Evaluation of Susceptibility Status of Some Clinical Bacterial Isolates to Generations of Cephalosporins Sold in Kano
Introduction: The circulation of substandard antibiotics is believed to aggravate the evil effect of Antibiotic resistance (AR) globally. AR knows no boundaries and pose a serious threat to existing antibiotics
Gap statement: Sabon Gari market is chosen due to reports of substandard antibiotics. It's a major distribution centre for pharmaceuticals yet research on its impact and extent of substandard drugs is lacking.
Aim: This study aims to evaluate the susceptibility status of some clinical Bacterial isolates (E. coli K. pneumoniae S. aureus S. pneumoniae P. aeruginosa and Salmonella sp.) to generations of Cephalosporins purchased from drug distributors in Sabon Gari Market Kano.
Methodology: Antimicrobial susceptibility pattern of the test isolates was determined by disc diffusion method. Fourier Transform Infrared Spectroscopy (FT-IR) analysis was used to confirm the functional group of the active ingredients of all the antibiotics tested. Molecular identification of resistant gene (CTX-M1) were carried out using PCR.
Results: Market survey reveals that Cephalexin 61% (first generation) Cefuroxime 72% (Second generation) and Cefexime 68% Cefpodoxime 79% Ceftriazone 63% Ceftazidime 70% and Cefotaxime 45% (third generation) and Cefepime 84% (fourth generation) were the most commonly sold Cephalosporins with different brands and company names. In all the antibiotics tested similar activity was observed in the branded antibiotics as compared with the standard antibiotics with no significant difference observed. Exactly 20% of E. coli and K. pneumoniae were resistant while 80% of S. aureus S. pneumoniae Pseudomonas and Salmonella sp. were susceptible. CTX-M1 resistant gene was identified E. coli and K. pneumoniae which further confirms their resistance to Cefotaxime and ceftriaxone antibiotics.
Conclusion: Branded cephalosporins sold in Kano were effective as standard antibiotics with good bioavailability and compliance with the standards formulation of medicine thus fit for human intake.
Methods to assess antibacterial, antifungal and antiviral surfaces in relation to touch and droplet transfer: a review, gap-analysis and suggested approaches.
To help assess whether a potentially antimicrobial material surface or coating provides antimicrobial efficacy a number of standardised test methods have been developed internationally. Ideally these methods should generate data that supports the materials efficacy when deployed in the intended end-use application. These methods can be categorised based on their methodological approach such as suspension tests agar plate/zone diffusion tests surface inoculation tests surface growth tests or surface adhesion tests. To support those interested in antimicrobial coating efficacy this review brings together an exhaustive list of methods (for porous and non-porous materials) exploring the methodological and environmental parameters used to quantify antibacterial antifungal or viral activity. This analysis demonstrates that antimicrobial efficacy methods that test either fungi or viruses are generally lacking whilst methods that test bacteria fungi and viruses are not designed to simulate end-use/lack realistic conditions. As such a number of applications for antimicrobial activity across medical touch screens medical textiles and gloves and transport seat textiles are explored as example applications providing guidance on modifications to existing methods that may better simulate the intended end-use of antimicrobial materials.
Identification of causative fungus from sterile abscess using metagenomics followed by in situ hybridization
Introduction: Invasive fungal infections require early diagnosis for treatment. Microscopic observation of biopsy and blood culture are the gold standard for identification of the causative fungus but it is difficult to identify the causative pathogen by a sterile abscess biopsy.
Case Presentation: We present a case report of breakthrough invasive trichosporonosis in a 65-year-old Japanese male with acute myeloid leukemia (AML) receiving antifungal prophylaxis. Blood cultures showed no fungal growth and a liver biopsy and a removed spleen with abscess showed fragmented fungi but no fungal identification was possible. This report demonstrates that retrospective analyses were able to identify the causative fungus.
Conclusion: We narrowed down the candidate fungi by deep sequencing of the ITS1 region of fungal genome and confirmed that the fungus observed in the specimen was T. asahii by in situ hybridization using a DNA probe targeting 26S rRNA.
Primary iliac bone tuberculosis: A case report
Tuberculosis is an infectious disease caused by the Mycobacterium tuberculosis complex. It is a major public health problem and one of the world's leading causes of morbidity and mortality. It occurs in both pulmonary and extra-pulmonary forms the pulmonary form being the most common. Primary iliac bone tuberculosis remains a rare clinical entity even in endemic areas. Its diagnosis can be challenging due to its similarity to other bone conditions. We report a rare case of primary iliac bone tuberculosis in a 63-year-old patient on peritoneal dialysis with the following medical history: hypertension type II diabetes complicated by diabetic retinopathy and diabetic kidney disease. Recent advances in molecular biology in particular with the advent of the Genexpert® have considerably improved patient management providing microbiological evidence in less than two hours.
Atypical presentation of varicella-zoster virus reactivation in a lung transplant patient: a case report
Background: Varicella zoster virus (VZV) is a human neurotropic virus which commonly causes infection during childhood. Later in life it may reactivate as herpes zoster. We report a rare manifestation of reactivation of VZV infection presenting as cutaneous vasculitis and varicella pneumonia in a lung transplant recipient.
Case presentation: A 65 year old man was lung transplanted bilaterally for emphysema and had repeated posttransplant chest infections and colonization with Pseudomonas aeruginosa. Nine months post-transplant he presented with dyspnea and a cutaneous vasculitis-like eruption. VZV reactivation was not suspected due to absence of the typical vesicular eruptions. The diagnosis was confirmed by VZV PCR from the swabs of the ulcer after skin punch biopsy of a lesion and from bronchoalveolar lavage (BAL). The histology of skin biopsy demonstrated epithelial and vascular damage but no typical epithelial virus associated changes. The patient responded to antiviral therapy with total remission of rash and VZV DNA was not detectable from repeated BAL after 29 days of therapy. However the pulmonary radiological features and dyspnea persisted due to reasons possibly unrelated to the VZV infection.
Conclusion: Had it not been for the patient to mention the resemblance of the vasculitic rash with his primary VZV infection the diagnosis would easily have been overlooked. In this case the biopsy did not show typical histopathologic findings of VZV-vasculitis. What led the diagnosis was PCR from the wound swab taken after punch biopsy. This case serves as a reminder for atypical presentation of common conditions in immunosuppressed patients and that extensive diagnostic sampling may be warranted in this group.
Sarcina Ventriculi in Association with Gastric Ulcer: A Case Report
Sarcina ventriculi is a gram positive bacteria which has been reported in patients with delayed gastric emptying as well as in association with cases of gastric ulcer and gastric carcinoma. Although it has been reported frequently in veterinary cases as a cause of fatal diseases exact pathogenesis in humans is yet to be identified. We report here a case of an elderly male who presented with hematemesis following which an upper gastrointestinal endoscopy was done and a gastric ulcer was revealed. Histopathological examination revealed Sarcina ventriculi in association with ulcer.
A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes
Infectious endophthalmitis is a severe ophthalmic emergency. It is known that this infection can be caused by bacteria and fungi. For efficient treatment the administration of antimicrobial drugs to which the microbes are susceptible is essential. The aim of this study was to identify microorganisms in biopsies of Mexican endophthalmitis patients using metagenomic next-generation sequencing and determine which antibiotic resistance genes were present in the biopsy samples. In this prospective case study 19 endophthalmitis patients were recruited. Samples of vitreous or aqueous humor were extracted for DNA extraction for metagenomic next-generation sequencing. Analysis of the sequencing results revealed the presence of a wide variety of bacteria in the biopsies. The resistome analysis showed that homologs of antibiotic resistance genes were present in several biopsy samples. Genes possibly conferring resistance to ceftazidime and vancomycin were detected in addition to various genes encoding efflux pumps. Our findings contrast with the widespread opinion that only one or a few bacterial strains are present in the infected tissues of endophthalmitis patients. These diverse communities might host many of the resistance genes that were detected which can further complicate the infections.
Genomic diversity of novel strains of mammalian gut microbiome derived Clostridium XIVa strains is driven by mobile genetic element acquisition
Despite advances in sequencing technologies that enable a greater understanding of mammalian gut microbiome composition our ability to determine a role for individual strains is hampered by our inability to isolate culture and study such microbes. Here we describe highly unusual Clostridium XIVa group strains isolated from the murine gut. Genome sequencing indicates that these strains Clostridium symbiosum LM19B and LM19R and Clostridium clostridioforme LM41 and LM42 have significantly larger genomes than most closely related strains. Genomic evidence indicates that the isolated LM41 and LM42 strains diverge from most other Clostridium XIVa strains and supports reassignment of these groups at genus-level. We attribute increased C. clostridioforme LM41 and LM42 genome size to acquisition of mobile genetic elements including dozens of prophages integrative elements putative group II introns and numerous transposons including 29 identical copies of the IS66 transposase and a very large 192 Kb plasmid. antiSmash analysis determines a greater number of biosynthetic gene clusters within LM41 and LM42 than in related strains encoding a diverse array of potential novel antimicrobial compounds. Together these strains highlight the potential untapped microbial diversity that remains to be discovered within the gut microbiome and indicate that despite our ability to get a top down view of microbial diversity we remain significantly blinded to microbe capabilities at the strain level.
Spectrum of Respiratory Viruses Identified from SARS-CoV-2 Negative Specimens in Watansoppeng, a Bat City in Eastern Indonesia
Respiratory infections account for millions of hospital admissions worldwide. Understanding the etiology could aid management and preventive strategies to reduce morbidity and mortality. Bats are reported as one of the animal reservoirs for many emerging respiratory viruses. SARS-CoV-2 negative specimens from Wattansoppeng city South Sulawesi a natural habitat for Acerodon celebensis and Pteropus alecto fruit bats were analyzed to study the spectrum of respiratory viruses. Samples were screened for influenza virus Enterovirus Paramyxoviridae Nipah virus Coronaviridae and Pneumoviridae. Of 210 specimens 19 were positive for Respiratory Syncytial Virus (RSV)-A RSV-B human parainfluenza (HPIV)-1 virus HPIV-2 human rhinovirus (HRV)-A HRV-B HRV-C human metapneumovirus (HMPV) influenza A virus and CV-A6. Influenza virus was of seasonal H3N2 subtype. The HMPVs were of genotype B1 and A2a while one of the RSV-A was ON-1 genotype. The viruses mostly affected children with unknown severity. No novel viruses were observed in this study.
Aspergillus esophagitis in a patient with solid tumors: a case report
Esophageal aspergillosis is a rare occurrence primarily documented in hematologic malignancies and only rarely occurring among patients with solid tumors. In this case report we present the unique case of an 81-year-old Lebanese man who had a remarkable medical history including four solid tumors. The patient sought medical attention due to dysphagia and weight loss prompting a gastroscopic examination that revealed a necrotic abscess at the esophagogastric junction. Initial treatment with fluconazole and Proton Pump Inhibitors was administered but the recurrence of similar symptoms led to a repeat gastroscopy unveiling a diagnosis of Aspergillus esophagitis. Intravenous Voriconazole was promptly initiated; however the patient developed a significant pericardial effusion and expired with Aspergillus species identified in the pericardial fluid. This exceptional case emphasizes the importance of considering esophageal aspergillosis in cancer patients who present with refractory symptoms such as epigastric pain dysphagia nausea and vomiting despite symptomatic treatment. Our findings underscore the need for increased awareness and the inclusion of gastrointestinal endoscopy as part of the diagnostic approach for this rare but potentially life-threatening condition.
Sequence and origin of the Streptomyces intergenetic-conjugation helper plasmid pUZ8002.
Conjugation of plasmids from Escherichia coli is essential for the genetic manipulation of Streptomyces spp. To facilitate intergeneric conjugation from E. coli to Streptomyces the conjugative machinery required for genetic transfer is usually provided by the non-transferable helper plasmid pUZ8002. Here we present the complete nucleotide sequence of pUZ8002 describe the previously undocumented creation process and provide details of the sequence relative to the parental pUZ8 plasmid and another previously published pUZ8002 sequence.
Enhancement of growth media for extreme iron-limitation in Escherichia coli
Iron is an essential nutrient for microbial growth and bacteria have evolved numerous routes to solubilise and scavenge this biometal which is often present at very low concentrations in host tissue. We recently used a MOPS-based medium to induce iron limitation in Escherichia coli K-12 during the characterisation of novel siderophore conjugated antibiotics. In this study we confirm that growth media derived from commercially-available M9 salts are unsuitable for studies of iron-limited growth likely through the contamination of the sodium phosphate buffer components with over 100 µM iron. In contrast MOPS-based media that are treated with metal-binding Chelex® resin allow the free iron concentration to be reduced to growth-limiting levels. Despite these measures a small amount of E. coli growth is still observed in these iron-depleted media. By growing E. coli in conditions that theoretically increase the demand for iron-dependent enzymes namely by replacing the glucose carbon source for acetate and by switching to a microaerobic atmosphere we can reduce background growth even further. Finally we demonstrate that by adding an exogeneous siderophore to the growth media which is poorly used by E. coli we can completely prevent growth perhaps mimicking situation in host tissue. In conclusion this short study provides practical experimental insight into low iron media and how to augment the growth conditions of E. coli for extreme iron-limited growth.
Characterization of Group A streptococci causing invasive diseases in Sri Lanka
Group A β haemolytic streptococci (GAS) or Streptococcus pyogenes is a human pathogen that causes an array of infections including pharyngitis cellulitis impetigo scarlet fever toxic shock syndrome and necrotizing fasciitis. The present study characterizes 51 GAS isolates from invasive infections in Sri Lanka focusing on resistance profiles genetic determinants of resistance and virulence markers.
Isolates were tested for sensitivity to penicillin erythromycin clindamycin and tetracycline. The presence of erm(A) erm(B) mef(A) was detected in erythromycin-resistant isolates while tet(M) was detected in the tetracycline-resistant isolates. PCR was used to identify SpeA SpeB SpeC SpeF SpeG smez and ssa as virulence markers. Selected GAS isolates were emm-typed using the updated CDC protocol.
All 51 isolates were susceptible to penicillin. The number of isolates non-susceptible to erythromycin was 16. The commonest resistant determinant identified was erm(B) (11/16). Tetracycline nonsusceptibility was found in 36 (70.6%) isolates and 26 of them contained the tet(M) gene. Thirteen (25.5%) isolates were resistant to both tetracycline and erythromycin while 12 (23.5%) isolates were sensitive to both antibiotics. The commonest virulence markers detected among the isolates was SpeB (44 86.3%) SpeG (36 70.6%) SpeF (35 68.6%) while SpeJ (15 29.4%) SpeA (10 19.6%) and ssa (59.8%) were less common.
In conclusion GAS isolates studied showed resistance to erythromycin and tetracycline while retaining universal susceptibility to penicillin. Additionally these isolates exhibited diverse genetic backgrounds displaying varying patterns of virulence genes and emm types.
A study on viruses and bacteria with particular interest on Mycoplasma pneumoniae in children with exacerbation of asthma from a tertiary care hospital in Sri Lanka
Asthma is a significant public health concern particularly in children with severe symptoms. Exacerbation of asthma (EOA) is life-threatening and respiratory infections (RIs) play a crucial role. Though viruses play a significant role in EOA patients are empirically treated with antibiotics which contribute to the development of antibiotic resistance. Although there are widely reported association of EOA with viral or M. pneumoniae infections there are no published data in Sri Lanka. The present study aimed to identify the association of common respiratory viruses typical respiratory bacterial pathogens and M. pneumoniae in children with EOA and relate them with the compatibility of antimicrobial use.
A case-control study was conducted in the pediatric unit of North Colombo Teaching Hospital Sri Lanka involving two groups of children between 5-15 years of age. Group-1: children with EOA Group-2: children with stable asthma (SA). Each group consisted of 100 children. Sputum/throat swabs were tested for common respiratory viruses using virus specific FITC-labelled monoclonal antibodies (MAbs) bacteria by routine culture and M. pneumoniae by RT-PCR. Macrolide-resistance in M. pneumoniae was detected using conventional PCR and sequencing specific genetic mutations in the 23S rRNA gene. M. pneumoniae was genotyped using nested multilocus sequence typing (MLST) which targeted eight housekeeping genes (ppa pgm gyrB gmk glyA atpA arcC adk).
There was no significant difference in age gender demographic or geographical locations between the two groups. In children with EOA antibiotics were used in 66% (66/100) and macrolides in 42% (42/100) in children with EOA. Samples consisted of 78% (78/100) sputum and 22% (22/100) throat swabs. Adenovirus was the most common virus identified and it was significantly higher in children with EOA compared to those with SA but no significant difference in typical bacteria findings between the two groups. M. pneumoniae was detected in one patient with EOA with none detected in the SA group. The M. pneumoniae was macrolide sensitive and it was ST14 by Multi Locus Sequence Typing. This study showed that the empiric use of antibiotics in children with asthma may be better targeted with prior pathogen screening to inform appropriate treatment to minimize antibiotic resistance.
The Y498T499-SARS-CoV-2 Spike (S) protein variant interacts with rat ACE2 but does not infect or induce responses in the rat lung when delivered as a S-protein pseudotyped lentivirus
The rat is a useful laboratory model for respiratory disease and SARS-CoV-2 proteins such as the spike (S) protein can induce inflammation. This study has investigated the ability of the Q498Y P499T (QP-YT) amino acid change described in the S-protein of the mouse adapted laboratory SARS-CoV-2 MA strain to interact with rat angiotensin converting enzyme-2 (ACE2) and stimulate responses in rat lung. Using a real-time S-ACE2 quantitative fusion assay ancestral S-protein fuses with human but not rat ACE2. The QP-YT S-protein retains ability to fuse with human ACE2 and interacts with rat ACE2 in the fusion assay and using a S-protein pseudotyped lentivirus infection system. L452R S-protein did not bind to rat ACE2. Although rat lower lung contains both ACE2 and TMPRSS2 target cells intratracheal delivery of ancestral or QP-YT S-protein pseudotyped lentivirus did not induce measurable respiratory changes inflammatory infiltration or innate mRNA responses. Isolation of primary cells from rat alveoli demonstrated the presence of cells expressing ACE2 and TMPRSS2. Infection of these cells however with ancestral or QP-YT S-protein pseudotyped lentivirus was not observed. Analysis of the amino acid changes across the S-ACE2 interface highlights the Y498 interaction with H353 as a likely facilitator of binding to rat ACE2 but also other amino acids that could improve this interaction.
Thus rat lungs contain cells expressing receptors for SARS-CoV-2 and the QP-YT S-protein variant can bind to rat ACE2 but this does not result in infection or stimulate responses in the lung. Further amino acid changes in S-protein could enhance this interaction to improve the utility of the rat model for defining the role of the S-protein in driving inflammation in the lung.
Using Photovoice to engage students in a non-major microbiology course
In the past decade it has become increasingly difficult to engage and encourage critical thinking and deeper learning in students who participate in higher education particularly in non-major subjects. Photovoice is a participatory action research methodology that has been used in community based research in many different areas including social science health science and education. In this study photovoice was used as a pedagogical tool in a third year BSc Bioscience non-major microbiology module at Dundalk Institute of Technology. In order to ascertain if photovoice was an effective way of engaging these students a qualitative descriptive methodological approach in the form of a focus group was employed. Six of the thirteen students who took the module participated in the focus group reporting a positive experience overall of using photovoice. Further analysis of the focus group data resulted in the overarching theme of choice with creativity and critical thinking and research skills as sub-themes to emerge. These findings suggest that photovoice is an effective way to engage students in microbiology as a non-major subject. However as it was a small sample size future research would need to use a larger cohort of students to provide further evidence of using photovoice as a pedagogical engagement tool for non-major subjects.
Notification of Bacterial Strains Made Available by the United Kingdom National Collection of Type Cultures in 2022
Here we report on the one hundred and twenty-five bacterial strains made available by the National Collection of Type Cultures in 2022 alongside a commentary on the strains their provenance and significance.
Bacterial profile of wound site infections and evaluation of risk factors for sepsis among road traffic accident (RTA) patients from Apex trauma centre, Northern India
Background: There is limited data about the bacterial contamination of Road traffic accident (RTA) wounds and their antibiotic susceptibility patterns.
Materials and Methods: This prospective study was conducted in a tertiary care centre in Northern India from January 2023 to January 2024. Wound deep swabs and aspirates were collected from RTA patients presenting to Apex Trauma centre. Gram stain and culture were performed and the isolates were subjected to antibiotic susceptibility testing. Organism identification was done using MALDI-TOF MS. Blood samples were also collected to rule out blood stream infections during follow up if patient became febrile or shown symptoms of systemic infection.
Results: A total of 189 wound samples were collected in which 97 (51.32%) samples showed the growth of microorganisms. The isolates included 69 (71.13%) Gram-negative bacilli in which majority were Klebsiella pneumoniae and 28 (28.86%) Gram-positive cocci in which majority were Staphylococcus aureus. 22 (11.64%) patients died during the hospital course. Sepsis developed in 50 (26.45%) patients in which Gram-negative bacilli were the predominant microorganism. Risk factors evaluated as significant for sepsis were raised procalcitonin level low Glasgow coma scale score (GCS) higher injury severity score (ISS) need for mechanical ventilation raised qSOFA (quick sequential organ failure assessment) score. Among the Gram negative isolates 100% susceptibility was seen for colistin. Among the Staphylococcus aureus 100% susceptibility was seen for vancomycin teicoplanin and levonadifloxacin.
Conclusion: It is essential to ascertain the profile of microorganism isolated from RTA wounds in order to reduce antimicrobial resistance and to deliver efficient treatment.
Detection of Hepatitis B Virus Genotypes in a Group of Hepatitis B Virus Infected Patients in Central and Northern Sri Lanka
Introduction
Hepatitis B infection causes a spectrum of clinical diseases varying from asymptomatic infection to severe or fulminant acute hepatitis chronic liver disease cirrhosis and hepatocellular carcinoma. Hepatitis B virus genotypes appear to influence transmission dynamics clinical outcomes and responses to antiviral therapy. However hepatitis B genotyping is a poorly investigated topic in Sri Lanka. This study intended to determine hepatitis B genotypes in a group of HBV-infected persons in central and northern Sri Lanka.
Methodology
The study was a laboratory-based descriptive cross-sectional study. Initial detection of HBV DNA in EDTA blood samples was done by a commercially validated quantitative real-time polymerase chain reaction kit (qPCR). Hepatitis B genotyping was performed by in-house conventional semi-nested multiplex PCR using genotype-specific primers (for genotypes A B C D E F). The serological profile was determined using a commercially validated ELISA/ CLIA assay. The results were evaluated for the genotype prevalence viral load association and HBeAg expression in the study population.
Results and Conclusion
The study detected that genotype C is most prevalent and infections with multiple genotypes (52%) were commoner than mono-genotype (23%) infections. In 25% of patients had no detectable genotype among genotype A-F. The mean viral load in asymptomatic patients with a single genotype was 3.28 log 10 copies/mL and in multiple genotypes was 4.18 log 10 copies/mL before treatment. Statistical significance was not detected in mean viral loads and HBeAg expression in these two groups. In the future chronic HBV infection may be effectively treated and managed according to the infected genotype.
A hydrocele revealing epididymal tuberculosis
Abstract: Genitourinary tuberculosis is a severe form of extrapulmonary tuberculosis. The most commonly affected organs are the epididymis and testicles. Clinical manifestations may include epididymitis orchid-epididymitis hydrocele associated with significant hematuria and leukocyturia in sterile urine. We report the case of a patient with a hydrocele that revealed epididymal tuberculosis. With the help of molecular biology the diagnosis of epididymal tuberculosis was made. The patient was treated conservatively with tuberculosis medication for six months.
Investigating the effectiveness of commercially available mouthwash on SARS-CoV-2 in-vivo using viable virus titre as the primary outcome. A randomised controlled trial.
This multi-arm parallel group single-blinded randomised controlled trial aimed to assess three commercially available mouthwashes effectiveness against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The manuscript has been written in accordance with the CONSORT statement. Methods Eligible participants were SARS-CoV-2 positive with a positive test in the last 72 hours. All participants had mild to moderate symptoms and could provide 5 saliva samples over a 60-minute period. Participants delivered a baseline saliva sample and then used a mouthwash as per manufacturer’s instructions. They provided further saliva samples at minute 1 10 30 and 60. Participants were randomised to one of four groups; OraWise+ Total Care Listerine Cool Mint Listerine and water (control). The lab-based research team were blind to the intervention. The research question was: Can SARS-CoV-2 be rendered inactive in saliva by using a mouthwash and how long does this effect last? The primary outcome was the amount of viable infectious SARS-CoV-2 virus in the sample compared to the baseline sample. The secondary outcome measure was the amount of genetic material from the SARS-CoV-2 virus in the sample measured via PCR testing. Results In total 100 participants were recruited (25 per group). Eight participants did not receive the allocated intervention and did not have saliva samples collected. There were no adverse events. In total 42 of the 92 participants had viable virus which could be cultured at baseline. Statistical analysis of the primary outcome was not advised due to the reduced level of viable virus at baseline and the positive skewness present in the distribution of log10(titre) data. Observational data of the primary outcome measure is presented. Analysis of the secondary outcome PCR measure showed that there was strong evidence for a decrease in SARS-CoV-2 RNA levels compared to water for all mouthwashes after 1 minute OraWise+ -0.49 (-0.92 -0.05) p-value 0.029 Cool Mint Listerine -0.81 (-1.25 -0.38) p-value <0.001 Total Care Listerine -1.05 (-1.48 -0.62) p-value <0.001. For the remaining timepoints there was generally no evidence of virus level reduction compared to water although there is weak evidence for a decrease at ten minutes using Total Care Listerine -0.44 (-0.88 0.01) p-value 0.053. Conclusion The three mouthwashes included in this trial observationally demonstrated a reduction in virus titre level 1 minute after use with virus levels normalising up to 60 minutes compared to the control. Although an interesting observation this result could not be statistically analysed. Using the secondary outcome PCR measure all three included mouthwashes reduced virus levels compared to water at 1 minute and these results were statistically significant. Clinically this result does not support the use of the included mouthwashes to reduce SARS-CoV-2 levels in saliva.
Whole-Genome Sequencing assisted outbreak investigation of Salmonella Enteritidis, at a hospital in South Africa, September 2022
Introduction Health authorities were notified of a suspected outbreak of foodborne disease in a hospital in South Africa. Staff and patients reported acute onset of abdominal cramps diarrhoea fever and rigors after eating a chicken pasta meal.
Aim To report on the use whole-genome sequencing (WGS) analysis of bacterial isolates to support an epidemiological investigation.
Methodology Epidemiological investigation of the outbreak was led by the Infection Control Manager of the hospital and supported by an outbreak response team. Standard microbiological procedures were used to process stool samples and culture/identify diarrhoeal pathogens. Bacterial cultures were investigated using WGS performed using Illumina NextSeq technology. WGS data were analyzed using multiple bioinformatics tools including those available at the Center for Genomic Epidemiology and EnteroBase. Core-genome multilocus sequence typing (cgMLST) was used to investigate the phylogeny of isolates.
Results Forty-nine cases were identified. Stool samples were collected from 21 cases and nontyphoidal Salmonella was isolated from 19/21 (90%) of the samples. All isolates were identified as Salmonella enterica serovar Enteritidis. All isolates differed from each other by allele differences on cgMLST indicating that isolates are highly genetically related. Delays in testing of food retention samples rendered the negative test results of limited value. A case control study was conducted; eating chicken pasta was strongly associated with developing gastroenteritis (Haldane-Anscombe Adjusted Odds Ratio 15.398)
Conclusion The epidemiological evidence suggests that the chicken pasta was the likely vehicle of transmission in this outbreak. The source of Salmonella enterica serovar Enteritidis remains unknown.
In silico analysis of Ffp1, an ancestral Porphyromonas spp. fimbrillin, shows differences with Fim and Mfa
Background: Scant information is available regarding fimbrillins within the genus Porphyromonas with the notable exception of those belonging to Porphyromonas gingivalis which have been extensively researched for several years. Besides fim and mfa a third P. gingivalis adhesin called filament-forming protein 1 (Ffp1) has recently been described and seems to be capital for outer membrane vesicle (OMV) production. Objective: We aimed to investigate the distribution and diversity of type V fimbrillin particularly Ffp1 in the Porphyromonas genus. Methods: A bioinformatic phylogenomic analysis was conducted using all accessible Porphyromonas genomes to generate a domain search for fimbriae using hidden Markov model (HMM) profiles. Results: Ffp1 was identified as the sole fimbrillin present in all analyzed genomes. After manual verification (i.e. biocuration) of both structural and functional annotations and 3D modeling this protein was determined to be a type V fimbrillin with a closer structural resemblance to a Bacteroides ovatus fimbrillin than to FimA or Mfa1 from P. gingivalis. Conclusion: It appears that Ffp1 is an ancestral fimbria transmitted through vertical inheritance and present across all Porphyromonas species. Additional investigations are necessary to elucidate the biogenesis of Ffp1 fimbriae and his potential role in OMV production and niche adaptation.
The Relationship between microbial population adenosine triphosphate and quantitative polymerase chain reaction bioburdens in diesel fuel microcosms
Historically fuel microbiology studies have relied on culture data. Potentially relevant but unculturable were not detected. Although adenosine triphosphate (ATP) can quantify total microbial bioburdens in fuels it cannot differentiate among the taxa present. Quantitative polymerase chain reaction (qPCR) testing promises to fill this gap by quantifying targeted amplicon sequences and thereby detecting both culturable and non-culturable taxa and quantifying specifically targeted taxa. In this study fluid samples drawn from the fuel interface and water phases of fuel over water microcosms were tested for cellular ATP concentration ([cATP]) and qPCR bioburdens. Additionally surface swab samples from steel corrosion coupon surfaces exposed to each of these three phases were collected and tested for total ATP concentration ([tATP]) and qPCR bioburdens. Statistical relationships between ATP and qPCR bioburdens were examined. Correlation coefficients between the two variables were matrix dependent and ranged from negligible (|r| = 0.2) to strong (|r| = 0.7). When results were categorized into negligible moderate and heavy bioburdens parameter agreement was again matrix dependent. Percent agreement between [ATP] and qPCR gene copies ranged from 11 % to 89 % – with qPCR-bioburden ratings typically being greater than ATP-bioburden ratings.
Antibiotic Use and Antimicrobial Resistance: KAP survey of medical students to evaluate undergraduate training curriculum
Introduction: A better understanding of knowledge attitude and practices of undergraduate medical students towards antimicrobial resistance (AMR) is necessary to identify gaps in current training curriculum.
Methods: A 20-point Likert scale-based questionnaire divided three parts on knowledge attitude and practices relating to antibiotic use and resistance was devised. Students attending each year of undergraduate medical program were approached to participate in the study over a one-week-period. KAP scores of each year were compared through logistic ordinal regression and Kruskal-Wallis (KW) test.
Results: Two hundred and eight students participated in the study. Overall knowledge of about intended use of antibiotics fixed drug combinations and awareness about AMR was good (average score of 73.75%). Steady improvement in knowledge scores was observed from first year (-0.441) to final year (0.00). The medical students had favorable attitude towards rational antimicrobial use (Likert score ³4) including the need to spread awareness about AMR amongst students and public and following doctor’s prescription. Self-medication was reported by 28.4% of students and hoarding of leftover doses by 49.1%. Attitude score had a direct correlation with the knowledge score on KW test (χ2 =29.6 p≤0.5) but had no significant correlation with antimicrobial practices (χ2 =3.9 p≥0.5). The gaps identified in students’ practices included self-medication skipping of dosing hoarding of leftover medication.
Conclusion: As improvement in knowledge did not correlate with better personal behaviours regarding antibiotics current curriculum needs to include AMR as a focus area to ensure good antibiotic prescribing practices in future practitioners.
Phenotypic antibiotics susceptibility profile of clinical Enterobacteriaceae isolates from Kaduna State, North-west Nigeria
Background: The increasing resistance of clinical Enterobacteriaceae infection to commonly prescribed antibiotics have been reported around the world. Data is generally lacking on the prevalence and antibiotic susceptibility profile of clinical Enterobacteriaceae isolates from Kaduna northwest Nigeria. This study thus aimed to determine the diversity of clinical Enterobacteriaceae isolates recovered from clinical specimens of patients admitted into two selected healthcare institutions in Kaduna Nigeria.
Methods: This was a prospective cross-sectional study conducted between September and December 2021. Non-duplicate clinical bacterial isolates recovered from various specimens were collected and identified using rapid biochemical identification kits. The susceptibility of identified Enterobacteriaceae to various antibiotics and phenotypic detection of carbapenemase enzymes were thereafter determined. The data were analyzed and visualized using the R software version 4.3.1.
Results: Of the 500 collected bacterial isolates 108 (21.6 %) were identified as Enterobacteriaceae with Pantoea agglomerans (52 48.1%) Klebsiella oxytoca (19 17.6%) as the most prevalent. The isolates exhibited high resistance to azithromycin (69%) and ceftazidime (42%) while exhibiting low resistance to amikacin (7%) and imipenem (10%). Among the carbapenem-resistant Enterobacteriaceae (CRE) isolates a significant proportion (66.6 %) tested positive for carbapenemase activity.
Conclusion: This study reports a high prevalence of multi-drug resistant Enterobacteriaceae in Kaduna northwest Nigeria. The emergence of pathogenic P. agglomerans and an alarmingly high prevalence of carbapenemase-producing CRE are also observed. The presence of carbapenemase producers in an area with low carbapenem usage and resistance rates raises significant concerns. Continuous surveillance and robust antibiotic stewardship policies are imperative to preserve the efficacy of carbapenems in this region.
Mycotic Aneurysms: Uncommon Pathogens and Treatment Conundrums
Introduction: Mycotic aneurysms characterized by vessel wall dilation resulting from infections including bacteria fungi and viruses are a rare yet severe consequence of systemic infections.These aneurysms accounting for 0.6% of Western countries' aneurysms carry a higher risk of rupture compared to uninfected conditions. While the femoral artery aorta and intracranial visceral arteries are commonly affected pathogens causing mycotic aneurysms vary across regions. Diagnostic challenges arise from nonspecific symptoms such as fever and discomfort. To prevent the substantial morbidity and mortality associated with mycotic aneurysms timely identification and treatment are paramount. We present a case series highlighting mycotic aneurysms caused by some rare pathogens - Salmonella Paratyphi A Streptococcus pneumoniae and Pseudomonas aeruginosa.
Materials & Methods: The case series involves three patients diagnosed with mycotic aneurysms due to unusual pathogens. We describe each patient's clinical presentation medical history physical examination findings laboratory results imaging studies and the diagnostic process leading to the identification of the causative pathogens.
Results: The first case depicts a 70-year-old male with a ruptured infra-renal abdominal aortic pseudoaneurysm caused by Salmonella Paratyphi A. The second case involves a 66-year-old male with a Streptococcus pneumoniae-associated descending thoracic aortic pseudoaneurysm. The third case pertains to a 70-year-old male with a ruptured descending thoracic aortic aneurysm into the esophagus due to Pseudomonas aeruginosa infection. Each case highlights unique clinical features laboratory findings imaging results and the management approaches undertaken.
Conclusion: Mycotic aneurysms stemming from infections involving diverse pathogens pose diagnostic challenges due to their nonspecific symptoms. Early identification and intervention are essential to mitigate the severe complications associated with these aneurysms. The presented cases underscore the need for a comprehensive approach to diagnosis and management ensuring optimal outcomes for patients affected by mycotic aneurysms.
Evaluation of optimal agar medium for detecting hypervirulent Klebsiella pneumoniae using string test
1. Abstract The string test is a screening method for detecting hypervirulent Klebsiella pneumoniae (hvKp). Agar media are typically used for string test; however the effect of media type on the test results remains unclear. We aimed to determine the optimal agar medium and cutoff value for the string test. We tested the string test for 99 Klebsiella strains using different agar media: sheep blood chocolate Drigalski's and MacConkey. Diagnostic accuracy was calculated in concordance with the rmpA rmpA2 or iuc gene levels. The diagnostic accuracy rates for sheep blood chocolate Drigalski's and MacConkey agar were 0.79 0.75 0.73 and 0.64 respectively. When the cutoff was changed from 5 mm to 10 mm the diagnostic accuracy rate for sheep blood agar decreased from 0.79 to 0.65. Our findings suggest that agar medium type affect the string test results and sheep blood agar with a cutoff of 5 mm is the optimal condition for detecting hvKp.
Staphylococcus aureus associated with post-operative wound infections in Western Kenya reveals genomic hotspots for pathogen evolution
Objectives. Staphylococcus aureus is one of the most common pathogens attributed to hospital infections. Although S. aureus infections have been well studied in developed countries far less is known about the biology of the pathogen in sub-Saharan Africa.
Methods. Here we report on the isolation antibiotic resistance profiling whole genome sequencing and genome comparison of six multi-drug resistant isolates of S. aureus obtained from a referral hospital in Kakamega Western Kenya.
Results. Five of the six isolates contained a 20.7-kb circular plasmid carrying blaZ (associated with resistance to b-lactam antibiotics). These five strains all belonged to the same sequence type ST152. Despite the similarity of the plasmid these isolates whole genome sequencing revealed that the strains differed depending on whether they were associated with hospital-acquired or community-acquired infections.
Conclusion. The intriguing finding is that the hospital acquired and the community acquired isolates of S. aureus belonging to the same genotype ST152 formed two separate sub-clusters in the phylogenetic tree and differed by the repertoire of accessory virulence genes suggesting an ongoing adaptive evolution and significant genomic plasticity.
Hollow-fibre infection model: adaptations for the culture and assessment of fastidious organisms
The Hollow-fibre Infection Model (HFIM) is a valuable in vitro platform for emulating antimicrobial drug (AMD) pharmacokinetic (PK) profiles. Despite its potential standardized protocols for HFIM operation especially concerning fastidious organisms are lacking. This study addresses this gap by examining challenges in culturing Pasteurella multocida and Actinobacillus pleuropneumoniae two fastidious organisms in the HFIM.
Our findings reveal effective strategies to prevent system clogging involving multiple freeze-thaw cycles of horse blood centrifugation and cell straining to enhance the clarity of the Mueller-Hinton fastidious (MH-F) medium defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI). Additionally we propose that the provision of a CO2 atmosphere along with the utilization of gas-permeable tubing and gas vent filters significantly facilitates the growth of fastidious organisms. Remarkably both P. multocida and A. pleuropneumoniae were sustained for a period of up to 10 days under these optimized conditions.
This study provides crucial insights into the modifications necessary to successfully culture fastidious organisms in the HFIM paving the way for more accurate and representative in vitro models for antimicrobial drug testing. These advancements hold promise for advancing research in the field of antimicrobial pharmacokinetics and efficacy against challenging pathogens.
Group A Streptococcus isolated in Guyana with reduced susceptibility toβ-lactam antibiotics
Introduction: Streptococcus pyogenes (Group A streptococci [GAS]) is the causative agent of pharyngitis and various other syndromes involving cellulitis streptococcal toxic shock syndrome (STSS) and necrotising fasciitis. Although the prevalence of GAS infections globally remains high necessitating the widespread use of b-lactam antibiotics GAS has remained largely susceptible to these agents. However there have been several reports of GAS with reduced susceptibility harbouring mutations in genes for penicillin-binding proteins (PBPs). The objectives of this study were to examine the in vitro b-lactam susceptibility patterns of Group A streptococci determine the prevalence of drug resistance and ascertain whether such resistance could be attributed to mutations in specific PBP genes.
Methods: In this study we sought to use Sanger sequencing to identify mutations in PBP genes of Streptococcus pyogenes isolated from patients that required inpatient and outpatient care that could confer reduced PBP affinity for penicillin and/or cephalosporin antibiotics. All isolates were screened for susceptibility to penicillin amoxicillin and cefazolin using E-test strips.
Results: While there were no documented cases of reduced susceptibility to penicillin or amoxicillin. Thirteen isolates had reduced susceptibility against cefazolin. Examination of pbp1a by Sanger sequencing revealed several isolates with single amino acid substitutions which could potentially reduce the affinity of PBP 1A for cefazolin and possibly other first-generation cephalosporins.
Conclusion: Penicillin and penicillin-derived antibiotics remain effective treatment options for GAS infections but active surveillance is needed to monitor for changes to susceptibility patterns against these and other antibiotics and understand the genetic mechanisms contributing to them.
Trend of Vancomycin resistance among Enterococcal meningitis patients in North India – an observational analysis
Introduction: Among bacterial meningitis enterococcal meningitis is extremely uncommon and typically nosocomial in origin.
Aim: This study was done to estimate the prevalence of Vancomycin-resistant Enterococcal meningitis and to assess the risk factors amongst these patients. Also resistance pattern of these Vancomycin resistant Enterococcal isolates towards other antibiotics were also assessed.
Materials and methods: This observational analysis was done in the Microbiology department of a tertiary care referral center from January 2021 to July 2023. Cerebrospinal fluid (CSF) samples of all cases of suspected meningitis were included in the study and sent to Microbiology lab for culture and sensitivity. Culture was done on chocolate agar 5% blood agar and MacConkey agar and incubated aerobically for 72 hours. After incubation the isolate was identified by MALDI-ToF MS. Sensitivity was done using Kirby Bauer disk diffusion method and interpreted using CLSI 2023 M-100 clinical breakpoints. The patients’ demographic details associated risk factors type of surgery done and the clinical outcome of the patients were analyzed.
Statistical analysis: Clinical data and values were entered in Excel sheet. Univariate analysis of the risk factors was done and p-values <0.05 were considered significant.
Results: A total of 2352 CSF samples were cultured of which 292 (12.4%) samples showed growth on culture. Enterococcus species were isolated in 30 (10.3%) samples. The predominant species was Enterococcus faecalis (n=17; 56.7%). Majority of the patients presented with fever (50%) and headache (33.3%). The risk factors in these patients were hypertension (40%) and diabetes mellitus (33.3%). All the patients had an extra-ventricular drain (EVD) present in them. Intracranial surgery was done in 15 patients. Only 1 (3.3%) patient died due to enterococcal meningitis. Of these 6 (20%) isolates were Vancomycin resistant. Statistically significant risk factors in these patients were hypertension prolonged hospital stay of >21 days. Majority of the isolates were resistant to Levofloxacin high level gentamicin doxycycline and ampicillin. Removal of the EVD helped in better prognosis of the patients
Conclusion: Early detection is crucial for a positive clinical result since vancomycin resistant enterococcal meningitis is associated with a high morbidity rate.
Interaction with refuse piles drives co-occurrence of core gut microbiota in workers of the ant Aphaenogaster picea
Comparing the diversity of gut microbiota between and within social insect colonies can illustrate interactions between bacterial community composition and host behavior. In many eusocial insect species different workers exhibit different task behaviors. Thus these workers may benefit from symbiotic relationships with certain bacteria that augment the metabolic processes underlying their specific behaviors. Evidence of compositional differences between core microbiota in different worker types could suggest a microbial association with division of labor among workers. Here we present the core microbiota of Aphaenogaster picea ant workers with different task behaviors. The genus Aphaenogaster is abundant worldwide yet the associated microbiota of this group is unstudied. Bacterial communities from A. picea gut samples in this study consist of 19 phyla dominated by Proteobacteria Cyanobacteria and Firmicutes. Analysis of 16S rRNA gene sequences reveals distinct similarity clustering of A. picea gut bacterial communities in workers that have more interactions with the refuse piles. Though gut bacterial communities of nurse and foraging ants are similar in overall composition and structure the worker groups differ in relative abundances of dominant taxa. Interaction with fecal matter via refuse piles seems to have the greatest impact on taxa distribution and this effect appears to be independent of worker type. This is the first report surveying the gut microbiome community composition of Aphaenogaster ants.
An atypical case of esophageal actinobacillosis in a cow
Present case report describes an unusual instance of esophageal actinobacillosis in an adult cow presented to the university hospital with a history of inability to drink and swallow. Clinical evaluation revealed a noticeable five-inch swelling in the Juglar groove while radiographic imaging indicated the presence of a small round and mildly radio-opaque lesion. In response an exploratory surgical excision was performed as a palliative measure and the excised tissue was subsequently preserved in 10% buffered formalin for histopathological examination. Histopathology revealed pyogranulomatous inflammation characterized by radiating eosinophilic club shaped bodies surrounding small colonies of coccobacilli. Grams and Zeil Neelson stains confirmed the presence of gram negative and non-acid fast coccobacilli. Additionally following a thorough review of relevant literature on atypical actinobacillosis the authors assert the rarity of esophageal involvement with this case representing only the second documented instance globally.
Comparative analysis of virulence gene profiles of Escherichia coli from clinical and non-clinical sources in Rivers State, Nigeria
Traditionally the presence of virulence features have been thought to be a key factor in differentiating pathogenic from commensal strains. An understanding of virulence potential of Escherichia coli isolates from various sources is essential to help shed light on potential contamination/transmission rates between the various sources. This study was therefore aimed at exploring the occurrence of specific virulence genes and gene profiles associated with Escherichia coli from clinical and non-clinical sources in Rivers State Nigeria.
Two hundred samples from clinical (urine and feces) and non-clinical (soil and poultry droppings) sources (50 each) were analyzed using standard microbiological procedures. DNA was extracted from isolates presumptively identified as Escherichia coli using PrestoTM Mini gDNA Bacteria-Kit Quick protocol following the manufacturer’s instructions. Isolate identities were confirmed using E. coli specific 16S rRNA primers and confirmed isolates screened for the presence of six virulence genes (Afimbriae binding adhesin (afa) type 1 fimbriae (fimH) P-fimbrial Usher Protein (papC)) iron acquisition systems: aerobactin (aer) Cytotoxic necrotizing factor I (cnf1) and alpha hemolysin (hly).
Results showed that all isolates haboured at least one of the tested virulence genes with fimH (97%) as the most prevalent virulence gene and papC the least commonly occurring (35%). A higher occurrence of virulence genes was noted in non-clinical isolates though hly and cnf were not detected at all in any of the isolates studied (0%). Ten different profiles were observed with the afaCc-aer-fimH profile the most commonly occurring virulence gene profile in general (33.3%). For non-clinical isolates however the aer-afaCc-fimH-papC was the most commonly occurring profile (42.9%).
This study shows that the test Escherichia coli from clinical and non-clinical sources do not carry distinct virulence gene profiles. Studies on a larger subset of isolates would however be necessary to determine if indeed the virulence genes tested for in this study really cannot be used to tell whether an isolate is from a clinical source or not in the South-South of Nigeria.
Variability of pMGA/vlhA sequences among Mycoplasma gallisepticum field strains isolated from laying hens and their deformed eggs.
Mycoplasmosis attributed to Mycoplasma gallisepticum poses a significant challenge to poultry farming leading to substantial economic losses and persistent infections within flocks. This bacterium harbors various surface proteins that are crucial for the adhesion transporter activity and evasion of the host immune response facilitating its pathogenicity. One such key surface lipoprotein referred to as pMGA or vlhA hemagglutinin plays a pivotal role in adhesion processes. In this study the clonal regions pMGA1.2 and pMGA1.3 as reported by Markham (M83178.1) were investigated to elucidate differences or similarities in the whole DNA sequences of Myc. gallisepticum field strains. The aim was to analyze sequence diversity within this region. Six internal primers were designed to amplify the target sequence and isolates were obtained from both eggs and chickens sourced from laying hen flocks. Identification revealed 17 strains of Myc. gallisepticum and four strains of Myc. synoviae which were confirmed through the mgc2 and 16S rRNA genes respectively. Positive and negative controls were established using the MGS6 and MSWUV1853 strains. Amplification results indicated a higher frequency of amplification proximal to the C-terminal region with segments 4 (33.3%) and 6 (27.8%) being the most prevalent. Notably none of the field strains exhibited the same amplification pattern as MGS6 and none of the strains characterized as Myc. synoviae amplified any primer set.
Upon translation the amino acid sequences from segments 4 and 6 were found to be compatible with conserved sequences within the Myco_haema protein domains of the genus Mycoplasma specifically corresponding to Q7NAP3_MYCGA VlhA.3.04. The observed homology suggests a potential genetic transfer while the variability identified in the pMGA or vlhA gene region of the field strains may have significant implications for protection against Myc. gallisepticum infection in chickens.
Exceptional association of two species of bacteria causing acute appendicitis: Haemophilus influenzae and Enterobacter cloacae
Appendicitis typically caused by appendiceal lumen obstruction is a prevalent abdominal surgical emergency worldwide. While most cases involve Enterobacterales Haemophilus influenzae primarily known for upper respiratory infections is infrequently associated with gastrointestinal infections. This article presents an exceptional case of acute appendicitis caused by both Haemophilus influenza and Enterobacter cloacae in a 15-year-old child highlighting the significance of recognizing uncommon pathogens in appendicitis and emphasizing the necessity for thorough microbiological investigations to refine diagnostic approaches.
Exploration and characterization of a newly isolated bacterium, Enterobacter quasihormaechei strain BDIFST24001, capable of producing rhamnolipids biosurfactant for oil remediation
Biosurfactants are naturally occurring compounds synthesized by microorganisms that increasingly attract attention due to both their living area and application in various industries. In this study we explore and characterize a novel bacterium Enterobacter quasihormaechei strain BDIFST24001 isolated for its ability to produce rhamnolipids biosurfactants with the aim of facilitating oil remediation processes. The isolation of this bacterium was carried out using Luria-Bertani broth (LB) media from environmental samples collected from oil-contaminated sites in Dhaka city. Screening tests including the oil spreading method and drop collapse assay were conducted to identify potential biosurfactant-producing strains leading to the selection of E. quasihormaechei strain BDIFST24001 based on its favorable performance. Subsequent molecular identification revealed a high similarity of the strain's 16S rRNA gene to E. quasihormaechei which was corroborated through phylogenetic analysis. Further analysis of the biosurfactant produced by this strain indicated its rhamnolipids nature as confirmed by FT-IR spectroscopy. The rhamnolipids exhibited promising surface-active properties including a significant reduction in surface tension and emulsification activity as evidenced by surface tension measurements and emulsification index assays. Optimization studies revealed that the optimal conditions for rhamnolipids production by E. quasihormaechei strain BDIFST24001 were a temperature of 37°C pH 10.0 and salinity of 4%. The rhamnolipids produced by this strain demonstrated effective oil remediation capabilities as observed through controlled experiments using petrol oil. The rhamnolipids effectively reduced the surface tension of the oil-water interface facilitating the dispersion and emulsification of the oil phase in water. Overall our findings highlight the potential of E. quasihormaechei strain BDIFST24001 as a promising candidate for biosurfactant-mediated oil spill cleanup and environmental remediation efforts.
Human Metapneumovirus (hMPV): An associated etiology of Severe Acute Respiratory Infection in Children of Eastern Uttar Pradesh, India.
Acute respiratory infections (ARIs) are a serious public health concern across the world causing considerable morbidity and mortality. Every year around 13 million children under the age of five die. Approximately 95% of them are from developing nations and ARIs are responsible for one-third of all deaths. Human Metapneumovirus (hMPV) is one of the causative agents associated with respiratory tract infections. There is lack of information about hMPV from the eastern region of Uttar Pradesh. In our centre Indian Council of Medical Research- Regional Medical Research Centre Gorakhpur (ICMR‐RMRC Gorakhpur) at Gorakhpur Uttar Pradesh India; we tested for respiratory pathogens in under-five patients presenting with ARI and severe acute respiratory illness (SARI) through semi nested PCR. A total of 100 nasal and throat specimens were collected from the OPD and IPD of Department of Paediatrics BRD Medical College Gorakhpur during from February 2022 to April 2022. Out of 100 enrolled pediatric patients 4 (4%) were found to be positive. Among the patients who tested positive for hMPV 25% (1/4) patient unfortunately died. The phylogenetic analysis of hMPV showed the close resemblance with the clade of Singapore and USA hMPV isolates. Our work underlines the importance of hMPV as the cause of acute respiratory infections in children and the need for routine testing for this virus in laboratories. Further comprehensive information regarding the incidence of hMPV in this area is needed.
Genome sequencing and analysis of Salmonella enterica subsp. enterica serotype Enteritidis PT4 578
Salmonella enterica serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. Salmonella Enteritidis causes self-limited gastroenteritis in humans which can progress to systemic infection in immunocompromised individuals. Poultry products are considered significant reservoirs of many Salmonella serotypes and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion intestinal colonization and intracellular survival. The genome harbors twelve Salmonella pathogenicity islands (SPIs) with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found with regions of intact prophages corresponding to Salmon_118970_sal3 and Gifsy-2. The genome also contains two CRISPR systems. Comparative genome analysis with three other serotypes of Salmonella demonstrates that most unshared genes are related to metabolism membrane and hypothetical proteins. Finally the phenotypic characterization evidenced differences among Salmonella Enteritidis PT4 578 and the other three serotypes regarding the expression of the red dry and rough (rdar) morphotype and biofilm formation. Overall the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in Salmonella Enteritidis PT4 578.
HIV combined with skin infection of Nocardia brasiliensis: A rare case report
Introduction. The HIV virus can attack and gradually damage the human immune system causing the host to be unprotected when infected. Nocardia is a type of opportunistic pathogenic bacteria that can easily cause infections in patients with chronic wasting diseases immune dysfunction and the use of immunosuppressants. Nocardia can invade various tissues and parts of the body causing corresponding clinical symptoms. There are few reports of HIV patients being infected with Brazilian Nocardia.
Case presentation. This article reports a case of an HIV patient with concurrent infection with Brazilian Nocardia. A patient with HIV developed a lump on the surface of their left skin without any obvious cause. Due to improper disinfection and treatment methods the condition worsened and they subsequently sought medical attention at our hospital. A series of laboratory related tests are conducted clinically based on the patient's medical history symptoms and signs. Based on the test results a reasonable treatment plan was adopted clinically ultimately achieving satisfactory treatment outcomes for patients.
Conclusion. HIV patients are prone to various types of infections even rare bacteria as their immune function decreases. With the popularity of new identification methods such as mass spectrometry laboratories should pay attention to traditional staining methods and use microscopes to detect pathogens.
Brief Report: Nasal colonization with Staphylococcus aureus and Methicillin resistant Staphylococcus aureus among community-dwelling older adults with comorbidities seeking follow-up medical care in Central Sri Lanka.
Older adults are more severely affected by infections caused by drug-resistant bacteria including Methicillin-Resistant Staphylococcus aureus (MRSA). We aimed to identify the MRSA colonization rates and associated factors among older adults aged more than 65-years-old. Among the 309 recruited 152 (49.2%) were males. Self-collected nasal swabs were used to isolate Staphylococcus aureus and MRSA with routine microbiological methods. Staphylococcus aureus was isolated from 36 (11.7%) participants while 11 (3.6%) were colonized with MRSA. We identified a significant association between the male sex and MRSA colonization (p=0.028 Chi-square test). However this needs careful interpretation given the smaller number of outcome events. Other factors studied had no statistically significant association with MRSA colonization.
Title of Manuscript: Prevalence of SARS- CoV-2 virus in saliva, stool, and urine samples of COVID-19 patients in Bihar, India
Introduction: The coronavirus illness caused by SARS- CoV-2 can cause multiple organ involvement with varying degrees of severity. Besides inhalation as a route for transmission feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue.
Objective: To detect SARS-CoV-2 RNA in non-respiratory samples (saliva urine and stool) collected from COVID-19 cases in Bihar.
Materials and methods: This Cross-Sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116) stool (97) and urine (132) were collected from 143 covid-19 cases. Samples were analyzed for SARS-CoV-2 by multiplex RT-PCR targeted against E ORF 1ab and RdRp gene.
Results: In this study out of 143 cases a total of 107(74.8%) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples.
Conclusion: There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.
Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07
Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as biocontrol biopesticides that promise improved sustainability and ecological safety in agriculture. Here we present a draft-quality genome sequence for Bacillus velezensis EU07 which shows growth-promotion in tomato plants and biocontrol against Fusarium head blight. We found that the genome of EU07 is almost identical to that of the commercially used strain QST713 but identified 46 single-nucleotide differences that distinguish these strains from each other. The availability of this genome sequence will facilitate future efforts to unravel the genetic and molecular basis for its beneficial properties.
Development of Recombinant Proteins for Vaccine Candidates Against Serotype O and A of Foot and Mouth Disease Virus in Bangladesh
Frequent vaccine failure leading to recurrent outbreaks of Foot-and-Mouth Disease (FMD) in livestock populations necessitates the development of a customizable vaccine platform comprising potential antigenic determinants of circulating lineages of FMD viruses. Artificially designed chimeric peptide-based recombinant vaccines are novel approaches to combat the phylogenetically diverse FMD Virus (FMDV) strains. Among seven recognized serotypes only serotypes O and A are dominantly circulating in Bangladesh and neighboring countries of Asia where transboundary transmission recurrent outbreaks and emergence of novel lineages of FMDV are highly prevalent. The objective of this study was to develop multi-epitope recombinant peptides procuring immunogenicity against circulating diverse genotypes of FMDV serotypes O and A. Two chimeric peptides named B1 (41.0 kDa) and B3 (39.3 kDa) have been designed to incorporate potential B-cell and T-cell epitopes selected from multiple FMDV strains including previously reported and newly emerged sub-lineages. After expression characterization and immunization of guineapigs with considerable antigen load of B1 and B3 followed by the serological assays revealed the significant protective immunogenicity developed from the higher (100 µg) doses of both antigens against most of the currently prevalent serotype O and A strains of FMDV. The efficient expression antigenic stability and multivalent immunogenic potency of the chimeric peptides strongly indicate their credibility as novel vaccine candidates for existing serotypes O and A of FMDV in Bangladesh and surrounding territories.
Deciphering the interaction surface between the West Nile virus NS3 and NS5 proteins
West Nile virus (WNV) is the most prevalent mosquito-borne disease and the leading cause of viral encephalitis in the continental United States. It belongs to the Flavivirus family which includes other important human pathogens such as dengue virus (DENV) Japanese encephalitis virus (JEV) and Zika viruses (ZIKV). Despite several decades of research no specific antiviral drugs are available to treat Flavivirus infections. The present study characterizes the interaction between the WNV NS3 and NS5 proteins for the purpose of identifying hotspots in the protein-protein interaction which could be targeted for the development of antiviral therapeutics. We previously developed an interaction model in silico based on data available in the literature. Here potential interacting residues on NS3 and NS5 were mutated in a WNV replicon and seven mutations in the NS3 protein were found to drastically reduce viral replication. In addition to being well conserved among mosquito-borne Flaviviruses these residues are located on the protein’s surface in two clusters which might be interesting new targets for future drug development.
An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
ChatGPT and Bard (now called Gemini) two conversational AI models developed by OpenAI and Google AI respectively have garnered considerable attention for their ability to engage in natural language conversations and perform various language-related tasks. While the versatility of these chatbots in generating text and simulating human-like conversations is undeniable we wanted to evaluate their effectiveness in retrieving biological knowledge for curation and research purposes. To do so we asked each chatbot a series of questions and scored their answers based on their quality. Out of a maximal score of 24 ChatGPT scored 5 and Bard scored 13. The encountered issues included missing information incorrect answers and instances where responses combine accurate and inaccurate details. Notably both tools tend to fabricate references to scientific papers undermining their usability.
In light of these findings we recommend that biologists continue to rely on traditional sources while periodically assessing the reliability of ChatGPT and Bard. As ChatGPT aptly suggested for specific and up-to-date scientific information established scientific journals databases and subject-matter experts remain the preferred avenues for trustworthy data.
Detection and significance of anti-Mycobacterium tuberculosis specific IgG antibody response for the diagnosis of pulmonary tuberculosis using enzyme-linked immunosorbent assay
Objective: Evaluation of an ELISA test for detection of IgG antibody response using in-house prepared Mycobacterium tuberculosis H37Rv soluble extract (MTSE) as antigen for rapid diagnosis of pulmonary tuberculosis and its clinical usefulness.
Methods: In this study a total of 758 pulmonary tuberculosis (TB) patients (652 AFB-positive and 106 AFB-negative) 276 healthy controls and 43 pulmonary infectious disease controls other than TB were recruited. IgG antibody level against MTB soluble extract was measured in sera samples of all study groups using an ELISA test. The level of IgG antibody responses was compared among groups by the Kruskal-Wallis test. The pairwise comparison was made by the Mann-Whitney test A positive score was represented by optical density above the cut–off value which was calculated from OD values of healthy controls by adding 2SD to the mean OD value. The evaluation of diagnostic value was considered based on sensitivity and specificity.
Results: Significantly higher levels of IgG antibody response were observed in PTB patients compared to healthy control and non-TB other pulmonary infectious disease control groups (p value<0.0001). The percent positivity for the IgG antibody response was higher in AFB-positive 574/652 (88.04%) and 79/106 (74.53%) AFB-negative PTB patients as compared to healthy control 9/276 (3.26%) and non-TB other pulmonary infectious disease control 3/43 (6.97%). The sensitivity of the test in PTB patients (AFB-positive and AFB-negative) was 86.15% (95% CI; 83.48-88.53) and the specificity was 96.74% (95% CI; 93.90-98.50).
Conclusion: This developed immunological test could be an efficient test in detecting IgG antibody response in PTB patients. Further this test could be useful for diagnosing AFB-negative presumptive TB cases.
Xanthomonas citri pv. eucalyptorum 4866-2_S43 strain (formerly X. axonopodis pv. eucalyptorum): Causal agent of bacterial leaf blight on eucalypt recovered in Argentina
We report here a draft genome assembly of strain 4866-2_S43 isolated from a eucalyptus lesion in Argentina and what until recently was caused by Xanthomonas axonopodis pv. eucalyptorum (Xae). The genome size is 5188607 bp with a G+C content of 64.66%. Comparative analysis reveals that the closest relative of strain 4866-2_S43 is Xae LPF 602 isolated in Brazil. Comparison of the whole genome sequences revealed an average nucleotide identity (ANI) of 99.96%. between the two strains. ANIs were determined between the whole genome sequence of strain 4866-2_S43 and the genomes of all currently validated Xanthomonas spp. These results revealed that strain 4866-2_S43 had greater than 95% with X. citri pv. citri and X. citri pv. phaseoli and less than 95% with X. euvesicatoria pv. alfalfae X. perforans and X. euvesicatoria pathovars euvesicatoria and eucalyptii.
PATHOGENECITY AND ENZYME SCREENING OF SOME SELECTED NON-DERMATOPHYTIC MOLDS
A total of 10 non-dermatophytic molds isolated from both symptomatic and asymptomatic cattle skin which includes Penicillum citrinum Aspergillus welwitschiae Aspergillus aculeatus Curvularia kusanol Cladosporium teniussmum Pestalotiopsis microspora Fusarium oxysporum Fusarium linchenicola Absidia sp. and Aspergillus fumigatuswere subjected to a pathogenicity test using albino mice. These isolates were also screened for five enzymes using standard plate method. Result from pathogenicity test showed that Absidia sp C. tenuissimum and Aspergillus welwitschiae were able to elicit discoloration lesion production and alopecia on the albino mice skin respectively which are evidences of clinical symptoms associated of cutaneous mycoses. The enzyme screening results revealed the highest zone of activity for keratinase (65mm) amylase (86mm) protease (60mm) lipase (60mm) and cellulase (86mm) which were observed on P. microspora A. welwitschiae C. tenuissimum A. welwitschiae and A. welwitschiae respectively. Pathogenicity test from this study shows that some of these molds may be virulent and that can be attributed to their ability to possess some virulent factors which includes secretion of hydrolytic enzymes.
Inducible clindamycin resistance among clinical Gram-positive cocci in a tertiary hospital in Niger Republic
Background. Macrolide-induced resistance to clindamycin is a well-described mechanism leading to treatment failure. Herein we determined the frequency and associated factors of inducible clindamycin resistance in Gram-positive cocci in a tertiary care hospital.
Methods. A cross-sectional descriptive study was carried out between January and December 2022. D tests were performed as recommended by EUCAST 2021 guidelines on 100 non-duplicate clinical isolates of Gram-positive cocci to determine the prevalence of methicillin resistance and inducible clindamycin resistance among the collected isolates.
Results. Of the 100 Gram-positive cocci isolates 56 (56.0 %) 17 (17.0 %) and 27 (27.0 %) were respectively coagulase-negative staphylococci Staphylococcus aureus and Streptococcus spp. Among Streptococcus spp. Group D Streptococci (15.0%) were the most isolated. Methicillin-resistant Staphylococcus aureus (MRSA) represented 9 (53.0 %) of S.aureus isolates. Constitutive (cMLSb) and inducible clindamycin resistance (iMLSb) phenotypes were detected in 36 (36.0%) and 14 (140%) of the isolates respectively. S. aureus exhibited 38.4% of cMLSb and 13.7% of iMLSb. The result of multivariate analysis showed that age groups gender type of samples provenance and bacteria were not significantly associated with Gram-positive cocci iMLSb phenotype.
Conclusion. The study reported for the first time a high prevalence of inducible resistance of Gram-positive cocci strains to clindamycin in Niger Republic. This suggests the urgent need for the implementation of regular screening of these isolates and the wise use of clindamycin in clinical practice.
Erysipelothrix spp. and other Erysipelotrichales detected by 16S rRNA microbial community profiling in samples from healthy conventionally reared chickens and their environment
Outbreaks of erysipelas a disease caused by infection with Erysipelothrix rhusiopathiae (ER) is a re-emerging problem in cage-free laying hen flocks. The source of ER infection in hens is usually unknown and serological evidence has indicated the presence of ER or other antigenically related bacteria also in healthy flocks. The aim of the present study was to evaluate sample collection culture methods and DNA-based methodology to detect ER and other Erysipelotrichales in samples from healthy chickens and their environment.
We used samples from a research facility with conventionally reared chickens with no history of erysipelas outbreaks where hens with high titers of IgY recognising ER previously have been observed. Microbial DNA was extracted from samples either directly or after pre-culture in nonselective or ER-selective medium. Real-time PCR was used for detection of Erysipelothrix spp. and high-throughput amplicon sequencing of 16S rRNA sequencing was used for detection of Erysipelotrichales. A pilot serological analysis of some Erysipelotrichales members with IgY from unvaccinated and ER vaccinated high biosecurity-chickens as well as conventionally reared chickens was also performed.
All samples were negative for ER E. tonsillarum and E. piscisicarius by PCR analysis. However 16S rRNA community profiling indicated the presence of several Erysipelotrichales genera in both environmental samples and chicken intestinal samples including Erysipelothrix spp. that were detected in environmental samples. Sequences from Erysipelothrix spp. were most frequently detected in samples pre-cultured in ER-selective medium. On species level the presence of E. anatis and/or E. aquatica was indicated. Serological results indicated that IgY raised to ER showed some cross-reactivity with E. anatis. Hence environmental samples pre-cultured in selective medium and analysis by 16S rRNA sequencing proved a useful method for detection of Erysipelotrichales including Erysipelothrix spp. in chicken flocks. The observation of such bacteria in environmental samples offers a possible explanation for the observation of high antibody titres to ER in flocks without a history of clinical erysipelas.
Galleria mellonella as a superficial model for Malassezia globosa and its treatment
Introduction. Malassezia globosa is a yeast species that belongs to the mycobiota of humans and animals associated with dermatological disorders such as dandruff. This is a chronic scalp skin disorder characterized by flaking and itching. Treatments include commercial shampoo with different formulations that contain antifungal activities like Zinc pyrithione or Piroctone Olamine. The effectiveness of these formulations have been evaluated for decades for dandruff symptom relief of volunteers. To date non-mammalian in-vivo methods exist to test formulations of these actives.
Aim. To evaluate in vivo in Galleria mellonella larva two commercial antifungal shampoos (Shampoo with 1% ZPT & 1.6% Zinc Carbonate and shampoo with 0.5% PO) against this species.
Methodology. G. mellonella larvae were inoculated with M. globosa on abraded cuticular surface. Then integument cell viability histological changes and fungal burden were evaluated.
Results. Larvae inoculated with M. globosa showed higher lesion melanization and tissue damage. In addition M. globosa population showed to increase over time. Concerning the shampoo’s effectiveness both formulations significantly reduced M. globosa burden and tissue damage.
Conclusion. G. mellonella larvae were allowed to evaluate M. globosa superficial infection and antifungal effectiveness. Shampoos with ZPT and PO showed a positive effect on inoculated larvae.
Retrospective analysis of Acinetobacter baumannii bacteraemia risk factors, complications, and mortality in a tertiary university hospital in Saudi Arabia
Introduction. Acinetobacter baumannii is a nosocomial pathogen of which many isolates are multidrug resistant. A. baumannii is a major cause of healthcare-acquired infections in patients who are critically ill and A. baumannii bacteraemia (ABB) is associated with high mortality. Several factors are known to play a role in A. baumannii transmission and the emergence of resistance.
Aim. This study aimed to retrospectively analyse ABB cases in Saudi Arabia where little is known about the prevalence risk factors clinical disease treatment outcomes and mortality associated with this infection.
Methods. A retrospective chart review was performed from January 1 2015 until December 31 2022 to identify all patients 14 years and above with ABB. Demographic and clinical data as well as results from laboratory analyses were collected from patients’ electronic charts. Statistical analyses were performed on the data to identify factors associated with 90-day mortality.
Results. In total 112 ABB cases were identified with a mean age of 58.0 years of which 66.1% were males. Of these cases 71 (63.4%) died. The factors that were found to be associated with 90-day mortality were the Charlson comorbidity score Pitt bacteraemia score quick Sequential Organ Failure Assessment (qSOFA) score (p < 0.001 for each) hospital ward (p < 0.02) short duration of antibiotic treatment (p < 0.01) and higher age (p < 0.05). The most common source of infection was Central Line-associated Bloodstream Infection in 52.7%. Also associated with mortality were inappropriate antimicrobial therapy (p < 0.02) and empirical use of colistin (p < 0.05). In many patients ABB was caused by carbapenem-resistant A. baumannii (CRAB) (69.6%) and 74.4% of those patients died.
Conclusion. CRAB is a growing threat in hospitals in Saudi Arabia especially in the critical care setting and carries a very high risk of mortality. Future studies should focus on novel ways of preventing CRAB infections and on the assessment of promising new antimicrobials such as cefiderocol or sulbactam-durlobactam and other treatment options such as bacteriophages.
Fatal Clostridium septicum gas gangrene complicating ECMO : case report and review of literature
Clostridium septicum gas gangrene is a severe and deadly infection caused by an anaerobic spore-forming Gram-positive bacillus. As previously described two entities are observed: traumatic and spontaneous (or non-traumatic) forms. In this report we aim to describe the case of a fulminant and ultimately fatal C. septicum myonecrosis occurring in a patient who was first admitted for refractory cardiac arrest and placed on veino-arterial extracorporeal membrane oxygenation (ECMO). Building upon prior studies that have documented cases of spontaneous gas gangrene caused by C. septicum we provide an updated compilation focusing on microbiological characteristics of C. septicum along with the diagnostic and therapeutic challenges associated with spontaneous gas gangrene. Additionally the specific clinical situation of our case illustrates the seriousness of this infectious complication that combined both spontaneous and traumatic gas gangrene risk factors. We thus discuss the antibiotic coverage prior to the initiation of ECMO procedure.
Isolation of Bioactive Compounds from Low-cost Agricultural Resources and its Utilization in Daily Life.
The ethanolic (80%) methanolic (80%) and aqueous decoction (100% distilled water) of whole plant of Oxalis corniculata Linn (Indian Sorrel) was evaluated for its anti‐microbial and antioxidant properties by in vitro methods. Methanolic (80%) and ethanolic (80%) decoctions showed significant antibacterial property against Staphylococcus aureus Bacillus subtilis Escherichia coli Salmonella typhi bacterial strains. In comparison to Chloramphenicol (C30) against bacteria 80% ethanolic decoctions showed significant effect among the decoctions. Nowadays though the standard soap is in a huge demand but it’s also facing major backlashes due to the presence of synthetic compounds in it which over long use may cause harmful effects on the skin health. Therefore the organic soaps which are made up of natural ingredients herbs or any sort ayurvedic compound have less side effects on the human skin and are much safer than standard daily soap. The formulated therapeutic soap exhibits significant amount of reducing potential (high FRAP and TAC values) and antioxidant activity (DPPH ABTS assay).
Identification of anaerobic and aerobic bacteria that can be associated with DFI and their therapeutic in Elnaw teaching hospital
Diabetic foot infection (DFI) is one of the commonest diabetic complications which considered a major public health concern around the world with the rising prevalence especially in developing countries. Globally adults with diabetes accounted for 463 million in 2019 according to the International Diabetes Federation.
The aim of this study was to identify the anaerobic and aerobic bacteria that causing DFI and their therapeutic regimen on diabetic patients in diabetic clinic room in Elnaw teaching hospital - Khartoum state.
The study showed that there was no infection by anaerobic organism and the most frequently isolated organisms were gram negative rods (70%) which represents (65%) on diabetic patients. The commonest isolated organism was S.aureus (30%) followed by E.coli (25%) in control group (non-diabetic) while Klebsiella.spp and S.aureus with (20%) for each; were isolated from the clinic room swabs.
Early diagnosis optimal management and effective antibiotic therapy are necessary to prevent DFI and amputation.
ELISA for leptospiral 3-hydroxyacyl-CoA dehydrogenase in urine is a promising screening tool for acute leptospirosis
Introduction: Leptospirosis is a zoonotic disease that is prevalent worldwide. The leptospiral 3-hydroxyacyl-CoA dehydrogenase (3-HADH) is excreted in the urine of infected individuals. However the potential use of 3-HADH as a biomarker for the diagnosis of leptospirosis using enzyme-linked immunosorbent assay (ELISA) has not been investigated. A technique that identifies Leptospira in a patient in urine sample will be valuable in regular diagnostics and epidemic scenarios as opposed to existing serological approaches. This study aimed to develop and evaluate an ELISA that can detect 3-HADH in the urine of patients with confirmed acute leptospirosis and to assess its potential as a screening test for leptospirosis.
Methods: Laboratory confirmation of acute leptospirosis was done by flaB-nested polymerase chain reaction (PCR) of plasma samples from suspected patients. ELISA-based determination of the presence of 3-HADH in the urine of PCR-positive patients versus PCR-negative patients matched for fever date was performed by coating ELISA plates with urine supernatants and using rabbit anti-3-HADH as the primary antibody. Receiver operating characteristic curve analysis was used to determine the cutoff values for the ELISA. The diagnostic measures between the PCR-positive and PCR-negative patients were compared using the Mann-Whitney U test.
Results: In total 158 febrile patients were assessed of whom 121 (76.6%) were male. Of the 15 flaB-nested PCR-positive patients 12 were in the acute phase of the febrile illness. The best cutoff was an average optical density (ODav) value of 0.2200 for febrile patients. Sensitivity and specificity were 83.33% (95% confidence interval [CI] 51.59–97.91%) and 83.33% (95% CI 76.05–89.13%) respectively. The ODav values for PCR-positive patients in the acute phase of the disease (≤7 days of fever) were significantly higher than those for PCR-negative patients (p<0.001 U=114.0 z= -4.946).
Conclusion: Detection of 3-HADH in urine by ELISA appears promising for the screening of acute leptospirosis in suspected patients.
A Case of Persistent Pasteurella Multocida Cellulitis Complicated with Large Endocarditis Vegetation
Introduction: A distinct and infrequent player emerges in the realm of infective endocarditis Pasteurella multocida now warranting careful consideration in this unique case report. Disseminated P.multocida infection seeded into the heart valve has only been reported in about one case per year worldwide with only 42 cases were found in the literature and only 5 cases reported to have underlying liver cirrhosis as in our case.
Case Presentation: A 73-year-old female with past medical history of liver cirrhosis secondary to primary biliary cholangitis with splenomegaly and pancytopenia presented to hospital with weakness fever and leg rash. She had recent admission with lower extremity cellulitis and P.multocida bacteremia treated with 14 days high dose oral amoxicillin-clavulanate after negative blood culture prior to discharge. The repeat blood culture showed P.multocida. Echocardiogram showed a 1.9 cm x 1 cm mobile mass attached to the mitral valve. She was not a suitable candidate for valve surgery due to her comorbidities. She was ultimately discharged with a two-week course of ceftriaxone continued with levofloxacin to complete six weeks of total treatment and followed by long-term penicillin.
Conclusion: In this case report we delve into a rare clinical presentation of Pasteurella multocida case. Our patient is the second reported case which showed complication of native mitral valve endocarditis even in the setting of bacteremia resolution. This report sheds light on the challenging diagnosis and management of this uncommon yet clinically significant condition highlighting the importance of vigilant and prompt intervention in endocarditis cases with atypical agents.
Cutaneous tuberculosis an unusual localization: A case report
Tuberculosis is a major public health concern. Morocco is a tuberculosis endemic country; nearly 30000 cases are recorded each year. Pulmonary tuberculosis accounts for 57% extrapulmonary tuberculosis 43%. Cutaneous localization is exceptional; it accounts for 0.5% to 2% of cases of tuberculosis. It is very difficult to diagnose given the variability of clinical presentation. We report a rare case of cutaneous tuberculosis in a patient with a history of pulmonary and cutaneous sarcoidosis.
Bloodstream infections in cancer patients in central India: study of pathogens and trend of antimicrobial resistance over five years
Bloodstream infection (BSI) is a prevalent complication with a high fatality rate in cancer patients. Over time and in different countries there are noticeable changing trends in the epidemiology of BSI. With this context our goal was to investigate the antibiogram and distribution of bacterial pathogens causing BSI in central Indian cancer patients. This single-center retrospective observational study was conducted in an Indian cancer hospital that offers tertiary care. Patients with solid organ and haematological cancers in both adults and children who had blood cultures sent to the microbiology laboratory were all included. In accordance with the recommendations of the Clinical and Laboratory Standards Institute (CLSI) blood cultures were processed using the BacT/ALERT 3D system (BioMerieux France) and identification of bacteria to species level and antimicrobial susceptibility (AST) was carried out using the Vitek 2 compact system (BioMerieux France). Electronic medical records and microbiology lab records were used to retrieve the demographic and microbiological data. Microsoft Excel (Microsoft Excel RRID: SCR_016137) was used to enter and tabulate the data while SPSS (RRID: SCR_002865) was used to conduct the statistical analysis. Hemato-lymphoid cancer had a higher culture positive rate than solid organ cancer. In cancer patients BSI was more frequently caused by gram-negative bacteria.
An improved genome editing system for Sphingomonadaceae
The sphingomonads encompass a diverse group of bacteria within the Sphingomonadaceae family with the presence of sphingolipids on their cell surface instead of lipopolysaccharide as their main common feature. They are particularly interesting for bioremediation purposes due to their capability to degrade or metabolise a variety of recalcitrant organic pollutants. However the research and development of their full bioremediation potential has been hampered because of the limited number of tools available to investigate and modify their genome. Here we present a markerless genome editing method for Sphingopyxis granuli which can be further optimised for other sphingomonads. This procedure is based on a double recombination triggered by a DNA double strand break in the chromosome. The strength of this protocol lies in forcing the second recombination rather than favouring it by pressing a counterselection marker thus avoiding laborious re-streaking or passaging screenings. Additionally we introduce a modification with respect to the original protocol to increase the efficiency of the screening after the first recombination event. We show this procedure step by step and compare our modified method with respect to the original one by deleting ecfG2 the master regulator of the general stress response in S. granuli. This adds onto the genetic tool repertoire that can be applied to sphingomonads and stands as an efficient option for fast genome editing of this bacterial group.
Seroprevalence of Herpes simplex virus Type-1 IgG antibodies among pregnant women with recurrent abortions
Herpes Simplex Virus Type 1 (HSV-1) is a nuclear replicating enveloped virus usually acquired through direct contact with infected lesions or body fluids (typically saliva). The prevalence of HSV-1 infection increases progressively from childhood and inversely related to socioeconomic background. The infections among children are either asymptomatic or following an incubation period of about 1 week gives rise to mucocutaneous vesicular eruptions. Herpetic gingivostomatitis typically affects the tongue lips gingival buccal mucosa and the hard and soft palate. The main aim of this study is to study the seroprevalence of herpes simplex virus type-1 IgG antibodies among pregnant women with recurrent abortions. The study demonstrated a 29 (58%) were positive HSV-1-IgG and 21 (42%) were negative among cases (pregnant women) while 25 (100%) in control subject were negatives and the possible risk factors i.e. age Abortion Blood transfusion Contraceptive Rash have been examined in this study and showed no effect except previous history of TORCH test examination. The study concluded more than half pregnant women was found to be infected in our study and we recommended to screen both IgM and IgG followed by viral detection and load by molecular technique in case of positive ELISA.
Invasive Streptococcus pyogenes Infection: A case report
The Group A Streptococcus also known as Streptococcus pyogenes is a human pathogen causing various infections ranging from mild such as tonsillitis and impetigo to severe and invasive conditions like septicemia and necrotizing fasciitis. Despite a decline in incidence and severity during the 20th century due to antibiotics there has been a reported increase in severe cases since the 1980s in industrialized countries.
Streptococcus pyogenes (S. pyogenes) is a human pathogen with a natural reservoir in the 26 pharynx and skin exhibits asymptomatic carriage in various body sites. It is responsible for a 27 spectrum of clinical manifestations from asymptomatic carriage to severe invasive infections. 28 Transmission occurs through respiratory droplets or direct contact with skin lesions. 29 Bacteriologically S. pyogenes is a gram-positive β-hemolytic streptococcus. This summary highlights a case of invasive Group A Streptococcus infection in a 28-year-old diagnosed at the microbiology laboratory of the Mohammed V Military Training Hospital in Rabat Morocco.
A 28-year-old patient with a history of chickenpox presented with acute febrile oligoarthritis. Following a recent flu-like syndrome and febrile tonsillitis the patient experienced asymmetric inflammatory oligoarthralgia affecting the left knee left ankle and right shoulder accompanied by functional impairment of the left lower limb. Upon admission clinical examination revealed swelling positive patellar tap and sternal involvement. Laboratory and imaging findings indicated an abscessed collection in the left knee and anterior mediastinitis. Emergency aspirations revealed Group A Streptococcus specifically Streptococcus pyogenes leading to a diagnosis of septic arthritis. Dual antibiotic therapy and knee joint drainage resulted in symptom resolution after 45 days.
The rise in severe Group A Streptococcus infection underscores the need for early detection and treatment. Widely sharing the French High Council for Public Health’s antibiotic prophylaxis recommendations is crucial for awareness. Collaborating between clinicians and microbiologists is essential for effective management.
Phenotypic and genotypic characterization of ESBL Enterobacteriaceae clinical isolates in a Moroccan hospital
Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) are a major public health problem in hospitals and in the community. The objective of this work was to describe the epidemiology of ESBL enterobacteria to study their resistance profile and to determine the genes encoding the ESBL phenotype.
This is a retrospective study conducted in the bacteriology laboratory of the Military Hospital of Instruction Mohamed V of Rabat and covering all isolates of Enterobacteriaceae from 01/01/2018 to 31/12/2020. The molecular study of ESBL genes involved a representative sample of all ESBL isolates.
The overall prevalence of ESBLs in isolated Enterobacteriaceae (1402/10268) is 13.65%. The urinary tract was the main site of isolation of ESBL (61%). The bacterial species most concerned are essentially Escherichia coli (419%) Klebsiella pneumoniae (422%) and Enterobacter cloacae (119%). The study of antibiotic susceptibility showed a resistant profile marked mainly by 100% resistance to C1G and C3G 55% to piperacillin-tazobactam 16% to imipenem 87% to fluoroquinolones. Molecular typing of ESBL strains showed a prevalence of CTX-M (95%) SHV (50%) and TEM (56%). The CTX-M-1 and the CTX-M-9 groups were the most common (9619% and 762 % respectively) and CTX-M15 was found in 7810% CTX-M-1 ESBL positive isolates. Most strains had more than two coexisting resistance genes.
The prevalence rate of ESBL-E is critical and preventive action at different levels (prescriber biologist hospital patient etc.) is necessary in order to limit their spread and to manage a better therapeutic strategy.
Molecular characterization of HBV infected Nigerians reveal diverse mutational profiles within the BCP/PC regions
Background; Hepatis B virus (HBV) is the most implicated cause of severe liver disease and hepatocellular carcinoma worldwide. Studies have shown that the basal core protein (BCP) and pre-core protein (PC) of HBV play a significant role in HBV related carcinogenesis. There is paucity of data on type and effect of BCP and PC mutations in Nigeria. This study aims to genotype HBV and investigate any mutations within the BCP and PC among HBV patients in Ibadan Nigeria.
Methods; Forty HBV DNA positive were recruited into this study viral load assay and genotyping by nested multiplex PCR was done. The partial X gene region was amplified and Sanger sequenced. The BPC and PC genomic regions were then analyzed using bioinformatics.
Results; Twenty-three participants recorded HBV DNA viral load of >20000 International Units (IU) while 17 had <20000 IU while 28 samples were genotyped. Five genotypes A B C D and E and 4 mixed genotypes AC AD ACD and ABCD were detected. Genotype AC was the most frequently encountered while genotypes E and B were the least encountered. Mutation was highest in ages 34 to 45 years. Double mutation A1762T and G1764A within the BCP region was the most encountered mutation.
Conclusions; We report a diverse HBV genetic landscape with mixed infections between genotypes with BCP double mutation A1762T/G1764A signaling the likelihood of poor HBV related liver disease prognosis. Our findings contribute to our understanding of the molecular characteristics of HBV and its potential implications for disease progression and management among HBV infected Nigerians.
Comparative genome analyses of Staphylococcus aureus from platelet concentrates reveal rearrangements involving loss of type VII secretion genes
Staphylococcus aureus has been involved in transfusion-transmitted fatalities associated with platelet concentrates (PCs) due to its heightened pathogenicity enhanced by genome-encoded virulence and antibiotic resistance genes. This may be facilitated by mobile genetic elements (MGEs) that can cause rearrangements. Several factors contribute to S. aureus virulence including the type VII secretion system (T7SS) which is comprised of twelve genes six of which form the T7SS core and are conserved across S. aureus strains. In this study we conducted comparative genome analyses of five S. aureus isolates from PCs (CI/BAC/25/13/W PS/BAC/169/17/W and PS/BAC/317/16/W were detected during PCs screening with the BACT/ALERT automated culture system and ATR-20003 and CBS2016-05 were missed during screening and caused septic transfusion reactions). Multiple alignments of the genomes revealed evidence of rearrangements involving phage ɸSa3 in PS/BAC/169/17/W and PS/BAC/317/16/W. While the former had undergone translocation of its immune evasion cluster (IEC) the latter had lost part of the phage leaving behind the IEC. This observation confirms S. aureus genome plasticity. Unexpectedly strain CBS2016-05 was found to encode a pseudo-T7SS that had lost five of the conserved core genes (esxA esaA essA esaB and essB) and contained a 5’ truncated essC. Since these genes are essential for the function of the T7SS protein transport machinery which plays a key role in S. aureus virulence CBS2016-05 probably compensates by recruiting other export mechanisms and/or alternative virulence factors such as neutralizing immunity proteins. This study unravels genome rearrangements in S. aureus isolated from PCs and reports the first S. aureus isolate lacking conserved T7SS core genes.
Trends and antibiotic susceptibility patterns of diarrhoeal pathogens - an experience of fourteen years in Southern India
INTRODUCTION:
Enteric pathogens contribute largely to morbidity in a developing country like India. Early and prompt diagnosis of diarrhoeal diseases can reduce the mortality rate particularly in children. The pattern of sensitivity to antimicrobials for the common pathogens can vary from time to time. The present study was conducted to study the pathogen distribution and antimicrobial susceptibility pattern during the study period (January 2010 to December 2023).
HYPOTHESIS/GAP STATEMENT:
Studying the changing trend in the antimicrobial sensitivity pattern of diarrhoeal pathogens over a decade can help to plan future treatment options.
AIM:
This study was undertaken to provide insight into the changing pattern of pathogen distribution and antimicrobial susceptibility of enteric pathogens over 14 years.
METHODS:
A retrospective observational cohort analysis was conducted on all the stool pathogens isolated from the samples received in the Microbiology department of a tertiary care hospital from the year 2010 to 2023. The demographic details stool microscopy culture reports and antimicrobial susceptibility patterns were noted.
RESULTS:
18336 stool specimens were received in the Microbiology laboratory between January 2010 to December 2023. A total of 591 Salmonella 471 Shigella181 Vibrio and 80 Aeromonas species were isolated. 93% of Salmonella species 89% of Shigella species and 95 % of Vibrio species were susceptible to Ceftriaxone.91% of Aeromonas isolates were susceptible to Chloramphenicol. Some major parasites were also observed on microscopy.
CONCLUSION:
Timely diagnosis of diarrhoeal pathogens can be life-saving for patients belonging to extremes of age. Pathogens can exhibit a changing susceptibility pattern to antibiotics which should be regularly observed to plan future therapy.
Effect of CHIKV capsid protein nucleolar localisation on host gene modulation
Host cell nuclear localisation of alphaviral proteins has been shown to be important for host transcriptional shut off antagonising type I interferon induction and inhibiting the antiviral response. Our previous studies demonstrate that mutation of the nucleolar localisation sequence (NoLS) of chikungunya virus (CHIKV) capsid protein significantly attenuates CHIKV replication. However the reason for this attenuation remains unclear. In this study we investigated the impact of CHIKV capsid protein on host gene expression using Nanostring analysis and determined whether nucleolar localisation of capsid protein is required for host gene modulation. Little significant change in differential gene expression (adjusted p value <0.05) was observed in Capsid-WT-EGFP and mutant Capsid-NoLS-EGFP transfected HEK293T cells compared to mock EGFP transfected cells. To explore minor changes to host gene modulation in response to capsid protein differential gene expression analysis was performed under a reduced arbitrary threshold (unadjusted P value < 0.01). Results suggest that expressed as a recombinant protein CHIKV capsid has limited impact on host gene expression regardless of its ability to localise to the nucleolus. Results further suggest that attenuation of CHIKV resulting from mutation of the capsid protein NoLS is largely dependent on viral rather than host factors.
Multiple novel Caliciviruses identified from stoats (Mustela erminea) in the United Kingdom
The Caliciviridae family comprising positive-sense RNA viruses is characterised by its non-enveloped small virions broad host range and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from Stoats (Mustela erminea) identifying two novel Calicivirus species tentatively named Stoat vesivirus and Stoat valovirus. Stoat vesivirus was identified in three samples (ST008 ST006 ST004) exhibiting a genome wide nucleotide identity of approximately 92%. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length respectively. Each comprised three open reading frames (ORF) closely resembling the Vesivirus mink calicivirus (China/2/2016) with 70-72% similarity in ORF1 61-62% in ORF2 and 71% in ORF3. Phylogenetic analysis robustly supported Stoat vesivirus as belonging within the Vesivirus genus. The second Calivicirus (Stoat valovirus) detected solely in sample ST008 was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valerien swine virus and Marmot norovirus HT16 showing 39.5% and 38.8% protein identity with ORF1 and 43.3% and 42.9% for VP1. Phylogenetic analysis suggested that while Stoat valovirus is borderline for new genus demarcation criteria with greater than 60% divergence at ORF1 it clusters basally within the Valovirus genus supporting its inclusion in this genus.
First Case Report of Disseminated Gonococcal Arthritis in Newfoundland & Labrador
Introduction: Disseminated gonococcal infections (DGIs) are a rare but often debilitating complication of N. gonorrhoeae infections. Often presenting as arthritis-dermatitis syndrome true suppurative joint infections are an even more rare form of DGI. Here we present the first known case of DGI in Newfoundland and Labrador in over 10 years.
Case report: A 50-year-old man who is known to inject drugs with multiple housing and social challenges presented to the emergency department with a two-day history of an isolated painful erythematous knee. After being assessed by orthopedics and undergoing an operative debridement intraoperative cultures grew N. gonorrhoeae. He was treated with IV ceftriaxone and his course in hospital was complicated by inadequate pain control and a lack of stable housing.
Conclusion: DGIs while rare need to remain on any clinician’s differential for septic arthritis given the increasing prevalence of gonorrheal infections in Canada and in Newfoundland and Labrador. In addition patients who are at risk of delaying accessing care such as people who inject drugs and unhoused individuals are at higher risk of complicated hospital stays.
Modelling SARS-CoV-2 infection in a human alveolus microphysiological system
The COVID-19 pandemic has highlighted the importance of physiologically relevant in vitro models to assist preclinical research. Here we describe the adaptation of a human alveolus microphysiological system (MPS) model consisting of primary human alveolar epithelial and lung microvascular endothelial cells to study infection with SARS-CoV-2 at Biosafety Level 3 (BSL3) facility. This infection model recapitulates breathing-like stretch and culture of epithelial cells at the air-liquid interface (ALI) and resulted in clinically relevant cytopathic effects including cell rounding of alveolar type 2 cells (AT2) and disruption of the tight junction protein occludin (OCLN). Viral replication was confirmed by immunocytochemical nucleocapsid staining in the epithelium and increased shedding of SARS-CoV-2 virus within two days post-infection associated with changes in innate host immune responses. Together these data demonstrate that under the experimental conditions used in this work this human alveolus MPS chip can successfully model SARS-CoV-2 infection of human alveolar lung cells.
Epidemiological and virological characteristics of people living with HIV on antiretroviral treatment for more than six months in virological failure in Brazzaville, Republic of Congo
Introduction Virological failure is one of the major causes of treatment failure and better management of HIV infection requires understanding and controlling the factors that contribute to this phenomenon. The main objective was to characterize the patients of the active file of the Brazzaville Outpatient Treatment Center in virological failure in order to identify predictive factors that lead to virological failure.
Methods This was a cross-sectional study conducted between June and December 2020. Patients enrolled were HIV-1 infected patients from the Brazzaville Outpatient Treatment Center receiving a potent combination therapy for at least 6 months but experiencing virological failure. Viral load was determined with the automated Abbott Real-time HIV-1 m2000rt System. Sociodemographic and clinical data were collected from a computerized patient record software called Santia. Statistical analysis was performed to identify independent predictors of virological failure.
Results A total of 109 patients with virological failure were recruited. The median age of the patients was 45 years (IQR: 37-52 years) and women were more represented (74%). More than half of the patients had WHO stage IV HIV and the median duration on ARV treatment was 96 months. The most followed treatment regimen was AZT+3TC+EFV (or NVP) with 48% while the median viral load was 12985 copies/mL.
Conclusion In our study we did not identify any sociodemographic or clinical variables predictive of virological failure. However we felt that it would be desirable to carry out a study with temporal follow-up and the possibility of sequencing in order to identify the different circulating genotypes and resistance mutations.
HIV-DRIVES: HIV Drug Resistance Identification, Variant Evaluation, & Surveillance Pipeline
The global prevalence of resistance to antiviral drugs combined with antiretroviral therapy (cART) emphasizes the need for continuous monitoring to better understand the dynamics of drug-resistant mutations to guide treatment optimization and patient management as well as check the spread of resistant viral strains. We have recently integrated next-generation sequencing (NGS) into routine HIV drug resistance (HIVDR) monitoring with key challenges in the bioinformatic analysis and interpretation of the complex data generated while ensuring data security and privacy of patient information. To address these challenges here we present HIV-DRIVES (HIV Drug Resistance Identification Variant Evaluation and Surveillance) an NGS-HIVDR bioinformatics pipeline that has been developed and validated using Illumina short-reads FASTA and Sanger ab1.seq files.
Reducing Blood Culture Contamination Rates: Introduction of a Combined Education and Skin Antisepsis Intervention
Background Blood culture contamination (BCC) is an important quality concern in clinical microbiology as it can lead to unnecessary antimicrobial therapy in patients and increased workload for laboratory scientists. The Clinical Laboratory and Standards Institute recommend BCC rates to be <3% and recently updated guidelines have set a new goal of 1%. The aim of this project was to design and implement interventions to reduce BCC rates at our institution.
Methods We introduced a combined education and skin antisepsis intervention in a large Model 4 academic teaching hospital in the South of Ireland. BD ChloraPrep™ skin antisepsis applicators (2% chlorhexidine gluconate/70% isopropyl alcohol) licensed for use for blood culture collection were introduced replacing Clinell® (2% chlorhexidine gluconate/70% isopropyl alcohol) wipes. In addition a multimodal education programme was designed and delivered. This consisted of a video demonstrating the recommended blood culture collection technique using the new applicators as well as simulation training for all interns. The video was uploaded to the intranet as an educational resource available to all staff.
Results The interventions were implemented in July 2022 and BCC rates pre- and post-intervention were calculated. The average BCC rate for the 12 months preceding the intervention (July 2021-July 2022) was 2.56% with highest rates in the emergency department. This compared to an average rate of 2.2% in the 12 months post-intervention (July 2022-July 2023). In comparing the two rates the reduction in BCC rates between the two periods was not statistically significant (p=0.30).
Conclusion Overall BCC rates reduced but the difference between the two periods did not reach statistical significance. The resource intensive nature of providing regular and timely feedback of contamination rates and the larger impact of in–person education and training over virtual modalities may explain the modest reduction. Further investments in these areas particularly in the emergency department will be necessary to further reduce rates in line with new recommendations.
Virucidal activity of olanexidine gluconate against SARS-CoV-2
Antiseptics have been used for infection control against SARS-CoV-2. Ethanol (EtOH) was effective against SARS-CoV-2 while chlorhexidine gluconate (CHG) was less effective. Therefore there may be differences in virucidal activity between classes of antiseptic agents. Aim: In this study we evaluated the efficacy of antiseptics against SARS-CoV-2 and identified effective agents for infection control. Methods: The following antiseptics were used in this study: 1.5% olanexidine gluconate (OLG); 80% EtOH; 1% sodium hypochlorite (NaClO); 0.2% benzalkonium chloride (BKC); 1% povidone-iodine (PVP-I); 0.5% 1% and 1.5% chlorhexidine gluconate (CHG); and 0.5% alkyldiaminoethylglycine hydrochloride (AEG). Virucidal activity was evaluated at 0 30 s 1 2 and 3 min according to EN14476. Results: After 30 s of exposure 1.5% OLG 80% EtOH 1% NaClO 0.2% BKC and 1% PVP-I inactivated SARS-CoV-2 below the detection limit. In contrast the virus was survived in 0.5% CHG 1% CHG and 0.5% AEG after 3 min of exposure. However the virucidal activity of 1.5% CHG was insufficient after 30 s of exposure. Conclusion: This study showed that the virucidal activity against SARS-CoV-2 differs depending on the class of antiseptic agent. Despite belonging to the same class of biguanide antiseptics OLG was more effective against SARS-CoV-2 than CHG.
Gummatous mitral valve endocarditis from tertiary syphilis
A 50-year old Romanian gentleman presented with fever myalgia and 30kg weight loss. He was treated for syphilis previously after acquiring it from his ex-wife 16 years ago. On examination there was a pansystolic murmur in the axilla and the patient had an ataxic gait. Blood tests showed raised inflammatory markers. However standard investigations for infective endocarditis including multiple blood cultures serological titres for fastidious organisms and antibody tests were negative.
CT of the chest abdomen and pelvis demonstrated hepatosplenomegaly with multiple splenic infarcts. MRI of the head with contrast showed multiple punctate enhancement in the bilateral hemispheres with leptomeningeal enhancement. Transthoracic echocardiogram demonstrated large vegetation leading to severe mitral regurgitation. Serum treponemal antibodies were positive; TPPA was positive at 1:1280 and RPR: 1:4 Treponemal IgM was negative; lumbar puncture syphilis serology was negative. The patient was treated with an extensive period of intravenous antibiotics in addition to a prosthetic metallic valve replacement where unusual ragged calcified valvular tissue was observed.
Tertiary syphilis is a difficult diagnosis to confirm since it can often be indolent and occur in areas of the body where they may go unnoticed. In our case a diagnosis of syphilitic endocarditis was made from a combination of the history an initial increase in size of the lesion following antibiotic therapy and observation of likely gumma on the mitral valve during surgery. In such cases surgery in addition to optimal antimicrobial therapy is necessary for effective treatment.
Antimicrobial activity of CO2 and Er:YAG lasers against Staphylococcus aureus and Escherichia coli
The antimicrobial effect of CO2 and Erbium-doped yttrium aluminium garnet (Er:YAG) lasers against Escherichia coli Staphylococcus aureus and a mixed culture of both organisms was assessed. Bacterial isolates were exposed to lasers utilising a range of parameters. Both lasers demonstrated a reduction in bacterial viability with increased number of passes and increased power. Against the individual bacterial cultures the CO2 laser demonstrated greater a reduction in bacterial numbers with higher density and pulse durations. At a lower power and pulse duration the CO2 laser demonstrated a complete reduction against combined bacterial species with increased passes. Use of the Er:YAG laser against the individual bacterial species demonstrated that the reduction in bacterial viability was increased with an increased overlap. The Er:YAG laser was the most effective at reducing the bacterial co-cultures and was influenced by the power overlap and number of passes. Throughout this study S. aureus was more difficult to eradicate than E. coli. The findings from this work showed promising antimicrobial effects of both the CO2 and Er:YAG lasers and demonstrates that the use of such instruments is one potential avenue to be explored to develop effective novel therapies to reduce bacterial viability in infections.
Bacillus subtilis comparative genomics
As a producer of industrial enzymes and secondary metabolites Bacillus subtilis is generally considered to be more beneficial for humans animals and notably industry. Consequently it is imperative to investigate various Bacillus spp at the genome level. The comparative genomics of Bacillus spp is the subject of this manuscript. Wherein various Bacillus spp genomes were collected and examined. The sources of the bacteria included fermented foods soil and liquid wastes. A wide range of bioinformatics resources and tools were used in the study for genome annotation assembly and comparison. The isolate B. subtilis S2 is closely linked to the B. subtilis SRCM103571 and B. subtilis SRCM104005 species cluster according to the phylogenetic tree analysis. The WGS is also unique in that it produces two bacteriocins Sublancin and Subtilosin A according to antiSMASH & BAGEL-4 analysis. Subsequent investigation revealed that it has the fewest rRNA -just nine-and tRNA -72. However at 4438 it has the highest number of genes which makes the S2 strain distinct at the genome level. We conclude by noting the different nature of B. subtilis S2.
Phenotypic Characterization of Carbapenem-Resistant Enterobacteriaceae in Presumptive Tuberculosis Patient across One Health Interface
Introduction: Globally Nigeria remains one of the 30 countries highly burdened with tuberculosis (TB) TB/Human immunodeficiency virus and multidrug-resistant TB (MDR-TB). Objective: This study aimed to characterize carbapenem-resistant Enterobacteriaceae (CRE) in presumptive tuberculosis patients across one health interface. Methods: Sixty-six sputum samples from presumptive tuberculosis patients fecal samples of animals loitering the hospital and environmental soil samples were collected and characterized. Isolated Enterobacteriaceae were screened for multidrug resistance and characterized for carbapenemase production. Result: Fifty-seven enterobacteriaceae were isolated from 66 samples of sputum fecal and soil samples. The frequency of occurrence of Klebsiella pneumoniae was 66.7% and 100% in sputum and fecal samples respectively while 60% of the soil sample was Proteus mirabilis. Multidrug resistance was exhibited with ceftizidime showing the highest resistance of 100% augumentin (95.7%) and nitrofurantoin (59.6%) in sputum samples. Animal and fecal samples showed similar resistance patterns to antibiotics with gentamicin cefixime augementin and nitrofurantin. Majority (70.2%) were carbapenemase-producing Enterobacteriaceae while only 34% were producing metallo-beta lactamase from sputum samples. Conclusions: The interconnectivity and frequency of CRE occurrence was found to be high in this study across the three pillars of One Health.
Bacteriological profile of community peritonitis operated in a Moroccan Hospital
Introduction. Peritonitis is characterized by acute inflammation of the peritoneum often resulting from digestive organ perforation or intra-abdominal septic focus. It may be either of infectious or noninfectious origin. The germs involved are those of the digestive flora (Enterobacteriaceae and Anaerobic) while gram-positive cocci and yeasts can be isolated in nosocomial infections. Our study aims to isolate and identify the germs involved in community-acquired peritonitis in order to assess their susceptibility to the antibiotics available in our Country.
Methods. This is a retrospective study of bacteriological profile of community peritonitis in Rabat Morocco. A total of 150 adult patients with peritonitis were admitted and samples were collected intraoperatively for bacteriological examination between July 1 2022 and April 30 2023.
Results. Among the 150 patients 101 (67.8%) were males and 48 (32.2%) were females with sex/ratio of 2.1. The mean age of the patients was 40.5 years +/- 20.12. The distribution of germs was dominated by Escherichia coli (44%). Overall 70% of Escherichia coli isolated had a resistance to Ampicillin but no resistance to Ampicillin has been reported by Enterococcus.
Discussion. In the present study we were interested in the bacteriological profile of community peritonitis in order to adapt the antibiotic therapy to our bacterial ecology. Our findings indicate a concerning trend of increasing resistance among Escherichia coli to the commonly used Amoxicillin/Clavulanic Acid combination in our clinical setting.
Conclusion. Consequently there is a need to reassess the empiric antibiotic prescribed for the management of community-acquired peritonitis.
Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial.
Even though dietary fibers are often used as prebiotic supplements in dogs the effect of individual types of fibers on canine microbiota composition is unknown. The objective of this study was to assess changes in fecal microbiota richness diversity and taxonomic abundance with 3 different fiber supplements in dogs. These were psyllium husk resistant starch from banana flour and methylcellulose. They were administered to 17 healthy dogs in a cross-over trial after transition to the same complete feed. Fecal scores and clinical activity indices were recorded and fecal samples collected before and at the end of supplementation as well as 2 weeks after each supplement (washout). Illumina NovaSeq paired-end 16S rRNA gene sequencing was performed on all samples. After quality control and chimera removal alpha diversity indices were calculated with QIIME. Differences in specific taxa between groups were identified using Metastats. Methylcellulose significantly increased fecal scores but had no effect on microbiota. Psyllium resulted in minor changes of specific taxa abundance but with questionable biological significance. Resistant starch reduced microbiota richness and resulted in the most abundant changes in taxa mostly a reduction in short-chain fatty acid producing genera of the Bacillota phylum with an increase in genera within the Bacteroidota Pseudomonadota Actinomycetota and Saccharibacteria. In conclusion while psyllium and methylcellulose led to few changes in the microbiota composition the taxonomic changes seen with resistant starch may indicate a less favorable composition. Based on this the type of resistant starch used here cannot be recommended as a prebiotic in dogs.
Investigating the impact of temperature on growth rate of the root rot fungus, Gymnopus fusipes
Gymnopus fusipes is an understudied root rot pathogen associated with multiple tree species and is linked to episodes of oak decline across the United Kingdom and Europe. Although the reported distribution of G. fusipes is broad many observations rely solely on visual identification of fruiting bodies which can be unreliable and lack confirmation by molecular and/or isolation data to verify this broad ecological range. Given the paucity of information regarding the true ecological distribution of G. fusipes it is difficult to predict and model the potential distribution of the species under both current and future climate scenarios. In this study to determine the growth capabilities of G. fusipes across a range of ecologically relevant temperatures five geographically diverse isolates of G. fusipes were grown at five different temperatures ranging from 4˚C to 37˚C to determine the optimal temperature for G. fusipes growth and to establish whether geographically diverse isolates exhibit local adaptation to temperature tolerance. Incubation temperature had a significant effect on G. fusipes growth rate with 25˚C representing the optimum (p < 0.001). Isolates had differing growth rates at each of the temperatures with an isolate from the UK having the highest overall growth rate across all five temperatures tested (p < 0.001) and at the optimum increased by a mean value of over 4915 mm2. Local adaptation to temperature tolerance was not found in the isolates tested. These data demonstrate the optimal incubation temperature for future laboratory studies on G. fusipes and provide the first data on the growth rate of this pathogen across ecologically relevant climate ranges that may inform land managers modellers and policy makers in predicting the current and potentially future geographical limits of this widespread root rot pathogen.
Fannyhessea vaginae causing bacteraemia and vertebral osteomyelitis: first report of invasive disease in a male
Introduction. Fannyhessea vaginae (formerly Atopobium vaginae) is an anaerobic organism commonly associated with female genital flora with rare cases of invasive disease reported in females.
Case report. We discuss the case of an 81-year-old male who presented with an acute history of back pain and signs of urinary tract infection in the context of intermittent self-urinary catheterisation. Multiple blood cultures grew Fannyhessea vaginae with a later finding of lumbar vertebral osteomyelitis as the cause of back pain. Treatment was commenced with ampicillin later switched to ceftriaxone with improvement of acute signs of infection.
Conclusion. Gram positive anaerobic organisms including Fannyhessea vaginae are possibly under-recognised causes of urinary tract particularly in older males. These bacteria may prove challenging to grow in standard protocols for urine culture; anaerobic or extended incubation could be considered particularly in complicated cases of urinary tract infection without an identifiable pathogen.
Disseminated hydatidosis an unusual presentation: A case report
Hydatidosis also known as cystic Echinococcosis is a widespread zoonosis caused by a tapeworm of the genus Echinococcus. It presents a significant public health concern particularly in endemic areas. The occurrence of disseminated hydatid disease is uncommon even in regions where it is endemic with an incidence ranging from 1 to 8%. The definitive diagnosis relies on parasitological method. In this work we present an unusual case of disseminated hydatid disease that was diagnosed in the central parasitology-mycology laboratory of “The Ibn Sina University Hospital”. This is a 21-year-old patient residing in a rural area who presented with heaviness-type pain in the right hypochondrium accompanied with nausea and vomiting. During the examination the patient mentioned the contact with dogs. Abdominal radiography (Ultrasound and CT) revealed findings suggestive of multiple hydatid cysts located in the liver and peritoneum. This suspicion was confirmed by positive hydatid serology. After 9 months of treatment with albendazole the patient underwent surgery for excision of the cysts shown on the x-ray as well as other cysts incidentally discovered intraoperatively at the pelvic and rectal levels. All of the extracted specimens were sent to the parasitology laboratory. The direct examination along with the viability test revealed the presence of hooks and scolex of non-viable Echinococcus granulosus. Disseminated hydatidosis is a rare but serious presentation and the positive diagnosis relies on several epidemiological clinical radiological and parasitological arguments. Medical and surgical treatments play a crucial role in determining the patient's prognosis.
Clinical Presentation and Outcome of Enteric Fever in Adult Patients with Cancer; A Perspective from Pakistan
Introduction:
Enteric fever is a significant health concern in endemic countries. While extensive research has been conducted to understand its presentation and outcomes in non-cancer patients limited data exist on its impact on cancer patients. This descriptive study aims to investigate the clinical presentation and outcome in cancer patients.
Methodology:
This retrospective observational study analysed 90 adult cancer patients from a single centre in Pakistan from January 2017 to December 2022. Inclusion criteria involved documented blood culture infections with Salmonella typhi or paratyphi A B or C. We examined clinical presentation laboratory parameters antimicrobial resistance complications and outcomes. Additionally we explored the effects of chemotherapy comorbidities type of malignancy and patient age on complications and mortality.
Results:
Salmonella typhi was the most prevalent organism (72.2%) followed by Salmonella paratyphi A (22.2%) and B (5.5%). Non-resistant isolates constituted 51.5% multi-drug resistant (MDR) isolates accounted for 20% extensively drug resistant (XDR) for 14.4% and ESBL-producing for 15.5% of all enteric fever infections.. Enteric fever-associated complications were observed in 21.1% of cases. Chemotherapy in the preceding month did not affect mortality nor did age gender or malignancy type. However comorbidities were statistically significant for mortality (p-value 0.03). A total of 8.8% of patients required ICU care and the all-cause 30-day mortality rate was 13.3%
Conclusion:
Enteric fever remains prevalent in our geographical region. Unlike Non-Typhoidal Salmonella (NTS) enteric fever does not behave differently in an immunocompromised population including cancer patients.
The role of nutrition in the pathogenesis of neglected tropical diseases: systematic review and meta-analysis
Background: According to the WHO neglected tropical diseases (NTDs) affect over 2 billion people worldwide. While the links between nutrition and many diseases have become clear over recent decade NTDs have lagged behind and the linkage with nutrition is largely unknown. We conducted this systematic review with meta-analysis to determine the current status of research on the role of diet in the pathogenesis of NTDs.
Methodology: PubMed Embase Scopus and African Journal online databases were searched using predefined search terms. We included all original articles with a case-control design and at least one NTD. The studies had to compare the nutritional parameters between the infected and uninfected. Articles that did not report original data were excluded. The quality of the studies was assessed using the Newcastle-Ottawa scale. Pooled estimates were conducted using the random-effects model. The publication bias of studies was determined by funnel plots. Q and I2 statistics were used to assess the heterogeneity of the studies.
Results: After screening 1294 articles only 16 qualified for the systematic review and 12 for meta-analysis. These predominately had a focus on soil-transmitted helminthiasis (ascariasis hookworm diseases trichuriasis) and schistosomiasis with a minority concerning leishmaniasis and leprosy. Pooled estimates showed an association between intestinal parasites and stunting in children (OR= 1.38 95%CI: 1.14-1.66 I2 = 0%). We also identified a moderate association established between blood iron deficiency (OR=4.67 95%CI: 1.91-11.44) and intestinal parasites.
Conclusions/Significance: Of the 20 NTDs the links between diet and disease have been explored only for a very few. There is a paucity of data from low and middle-income countries and least developed countries where the NTD burden is high. Therefore more research into the role of nutrition in NTD infection is recommended.
The Microbiome of C. elegans Enhances Growth of S. aureus During Infection
Staphylococcus aureus is a significant human pathogen associated with a wide range of infections. The microbiome consisting of diverse microbial communities has been recognized as a critical factor in modulating host-pathogen interactions. This study aimed to investigate the role of the Caenorhabditis elegans microbiome in Staphylococcus aureus infection by transferring worms from the standard laboratory food source (OP50) or a microbiome sample to S. aureus cultures. Our findings revealed that the C. elegans microbiome paradoxically enhanced Staphylococcus aureus colonization resulting in increased pathogen burden compared to worms transferred from E.coli OP50. These results underscore the importance of the microbiome in modulating host susceptibility.
Genomic analysis of Oceanotoga teriensis strain UFV_LIMV02, a multidrug-resistant thermophilic bacterium isolated from an offshore oil reservoir
Bacteria of the species Oceanotoga teriensis belong to the Family Petrotogaceae are moderately thermophilic and are included in the group of thiosulfate-reducing bactéria (TRB) being able to accelerate corrosion in metallic structures significantly. The O. teriensis strain UFV_LIMV02 was isolated from water samples from the separator of an offshore oil extraction platform in the Campos basin in Rio de Janeiro (Brazil). In this work we describe the man phenotypic and genotypic characteristics mainly related to hydrogen sulfide production and antimicrobial resistance to different classes of antibiotics. We also systematically investigate the presence of CRISPR-Cas loci and prophages. Through H2S titration it was possible to verify thexistence of 150 ppm of hydrogen sulfide in the solution. It presented a genome with 2812778 bp in size with 26% of GC content organized into 34 contigs 2629 genes encoding candidate proteins and identified 51 genes of different RNAs. The search for CRISPRs systems in the genome of the isolate allowed us to identify the presence of four CRISPRs arrays classified as type I-B and III-B with the presence of 272 different spacers which could provide the strain with immunity to other mobile genetic elements and infection by bacteriophages. Genomic analysis using RAST revealed the presence of resistance genes for the class of beta-lactams and fluoroquinolones; however when evaluating the antimicrobial resistance of the isolate using the disk diffusion technique it was possible to confirm not only the resistance to B-lactams and fluoroquinolones but also to four other classes of antibiotics: aminoglycoside sulfonamide lincosamide and rifamycin a total of 14 antibiotics probably due to the presence of mechanisms capable of expelling the antibiotic from the cells such as efflux pumps allowing them to grow in the presence of these antimicrobials. The results found in this study provide indications that residues from offshore oil exploration may represent a risk for the dissemination of ARGs due to the presence of multidrug-resistant bacteria. More comprehensive studies are needed on the microbial community present in oil tailings to assess the risks to public health.
Science in Schools: combining language and microbiology engagement during a pandemic
This paper presents an public engagement pedagogy designed to engage Key Stage-one and -two students. The activities were developed for a British Council Science-in-Schools visit allowing UK-based researchers to visit French territory schools delivering activities in English. Focusing on infection transmission our event aimed to enhance understanding of infection transmission concepts (coughing sneezing handwashing and surface contamination). Additionally we hosted a "masterclass" session for teachers demonstrating the activities and discussing their integration into classroom settings. Here we present lesson plans for both student- and teacher-focused sessions and detailed protocol and demonstration video for each activity. We also include vocabulary lists and flashcards which were used within the sessions to aid student comprehension of the activities and support further discussion around key concepts and findings. Finally we present a brief reflective evaluation of the visit and offer considerations for others wishing to use the materials as part of their pedagogy practice. There was a positive reception to the activities among both students and teachers. Here the activities were used with French-speaking students developing English language skills but we believe that these activities could be used with a wide range of ages scientific literacy and event types. In conclusion this paper underscores the significance of public engagement pedagogy in fostering health literacy and empowering young learners to make informed decisions regarding personal and community well-being. By combining interactive methodologies with targeted public health interventions we aim to inspire a generation of proactive global citizens equipped to address contemporary health challenges.
A comparative in silico analysis of the vlhA gene regions of Mycoplasma gallisepticum and Myc. synoviae isolates from commercial hen farms in Mexico.
Avian mycoplasmosis caused by Mycoplasma synoviae and Myc. gallisepticum poses significant economic challenges due to respiratory issues reduced production and soft eggshells. The hemagglutinin (vlhA) protein crucial for pathogenicity comprises conserved (MSPB) and variable (MSPA) regions. In this study we examined vlhA sequences from field strains in Mexico's central region (Jalisco and Mexico City) revealing a close cluster relationship distinct from sequences in GeneBank. We analyzed 124 deformed eggs and 10 laying hens from nine farms with Hy-line and Bovans breeds. Using PCR targeting mgc2 and 16S RNAr genes we characterized 24 field strains Mycoplasma synoviae (4) and Myc. gallisepticum (20). The vlhA regions based on AF035624.1 sequences were analyzed with ATTC strains as positive controls. Additionally 20 negative samples at Mycoplasma isolation validated the sensitivity of PCR testing without the need of cultivation. Two amplification regions were identified: the 1st MSPB and 2nd MSPA. Bioanalysis revealed relationships with relatives avian Mycoplasma sequences in GenBank alongside similarities with Acholeplasma laidlawii PG8 and Escherichia coli. Given vlhA's significance in pathogenicity and immune evasion the identified conserved sequences hold potential as therapeutic targets and for phylogenetic studies.
Emerging challenge of Linezolid and Vancomycin resistant Enterococci faecium:First case report from Northern Pakistan
Enterococcus faecium are among the most versatile pathogens found to infect hospitalized patients. Resistance against anti-enterococcal antibiotics is gaining access day to day and among them linezolid resistant vancomycin resistant Enterococcus faecium is a nightmare for the clinicians especially in a resource limited country like Pakistan.
A 72 year old patient presented with collection of pus and necrosis around the head of pancreases. These pockets of pus resulted as acute postsurgical complication along with surgical site infection. Pus was processed according to clinical guidelines. Enterococcus faecium was identified and confirmed by VITEK. Isolate was resistant to vancomycin and linezolid. Tigecyclin was the only option for this patient due to unavailability of quinupristin/dalfopristin as a treatment option. A regular follow up was done and patient was discharged after recovery.
Linezolid and Vancomycin resistant Enterococci (LRVRE) is the result of non-implementation of antimicrobial stewardship and it can be followed with further resistance in Enterococcus which can be havoc. Clinicians infection control team and microbiologist should work together to overcome antimicrobial resistance crises.
Meropenem resistant Burkholderia pseudomallei - A concerning single case in Australia with no prior meropenem exposure
We report a case of cutaneous melioidosis in a 54-year-old male with a meropenem resistant sub-population. He was empirically treated with episodic doxycycline and trimethoprim-sulfamethoxazole however the abscess re-accumulated. The patient had no prior exposure to meropenem. A sub-population of the isolate was meropenem resistant with an MIC>32 µg/ml and the identification was re-confirmed as B. pseudomallei. Whole genome sequencing with ARDaP analysis only revealed a resistance determinant to doxycycline and it didn’t reveal a resistance determinant to meropenem. Furthermore no carbapenemases were detected through multiple bioinformatics tools. To date this is the first reported case in Australia of a B. pseudomallei isolate resistant to meropenem without previous carbapenem exposure.
Characteristics of soil origin Pseudomonas batumici Koz11 isolated from a remote island in Japan
Soil samples from a remote Japanese island (Kozushima) were processed and investigated for organisms exhibiting antimicrobial activity against pathogenic strains. A Pseudomonas strain demonstrating antimicrobial activity against Staphylococcus aureus (S. aureus) was observed leading to further investigation. Whole-genome sequencing was used to identify species and phylogenetic analysis followed by in silico molecular analysis. Chemotaxonomic and biochemical analyses were conducted to characterize the strain further. Genomic analysis identified a strain of interest Pseudomonas batumici (P. batumici) a strain initially isolated from soil of the Black Sea coast of the Caucasus in 1980. P. batumici Koz11 is the second P. batumici strain isolated and identified outside the area where it was first found. Similar to the type strain P. batumici Koz11 showed antimicrobial activity against various S. aureus strains including vancomycin-resistant S. aureus. However the previously reported gene cluster known as the "batumin gene cluster" which synthesizes antimicrobial compounds was absent from P. batumici Koz11. This study provides insights on P. batumici that were not previously known. Since the type of strain of P. batumici is exclusively deposited in the Ukrainian Collection of Microorganisms the Koz11 strain may be a surrogate to facilitate continued study of P. batumici.
Development of selective isolation media for detecting Actinomyces and Schaalia genera from oral specimens containing indigenous bacteria
To isolate specific bacteria from samples constituting the microbiota it is essential to employ selective media that suppress the growth of resident bacteria other than specific target bacteria. Selective media for clinically important Actinomyces (including Schaalia which was previously taxonomically classified as part of the Actinomyces genus) have been limited because they have been designed for a limited range of species within the genus and require ingredients which are difficult to prepare and handle. This study aimed to develop a selective medium (referred to as Actinomyces and Schaalia Selective Medium (ASSM)) for the isolation of a broad range of Actinomyces and Schaalia species from samples mixed with resident bacteria. The composition of ASSM includes yeast extract agar brain heart infusion (BHI) levofloxacin (LVFX) fosfomycin (FOM) colistin (CL) and metronidazole (MNZ). Evaluation of the medium using 24 swab samples serially collected from the roots of the teeth of a healthy individual for whom metagenome sequencing data of a saliva sample are publicly available revealed that ASSM adjusted to concentrations of LVFX 0.5 mg/L FOM 5 mg/L CL 1 mg/L and MNZ 2 mg/L and cultured anaerobically at 35°C for 7 days enabled the isolation of Actinomyces species from 37.5% of the samples. The inclusion of CL and MNZ in ASSM can also be useful for samples suspected of harbouring other bacterial species. The selective isolation medium is expected to contribute to studies investigating the relationship between these bacteria and their pathogenesis or disease.
Kaposi’s sarcoma herpesvirus viral FLICE inhibitory protein modulates A20 deubiquitinase activity
KSHV viral FLICE inhibitory protein (vFLIP) is a potent activator of NF-κB signaling and an inhibitor of apoptosis and autophagy. Inhibition of vFLIP function and NF-κB signaling promotes lytic reactivation. Here we provide evidence for a novel function of vFLIP through inhibition of the deubiquitinating (DUB) activity of the negative regulator A20. We demonstrate direct interaction of vFLIP with Itch and A20 and provide evidence for subsequent loss of A20 DUB activity. Our results provide further insight into the function of vFLIP in the regulation of NF-κB signaling.
Unearthing New Learning Opportunities: Adapting and Innovating through the “Antibiotics Under Our Feet” Citizen Science Project in Scotland during COVID-19
“Antibiotics under our feet” is a Scottish citizen science project that aimed to raise science capital in primary school learners and their teachers through measurement of microbial diversity in urban soil samples in the search for novel antimicrobial compounds. Resistance to antibiotics is rising posing a global threat to human health. Furthermore science technology engineering and mathematics (STEM) skills are in crisis jeopardising our capacity to mobilise as a society to fight antimicrobial resistance (AMR). Originally conceived as a response to the AMR and STEM emergencies our project was hit by the unprecedented challenge of engaging with schools during the COVID-19 pandemic. We describe how we adapted our project to enable remote participation from primary schools and youth groups utilising COVID-19 response initiatives as opportunities for multi-level co-creation of resources with learners in primary secondary and higher education. We produced portable kit boxes for soil sample collection with learning activities and videos linked to the Scottish Curriculum for Excellence. We also addressed glaring project specific content gaps relating to microbiology on English and Simple English Wikipedia. Our hybrid model of working extended our geographical reach and broadened inclusion. We present here the inception implementation digital resource outputs and evaluation of pedagogical aspects of “Antibiotics under our feet”. Our strategies and insights are applicable post-pandemic for educators to develop STEM skills using soil microbes and antibiotics as a theme.
How suitable is freshwater sponge Ephydatia fluviatilis (Linnaeus, 1759) for time-integrated biomonitoring of microbial water quality?
Faecal pollution of water by bacteria has a negative effect on water quality and can pose a potential health hazard. Conventional surveillance of microbial water quality relies on the analysis of low frequency spot samples and is thus likely to miss episodic or periodic pollution. This study aimed to investigate the potential of filter feeding sponges for time-integrated biomonitoring of microbial water quality. Laboratory trials tested the effects of different ratios of bacterial abundance and the sequence of exposure on bacterial retention by the freshwater sponge Ephydatia fluviatilis (Linnaeus 1759) to establish its potential to indicate bacterial exposure.
Gemmule grown sponges were simultaneously exposed to Escherichia coli and Enterococcus faecalis but at different ratios (Trial 1) or individually exposed to each bacterial species but in different sequential order (Trial 2). The E. coli and E. faecalis retained in each sponge was quantified by culture on selective agars. Data analysis was conducted using the Kruskal- Wallis test and/ or the Mann Whitney U test to compare between the numbers of bacteria retained in each treatment. Additionally the Wilcoxon Matched-Paired Signed-Rank test was used for comparison of the different bacterial abundances retained within each individual sponge.
Sponges from all trials retained E. coli and E. faecalis in small numbers relative to the exposure (<0.05% Trial 1 and <0.07% Trial 2) but exhibited higher retention of E. coli. Higher abundance of either bacterial species resulted in significantly lower (p<0.005) retention of the same species within sponges (Trial 1). An initial exposure to E. coli resulted in significantly higher (p=0.040) retention of both bacterial species than when sponges were exposed to E. faecalis first (Trial 2).
Bacterial retention by sponges was neither quantitatively representative of bacterial abundance in the ambient water nor the sequence of exposure. This implies either selective filtration or an attempt by sponges to prevent infection. However freshwater sponges may still be useful in biomonitoring as qualitative time-integrated samplers of faecal indicator bacteria as they detect different bacteria present in the water even if their quantities cannot be estimated.
Draft genome sequence of Lactiplantibacillus pentosus isolated from traditional fermented rice
Lactiplantibacillus pentosus is a probiotic bacterium reported to be present in various fermented foods such as fermented olives and it significantly influences human health. The present study concerns a lactic acid bacterial strain designated L. pentosus isolated from traditional fermented rice and has been shown to have an assortment of beneficial attributes. Using Illumina technologies we have sequenced and investigated the whole genome sequence of L. pentosus for an accurate understanding of its functionality and safety. The chromosomal genome was 3.7 Mbp in size with 46% GC (Guanine-Cytosine) content and 3192 protein-coding sequences. In accordance with this additional extensive bioinformatics investigations were carried out involving whole genome sequence assembly and annotation.
Comparative virulome analysis of four Staphylococcus epidermidis strains from human skin and platelet concentrates using whole genome sequencing
Staphylococcus epidermidis is one of the predominant bacterial contaminants in platelet concentrates (PCs) a blood component used to treat bleeding disorders. PCs are a unique niche that triggers biofilm formation the main contributor to S. epidermidis infections. We performed whole genome sequencing of four S. epidermidis strains isolated from the skin of healthy human volunteers (AZ22 and AZ39) and contaminated PCs (ST10002 and ST11003) to unravel phylogenetic relationships and decipher virulence mechanisms compared to 25 complete S. epidermidis genomes in GenBank. AZ39 and ST11003 formed a separate unique lineage with 14.1.R1 and SE95 strains while AZ22 formed a cluster with 1457 and ST10002 closely grouped with FDAAGOS_161. The four isolates were assigned to sequence types ST1175 ST1174 ST73 and ST16 respectively. All four genomes exhibited biofilm-associated genes ebh ebp sdrG sdrH and atl. Additionally AZ22 had sdrF and aap whereas ST10002 had aap and icaABCDR. Notably AZ39 possesses truncated ebh and sdrG and harbors a toxin encoding gene. All isolates carry multiple antibiotic resistance genes conferring resistance to fosfomycin (fosB) β-lactams (blaZ) and fluoroquinolones (norA). This study revealed a unique lineage for S. epidermidis and provided insight into the genetic basis of virulence and antibiotic resistance in transfusion-associated S. epidermidis strains.