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.
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.
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.
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.
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.
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.
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.