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.
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.
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.
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.
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.
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.
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.
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.
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.
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.