Whole genome sequencing and genotyping Klebsiella pneumoniae multi-drug resistant hospital isolates from Western Kenya.

Objectives: Klebsiella pneumoniae are a frequent cause of nosocomial infections worldwide. Sequence type 147 (ST147) has been reported as a major circulating high-risk lineage in many countries, and appears to be a formidable platform for the dissemination of antimicrobial resistance (AMR) determinants. However, the distribution of this pathogen in Western African hospitals has been scarcely studied. The main objective of this work was to perform whole genome sequencing of K. pneumoniae isolates from a referral hospital in Kakamega (Kenya) for genotyping and identification of AMR and virulence determinants. Methods: In total, 15 K. pneumoniae isolates showing a broad spectrum antimicrobial resistance were selected for whole genome sequencing by Illumina HiSeq 2500 platform. Results: ST147 was the dominant lineage among the highly-resistant K. pneumoniae isolates that we sequenced. ST147 was associated with both community- and the hospital-acquired infections, and with different infection sites, whereas other STs were predominantly uropathogens. Multiple antibiotic resistance and virulence determinants were detected in the genomes including extended-spectrum ß-lactamases (ESBL) and carbapenemases. Many of these genes were plasmid-borne. Conclusions: Our data suggest that the evolutionary success of ST147 may be linked with the acquisition of broad host-range plasmids, and their propensity to accrue AMR and virulence determinants. Although ST147 is a dominant lineage in many countries worldwide, it has not been previously reported as prevalent in Africa. Our data suggest an influx of new nosocomial pathogens with new virulence genes into African hospitals from other continents.

Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya.

Many low-middle income countries in Africa have poorly-developed infectious disease monitoring systems. Here, we employed whole genome sequencing (WGS) to investigate the presence/absence of antimicrobial resistance (AMR) and virulence-associated (VA) genes in a collection of clinical and municipal wastewater Escherichia coli isolates from Kakamega, west Kenya. We were particularly interested to see whether, given the association between infection and water quality, the isolates from these geographically-linked environments might display similar genomic signatures. Phylogenetic analysis based on the core genes common to all of the isolates revealed two broad divisions, corresponding to the commensal/enterotoxigenic E. coli on the one hand, and uropathogenic E. coli on the other. Although the clinical and wastewater isolates each contained a very similar mean number of antibiotic resistance-encoding genes, the clinical isolates were enriched in genes required for in-host survival. Furthermore, and although the chromosomally encoded repertoire of these genes was similar in all sequenced isolates, the genetic composition of the plasmids from clinical and wastewater E. coli was more habitat-specific, with the clinical isolate plasmidome enriched in AMR and VA genes. Intriguingly, the plasmid-borne VA genes were often duplicates of genes already present on the chromosome, whereas the plasmid-borne AMR determinants were more specific. This reinforces the notion that plasmids are a primary means by which infection-related AMR and VA-associated genes are acquired and disseminated among these strains.

Co-occurrence of Helicobacter pylori with faecal bacteria in Nairobi river basin: public health implications.

INTRODUCTION: Overwhelming evidence implicates Helicobacter pylori (H. pylori) as an etiologic agent of gastrointestinal diseases including gastric cancer. The mode of transmission of this pathogen remains poorly understood. OBJECTIVE: This investigation is to establish the presence of H. pylori in the waters of the Nairobi river basin and the predictive value the presence of fecal indicator bacteria would have for H. pylori. METHODOLOGY: Physical, chemical and biological assessment of water quality of rivers in Nairobi were carried out using standard methods. H. pylori DNA in water was detected using highly specific primers of glmM gene (294pb). RESULTS: There was high presence of faecal bacteria in the waters sampled. H. pylori DNA was detected in two domestic wells and one river. The wells were located in two different regions of the water basin but influenced by similar human activities. CONCLUSION: The high presence of faecal bacteria in the waters sampled did not parallel the H. pylori detection in the same waters. H. pylori was detected in the Nairobi river basin, but there was no relationship between the numerical levels of fecal bacteria and H. pylori.

Pattern of pathogens and their sensitivity isolated from surgical site infections at the Aga Khan University Hospital, Nairobi, Kenya.

BACKGROUND: In low income countries, surgical site infections (SSIs) are costly and impose a heavy and potentially preventable burden on both patients and healthcare providers. This study aimed to determine the occurrence of SSI, pathogens associated with SSI, the antibiogram of the causative pathogens and specific risk factors associated with SSI at the hospital. METHODS: Two hundred and sixty-eight respondents admitted for general surgical procedures (other than neurological and cardiothoracic surgeries) at the Aga Khan University Hospital were eligible to take part in the study. Post-surgery patients were observed for symptoms of infection. Follow ups were done through the consulting clinics, breast clinic and casualty dressing clinic by a team of surgeons. In cases of infection, pus swabs were collected for culture. RESULTS: SSI incidence rate was 7.0%, pathogens isolated from SSI included gram negative enteric bacilli and S. aureus which was the most prevalent bacterial isolate. Only one isolate of MRSA was found and all staphylococci were susceptible to Vancomycin. Preoperative stay ≥ 2 days and wound class were the risk factors associated with SSI. CONCLUSION: The SSI incidence rates (7.0%) observed in this study were relatively lower than the ones documented in other studies in Kenya. S. aureus is the most prevalent pathogen associated with SSI. Similar to findings from other studies done in the region; prolonged hospital stay and dirty wounds were the risks associated with postsurgical sepsis at the hospital.