Staphylococcus aureus associated with surgical site 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 ß-lactam antibiotics). These five strains all belonged to the same sequence type, ST152. Despite the similarity of the plasmid in 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. These data suggest ongoing adaptive evolution and significant genomic plasticity.

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.

Hygiene Practices and Early Childhood Development in the East Asia-Pacific Region: A Cross-Sectional Analysis.

Poor hygiene might be a risk factor for early childhood development (ECD). This study investigated the associations of three hygiene practices ('wash hands before a meal,' 'wash hands after going to the toilet,' and 'brush teeth'), separately and combined, with ECD. Six thousand six hundred ninety-seven children (4 [0.8] years) from the East Asia-Pacific Early Child Development Scales validation study were included in this cross-sectional analysis. The hygiene variables were recoded to have comparable values as 'always,' 'sometimes,' and 'never.' These variables were then grouped to create combined categories. The binary outcome variables, poor ECD, were defined as a score < age-specific 25th centile. Modified Poisson regression models were used to analyse the associations. Data collection was performed between 2012 and 2014, and the analyses were conducted in April 2022. Compared with children who 'always' washed their hands before a meal, those who did it 'sometimes' (Prevalence Ratio [PR]: 1.30 [95% CI: 1.16-1.46]) or 'never' (PR: 1.35 [1.18-1.55]) had a higher likelihood of poorer overall development. Comparable results were identified for the other two hygiene practices and the other four domain-specific outcomes (p < 0.05). Compared with children who always followed the three hygiene practices, the likelihood of poor overall ECD increased as the combined hygiene practice decreased among children with poor hygiene practices (PRnever: 1.67 [1.40-2.00]; PRrarely: 1.49 [1.30-1.71]; PRsometimes: 1.30 [1.14-1.49]). Children who did not always follow good hygiene practices had a higher likelihood of poor ECD independently of sociodemographic factors. Considering these findings, future hygiene practice interventions and trials should consider including ECD outcomes.

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.