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 β-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.

Surgical Site Infections remain a significant burden in healthcare settings, contributing to prolonged hospital stays, increased healthcare costs, and increased morbidity and mortality rates. Among the various pathogens implicated in these infections, Pseudomonas aeruginosa remains a particularly formidable bacterium due to its intrinsic resistance to many antibiotics and its ability to acquire additional resistance mechanisms. Despite this incidence, there is a geographical limitation of surveillance programs on this pathogen continues to cripple infection control and prevention in sub-Saharan Africa, crippling surveillance data on the infection management. We aimed at understanding the role of Pseudomonas aeruginosa (PA) on the seemingly growing and concerning infections of surgical site in sub-Saharan Africa (SSA). This study adopted systematic review and meta-analysis design in line with PRISMA guidelines. For data collection, therefore, we systematically searched PubMed and other relevant databases for articles (2015-2023) relevant to antimicrobial resistance (AMR) and predominance of Pseudomonas aeruginosa (PA) in sub-Saharan Africa (SSA). We examined 26 relevant articles out of 225 that matched the initial search. A standardized data extraction form was developed to capture relevant information from the selected studies. Data collected from the studies included were synthesized narratively and reported through Systematic Reviews and Meta Analyses (PRISMA). Through an in-depth analysis of the relevant literature, the low number of studies in the region focused on PA and AMR. Nevertheless, the relatively few studies demonstrate the high rates of PA involvement in surgical site infections. The studies further show high levels of multi-drug resistance and points to subsequent nosocomial clinical outcomes. In conclusion, the study underscores the burden posed by PA in SSA, highlighting on the prevalence, multi-drug resistance and virulence. Clearly, its surveillance remains geographically limited especially in the regions that are underrepresented. The study recommends that infections prevention and control programs (IPCs) be strengthened, that antimicrobial stewardship be sensitised to regulate antibiotic use, and that surveillance and research on PA be expanded in SSA.

Staphylococcus aureus is one of the most common pathogens associated with hospital infections. Although S. aureusinfections have been well studied in developed countries, far less is known about the biology of the pathogen in sub-Saharan Africa. 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. 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. The most striking difference was the larger number of horizontally-acquired genomic islands (GIs) in the nosocomial isolates. The data indicate that adaptation to the hospital environment may also be linked with mutations in the uvrAB genes.

Pseudomonas aeruginosa is an important cause of surgical site infections (SSIs) and is characterized by extensive antimicrobial resistance and genomic plasticity. We analyzed 13 whole‐genome sequences of clinical P. aeruginosa isolates recovered from SSIs at a Level 5 referral hospital in Western Kenya and integrated genomic analyses with antimicrobial susceptibility tests and phenotyping of quorum‐sensing (QS). Multidrug resistance was common, with resistance observed primarily against ciprofloxacin, piperacillin, ceftazidime, and amikacin, whereas meropenem and piperacillin/tazobactam retained the greatest in vitro activity. Genomic analyses identified diverse sequence types, extensive variability in insertion sequences and genomic islands, and widespread conservation of intrinsic resistance determinants, whereas accessory antimicrobial resistance genes were infrequently detected and largely associated with genomic islands. Virulence‐associated genes were predominantly chromosomal, although several showed strain‐specific genomic island localizations. Functional QS analyses demonstrated that isolates with intact lasR and rhlR produced significantly higher levels of acyl‐homoserine lactone signals than isolates carrying predicted loss‐of‐function mutations, whereas Pseudomonas quinolone signal production remained comparatively conserved. These findings provide a genomic baseline for P. aeruginosa causing SSIs in Western Kenya and highlight the importance of integrating whole‐genome sequencing with phenotypic analyses to strengthen surveillance and inform antimicrobial stewardship and infection prevention strategies.

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. aureusbelonging 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.

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. aureusbelonging 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.