Botany

Permanent URI for this collectionhttps://repository.chuka.ac.ke/handle/123456789/22650

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Browsing Botany by Subject "Staphylococcus aureus"

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    Determination of bacterial resistance profile of chronic wound pathogens and genetic characterisation of staphylococcus aureus from patients at meru teaching and referral hospital, Meru county, Kenya
    (Chuka University, 2025) Silas Rael Gacheri
    Chronic wound infections remain a major public health concern, particularly in low- and middle-income countries, where they are often complicated by polymicrobial colonization and the emergence of multidrug-resistant (MDR) pathogens. Effective management is challenged by incomplete pathogen identification, which hampers accurate diagnosis and treatment. This study aimed to determine the prevalence, bacterial profile, and antimicrobial resistance patterns of pathogens associated with chronic wound infections at Meru Teaching and Referral Hospital (MeTRH) in Kenya, and to provide genomic insights into their resistance and virulence determinants. A cross-sectional survey design was employed, in which 68 wound swab samples were collected from a stratified random sample of 293 patients over eight months, following consent. Data were analyzed using SPSS for epidemiological trends, R for visualization, and bioinformatics pipelines for sequencing data processing, assembly, annotation, and phylogenetic reconstruction to characterize antimicrobial resistance and virulence profiles. The findings indicate that the highest burden of chronic wounds occurred among patients aged 21–30 years (22%) and 51–60 years (19.2%). The predominant pathogens were Staphylococcus aureus (26.6%), Pseudomonas aeruginosa (13.2%), and Escherichia coli (10.3%). Clinically significant MDR organisms included Klebsiella pneumoniae, Proteus hauseri, Morganella morganii, Acinetobacter baumannii, and Enterococcus faecalis, while 20.5% of wounds showed no bacterial growth despite clinical evidence of infection. Notably, 50% Staphylococcus aureus isolates exhibited resistance to multiple antibiotics. Distinct susceptibility patterns were observed for Morganella morganii and Proteus spp, whereas coagulase-negative staphylococci displayed variable meropenem resistance reaching up to 100% in some cases. Klebsiella and Pseudomonas spp. were largely sensitive to meropenem, although resistance ranged from 0% to 11%, depending on the species. Whole-genome sequencing revealed frequent resistance determinants, including MecA (60%), blaZ (60%), aadD/aphA-3 (60%), mrsA (70%), ermB (30%), ermC (10%), ermA (20%), rpob_H481N (20%), and grlA_S80F; GrA_S84L (20%), reflecting co-occurrence of beta-lactam, MLS, sulfonamide/trimethoprim, tetracycline, aminoglycoside and quinolone resistance genes. Virulence markers such as aureolysin and toxin/exoenzyme genes (edinB, hlgA/B/C, lukPV, sak, scn, splA/B/E) were identified, alongside diverse spa types (t355-centered clusters), mosaic SCCmec elements, and varied MLST lineages (MLST/spa) were observed across Staphylococcus aureus. Plasmid replicons detected included Rep5a (n = 5), Rep16 (n = 4), Rep7a, Rep10, Rep9a, Rep9b, RepUS70, Rep21, Rep13, and Rep15, suggesting circulation of MRSA and MRSA-like lineages with mobile genetic elements. Clonal complexes CC30, CC121, CC45, and MLST 152 reflected both community- and hospitalassociated strains, indicating dynamic Staphylococcus aureus populations shaped by clonal expansion and horizontal gene transfer. The findings highlight the substantial antimicrobial resistance burden in chronic wound infections, the importance of integrating advanced molecular diagnostics with traditional surveillance, and the need for antibiotic stewardship programs. Moreover, the genomic diversity and virulence architecture revealed here highlight the necessity for localized surveillance strategies and virulence-informed risk stratification to guide infection control and therapeutic interventions.