Diversity of Nasal Cavity Bacteria and Molecular Characterization of Methicillin Resistant Staphylococcus Spp. Isolated from Pastoralists in Kajiado Central Sub-County

Abstract

Antimicrobial resistance (AMR) remains a major global health challenge. This cross-sectional study aimed to establish baseline data on nasal bacterial diversity, Staphylococcus spp. resistance patterns, and associated risk factors for MDR among pastoralists in Kajiado Central Sub-County, Kenya, using molecular and bioinformatics approaches. A total of 176 nasal swabs were analyzed through standard phenotypic, biochemical, and molecular methods. Antimicrobial susceptibility of Staphylococcus spp. was assessed using the Kirby-Bauer disk diffusion method against 14 commonly used antibiotics. Methicillin resistance genes (mecA and mecC) were detected by PCR. The prevalence of coagulase-negative Staphylococcus (CoNS) and S. aureus was 44.9% and 8%, respectively. Other nasal bacteria isolated included Enterococci spp., Bacillus spp., Corynebacterium spp., Morganella spp., Lactobacillus spp., Proteus mirabilis, Pantoea spp., and Aeromonas hydrophila. High resistance was observed among CoNS and S. aureus to amoxicillin (78.7%) and ceftazidime (76%), with S. aureus showing additional resistance to streptomycin and vancomycin. Oxacillin resistance was recorded at 49.3% (CoNS) and 28.6% (S. aureus); cefoxitin resistance was 28.0% and 21.4%, respectively. Methicillin resistance genes mecA and mecC were found in 12% and 8% of CoNS isolates, respectively.16S rRNA sequencing revealed >99.5% homology with S. epidermidis, S. caprae, and uncultured bacteria. Phylogenetic analysis identified three MR-CoNS clades: one globally distributed (2002–2022), one regional (Kenya/Tanzania, 2009–2014), and one unique to the study area. Risk factors predicted for acquisition of MDR strains were age, gender, habitual intake of raw milk, frequent contact with livestock. Correlation analysis revealed the significant risk factors for MDR carriage as male gender (p = 0.02, OR = 1.3) and raw milk consumption (p = 0.02, OR = 1.82). These findings highlight both the global transmission and local emergence of methicillin-resistant coagulase-negative staphylococci (MR-CoNS). The study provides important baseline data to inform public health interventions, including community education on antibiotic misuse, promotion of hygiene and safe milk handling practices, and the integration of routine culture and susceptibility testing into clinical care. This study recommends use of targeted antibiotic therapy favoring agents such as Augmentin, ciprofloxacin, and cefotaxime based on susceptibility profiles can aid in mitigating resistance. Additionally, the findings underscore the importance of incorporating alternative methicillin resistance markers(mecC/B) in diagnostic laboratories when screening for MRSA. Likewise, the observed regional transmission dynamics call for coordinated efforts to combat AMR between Tanzania and Kenya. This study also establishes a foundation for future molecular characterization of SCCmec elements and clonal lineages circulating within the region.