Prevalence, Genetic Diversity and Antimicrobial Susceptibility Pattern of Clinical Salmonella Isolates from Kapsabet and Kisumu District Hospitals in Kenya

Abstract

The re-emergence of invasive non typhoidal Salmonella (NTS) is exacerbated by antimicrobial resistance (AMR) to most commonly available antimicrobials. Extreme climatic changes, in addition to increase in susceptible host population risk factors has resulted in the emergence of successful clones of Salmonella. Prevalence of S. Typhimurium is documented at 4.2% while bacteria caused diarrhea at 8.5% in Kapsabet region. Prevalence of NTS in Kisumu is documented at 39% and MDR at 76%. This warranted the appraisal of antibiotic susceptibility patterns of clinical Salmonella isolates and determining correlation between antimicrobial susceptibility and genetic diversity. This study aimed to determine the prevalence, genetic diversity and antimicrobial susceptibility pattern of clinical Salmonella isolates from Kapsabet and Kisumu District hospitals. A cross sectional study design was adopted. Systematic random sampling technique was used and a total of 400 stool specimens were collected from each study site. Salmonella isolates were identified based on their morphological appearance, biochemical reaction on various bacteriological culture media in addition to indole, methyl red, voges proskauers, citrate (IMVIC) and Salmonella a nalytical profile index (API) 20E system and confirmed by invA gene sequencing. Antimicrobial susceptibility was done using disk diffusion method. Polymerase chain reaction was used to detect the presence of blareu and sul2 genes in addition to spv virulence genes. Single locus sequence typing was used to determine genetic diversity among S. Typhimurium isolates based onjliC gene. A total of 174 Salmonella species were isolated, 55.75% (971174) and 44.25% (771174) from patients treated at Kapsabet and Kisumu District hospitals respectively. The predominant Salmonella from Kapsabet was serovar S. Typhimurium 52.6% (51/97) followed by s.. Enteritidis 26.8% (26/97). The highest Salmonella isolate from Kisumu was S. Typhimurium 57.1% (44177), followed by S. Enteritidis 24.6% (19177). The other serovars constituted a small proportion in both sites. Kapsabet had high distribution of serovars, p=0.0288. The difference in prevalence ofNTS among patients was not significant, p=0.0793. Approximately 70% of Salmonella isolates were MDR, the resistant phenotype was; ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline (ACSSuT). Kisumu had high resistance to antimicrobials tested p<O.OOO1.blarsu and sul2 genes were associated with antimicrobial susceptibility p< 0.001. A total of 4.54% (2/44) of S. Typhimurium from Kisumu lacked spv genes while 4.54% (2/45) of all S. Enteritidis lacked spv genes. Genetic diversity in S. Typhimurium strains correlated with AMR, p= 0.0258. Isolates exhibited geographic restriction. The overall interclade diversity was p< 0.001. Use of Multi locus sequence typing is recommended to mitigate phylogenetic discordance. Development of vaccines for human and vetenary use may be best alternative to antibiotics