Frequency of Antimicrobial Resistance Among Fecal Bacteria Pathogens in an Informal Settlement in Nairobi, Kenya, 2018 to 2020

Multidrug-resistant bacterial enteric pathogens such as Salmonella and Shigella have the potential to cause significant mortality and represent a major issue facing the global health community. This is particularly concerning in low-and middle-income countries where access to clean water and antimicrobials is limited. We aimed to determine the frequency, antimicrobial resistance, and presence of resistance genes among Salmonella, Shigella, Vibrioand Campylobacter recovered from patients presenting with diarrhea in an informal settlement in Nairobi, Kenya, from 2018 to 2020. Conventional bacteriologic methods were used for bacterial culture and isolation. BD Phoenix M50 technology was used for the identification and speciation of bacteria recovered from stool samples and for determining minimum inhibitory concentrations to both clinically relevant antimicrobials and agents of epidemiologic significance. PCR testing was subsequently performed to identify resistance genes. The key pathogenic bacteria recovered were: Shigella flexneri (58.3%), Salmonella enterica serovar Typhi (8.3%), Shigella dysenteriae (6.7%), Shigella boydii (6.7%), and Shigella sonnei (6.7%); no Campylobacter or Vibrio were isolated. Overall resistance among Shigella spp. and Salmonella spp. was determined to be highest to ampicillin (83%), followed by tetracycline (50%), cotrimoxazole (47%), chloramphenicol (17%), ceftriaxone (7%), gentamycin (5%), meropenem (2%), ciprofloxacin (0%) and amoxicillin-clavulanic acid (2.0%). Resistance genes detected included β-lactamases (blaTEM and blaSHV), aminoglycoside 3-N acetyltransferase acc(3), sulfonamide resistance genes (sul1, sul2), and tetracycline resistance genes tet(A) and tet(B). Results emphasize the critical need for active and continuous surveillance of pathogenic enteric bacteria to improve patient management and inform the development of empiric therapy guidelines.