Carriage of antimicrobial-resistant bacteria in a high-density informal settlement in Kenya is associated with environmental risk-factors

Abstract

Background: The relationship between antibiotic use and antimicrobial resistance varies with cultural, socio-economic, and environmental factors. We examined these relationships in Kibera, an informal settlement in Nairobi-Kenya, characterized by high population density, high burden of respiratory disease and diarrhea.

Methods: Two-hundred households were enrolled in a 5-month longitudinal study. One adult (≥ 18 years) and one child (≤ 5 years) participated per household. Biweekly interviews (n = 1516) that included questions on water, sanitation, hygiene, and antibiotic use in the previous two weeks were conducted, and 2341 stool, 2843 hand swabs and 1490 drinking water samples collected. Presumptive E. coli (n = 34,042) were isolated and tested for susceptibility to nine antibiotics.

Results: Eighty percent of presumptive E. coli were resistant to ≥ 3 antibiotic classes. Stool isolates were resistant to trimethoprim (mean: 81%), sulfamethoxazole (80%), ampicillin (68%), streptomycin (60%) and tetracycline (55%). Ninety-seven households reported using an antibiotic in at least one visit over the study period for a total of 144 episodes and 190 antibiotic doses. Enrolled children had five times the number of episodes reported by enrolled adults (96 vs. 19). Multivariable linear mixed-effects models indicated that children eating soil from the household yard and the presence of informal hand-washing stations were associated with increased numbers of antimicrobial-resistant bacteria (counts increasing by 0·27-0·80 log₁₀ and 0·22-0·51 log₁₀ respectively, depending on the antibiotic tested). Rainy conditions were associated with reduced carriage of antimicrobial-resistant bacteria (1·19 to 3·26 log₁₀ depending on the antibiotic tested).

Conclusions: Antibiotic use provided little explanatory power for the prevalence of antimicrobial resistance. Transmission of resistant bacteria in this setting through unsanitary living conditions likely overwhelms incremental changes in antibiotic use. Under such circumstances, sanitation, hygiene, and disease transmission are the limiting factors for reducing the prevalence of resistant bacteria.

Keywords: Antimicrobial resistance; E. coli; Informal settlement; Kenya; Sanitation.

Fig. 1

Distribution of 6674 samples (2843 hand swabs, 2341 stool, 1490 water) collected from 200 study households over a 5-month study period. Sample collection on visits 8 and 9 was impacted by temporary migration of study respondents to other areas for holiday festivities. Visits 1 to 8 occurred between August and December 2015 while Visit 9 occurred in January 2016

Fig. 2

Aggregate distribution of antibiotic use by households and by enrolled children over the study period (includes second antibiotic if use was reported). Asterisk* indicates beta-lactam antibiotic

Fig. 3

Prevalence of resistant E. coli (mean and standard error) in stool, hand swabs, and water samples. Stool and hand swab values are pooled estimates for adults and children. Amp, ampicillin; Caz, ceftazidime, Chl, chloramphenicol; Cip, ciprofloxacin; Kan, kanamycin, Str, streptomycin; Sul, sulfamethoxazole; Tet, tetracycline; Tmp, trimethoprim

Fig. 4

Aggregate distribution of AMR profiles identified in 2318 stool samples. This includes individuals who reported using (users) or not using an antibiotic (non-users) during the study period; not all (non)users provided stool samples

Fig. 5

Load of resistant E. coli (mean and standard error) in adult and child stool samples. Amp, ampicillin; Caz, ceftazidime, Chl, chloramphenicol; Cip, ciprofloxacin; Kan, kanamycin, Str, streptomycin; Sul, sulfamethoxazole; Tet, tetracycline; Tmp, trimethoprim