Epidemiology of Clinically Relevant Antimicrobial Resistance at the Wildlife-Livestock-Human Interface in Nairobi

Hassell, James, Ward, Melissa, Muloi, Dishon, Bettridge, Judy, Robinson, Timothy, Kariuki, Sam, Ogendo, Allan, Kiiru, John, Imboma, Titus, Kang'ethe, Erastus, Öghren, Elin, Williams, Nicola, Begon, Michael, Woolhouse, Mark and Fevre, Eric (2019) Epidemiology of Clinically Relevant Antimicrobial Resistance at the Wildlife-Livestock-Human Interface in Nairobi. [Data Collection]

Description

Background Antimicrobial resistance (AMR) represents one of the great challenges facing global health security in the modern era. Wildlife species, particularly those that utilise urban environments, are an important but understudied component of AMR epidemiology. This study investigated AMR overlap between sympatric wildlife, humans, livestock and their shared environment across the developing city of Nairobi, Kenya. We use these data to examine the role of urban wildlife in the spread of clinically relevant AMR. Methods 99 households across Nairobi were randomly selected on the basis of socioeconomic stratification. A detailed survey was administered to household occupants, and samples (n=2102) were collected from the faeces of 75 wildlife species inhabiting household compounds (n=849), 13 livestock species (n=656) and humans (n=333), and from the external environment (n=288). E. coli, our sentinel organism, was cultured, and a single isolate from each sample tested for sensitivity to 13 antibiotics. Diversity of AMR phenotypes were compared between urban wildlife, humans, livestock and the environment, to investigate whether wildlife are a net source for antimicrobial resistance in Nairobi. Generalised linear mixed models were used to determine whether the prevalence of AMR phenotypes and multi-drug resistant (MDR) E. coli carriage in urban wildlife is this linked to variation in ecological traits, such as foraging behaviour, and to determine household-level risk factors for sharing of AMR between humans, wildlife and livestock. Findings E. coli were isolated from 485 samples collected from wildlife, between September 2015 and September 2016. Wildlife carried a low prevalence of pan-susceptible E. coli isolates [9.3% (45/485) susceptible to all antibiotics tested] and a high prevalence of clinically relevant multi-drug resistance (MDR) [52% (252/485)], which varied between taxa and by foraging traits. Multiple isolates resistant to at least one agent in seven or more of the nine antimicrobial classes tested for, and a single isolate resistant to all antibiotics tested for in the study, were also present. The phenotypic diversity of AMR-E. coli in wildlife was lower than in livestock, humans and the environment. Within household perimeters, statistical models identified two “interfaces” for AMR exchange; i) between rodents/seed-eating birds, humans and their rubbish, and ii) between seed-eating birds, cattle and bovine manure. Interpretation Urban wildlife carry a high burden of clinically relevant AMR-E. coli in Nairobi, exhibiting resistance to drugs considered critically important for human medicine by the World Health Organisation. Identifiable traits of the wildlife contribute to this exposure. However, compared to humans, livestock and the environment, low phenotypic diversity in wildlife is consistent with the hypothesis that they are a net ‘sink’ rather than source of clinically relevant resistance. Wildlife that interact closely with humans, livestock and their waste within households, are exposed to more AMR phenotypes, and could therefore act as conduits for the dissemination of clinically relevant AMR to the wider environment. These results provide novel insight into the broader epidemiology of AMR in complex urban environments, characteristic of lower-middle income countries.

Keywords: antimicrobial resistance, AMR, wildlife, humans, livestock, kenya, environment, urban
Divisions: Faculty of Health and Life Sciences
Depositing User: Eric Fevre
Date Deposited: 30 Apr 2019 09:34
Last Modified: 30 Apr 2019 09:34
DOI: 10.17638/datacat.liverpool.ac.uk/729
URI: https://datacat.liverpool.ac.uk/id/eprint/729

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