Dataset Information

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.

ABSTRACT:

Background

Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism.

Methods

We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311 human, 606 livestock and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated household-level risk factors for the exchange of AMR genes between sympatric humans and livestock.

Results

We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households.

Conclusions

Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided an in-depth understanding of AMR determinants at the interfaces of One Health sectors that will inform AMR prevention and control.

SUBMITTER: Muloi DM

PROVIDER: S-EPMC9730568 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Publications

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.

Muloi Dishon M DM Hassell James M JM Wee Bryan A BA Ward Melissa J MJ Bettridge Judy M JM Kivali Velma V Kiyong'a Alice A Ndinda Christine C Gitahi Nduhiu N Ouko Tom T Imboma Titus T Akoko James J Murungi Maurice K MK Njoroge Samuel M SM Muinde Patrick P Alumasa Lorren L Kaitho Titus T Amanya Fredrick F Ogendo Allan A van Bunnik Bram A D BAD Kiiru John J Robinson Timothy P TP Kang'ethe Erastus K EK Kariuki Samuel S Pedersen Amy B AB Fèvre Eric M EM Woolhouse Mark E J MEJ

BMC medicine 20221208 1

<h4>Background</h4>Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here, we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in Escherichia coli, regarded as a sentinel organism.<h4>Methods</h4>We conducted a structured epidemiological survey of 99 househ ...[more]

PMID: 36482440

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Dataset Information

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.

Background

Methods

Results

Conclusions

Publications

Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya.

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