OHEJP-RaDAR-D-JRP3-5.3 Attributable sources of community-acquired carriage of Escherichia coli containing β-lactam antibiotic resistance genes

Published in: Lancet Planet Health 2019: 3: 357–69

Summary
Background

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC), plasmid-mediated AmpCproducing
E coli (pAmpC-EC), and other bacteria are resistant to important β-lactam antibiotics. ESBL-EC and
pAmpC-EC are increasingly reported in animals, food, the environment, and community-acquired and health-careassociated
human infections. These infections are usually preceded by asymptomatic carriage, for which attributions
to animal, food, environmental, and human sources remain unquantified.

Methods

In this population-based modelling study, we collected ESBL and pAmpC gene data on the Netherlands
population for 2005–17 from published datasets of gene occurrences in E coli isolates from different sources, and
from partners of the ESBL Attribution Consortium and the Dutch National Antimicrobial Surveillance System. Using
these data, we applied an established source attribution model based on ESBL-EC and pAmpC-EC prevalence and
gene data for humans, including high-risk populations (ie, returning travellers, clinical patients, farmers), farm
and companion animals, food, surface freshwater, and wild birds, and human exposure data, to quantify the overall
and gene-specific attributable sources of community-acquired ESBL-EC and pAmpC-EC intestinal carriage. We also
used a simple transmission model to determine the basic reproduction number (R0) in the open community.
 

Findings

We identified 1220 occurrences of ESBL-EC and pAmpC-EC genes in humans, of which 478 were in clinical
patients, 454 were from asymptomatic carriers in the open community, 103 were in poultry and pig farmers, and
185 were in people who had travelled out of the region. We also identified 6275 occurrences in non-human sources,
including 479 in companion animals, 4026 in farm animals, 66 in wild birds, 1430 from food products, and 274 from
surface freshwater. Most community-acquired ESBL-EC and pAmpC-EC carriage was attributed to human-to-human
transmission within or between households in the open community (60·1%, 95% credible interval 40·0–73·5), and
to secondary transmission from high-risk groups (6·9%, 4·1–9·2). Food accounted for 18·9% (7·0–38·3) of carriage,
companion animals for 7·9% (1·4–19·9), farm animals (non-occupational contact) for 3·6% (0·6–9·9), and
swimming in freshwater and wild birds (ie, environmental contact) for 2·6% (0·2–8·7). We derived an R0 of 0·63
(95% CI 0·42–0·77) for intracommunity transmission.

Interpretation

Although humans are the main source of community-acquired ESBL-EC and pAmpC-EC carriage, the
attributable non-human sources underpin the need for longitudinal studies and continuous monitoring, because
intracommunity ESBL-EC and pAmpC-EC spread alone is unlikely to be self-maintaining without transmission to
and from non-human sources.
 

Funding 1Health4Food, Dutch Ministry of Economic Affairs, and the EU’s Horizon-2020 through One-Health
European Joint Programme.
Copyright © 2019 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND
4.0 license.