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. 2021 May;68(3):194-202.
doi: 10.1111/zph.12805. Epub 2021 Jan 17.

Antimicrobial resistance clusters in commensal Escherichia coli from livestock

Ayla Hesp  1   2 , Cajo Ter Braak  3 , Jeanet van der Goot  4 , Kees Veldman  1 , Gerdien van Schaik  5   6 , Dik Mevius  1   2
Affiliations

Antimicrobial resistance clusters in commensal Escherichia coli from livestock

Ayla Hesp et al. Zoonoses Public Health. 2021 May.

Abstract

To combat antimicrobial resistance (AMR), policymakers need an overview of evolution and trends of AMR in relevant animal reservoirs, and livestock is monitored by susceptibility testing of sentinel organisms such as commensal E. coli. Such monitoring data are often vast and complex and generates a need for outcome indicators that summarize AMR for multiple antimicrobial classes. Model-based clustering is a data-driven approach that can help to objectively summarize AMR in animal reservoirs. In this study, a model-based cluster analysis was carried out on a dataset of minimum inhibitory concentrations (MIC), recoded to binary variables, for 10 antimicrobials of commensal E. coli isolates (N = 12,986) derived from four animal species (broilers, pigs, veal calves and dairy cows) in Dutch AMR monitoring, 2007-2018. This analysis revealed four clusters in commensal E. coli in livestock containing 201 unique resistance combinations. The prevalence of these combinations and clusters differs between animal species. Our results indicate that to monitor different animal populations, more than one indicator for multidrug resistance seems necessary. We show how these clusters summarize multidrug resistance and have potential as monitoring outcome indicators to benchmark and prioritize AMR problems in livestock.

Keywords: E. coli; antimicrobial drug resistance; cluster analysis; epidemiological monitoring; multidrug resistance; policy making.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIGURE 1
FIGURE 1
Heatmap showing the resistance probability for the ten tested antimicrobialsa per cluster in the four clusters from model‐based clustering, in commensal E. coli isolates (N = 12,986) from broilers, dairy cows, slaughter pigs and veal calves from the Netherlands, 2007–2018. aGEN, gentamicin; TAZ, ceftazidime; FOT, cefotaxime; CHL, chloramphenicol; TMP, trimethoprim; SMX, sulfamethoxazole; TET, AMP, ampicillin; NAL, nalidixic acid; CIP, ciprofloxacin
FIGURE 2
FIGURE 2
Proportion of isolates in the four clusters (1–4) derived from model‐based clustering of multidrug resistance in commensal E. coli isolates (N = 12,986) of broilers, dairy cows, slaughter pigs and veal calves from the Netherlands, 2007–2018
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