An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species

Chung, Henri C.; Foxx, Christine L.; Hicks, Jessica A.; Stuber, Tod P.; Friedberg, Iddo; Dorman, Karin S.; Harris, Beth; Sattar, ed., Adeel

doi:10.1371/journal.pone.0290473

Title: An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species

Journal Article · Thu Aug 24 00:00:00 EDT 2023 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0290473· OSTI ID:1996589

Chung, Henri C.; Foxx, Christine L.; Hicks, Jessica A.; Stuber, Tod P.;

; Dorman, Karin S.;

; Sattar, ed., Adeel

Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F ₁ score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0014664

OSTI ID:: 1996589

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Vol. 18 Journal Issue: 8; ISSN 1932-6203

Publisher:: Public Library of Science (PLoS)Copyright Statement

Country of Publication:: United States

Language:: English

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