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Guts of healthy humans, livestock, and pets harbor critical-priority and high-risk Escherichia coli clones
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Idris Nasir Abdullahi, Islem Trabelsi
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Epidemiol Health. 2025;47:e2025013. Published online March 22, 2025
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DOI: https://doi.org/10.4178/epih.e2025013
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 Abstract
 PDF Supplementary Material
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Abstract
OBJECTIVES
In May 2024, the World Health Organization classified carbapenem (CARB)- and third-generation cephalosporin (3GC) resistance (R) in <italic>Escherichia coli</italic> as a critical priority, whereas colistin (COL) is a “last resort” antibiotic for their treatment. This meta-analysis evaluated the pooled prevalence, high-risk lineages, genetic relatedness, and mechanisms of CARB<sup>R</sup>, COL<sup>R</sup>, and 3GC<sup>R</sup> in <italic>E. coli</italic> from healthy humans and animals.
METHODS We conducted a systematic review and meta-analyses following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) criteria on all eligible studies that reported the analysis of <italic>E. coli</italic>, and antimicrobial susceptibility to CARB, COL and 3GC in <italic>E. coli</italic> from gut samples of clinically healthy humans, livestock, and pets from June 2014 to June 2024. Random-effect models and conserved signature indels phylogeny 1.4 were used to determine pooled prevalence rates (PPs) and the relatedness of publicly available <italic>E. coli</italic> genomes, respectively.
RESULTS Of the 5,034 identified articles, 64 studies were deemed eligible. The overall PPs of 3GC<sup>R</sup>, CARB<sup>R</sup>, and COL<sup>R</sup> <italic>E. coli</italic> were 22.5% (95% confidence interval [CI], 17.5 to 28.3), 2.2% (95% CI, 1.0 to 4.7), and 15.5% (95% CI, 10.8 to 21.8), respectively. The PPs of 3GC<sup>R</sup>-, COL<sup>R</sup>- and CARB<sup>R</sup> <italic>E. coli</italic> significantly varied by hosts, continent, and year of studies (p<0.05). Diverse <italic>E. coli</italic> lineages were found, including 13 high-risk <italic>E. coli</italic> sequence types (STs), within which ST10 predominated. Phylogenomic analyses produced 4 clusters of related CARB<sup>R</sup>- and COL<sup>R</sup> <italic>E. coli</italic> strains (<25 single nucleotide polymorphism): ST940-<italic>bla</italic><sub>OXA-181</sub> from humans in Lebanon, ST617-<italic>mcr</italic>-1 from pigs in China, ST46-<italic>mcr</italic>-1 from poultry in Tanzania, and ST1720-<italic>mcr</italic>-1 from goats in France.
CONCLUSIONS COL<sup>R</sup> and 3GC<sup>R</sup> are more frequent than CARB<sup>R</sup> in gut <italic>E. coli</italic>. These 10-year epidemiological data highlight the persistence and transmission of critical priority and high-risk <italic>E. coli</italic> strains in healthy humans and animals, raising significant One Health concerns.
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