Sharing ofalleles betweenandassociated with extensive drug resistance inisolates from infants and poultry in the Peruvian Amazon.

Abstract

is a serious health threat because of the rapid progressive evolution of antimicrobial resistance and efficient transmission from zoonotic as well as human sources. Resistance to fluoroquinolones and macrolides is particularly concerning as this compromises the two most effective oral antibiotic agents currently available for human campylobacteriosis. Here, we report on the prevalence and worldwide distribution of the operon, which encodes an efflux pump conferring high levels of combined resistance to fluoroquinolones and macrolides instrains isolated from poultry (= 75) and children (= 177). These mutations were found to be highly prevalent in isolates from poultry (62.7%) and children (29.4%) in Iquitos, Peru. We investigated the population structure of genes in theoperon and identified a potential genetic bottleneck for theandgenes. While mostalleles segregate by species, alleles associated with high resistance to fluoroquinolones and macrolides were found in bothand. We inferred that the likely ancestry of these alleles was fromand was later acquired bythrough recombination. Publicly accessible global genomic data from 16,120genomes identified these mutations in approximately 6% ofandisolates globally, with higher prevalence in samples from poultry in many countries, including Peru. Our findings suggest that these extensively drug-resistantstrains originated fromin poultry.IMPORTANCEAntimicrobial resistance inis a growing public health concern, driven by the rapid evolution and zoonotic transmission of resistant strains. This study focuses on mutations in the cmeABC efflux pump, which confer high resistance to fluoroquinolones and macrolides, the two most effective oral antibiotics for human campylobacteriosis. By analyzing genomes from poultry and children in Iquitos, Peru, as well as global genomic data sets, we identified a significant prevalence of these resistance-associated mutations, particularly in poultry and children. Our findings suggest that these mutations originated inand spread tothrough recombination. Globally, these mutations are found in approximately 6% of isolates, with higher prevalence in poultry in multiple countries. This research underscores the critical role of genomic epidemiology in understanding the origins, evolution, and dissemination of antimicrobial resistance and highlights the need to address poultry as a reservoir for resistant.