Sharing of
cmeRABC
alleles between
C. coli
and
C. jejuni
associated with extensive drug resistance in
Campylobacter
isolates from infants and poultry in the Peruvian Amazon
Authors: Cooper Kerry K. , Mourkas Evangelos , Schiaffino Francesca , Parker Craig T. , Pinedo Vasquez Tackeshy N. , Garcia Bardales Paul F. , Peñataro Yori Pablo , Paredes Olortegui Maribel , Manzanares Villanueva Katia , Romaina Cachique Lucero , Silva Delgado Hermann , Hitchings Matthew D. , Huynh Steven , Sheppard Samuel K. , Pascoe Ben , Kosek Margaret N. 
Published: December 2024

Campylobacter
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
cmeRABC
, which encodes an efflux pump conferring high levels of combined resistance to fluoroquinolones and macrolides in
Campylobacter
strains isolated from poultry (
n
= 75) and children (
n
= 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 the
cmeRABC
operon and identified a potential genetic bottleneck for the
cmeA
and
cmeB
genes. While most
cmeB
alleles segregate by species, alleles associated with high resistance to fluoroquinolones and macrolides were found in both
Campylobacter jejuni
and
Campylobacter coli
. We inferred that the likely ancestry of these alleles was from
C. jejuni
and was later acquired by
C. coli
through recombination. Publicly accessible global genomic data from 16,120
Campylobacter
genomes identified these mutations in approximately 6% of
C. jejuni
and
C. coli
isolates globally, with higher prevalence in samples from poultry in many countries, including Peru. Our findings suggest that these extensively drug-resistant
Campylobacter
strains originated from
C. jejuni
in poultry.

IMPORTANCE

Antimicrobial resistance in
Campylobacter
is 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 in
Campylobacter jejuni
and spread to
C. coli
through 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
Campylobacter
.