Abstract
Campylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.
Highlights
Campylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals. antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern
Point mutations at multiple positions of the DNA gyrase A (GyrA) region can cause resistance towards fluoroquinolones in Campylobacter[8], the Thr86Ile GyrA mutation has been reported as the most prevalent mechanism in Campylobacter from animal and human sources[8,28,29,30]. This is in agreement with the results presented here and with previous studies where this mutation was detected by SNP-PCR in fluoroquinoloneresistant C. jejuni isolated from ruminants and poultry in the region[5,11]
whole genome sequencing (WGS) was used to characterise and predict AMR in a collection of C. jejuni and C. coli with different resistance phenotypes isolated from a representative sample of beef cattle, dairy cattle, and sheep farms in the Basque Country
Summary
Campylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals. antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Campylobacter is a leading cause of bacterial gastroenteritis throughout the industrialized world, most cases being attributed to infection with Campylobacter jejuni and to a lesser extent with Campylobacter coli[1,2] Both species asymptomatically colonise the intestinal tract of a wide range of wild and domestic mammals and birds, and livestock constitute a significant source for human infection through consumption of contaminated food and water, or by contact with animals[1]. The aim of this study was to characterise by whole genome sequencing (WGS) the mechanisms of AMR in C. jejuni and C. coli recovered from beef cattle, dairy cattle, and sheep, focusing on the genetic diversity and population structure of resistant isolates
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