Whole genome-based characterisation of antimicrobial resistance and genetic diversity

This study is about 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 resistantCampylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni andCampylobacter 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.

figure1Fig: Heat map showing the distribution of antimicrobial resistance (AMR) genes detected by WGS in each isolate: (A) C. jejuni; (B) C. coli. Within eachCampylobacter species, samples were grouped based on their antimicrobial resistance pattern according to the result of the hierarchical clustering using the average linkage method (UPGMA) on the Euclidean distance matrix. Genetic determinants of resistance are grouped according to their corresponding antimicrobial classes, which are colour coded. Assignation of each isolate to MLST profiles is indicated (ST, sequence type; CC, clonal complex). In cells corresponding to blaOXA-61-like genes, the nucleotide (G = guanine, T = thymine) at the promoter region (57 bp upstream of the start codon) is indicated (a G T mutation is associated with high-level ampicillin resistance). Plasmid location oftet genes is indicated by the letter “P” in the corresponding cell.

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.

Ocejo, M., Oporto, B., Lavín, J.L. et al. Whole genome-based characterisation of antimicrobial resistance and genetic diversity inCampylobacter jejuni and Campylobacter coli from ruminants. Sci Rep 11, 8998 (2021). https://doi.org/10.1038/s41598-021-88318-0

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