Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution

Authors: VAN DER GRAAF, LINDA - Utrecht University; DUIM, BIRGITTA - Utrecht University; Looft, Torey; VELDMAN, KEES - Wageningen University And Research Center; ZOMER, ALDERT - Utrecht University; WAGENAAR, JAAP - Utrecht University

Submitted to: Microbial Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2022
Publication Date: 2/3/2023
Citation: van der Graaf-van Bloois, L., Duim, B., Looft, T.P., Veldman, K.T., Zomer, A.L., Wagenaar, J.A. 2023. Antimicrobial resistance in Campylobacter fetus: emergence and genomic evolution. Microbial Genomics. 9(3). https://doi.org/10.1099/mgen.0.000934.
DOI: https://doi.org/10.1099/mgen.0.000934

Interpretive Summary: The increase in antimicrobial resistance in Campylobacter is a worldwide public-health concern. Campylobacter fetus (C. fetus) is primarily associated with fertility problems in sheep and cattle but can also cause severe infections in humans that require antimicrobial treatment. There is little knowledge about the level of antimicrobial resistance development in C. fetus. In this study we used whole genome sequencing to investigate the emergence of resistance in an extensive set of 295 C. fetus strains, isolated from the pre-antimicrobial era (1939) until present. Most antibiotic resistance was detected in Campylobacter fetus subspecies fetus (Cff) isolates from human origin. C. fetus strains carry plasmids harboring antibiotic resistance genes that most likely are shared with other Campylobacter species. Cff strains showed elevated resistance for cefotaxime and cefquinome in isolates from 1943 and later, followed by the detection resistance to tetracyclines in 1999 and aminoglycosides in 2003. The emergence of AMR in C. fetus increased after the early 2000s and was found in strains isolated from around the world. Studies like this are needed to understand how pathogens of animal and public health significance change in susceptibility to drug treatments over time.

Technical Abstract: Campylobacter fetus (C. fetus) is an important pathogen for both humans and animals, but little is known about the development of antimicrobial resistance in C. fetus. Moreover, no epidemiological cut-off values (or clinical breakpoints) are available to distinguish between the wild type (susceptible) and non-wild type (reduced susceptible or resistant) population. The aim of this study was to determine the phenotypic susceptibility pattern of C. fetus strains and reveal the genomic basis of resistance to antimicrobial agents. Whole genome sequences of 295 C. fetus isolates, including strains isolated in the period 1939 till mid 1940’s before the usage of non-synthetic antimicrobials, were analysed for the presence of resistance markers and phenotypic antimicrobial susceptibility was obtained for a selection of 47 strains. In general, Campylobacter fetus subspecies fetus (Cff) strains (n=166) more often showed antimicrobial resistance compared to Campylobacter fetus subspecies venerealis (Cfv) strains (n=129) and resistance genes were only found in Cff strains, mainly isolated from human cases. Non-wildtype Cff strains showing elevated MICs for cefotaxime and cefquinome were detected in isolates from 1943 and onwards, followed by the detection of reduced susceptibility to tetracyclines in 1999 and aminoglycosides in 2003, and from then, the emergence of AMR in C. fetus is increasing. Resistance genes encoding for resistance to streptomycin (ant(6)) and tetracycline (tet(44)) were identified on chromosomal islands of 11 out of 295 strains, and genes causing resistance to kanamycin (aph(3')-III), neomycin (aph(3')-III) and tetracycline (tet(O)) were determined to be located both on chromosomal islands and plasmids, whereas a chloramphenicol resistance gene (cat) was only found on a plasmid. Plasmids harboring tetracycline and aminoglycoside resistance genes are most likely shared with other Campylobacter species given their gene homology. Silent mutations in the chromosomal DNA gyrase A appeared in the 1960s in ovine C. fetus isolates, and three gyrA substitutions in the Quinolone Resistance Determining Region (D91N, D91Y and T87I) conferring ciprofloxacin resistance were identified from 2008 onwards.