Whole Genome-based Characterisation of Antimicrobial Resistance and Genetic Diversity in Campylobacter Jejuni and Campylobacter Coli from Ruminants

Overview

Journal Sci Rep

Specialty Science

Date 2021 Apr 27

PMID 33903652

Citations 21

Authors

Medelin Ocejo

Beatriz Oporto

Jose Luis Lavin

Ana Hurtado

Affiliations

Soon will be listed here.

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 bla-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.

Citing Articles

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References

Gupta S, Padmanabhan B, Diene S, Lopez-Rojas R, Kempf M, Landraud L . ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2013; 58(1):212-20. PMC: 3910750. DOI: 10.1128/AAC.01310-13. View

Roux F, Sproston E, Rotariu O, Macrae M, Sheppard S, Bessell P . Elucidating the aetiology of human Campylobacter coli infections. PLoS One. 2013; 8(5):e64504. PMC: 3667194. DOI: 10.1371/journal.pone.0064504. View

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2015; 44(D1):D7-19. PMC: 4702911. DOI: 10.1093/nar/gkv1290. View

Englen M, Hill A, Dargatz D, Ladely S, Fedorka-Cray P . Prevalence and antimicrobial resistance of Campylobacter in US dairy cattle. J Appl Microbiol. 2007; 102(6):1570-7. DOI: 10.1111/j.1365-2672.2006.03189.x. View

Bock A . Biosynthesis of selenoproteins--an overview. Biofactors. 2000; 11(1-2):77-8. DOI: 10.1002/biof.5520110122. View

Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R . The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9:75. PMC: 2265698. DOI: 10.1186/1471-2164-9-75. View

Sheppard S, Dallas J, Strachan N, MacRae M, McCarthy N, Wilson D . Campylobacter genotyping to determine the source of human infection. Clin Infect Dis. 2009; 48(8):1072-8. PMC: 3988352. DOI: 10.1086/597402. View

Chatre P, Haenni M, Meunier D, Botrel M, Calavas D, Madec J . Prevalence and antimicrobial resistance of Campylobacter jejuni and Campylobacter coli isolated from cattle between 2002 and 2006 in France. J Food Prot. 2010; 73(5):825-31. DOI: 10.4315/0362-028x-73.5.825. View

10.

Nascimento M, Sousa A, Ramirez M, Francisco A, Carrico J, Vaz C . PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics. 2016; 33(1):128-129. DOI: 10.1093/bioinformatics/btw582. View

11.

Brocchieri L, Karlin S . Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res. 2005; 33(10):3390-400. PMC: 1150220. DOI: 10.1093/nar/gki615. View

12.

McArthur A, Waglechner N, Nizam F, Yan A, Azad M, Baylay A . The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013; 57(7):3348-57. PMC: 3697360. DOI: 10.1128/AAC.00419-13. View

13.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

14.

Overbeek R, Olson R, Pusch G, Olsen G, Davis J, Disz T . The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2013; 42(Database issue):D206-14. PMC: 3965101. DOI: 10.1093/nar/gkt1226. View

15.

Luangtongkum T, Jeon B, Han J, Plummer P, Logue C, Zhang Q . Antibiotic resistance in Campylobacter: emergence, transmission and persistence. Future Microbiol. 2009; 4(2):189-200. PMC: 2691575. DOI: 10.2217/17460913.4.2.189. View

16.

Jolley K, Maiden M . BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010; 11:595. PMC: 3004885. DOI: 10.1186/1471-2105-11-595. View

17.

Zeng X, Brown S, Gillespie B, Lin J . A single nucleotide in the promoter region modulates the expression of the β-lactamase OXA-61 in Campylobacter jejuni. J Antimicrob Chemother. 2014; 69(5):1215-23. DOI: 10.1093/jac/dkt515. View

18.

Brettin T, Davis J, Disz T, Edwards R, Gerdes S, Olsen G . RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015; 5:8365. PMC: 4322359. DOI: 10.1038/srep08365. View

19.

Fabre A, Oleastro M, Nunes A, Santos A, Sifre E, Ducournau A . Whole-Genome Sequence Analysis of Multidrug-Resistant Campylobacter Isolates: a Focus on Aminoglycoside Resistance Determinants. J Clin Microbiol. 2018; 56(9). PMC: 6113490. DOI: 10.1128/JCM.00390-18. View

20.

Lopes B, Strachan N, Ramjee M, Thomson A, Macrae M, Shaw S . Nationwide Stepwise Emergence and Evolution of Multidrug-Resistant Campylobacter jejuni Sequence Type 5136, United Kingdom. Emerg Infect Dis. 2019; 25(7):1320-1329. PMC: 6590748. DOI: 10.3201/eid2507.181572. View