Whole-genome comparison using complete genomes from Campylobacter fetus strains revealed single nucleotide polymorphisms on non-genomic islands for subspecies differentiation

Chian Teng Ong; Patrick J Blackall; Gry B Boe-Hansen; Sharon deWet; Ben J Hayes; Lea Indjein; Victoria Korolik; Catherine Minchin; Loan To Nguyen; Yusralimuna Nordin; Hannah Siddle; Conny Turni; Bronwyn Venus; Mark E Westman; Zhetao Zhang; Ala E Tabor

doi:10.3389/fmicb.2024.1452564

Whole-genome comparison using complete genomes from Campylobacter fetus strains revealed single nucleotide polymorphisms on non-genomic islands for subspecies differentiation

Front Microbiol. 2024 Sep 12:15:1452564. doi: 10.3389/fmicb.2024.1452564. eCollection 2024.

Authors

Chian Teng Ong¹, Patrick J Blackall², Gry B Boe-Hansen³, Sharon deWet⁴, Ben J Hayes¹, Lea Indjein³, Victoria Korolik⁵, Catherine Minchin⁶, Loan To Nguyen¹, Yusralimuna Nordin¹, Hannah Siddle¹, Conny Turni², Bronwyn Venus¹, Mark E Westman⁷, Zhetao Zhang¹, Ala E Tabor^{1

8}

Affiliations

¹ Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD, Australia.
² Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Dutton Park, QLD, Australia.
³ School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia.
⁴ Department of Agriculture and Fisheries, Biosecurity Sciences Laboratory, Coopers Plains, QLD, Australia.
⁵ Institute for Glycomics, Griffith University, Nathan, QLD, Australia.
⁶ Department of Agriculture and Fisheries, Agri-Science Queensland, Animal Science, Dutton Park, QLD, Australia.
⁷ Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia.
⁸ School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.

Abstract

Introduction: Bovine Genital Campylobacteriosis (BGC), caused by Campylobacter fetus subsp. venerealis, is a sexually transmitted bacterium that significantly impacts cattle reproductive performance. However, current detection methods lack consistency and reliability due to the close genetic similarity between C. fetus subsp. venerealis and C. fetus subsp. fetus. Therefore, this study aimed to utilize complete genome analysis to distinguish genetic features between C. fetus subsp. venerealis and other subspecies, thereby enhancing BGC detection for routine screening and epidemiological studies.

Methods and results: This study reported the complete genomes of four C. fetus subsp. fetus and five C. fetus subsp. venerealis, sequenced using long-read sequencing technologies. Comparative whole-genome analyses (n = 25) were conducted, incorporating an additional 16 complete C. fetus genomes from the NCBI database, to investigate the genomic differences between these two closely related C. fetus subspecies. Pan-genomic analyses revealed a core genome consisting of 1,561 genes and an accessory pangenome of 1,064 genes between the two C. fetus subspecies. However, no unique predicted genes were identified in either subspecies. Nonetheless, whole-genome single nucleotide polymorphisms (SNPs) analysis identified 289 SNPs unique to one or the C. fetus subspecies. After the removal of SNPs located on putative genomic islands, recombination sites, and those causing synonymous amino acid changes, the remaining 184 SNPs were functionally annotated. Candidate SNPs that were annotated with the KEGG "Peptidoglycan Biosynthesis" pathway were recruited for further analysis due to their potential association with the glycine intolerance characteristic of C. fetus subsp. venerealis and its biovar variant. Verification with 58 annotated C. fetus genomes, both complete and incomplete, from RefSeq, successfully classified these seven SNPs into two groups, aligning with their phenotypic identification as CFF (Campylobacter fetus subsp. fetus) or CFV/CFVi (Campylobacter fetus subsp. venerealis and its biovar variant). Furthermore, we demonstrated the application of mraY SNPs for detecting C. fetus subspecies using a quantitative PCR assay.

Discussion: Our results highlighted the high genetic stability of C. fetus subspecies. Nevertheless, Campylobacter fetus subsp. venerealis and its biovar variants encoded common SNPs in genes related to glycine intolerance, which differentiates them from C. fetus subsp. fetus. This discovery highlights the potential of employing a multiple-SNP assay for the precise differentiation of C. fetus subspecies.

Keywords: Campylobacter fetus; SNPs; complete genomes; genome comparison; glycine; subspecies; veterinary science.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Meat and Livestock Australia Donor Company (grant number: P.PSH.0799) and the Queensland Department of Agriculture and Fisheries.