Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events

Alexander Byrne; Séverine Ollier; Kapil Tahlan; Franck Biet; Nathalie Bissonnette

doi:10.3389/fgene.2023.1043598

Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events

Front Genet. 2023 Feb 2:14:1043598. doi: 10.3389/fgene.2023.1043598. eCollection 2023.

Authors

Alexander Byrne¹, Séverine Ollier², Kapil Tahlan¹, Franck Biet³, Nathalie Bissonnette²

Affiliations

¹ Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
² Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada.
³ INRAE, ISP, Université de Tours, Nouzilly, France.

Abstract

Mycobacterium avium subsp. paratuberculosis (MAP) is the pathogen responsible for paratuberculosis or Johne's Disease (JD) in ruminants, which is responsible for substantial economic losses worldwide. MAP transmission primarily occurs through the fecal-oral route, and the introduction of an MAP infected animal into a herd is an important transmission route. In the current study, we characterized MAP isolates from 67 cows identified in 20 herds from the provinces of Quebec and Ontario, Canada. Whole genome sequencing (WGS) was performed and an average genome coverage (relative to K-10) of ∼14.9 fold was achieved. The total number of SNPs present in each isolate varied from 51 to 132 and differed significantly between herds. Isolates with the highest genetic variability were generally present in herds from Quebec. The isolates were broadly separated into two main clades and this distinction was not influenced by the province from which they originated. Analysis of 8 MIRU-VNTR loci and 11 SSR loci was performed on the 67 isolates from the 20 dairy herds and publicly available references, notably major genetic lineages and six isolates from the province of Newfoundland and Labrador. All 67 field isolates were phylogenetically classified as Type II (C-type) and according to MIRU-VNTR, the predominant type was INMV 2 (76.1%) among four distinct patterns. Multilocus SSR typing identified 49 distinct INMV SSR patterns. The discriminatory index of the multilocus SSR typing was 0.9846, which was much higher than MIRU-VNTR typing (0.3740). Although multilocus SSR analysis provides good discriminatory power, the resolution was not informative enough to determine inter-herd transmission. In select cases, SNP-based analysis was the only approach able to document disease transmission between herds, further validated by animal movement data. The presence of SNPs in several virulence genes, notably for PE, PPE, mce and mmpL, is expected to explain differential antigenic or pathogenetic host responses. SNP-based studies will provide insight into how MAP genetic variation may impact host-pathogen interactions. Our study highlights the informative power of WGS which is now recommended for epidemiological studies and to document mixed genotypes infections.

Keywords: John’s disease; MIRU-VNTR analysis; MLSSR typing; molecular epidemiology; mycobacterium avium subsp. paratuberculosis; phylogenetic SNP based analysis; strain typing; whole genome sequencing (WGS).

Grants and funding

This research was supported by a contribution from Agriculture and Agri-Food Canada for collecting biological samples and phenotypes during two overlapping longitudinal studies (J-000075 and J-000079, NB). The microbiological cultures and WGS analysis were supported by the Dairy Research Cluster 3 Activity 9 (Dairy Farmers of Canada, Canadian Dairy Network and Agriculture and Agri-Food Canada J-002095, NB and KT) under the Canadian Agricultural Partnership AgriScience Program. The MIRU-VNTR typing was supported by the GALACTINOV funding (NB and FB). Memorial University of Newfoundland also provided student support to AB. As per the research agreement, aside from providing financial support, the funders have no role in the design and conduct of the studies, data collection and analysis or interpretation of the data. Researchers maintain independence in conducting their studies, own their data, and report the outcomes regardless of the results. The decision to publish findings rests solely with the researchers.