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

• Main Authors: Byrne, Alexander, Ollier, Séverine, Tahlan, Kapil, Biet, Franck, Bissonnette, Nathalie
• Other Authors: Memorial University of Newfoundland = Université Memorial de Terre-Neuve St. John's, Canada (MUN), Agriculture and Agri-Food Canada, Saskatoon Research Centre, Agriculture and Agri-Food (AAFC), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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).
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2023
• Subjects: mycobacterium avium subsp. paratuberculosis; whole genome sequencing (WGS); molecular epidemiology; phylogenetic SNP based analysis; strain typing; MIRU-VNTR analysis; MLSSR typing; John's disease; [SDV]Life Sciences [q-bio]; [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry; Molecular Biology/Genomics [q-bio.GN]; Canada; Newfoundland
• Online Access: https://hal.inrae.fr/hal-04004244; https://hal.inrae.fr/hal-04004244/document; https://hal.inrae.fr/hal-04004244/file/2023_Byrne_Front-Genet_vol-14_art-1043598.pdf; https://doi.org/10.3389/fgene.2023.1043598

International audience 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. ...