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


Byrne, A., Ollier, S., Tahlan, K., Biet, F., Bissonnette, N. (2023). Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events. Frontiers in Genetics, [online] 14

Plain language summary

Bovine paratuberculosis (also called Johne’s disease) is widespread throughout the world. It is caused by the bacterium Mycobacterium avium subsp. paratuberculosis (MAP). In Canada, the prevalence of MAP-positive dairy herds ranges from 24% to 60% depending on the region. What’s more, MAP poses a risk to humans—it has been implicated in Crohn’s disease. In dairy cows, MAP causes a debilitating disease with a major economic impact on industry. The course of the disease is often unpredictable. At present, little is known about the diversity of strains present in herds. In addition, it is not clear whether transmission between herds is a significant issue. In the present study, we assessed outbreaks in 20 herds in the provinces of Quebec and Ontario, Canada. The MAP strain from 67 cows was isolated and analyzed using precise molecular tools as well as whole-genome sequencing (WGS). Using WGS, we identified genetic variations in the virulence genes of the MAP bacterium. It turns out that the WGS approach was far more discriminating than the molecular tools commonly used in epidemiology. WGS was the only method capable of documenting disease transmission between herds. Transmission of MAP occurs mainly via the fecal-oral route from an infectious animal. The introduction of a sub-clinical animal into a herd is undoubtedly an important transmission route. This is the first validation of the fact that the movement of MAP-infected animals in Canada can generate new outbreaks of infection in herds. Future studies based on strain signatures and impact on host-pathogen interactions (virulence) are planned and are very promising.


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.

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