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

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.

High clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis

“…paratuberculosis (MAP) is a microorganism characterised by an extremely slow growth rate both in a controlled environment ( in vitro ) and within living organisms ( in vivo ). One of the consequences of this slow pace is a low mutation rate and the extremely well-conserved and closed core genome ( 14 , 15 , 17 , 20 ). In the field of MAP epidemiology, traditional population genetic and diversity analysis methods such as VNTR or SSR analysis have currently been largely supplanted by WGS approaches.…”

“…The first genome-wide single-nucleotide polymorphism (SNP) analysis of 141 global MAP isolates provided a greater resolution than the previous genotyping methods and confirmed a restricted genetic diversity with a low substitution rate ( 14 , 15 ). This study, together with the dropping costs of the whole-genome sequence (WGS) analysis, paved the way for further MAP epidemiological studies ( 16–20 ).…”

Strain diversity in Mycobacterium avium subsp. paratuberculosis-positive bovine fecal samples collected in Switzerland

“…Homoplasy is the occurrence of genotypes that are identical by state but not by descent and can appear due to different reasons, such as convergent and reverse evolution or horizontal gene transfer ( 33 ), possibly interfering with the interpretation of data derived from VNTR analysis. In a recent study of Byrne et al, the presence of multiple distantly related strains within individual farms was shown, suggesting different infection events with distinct MAP strains ( 7 ). No clonal isolates were identified on the same farm revealing each isolate to have its own pattern of variants ( 7 ).…”

“…In a recent study of Byrne et al, the presence of multiple distantly related strains within individual farms was shown, suggesting different infection events with distinct MAP strains ( 7 ). No clonal isolates were identified on the same farm revealing each isolate to have its own pattern of variants ( 7 ). In our study, intra-herd variability was observed in four out of 11 herds, of which multiple samples per farm were analyzed.…”

“…Two major lineages, which were named according to the host species from which they were first isolated, are called “Sheep-type” (S-type/Type I and Type III) or “Cattle-type” (C-type/Type II) strains ( 5 , 6 ). C-type strains include also bison-type (B-type) isolates, which are based on differences in the IS 1311 insertion sequence ( 7 ). It has been recorded that MAP isolates belonging to different lineages are not host-specific ( 8 , 9 ).…”