Exploration of phylogenetic relationships between strains of mycobacterium avium subspecies paratuberculosis using genome sequencing
Résumé
The differentiation of isolates is essential for an in depth understanding of the epidemiology and pathogenesis of Mycobacterium avium subspecies paratuberculosis (MAP). Different strain groups have been identified using various molecular typing techniques, but some confusion exists as to the phylogenetic relationships between these strain groups. Genome sequencing was undertaken to investigate the genetic diversity and phylogenetic relationships between 134 MAP isolates of different provenance, representing 17 countries and 9 host species. The study confirmed the existence of two major lineages corresponding to the previously described S-type and C-type strains. The Type I and III strains identified by pulsed-field gel electrophoresis and Gyr SNP analysis comprised two distinct phylogenetic clusters within the S-type lineage. ‘Bison type’ strains did not comprise a distinct phylogenetic cluster and were scattered among different clusters within the C-type lineage. The majority of isolates in the panel were typed by pulsedfield electrophoresis and Mycobacterial Interspersed Repetitive Unit-Variable Nucleotide Tandem Repeat (MIRU-VNTR) analyses. The MIRU-VNTR data based on eight loci was mapped to the phylogenetic tree and showed poor concordance with the SNP-based phylogeny.
This suggests that while MIRU-VNTR typing can distinguish between some strain types, it detects diversity within a limited region of the genome and should not be the typing technique of choice for tracing the source of infections or transmission studies. Genome sequencing is clearly the most effective technique for strain differentiation but is expensive and impractical in many circumstances. However, as more isolates are sequenced, a SNP-based approach may offer a suitable alternative.