Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.

Josephine M Bryant,Karen Stevenson,Iker A Sevilla,Julian Parkhill,Franck Biet,Stephen D Bentley,Ian Heron,Virginie C Thibault,Duncan J Maskell,Joyce Mcluckie,David G E Smith,Simon R Harris

doi:10.1186/s12864-015-2234-5

Abstract

BackgroundMycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne’s disease in livestock. Determining genetic diversity is prerequisite to understanding the epidemiology and biology of Map. We performed the first whole genome sequencing (WGS) of 141 global Map isolates that encompass the main molecular strain types currently reported. We investigated the phylogeny of the Map strains, the diversity of the genome and the limitations of commonly used genotyping methods.ResultsSingle nucleotide polymorphism (SNP) and phylogenetic analyses confirmed two major lineages concordant with the former Type S and Type C designations. The Type I and Type III strain groups are subtypes of Type S, and Type B strains are a subtype of Type C and not restricted to Bison species.We found that the genome-wide SNPs detected provided greater resolution between isolates than currently employed genotyping methods. Furthermore, the SNP used for IS1311 typing is not informative, as it is likely to have occurred after Type S and C strains diverged and does not assign all strains to the correct lineage. Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) differentiates Type S from Type C but provides limited resolution between isolates within these lineages and the polymorphisms detected do not necessarily accurately reflect the phylogenetic relationships between strains.WGS of passaged strains and coalescent analysis of the collection revealed a very high level of genetic stability, with the substitution rate estimated to be less than 0.5 SNPs per genome per year.ConclusionsThis study clarifies the phylogenetic relationships between the previously described Map strain groups, and highlights the limitations of current genotyping techniques. Map isolates exhibit restricted genetic diversity and a substitution rate consistent with a monomorphic pathogen. WGS provides the ultimate level of resolution for differentiation between strains. However, WGS alone will not be sufficient for tracing and tracking Map infections, yet importantly it can provide a phylogenetic context for affirming epidemiological connections.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2234-5) contains supplementary material, which is available to authorized users.

Highlights

Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne’s disease in livestock
whole genome sequencing (WGS) alone will not be sufficient for tracing and tracking Map infections, yet importantly it can provide a phylogenetic context for affirming epidemiological connections
Two other isolates representing members of the Mycobacterium avium complex (Mycobacterium avium subspecies avium [Maa] and Mycobacterium avium subspecies silvaticum [Mas]) were included in the panel for WGS to place the Map strains in a wider mycobacterial context

Summary

Introduction

Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne’s disease in livestock. Mycobacterium avium subspecies paratuberculosis (Map) is an enteric pathogen causing Johne’s disease, which is responsible for considerable economic losses to the livestock and associated industries on a global scale [1]. It was proposed that these strain types be referred to as Type I (Type S) or Type II (Type C) [15], both designations are still in use. These two major strain groups can be differentiated based on their genotype, growth characteristics and pathogenesis [13, 16]

Methods

Results

Conclusion