Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain.

Claudia Perea,Alberto Allepuz,Suelee Robbe-Austerman,Bernat Pérez De Val,Tod Stuber,Giovanna Ciaravino,Tyler C Thacker

doi:10.3390/microorganisms9081629

Abstract

The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.

Highlights

Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex (MTBC), is responsible for causing tuberculosis (TB) in livestock, wildlife, and humans throughout the world
The objective of the present study is to characterize M. bovis isolates obtained from livestock and wildlife in Catalonia using Whole-genome sequencing (WGS) and single nucleotide polymorphisms (SNP) analysis to identify epidemiological clusters, as well as to investigate how the isolates from this region fit into the broader global phylogenetic structure
Investigation of M. bovis strains through WGS was useful for obtaining a highresolution overview of the population structure of this pathogen in Catalonia, which shows a heterogeneous distribution

Summary

Introduction

Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex (MTBC), is responsible for causing tuberculosis (TB) in livestock, wildlife, and humans throughout the world. As for shared pastures, this practice predisposes contact with other herds, thereby increasing the risk of disease transmission among herds either by animals that inter-mingle, have access to contaminated pasture and soil, and/or infected wildlife [64,65]. An important aspect to consider with respect to the potential spread of diseases on communal grazing areas is the level of mixing between animals from different origins. In this regard, [65] showed that the level of mixing might have an effect on bovine TB spread, which in turn may be influenced by herd size [66,67]. More studies are needed to properly estimate the mixing pattern between animals from different herds

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