Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates

Abstract

BackgroundBovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis complex (MTBC), a group of genetically monomorphic organisms featured by a remarkably high overall nucleotide identity (99.9%). Indeed, this characteristic is of major concern for correct typing and determination of strain-specific traits based on sequence diversity. Due to its historical economic dependence on cattle production, Uruguay is deeply affected by the prevailing incidence of Mycobacterium bovis. With the world’s highest number of cattle per human, and its intensive cattle production, Uruguay represents a particularly suited setting to evaluate genomic variability among isolates, and the diversity traits associated to this pathogen.ResultsWe compared 186 genomes from MTBC strains isolated worldwide, and found a highly structured population in M. bovis. The analysis of 23 new M. bovis genomes, belonging to strains isolated in Uruguay evidenced three groups present in the country. Despite presenting an expected highly conserved genomic structure and sequence, these strains segregate into a clustered manner within the worldwide phylogeny. Analysis of the non-pe/ppe differential areas against a reference genome defined four main sources of variability, namely: regions of difference (RD), variable genes, duplications and novel genes. RDs and variant analysis segregated the strains into clusters that are concordant with their spoligotype identities. Due to its high homoplasy rate, spoligotyping failed to reflect the true genomic diversity among worldwide representative strains, however, it remains a good indicator for closely related populations.ConclusionsThis study introduces a comprehensive population structure analysis of worldwide M. bovis isolates. The incorporation and analysis of 23 novel Uruguayan M. bovis genomes, sheds light onto the genomic diversity of this pathogen, evidencing the existence of greater genetic variability among strains than previously contemplated.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4249-6) contains supplementary material, which is available to authorized users.

Animal tuberculosis: impact of disease heterogeneity in transmission, diagnosis, and control

“…These studies have been proving that, besides the high nucleotidic similarity between M. bovis strains, several SNPs can be found that help to differentiate clinical isolates. The analysis of 186 whole‐genome sequences of MTC strains isolated worldwide revealed a highly clustered population in agreement with clustering based on clonal complexes (Lasserre et al, 2018). However, another study that analysed 823 genomes of M. bovis strains from different countries and hosts suggested the existence of three lineages (Lb1, Lb2 and Lb3) that do not fully represent the clonal complexes and are mainly clustered based on geographic location (Zimpel et al, 2019).…”

Global distribution and evolution ofMycobacterium bovislineages

“…In our previous study, we have also shown that few M. bovis genomes do not carry any CC genetic marker (Zimpel et al 2017a), a phenomenon that was recently observed in M. bovis isolates from one cattle herd in the USA and from slaughterhouse cattle in Eritrea (Ghebremariam et al 2018; Orloski et al 2018). These findings suggest that Clonal Complexes are unlikely to represent the whole diversity of M. bovis strains, warranting further evaluation of M. bovis molecular lineages (Zimpel et al 2017a; Lasserre et al 2018).…”

“…Since the whole-genome sequence of the first M. bovis strain became available in 2003 (Garnier et al, 2003), increasing efforts have been made to sequence additional strains and use whole-genome information to tackle bovine and/or wildlife TB transmission within specific outbreaks or countries (Bruning-Fann et al, 2017; Sandoval-Azuara et al, 2017; Ghebremariam et al, 2018; Kohl et al, 2018; Lasserre et al, 2018; Orloski et al, 2018a; Price-Carter et al, 2018; Razo et al, 2018). However, no studies to date have comprehensively analyzed M. bovis genomes at a global scale.…”

“…However, no studies to date have comprehensively analyzed M. bovis genomes at a global scale. Few studies that have compared transboundary M. bovis strains analyzed bacterial isolates obtained from a reduced number of countries (n<9) and included small sample sizes (Dippenaar et al, 2017; Patané et al, 2017; Zimpel et al, 2017a; Ghebremariam et al, 2018; Lasserre et al, 2018). Nevertheless, attained results suggest that M. bovis strains are likely to cluster based on geographical location (Dippenaar et al, 2017; Kraemer Zimpel et al, 2017; Lasserre et al, 2018).…”

“…Few studies that have compared transboundary M. bovis strains analyzed bacterial isolates obtained from a reduced number of countries (n<9) and included small sample sizes (Dippenaar et al, 2017; Patané et al, 2017; Zimpel et al, 2017a; Ghebremariam et al, 2018; Lasserre et al, 2018). Nevertheless, attained results suggest that M. bovis strains are likely to cluster based on geographical location (Dippenaar et al, 2017; Kraemer Zimpel et al, 2017; Lasserre et al, 2018). In our previous study, we have also shown that few M. bovis genomes do not carry any CC genetic marker (Zimpel et al, 2017a), a phenomenon that was recently observed in M. bovis isolates from one cattle herd in the USA and from slaughterhouse cattle in Eritrea (Ghebremariam et al, 2018; Orloski et al, 2018b).…”