Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates
Abstract Background Bovine 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...
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doaj-b6f2ba5ae8d54cb48a468dbaaea8adc42020-11-25T00:45:31ZengBMCBMC Genomics1471-21642018-01-0119111410.1186/s12864-017-4249-6Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolatesMoira Lasserre0Pablo Fresia1Gonzalo Greif2Gregorio Iraola3Miguel Castro-Ramos4Arturo Juambeltz5Álvaro Nuñez6Hugo Naya7Carlos Robello8Luisa Berná9Unidad de Biología Molecular, Institut Pasteur de MontevideoUnidad de Bioinformática, Institut Pasteur de MontevideoUnidad de Biología Molecular, Institut Pasteur de MontevideoUnidad de Bioinformática, Institut Pasteur de MontevideoDepartamento de Bacteriología, División de Laboratorios Veterinarios (DI.LA.VE.) “Miguel C. Rubino”Departamento de Bacteriología, División de Laboratorios Veterinarios (DI.LA.VE.) “Miguel C. Rubino”Departamento de Bacteriología, División de Laboratorios Veterinarios (DI.LA.VE.) “Miguel C. Rubino”Unidad de Bioinformática, Institut Pasteur de MontevideoUnidad de Biología Molecular, Institut Pasteur de MontevideoUnidad de Biología Molecular, Institut Pasteur de MontevideoAbstract Background Bovine 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. Results We 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. Conclusions This 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.http://link.springer.com/article/10.1186/s12864-017-4249-6Bovine tuberculosisComparative genomicsPhylogeneticsGenetically monomorphic bacteriaEuropean 1 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Moira Lasserre Pablo Fresia Gonzalo Greif Gregorio Iraola Miguel Castro-Ramos Arturo Juambeltz Álvaro Nuñez Hugo Naya Carlos Robello Luisa Berná |
spellingShingle |
Moira Lasserre Pablo Fresia Gonzalo Greif Gregorio Iraola Miguel Castro-Ramos Arturo Juambeltz Álvaro Nuñez Hugo Naya Carlos Robello Luisa Berná Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates BMC Genomics Bovine tuberculosis Comparative genomics Phylogenetics Genetically monomorphic bacteria European 1 |
author_facet |
Moira Lasserre Pablo Fresia Gonzalo Greif Gregorio Iraola Miguel Castro-Ramos Arturo Juambeltz Álvaro Nuñez Hugo Naya Carlos Robello Luisa Berná |
author_sort |
Moira Lasserre |
title |
Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates |
title_short |
Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates |
title_full |
Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates |
title_fullStr |
Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates |
title_full_unstemmed |
Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates |
title_sort |
whole genome sequencing of the monomorphic pathogen mycobacterium bovis reveals local differentiation of cattle clinical isolates |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2018-01-01 |
description |
Abstract Background Bovine 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. Results We 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. Conclusions This 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. |
topic |
Bovine tuberculosis Comparative genomics Phylogenetics Genetically monomorphic bacteria European 1 |
url |
http://link.springer.com/article/10.1186/s12864-017-4249-6 |
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