Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil

Abstract

Lack of routine surveillance in countries endemic for bovine tuberculosis (tB) and limited laboratory support contributes to the inability to differentiate the Mycobacterium tuberculosis complex species, leading to an underestimated burden of the disease. Here, Whole-Genome Sequencing of Mycobacterium bovis isolated from tissues with TB-like lesions obtained from cattle and buffalos at Marajó Island, Brazil, demonstrates that recent transmission of M. bovis is ongoing at distinct sites. Moreover, the M. bovis epidemiology in this setting is herein found to be dominated by an endemic and unique clade composed of strains evolved from a common ancestor that are now genetically differentiated from other M. bovis clades. Additionally, envisioning a rapid strain differentiation and tracing across multiple settings, 28 globally validated strain-specific SNPs were identified, three of which considered as robust markers for the M. bovis Marajó strain. In conclusion, this study contributes with data regarding the identification of a novel M. bovis phylogenetic clade responsible for ongoing transmission events in both cattle and buffalo species in Brazil, provides a framework to investigate the dissemination of this highly prevalent strain and, holds the potential to inform TB control strategies that may help to prevent the spread of bovine and zoonotic TB. Tuberculosis (TB) is a worldwide important infectious disease in humans and other animals resulting in substantial morbidity and mortality caused by the Mycobacterium tuberculosis Complex (MTBC) pathogens 1,2. Among these, Mycobacterium bovis is the main etiological agent of bovine TB (bTB) in herds and is associated with a decreased livestock productivity due to early disposal of animals of high zootechnical value with subsequent economic impact 3. The impact of bTB and M. bovis is not only restricted to economic aspects of livestock production. Although the economic losses can ascend to, e.g., US$18 200 in a single region as reported for Makurdi in Nigeria

Genetic Diversity and Potential Paths of Transmission of Mycobacterium bovis in the Amazon: The Discovery of M. bovis Lineage Lb1 Circulating in South America

“…Maximum likelihood (ML) phylogenetic tree from concatenated SNPs (single nucleotide polymorphisms) of Mycobacterium bovis genomes sequenced in this study and by Conceição et al ( 24 ) from Marajó Island. Blue tips: M. bovis genomes obtained from cattle and sequenced in this study; red tips: M. bovis genomes obtained from buffalo and sequenced in this study; green tips: M. bovis genomes from unknown hosts sequenced by Conceição et al ( 24 ) and obtained from cattle or buffalo from Marajó Island, Pará; black tips: Mycobacterium caprae genomes (outgroup). Purple bar, M. bovis genomes carrying markers of European 2 clonal complex; gray bar, M. bovis genomes carrying no markers of known clonal complexes.…”

“…As to evaluate genetic diversity of M. bovis in the geographic region, 15 quality-approved M. bovis genomes previously sequenced and obtained from cattle and buffalo of the Marajó Island ( 24 ) (ENA accession number ERP116404 ) were used to evaluate the phylogenetic relatedness with the M. bovis genomes sequenced in this study. The Marajó Island is geographically close to the targeted region analyzed herein ( Figure 1 ), together with the Lower Amazon River Basin are the regions of major concentration of bufallo in the country, and these M. bovis genomes ( 24 ) were the only strains of the North of Brazil sequenced up until this study. These genomes were quality-assessed and SNPs were obtained as described above.…”

“…Mycobacterium bovis genomes obtained from this study and those from Marajó Island ( 24 ) were compared against a collection of 106 genomes representing the four M. bovis lineages (Lb1–Lb4) and unknown groups 1, 2, and 3 from a recent study that evaluated worldwide distribution and evolution of M. bovis genomes ( 9 ) ( Supplementary Data Sheet 1 ). In addition, 21 quality-approved M. bovis genomes from France ( 39 ), which include representatives of the recently suggested CC called European 3 ( 40 ), were also included in the analysis ( Supplementary Data Sheet 1 ).…”

“…In addition, the knowledge regarding strain diversity within host species has special contribution in areas under risk of zoonotic TB occurrence, thereby providing new insights in strain distribution that may help establishing strategic measures for TB control and prevention ( 18 , 19 ). In Brazil, few and dispersed molecular epidemiologic studies of M. bovis have been reported ( 20 – 24 ), and the WGS characterization of the pathogen is just starting to be unraveled ( 24 – 26 ). While few studies focused on areas of high dairy herd productivity ( 25 , 26 ), a recent study evaluating M. bovis genomes obtained from buffalo and cattle of the Marajó Island, Northern Brazil, was performed and showed the existence of a monophyletic group without CC classification ( 24 ).…”

“…In Brazil, few and dispersed molecular epidemiologic studies of M. bovis have been reported ( 20 – 24 ), and the WGS characterization of the pathogen is just starting to be unraveled ( 24 – 26 ). While few studies focused on areas of high dairy herd productivity ( 25 , 26 ), a recent study evaluating M. bovis genomes obtained from buffalo and cattle of the Marajó Island, Northern Brazil, was performed and showed the existence of a monophyletic group without CC classification ( 24 ). Therefore, the aim of this study was to apply whole-genome and SNP-based phylogenomic analyses to obtain novel information regarding the genetic diversity of M. bovis strains circulating in buffalo and cattle from the region of the Lower Amazon River Basin.…”