Lineages of M. bovis

Evolution and distribution of Mycobacterium bovis lineages based on whole genome sequence analyses

This is one of the main research articles of our Morris Animal Foundation grant. It was a pleasure to work with this amazing team of researchers, led by the tireless dedication of Drs Cristina Zimpel and José Patané. The aim of this study was to perform a phylogenomic analysis to understand the populational structure of M. bovis worldwide and to provide dating estimates for the origin of this important pathogen. This manuscript turned out to be larger and more detailed than what we previously published on bioRXiv. Conclusions were not changed, but a larger sample size of M. bovis genomes was analyzed.

Accordingly, we have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains (one from a bison, one from a capybara e two from llamas), gathering 1,969 M. bovis genomes from 23 countries and at least 24 different host species to complete a phylogenomic analyses. Our phylogenetic reconstruction suggests the existence of at least four distinct lineages of M. bovis in the world, which we named Lb1 through Lb4. There were also three “unknown” groups for which we believe more data should be gathered. These lineages and groups are not fully represented by current clonal complexes (Eu1, Eu2, Af1, Af2), and we have proposed preliminary specific SNP markers. Future studies should evaluate additional deletion markers. 

Figure 1. Phylogenetic clustering, SNP (single nucleotide polymorphism) markers, and lineages of Mycobacterium bovis. Maximum likelihood phylogenetic tree based on SNPs of 1,201 Mycobacterium bovis genomes (reduced dataset), using Mycobacterium caprae and Mycobacterium orygis as outgroup. Source: Frontiers in Microbiology, doi: 10.3389/fmicb.2020.00843

These lineages tend to cluster according to geographical origin rather than host species. This finding reinforces the idea of M. bovis being a generalist bacterium, infecting different host species irrespective of its genetic makeup. Lb1 and Lb2 were found to occur mostly in Africa and Europe, Lb3 present mainly in the Americas, Europe and South Africa, and Lb4 dispersed worldwide.  Whether or not these lineages have different virulent profiles is still unknown and requires further investigation.

We also evaluated the evolutionary origin of M. bovis (i.e., time of the MRCA of M. caprae and M. bovis), which turned out to have occurred around 715 and 3,556 years BP (Before Present). This dating estimate is in accordance with independent archeological data, which indicates the presence of M. bovis in human skeletons in South Siberia dating from ~2,000 years ago. Additional dating estimates throughout the phylogenetic tree also match cattle introduction/importation into different countries worldwide, which is supportive evidence of the spread of the disease through animal trade. Inferring the precise timing of the origin of M. bovis and its distinct lineages is of great importance as it offers insights into which factors, at the time, facilitated the emergence of this infectious agent in the cattle and wildlife population. For example, it is very clear now that M. bovis introduction into South Africa occurred with infected cattle import and later spilled over to wildlife, with devastating effects.

Unfortunately, much of the world remains to have genomes of M. bovis sequenced from their animals. Genomic data is missing from Asia and most countries of Africa. This paucity of data hampers the estimation of M. bovis geographic origin. Even if ancestral state reconstruction with current genomes may provide results, these will be based on a minimal number of M. bovis genomes and on a biased world sample. We urge bovine TB researchers from all over the world to sequence M. bovis genomes, so we may all start to paint a complete picture of M. bovis history, geographic spread and host adaptation.

We strongly believe the results of this article will change how we evaluate the epidemiology of M. bovis moving forward. It opens doors to the an immense array of studies regarding virulence, disease transmission and spread, and diagnostics.

Source: Zimpel et al., 2020. Global distribution and evolution of Mycobacterium bovis lineages. Frontiers in Microbiology, 11:843.