Population structure and transmission of Mycobacterium bovis in Ethiopia

Abstract

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis , which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M . bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis , based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

Genomic and temporal analyses of Mycobacterium bovis in southern Brazil

“…The analysis of within-host diversity identified isolates from the same animal that were up to 26 SNPs apart, highlighting the likelihood of these animals suffering from mixed infections, higher rates of within-host evolution or long-term infections that are not being detected. This level of within-host diversity is similar to that observed in cattle in Ethiopia [91], although further analyses of multiple isolates from the same animals in other settings will be required to see if this is common to all animals infected with bTB. Examination of the pairwise SNP diversity amongst the defined fastBAPS clusters showed that there was much less diversity amongst cluster 1, which comprised Eu1 isolates, when compared to the other three clusters comprising Eu2 isolates which had similar levels of diversity ().…”

Whole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

“…The sports hunting industry has fueled high densities of wild boar and red deer in the Castelo Branco district, an agroforestry region, which thus may be more likely to experience transmission from wildlife, whereas in the rural settings of Portalegre, transmission involving extensively managed cattle may be more frequent. Other studies have also shown that the role of wildlife changes by location [23,[49][50][51][52][53][54]. These hypotheses are to be further demonstrated in future studies.…”

A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation

“…Raw M. bovis sequence files from Almaw et al [10], Loiseau et al [11], Orloski et al [12], Reis and Cunha [7], Rodrigues et al [13], Zwyer et al [14] and from BioProject PRJNA769553 were downloaded from the NCBI Sequence Read Archive. A full list of downloaded samples can be found in Supplemental File 1.…”