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.
Highlights
Mycobacterium bovis is one of several highly related subspecies of the Mycobacterium tuberculosis complex (MTBC) which causes tuberculosis (TB) in humans and a range of domesticated and wild animals [1]
Molecular dating of a collection of European 3 (Eu3) genomes which included the Ethiopian genomes in this study estimated the date of introduction of different Eu3 sub-lineages into Ethiopia and Eritrea during the same time period around the early 1970s (CI: 1958–1987)
To get a better understanding of how well the genomes analysed in this study represented the known population structure of M. bovis in Ethiopia, we collated spoligotype information for the vast majority of Ethiopian M. bovis isolates from animals published to date [67]
Summary
Mycobacterium bovis is one of several highly related subspecies of the Mycobacterium tuberculosis complex (MTBC) which causes tuberculosis (TB) in humans and a range of domesticated and wild animals [1]. In countries without adequate resources to control the disease, bTB is frequently endemic [2] This is the case for Ethiopia which has the fifth largest national cattle herd in the world with over 60 million animals, of which the vast majority are local zebu breeds reared in extensive farming systems [6]. BTB is endemic at a very low level in these extensive husbandry systems but thrives in the intensive dairy sector, with mainly high milk-yield Holstein-Friesian (H-F) or H-F/zebu cross-bred dairy cattle, where the prevalence is high [7]. Such expansion is associated with trading of dairy cattle between herds and regions, leading to increased risk of disease transmission in this sector
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