Population structure and transmission of Mycobacterium bovis in Ethiopia

Gizat Almaw, Getnet Abie Mekonnen, Adane Mihret, Abraham Aseffa, Hawult Taye, Andrew J.K. Conlan, Balako Gumi, Aboma Zewude, Abde Aliy, Mekdes Tamiru, Abebe Olani, Matios Lakew, Melaku Sombo, Solomon Gebre, Colette Diguimbaye, Markus Hilty, Adama Fané, Borna Müller, R. Glyn Hewinson, Richard J. EllisJavier Nunez-Garcia, Eleftheria Palkopoulou, Tamrat Abebe, Gobena Ameni, Julian Parkhill, James L.N. Wood, ETHICOBOTS Consortium, Stefan Berg, Andries J. van Tonder

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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.

Original languageEnglish
Article number000539
Number of pages12
JournalMicrobial Genomics
Volume7
Issue number5
DOIs
Publication statusPublished - 04 May 2021

Keywords

  • Bovine tuberculosis
  • Ethiopia
  • livestock
  • transmission
  • whole genome sequencing
  • Mycobacterium bovis/genetics
  • Europe
  • Genotype
  • Ethiopia/epidemiology
  • Minisatellite Repeats
  • Whole Genome Sequencing
  • Animals
  • Cattle
  • Bacterial Typing Techniques
  • Tuberculosis, Bovine/epidemiology
  • Livestock
  • Sequence Analysis

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