Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea

Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely. Spoligotyping, VNTR profiling, and whole genome sequencing (WGS) of M. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea's largest slaughterhouse in the capital Asmara, were conducted. The 14 M. bovis isolates were classified into three different spoligotype patterns (SB0120, SB0134 and SB0948) and six VNTR profiles. WGS results matched those of the conventional genotyping methods and further discriminated the six VNTR profiles into 14 strains. Furthermore, phylogenetic analysis of the M. bovis isolates suggests two independent introductions of BTB into Eritrea possibly evolving from a common ancestral strain in Europe.This molecular study revealed the most important strains of M. bovis in Eritrea and their (dis)similarities with the strains generally present in East Africa and Europe, as well as potential routes of introduction of M. bovis. Though the sample size is small, the current study provides important information as well as platform for future in-depth molecular studies on isolates from both the dairy and the traditional livestock sectors in Eritrea and the region. This study provides information onthe origin of some of the M. bovis strains in Eritrea, its genetic diversity, evolution and patterns of spread between dairy herds. Such information is essential in the development and implementation of future BTB control strategy for Eritrea.S1 Table. Accession numbers, Bioproject and sample numbers in ªFASTQº files from the isolates sequenced and uploaded into NCBI short read archive. The Eritrean M. bovis isolates are compared with the widely available M. bovis reference strains, the field strains from the collections of United States Department of Agriculture, Centre de Recercaen Sanitat Animal (CReSA)ÐInstitute de Recerca i Technologia AgroalimentaÂries (IRTA), Spain, and University of Ibadan, Nigeria, that shared the same common ancestor.S2 Table. SNP table comparing the Eritrean strains with Ethiopian, Spanish and American (USA) strains with reference to Bz-31150_Ref_Strain AF2_SB0133 and BCG_Ref_- Strain_SB0120.S1 Fig. Global comparison of spoligotypes in relation to the spoligotypes of the Eritrean M. bovis isolates.S2 Fig. The overall phylogenetic structure ofM. bovis isolates in the NVSL database with the Eritrean and related strains.Netherlands Foundation for International Cooperation (NUFFIC; Grant number: CF8608) and partially funded by the Eritrean Research Fund (ERF).http://www.plosntds.orgam2018Veterinary Tropical Disease