An African origin for Mycobacterium bovis

Chloé Loiseau; Fabrizio Menardo; Abraham Aseffa; Elena Hailu; Balako Gumi; Gobena Ameni; Stefan Berg; Leen Rigouts; Suelee Robbe-Austerman; Jakob Zinsstag; Sebastien Gagneux; Daniela Brites

doi:10.1093/emph/eoaa005

An African origin for Mycobacterium bovis

Evol Med Public Health. 2020 Jan 31;2020(1):49-59. doi: 10.1093/emph/eoaa005. eCollection 2020.

Authors

Chloé Loiseau^{1

2}, Fabrizio Menardo^{1

2}, Abraham Aseffa³, Elena Hailu³, Balako Gumi⁴, Gobena Ameni⁵, Stefan Berg⁶, Leen Rigouts^{7

8

9}, Suelee Robbe-Austerman¹⁰, Jakob Zinsstag^{1

2}, Sebastien Gagneux^{1

2}, Daniela Brites^{1

2}

Affiliations

¹ Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.
² University of Basel, Basel, Switzerland.
³ Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia.
⁴ Department of Animal Science and Range Management, Bule Hora University, Bule Hora Town, Ethiopia.
⁵ Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
⁶ Bacteriology Department, Animal & Plant Health Agency (APHA), Weybridge, Surrey, UK.
⁷ Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
⁸ Collection of Mycobacterial Cultures (BCCM/ITM), Institute of Tropical Medicine, Antwerp, Belgium.
⁹ Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium.
¹⁰ Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA.

Abstract

Background and objectives: Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens.

Methodology: We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age.

Results: Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world.

Conclusions and implications: Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented.

Lay summary: During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.

Keywords: Mycobacterium bovis; bovine tuberculosis; molecular clock; phylogeography; whole-genome sequencing; zoonosis.

Grants and funding

D43 TW009127/TW/FIC NIH HHS/United States