Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand

Abstract

The ability to DNA fingerprint Mycobacterium bovis isolates helped to define the role of wildlife in the persistence of bovine tuberculosis in New Zealand. DNA fingerprinting results currently help to guide wildlife control measures and also aid in tracing the source of infections that result from movement of livestock. During the last 5 years we have developed the ability to distinguish New Zealand (NZ) M. bovis isolates by comparing the sequences of whole genome sequenced (WGS) M. bovis samples. WGS provides much higher resolution than our other established typing methods and greatly improves the definition of the regional localization of NZ M. bovis types. Three outbreak investigations are described and results demonstrate how WGS analysis has led to the confirmation of epidemiological sourcing of infection, to better definition of new sources of infection by ruling out other possible sources, and has revealed probable wildlife infection in an area considered to be free of infected wildlife. The routine use of WGS analyses for sourcing new M. bovis infections will be an important component of the strategy employed to eradicate bovine TB from NZ livestock and wildlife.

An African origin forMycobacterium bovis

“…More recently, studies based on WGS have brought deeper insights into the population dynamics of M. bovis and showed that unlike M. tuberculosis , wild animals act as M. bovis reservoirs in different regions of the world [15-18]. However, most studies using WGS have aimed at investigating local epidemics, and little is known about the global population structure and evolutionary history of M. bovis .…”

Transboundary tuberculosis: Importation of alpacas infected with Mycobacterium bovis from the United Kingdom to Poland and potential for serodiagnostic assays in detecting tuberculin skin test false‐negative animals

“…comm. marian.price-carter@agresearch.co.nz; Price‐Carter et al, ). Our spoligotyping results and the fact that the two index alpacas showed advanced clinical disease leading to rapid fatal outcomes within 3 months of arrival to Poland support the conclusion that TB was imported with M. bovis ‐infected alpacas, most likely from the UK.…”

Animal tuberculosis: impact of disease heterogeneity in transmission, diagnosis, and control

“…In a recent work conducted in France, SNPs‐based phylogenetic analysis of 87 M. bovis isolates was congruent with clusters previously defined by spoligotyping and MIRU‐VNTR; however, some SNPs were specific of particular genotypic groups (Hauer et al, 2019). WGS is a higher resolution genotyping method, and the information generated is starting to be used to trace infection sources, to refine transmission networks and to improve knowledge concerning wildlife in TB transmission cycle, as well as in epidemiological scenarios with differential levels of complexity, from herd to multi‐host environment frameworks (Crispell et al, 2017; Price‐Carter et al, 2018).…”