Genome Sequences of Five Mycobacterium bovis Strains Isolated from Farmed Animals and Wildlife in Canada

Complete Genome Sequences of Mycobacterium bovis Strains Affiliated with Bovine Tuberculosis Outbreaks in Canada in 2016 and 2018

Mycobacterium bovis is the primary causative agent of bovine tuberculosis, a zoonotic infectious disease that presents a risk to public health, livestock, and wildlife. Here, we report complete genome sequences of two Mycobacterium bovis strains affiliated with bovine tuberculosis outbreaks in Canadian cattle farms in 2016 and 2018.

High female mortality caused by an atypical Mycobacterium species closely related to the Mycobacterium ulcerans-marinum complex in a colony of bearded dragons (Pogona vitticeps)

A commercial breeding colony of bearded dragons (Pogona vitticeps) experienced an increase in mortality that affected females only. Before death, the animals had lost appetite and weight, were dehydrated, and some had labored breathing. Necropsy revealed granulomas in many organs (ovaries, lungs, liver, kidneys, heart, bone marrow) in which numerous acid-fast bacteria were identified. Bacterial isolation confirmed Mycobacterium spp., which was identified by whole genome sequencing as closely related to the Mycobacterium ulcerans-marinum complex. Due to the zoonotic potential of this bacterium and the poor prognosis for the remaining sick animals, the entire colony was culled and 7 animals were evaluated. The possible routes for introduction of this bacterium, the female predisposition to the disease, as well as the zoonotic potential of this microorganism are discussed. Key clinical message: An atypical Mycobacterium species closely related to Mycobacterium ulcerans-marinum complex can cause high female morality in captive bearded dragons.

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial

Mycobacterium bovis (M. bovis) is a causative agent of bovine tuberculosis, a significant source of morbidity and mortality in the global cattle industry. The Randomised Badger Culling Trial was a field experiment carried out between 1998 and 2005 in the South West of England. As part of this trial, M. bovis isolates were collected from contemporaneous and overlapping populations of badgers and cattle within ten defined trial areas. We combined whole genome sequences from 1,442 isolates with location and cattle movement data, identifying transmission clusters and inferred rates and routes of transmission of M. bovis. Most trial areas contained a single transmission cluster that had been established shortly before sampling, often contemporaneous with the expansion of bovine tuberculosis in the 1980s. The estimated rate of transmission from badger to cattle was approximately two times higher than from cattle to badger, and the rate of within-species transmission considerably exceeded these for both species. We identified long distance transmission events linked to cattle movement, recurrence of herd breakdown by infection within the same transmission clusters and superspreader events driven by cattle but not badgers. Overall, our data suggests that the transmission clusters in different parts of South West England that are still evident today were established by long-distance seeding events involving cattle movement, not by recrudescence from a long-established wildlife reservoir. Clusters are maintained primarily by within-species transmission, with less frequent spill-over both from badger to cattle and cattle to badger.

Genomic and temporal analyses of Mycobacterium bovis in southern Brazil

Mycobacterium bovis is a causal agent of bovine tuberculosis (bTB), one of the most important diseases currently facing the cattle industry worldwide. Tracing the source of M. bovis infections of livestock is an important tool for understanding the epidemiology of bTB and defining control/eradication strategies. In this study, whole genome sequencing (WGS) of 74 M. bovis isolates sourced from naturally infected cattle in the State of Rio Grande do Sul (RS), southern Brazil, was used to evaluate the population structure of M. bovis in the region, identify potential transmission events and date the introduction of clonal complex (CC) European 2 (Eu2). In silico spoligotyping identified 11 distinct patterns including four new profiles and two CCs, European 1 (Eu1) and Eu2. The analyses revealed a high level of genetic diversity in the majority of herds and identified putative transmission clusters that suggested that within- and between-herd transmission is occurring in RS. In addition, a comparison with other published M. bovis isolates from Argentina, Brazil, Paraguay and Uruguay demonstrated some evidence for a possible cross-border transmission of CC Eu1 into RS from Uruguay or Argentina. An estimated date for the introduction of CC Eu2 into RS in the middle of the 19th century correlated with the historical introduction of cattle into RS to improve existing local breeds. These findings contribute to the understanding of the population structure of M. bovis in southern Brazil and highlight the potential of WGS in surveillance and helping to identify bTB transmission.

Whole Genome Sequencing of Mycobacterium bovis Isolated From Livestock in the United States, 1989-2018

The United States official bovine tuberculosis (bTB) eradication program has utilized genotyping for Mycobacterium bovis isolates since 2000 and whole genome sequencing was implemented in 2013. The program has been highly successful, yet as bTB prevalence has reached historic lows, a small number of new bTB-affected cattle herds occur annually. Therefore, understanding the epidemiology of bTB transmission is critically important, in order to target limited resources for surveillance and achieve eradication. This evaluation described the diversity and epidemiology of M. bovis isolates identified in the USA livestock. Isolates from animals within the bTB endemic area of Michigan were excluded. Broad diversity was found among 1,248 isolates, collected from affected cattle and farmed cervids herds and fed cattle during 1989–2018. Nearly 70% of isolates from 109 herds/cases during 1999–2018 were European clonal complex 1 and 30% were European clonal complex 2. The sources of infection based on the herd investigation were known for 41% of herds/cases and 59% were not epidemiologically linked to another USA origin herd. Whole genome sequencing results were consistent with the investigation findings and previously unrecognized links between herds and cases were disclosed. For herds/cases with an unknown source of infection, WGS results suggested several possible sources, including undocumented cattle movement, imported cattle and humans. The use of WGS in new cases has reduced the time and costs associated with epidemiological investigations. Within herd SNP diversity was evaluated by examining 18 herds with 10 or more isolates sequenced. Forty percent of isolates had not diverged or accumulated any SNPs, and 86% of the isolates had accumulated 3 or fewer SNPs. The results of WGS does not support a bTB reservoir in USA cattle. The bTB eradication program appears to be highly effective as the majority of herds/cases in the USA are unique strains with limited herd to herd transmission.