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 U.S. 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. Sixty-nine percent of isolates from 107 herds and cases during 1999-2018 were European clonal complex 1 and 32 percent were European clonal complex 2. The sources of infection based on the herd investigation were known for 42 percent of herds/cases and 58 percent were not epidemiologically linked to another U.S. origin herd. In all cases, whole genome sequencing results were consistent with the investigation findings. The use of WGS in new cases has reduced the time and costs associated with epidemiological investigations, and disclosed previously unrecognized links between herds and cases. 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 percent of the isolates had accumulated 3 or fewer SNPs. The results of WGS does not support a bTB reservoir in U.S. cattle. Most of the isolates recovered from imported fed cattle were not closely related to U.S. herds. This suggests there may be other vectors transmitting bTB to the U.S. national herd, such as humans or even imported dairy products, or undetected residual strains from historical cases. The bTB eradication program appears to be highly effective as the vast majority of herds/cases in the USA are unique strains with limited herd to herd transmission.