Investigating genetically-structured diversity in pathogen populations over time is important to better understand disease maintenance and spread. Herd-level surveillance of Mycobacterium bovis genotypes (multi-locus VNTR analysis types, MLVA types) from all culture-confirmed bovine tuberculosis (TB) herd cases was undertaken in Northern Ireland (NI), generating an unparalleled, longitudinal, population-level 14-year survey for this pathogen. Across this population, 295 genetically-distinct M. bovis MLVA types were identified in the 19,717 M. bovis isolates surveyed. Of these, the most frequent was MLVA type 002 (23.0%); 151 MLVA types were represented more than once, in groups ranging from 2 to 4438 isolates. Only 23 MLVA types were isolated in all 14 years. Investigating inter-annual frequency of M. bovis MLVA types, examples of statistically-significant expansions (MLVA types 002, 004, 006, 009 and 027), contractions (MLVA types 001, 007 and 011) and maintenance (MLVA types 003 and 005) were disclosed, during a period of fluctuating bovine TB herd-level incidence at the NI scale. The fixed period frequency distribution of MLVA types remained highly right-skewed. Novel VNTR copy number variant MLVA types (N = 242; an average of 17 per annum) were identified throughout the survey. The MLVA type distribution in the landscape was not random; MLVA types showed statistically-significant geographical localization and strong spatial associations with Divisional Veterinary Office (DVO) regions. There was also evidence of differential risk of particular MLVA types across breeds (Holstein/Friesian vs. other), age-class, and sex and some evidence of an association between the number of animals testing positive for bovine TB during the disclosing test and particular MLVA types, although there was substantial variation.

Veterinary Sciences Division Agri food and Biosciences Institute Agriculture House Dublin 2 Ireland

Veterinary Sciences Division Agri food and Biosciences Institute current address

Veterinary Sciences Division Agri food and Biosciences Institute Stoney Road Stormont Belfast BT4 3SD UK

Veterinary Sciences Division Agri food and Biosciences Institute Stoney Road Stormont Belfast BT4 3SD UK; School of Biological Sciences Queen's University Belfast Belfast BT7 1NN UK

Veterinary Sciences Division Agri food and Biosciences Institute Stoney Road Stormont Belfast BT4 3SD UK; Veterinary Service and Animal Health Group Department of Agriculture Environment and Rural Affairs Dundonald House Stormont Belfast BT4 3SB UK

Veterinary Service and Animal Health Group Department of Agriculture Environment and Rural Affairs Dundonald House Stormont Belfast BT4 3SB UK

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