Whole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

• Published in: Microorganisms (Basel) 2021-07, Vol.9 (8), p.1585
• Main Authors: Reis, Ana C, Salvador, Liliana C M, Robbe-Austerman, Suelee, Tenreiro, Rogério, Botelho, Ana, Albuquerque, Teresa, Cunha, Mónica V
• Format: Article
• Language: English
• Subjects: animal tuberculosis; Animals; Bayesian analysis; Cattle; Cervus elaphus; Datasets; Deer; Disease control; Disease hot spots; Epidemiology; Gene polymorphism; Gene sequencing; Genomes; Genotypes; Genotyping; Interfaces; Livestock; multi-host transmission; Mycobacterium bovis; Nucleotides; Pathogens; Phylogenetics; Phylogeny; Polymorphism; Population genetics; Population structure; Single-nucleotide polymorphism; Spoligotyping; Surveillance; Sus scrofa; Sympatric populations; Tuberculosis; Ungulates; Whole genome sequencing; Wildlife; wildlife-livestock interface
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms9081585

Classical molecular analyses of based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought the first insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. Previous surveillance provided valuable information on the prevalence and spatial occurrence of TB and highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric. However, links at the wildlife-livestock interfaces were established mainly via classical genotype associations. Here, we apply whole genome sequencing (WGS) to cattle, red deer and wild boar isolates to reconstruct the population structure in a multi-host, multi-region disease system and to explore links at a fine genomic scale between from wildlife hosts and cattle. Whole genome sequences of 44 representative isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this population into five genetic clades, three with apparent geographic specificities, as well as the establishment of an SNP catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to further structure this population by host species and TB hotspots, providing a baseline for network analyses in different epidemiological and disease control contexts. WGS of isolates from Portugal is reported for the first time in this pilot study, refining the spatiotemporal context of TB at the wildlife-livestock interface and providing further support to the key role of red deer and wild boar on disease maintenance. The SNP diversity observed within this dataset supports the natural circulation of for a long time period, as well as multiple introduction events of the pathogen in this Iberian multi-host system.