Genomic and temporal analyses of Mycobacterium bovis in southern Brazil

Abstract

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.

A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation

“…[12], Reis and Cunha [7], Rodrigues et al . [13], Zwyer et al . [14] and from BioProject PRJNA769553 were downloaded from the NCBI Sequence Read Archive.…”

“…Raw M. bovis sequence files from Almaw et al [10], Loiseau et al [11], Orloski et al [12], Reis and Cunha [7], Rodrigues et al [13], Zwyer et al [14] and from BioProject PRJNA769553 were downloaded from the NCBI Sequence Read Archive. A full list of downloaded samples can be found in Supplemental File 1.…”

Genomic analysis of an outbreak of bovine tuberculosis in a man‐made multi‐host species system: A call for action on wildlife in Brazil

“…The cattle transmission involved seven farms, the vast majority (40/48; 83.3%) of the transmission pairs occurred within the same farm, and all but two pairs of genomes shared the same spoligotype pattern (Table S3). The eight between-farm transmission events are further supported by field epidemiological data indicating animal movements between these farms (data not shown) (Rodrigues et al, 2021).…”

“…For comparison purposes, 71 sequencing reads (Illumina, paired‐end, 100 bp) obtained from 13 cattle herds in Rio Grande do Sul, the same state of the safari park, were included in the analysis. These M. bovis isolates were obtained and sequenced in an unrelated study (Rodrigues et al., 2021). Figure 1 indicates the location of the safari park in relation to these cattle herds.…”

“…To achieve these objectives, we sequenced M. bovis genomes of 19 deer culled in 2018 and added other two M. bovis genomes obtained from llamas in 2012, sequenced in a previous study (Zimpel et al., 2020). We also assessed 71 previously sequenced M. bovis genomes (Rodrigues et al., 2021) from nearby cattle farms to verify recent transmission events from the local area to the safari park. The events that took place in the safari park described in this study highlight many regulatory gaps of the current bTB control and animal welfare legislations in the country.…”