SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis

Abstract

Limited data are available for bovine tuberculosis and the infections it can cause in humans and other mammals. We therefore constructed a publicly accessible SITVITBovis database that incorporates genotyping and epidemiological data on Mycobacterium bovis. It also includes limited data on Mycobacterium caprae (previously synonymous with the name M. bovis subsp. Caprae) that can infect both animals and humans. SITVITBovis incorporates data on 25,741 isolates corresponding to 60 countries of origin (75 countries of isolation). It reports a total of 1000 spoligotype patterns: 537 spoligotype international types (SITs, containing 25 278 clinical isolates) and 463 orphan patterns, allowing a wide overview of the geographic distribution of various phylogenetical sublineages (BOV_1, BOV_2, BOV_3 and BOV_4-CAPRAE). The SIT identifiers of the SITVITBovis were compared to the SB numbers of the Mbovis.org database to facilitate crosscheck among databases. Note that SITVITBovis also contains limited information on mycobacterial interspersed repetitive units-variable number of tandem repeats when available. Significant differences were observed when comparing age/gender of human isolates as well as various hosts. The database includes information on the regions where a strain was isolated as well as hosts involved, making it possible to see geographic trends. SITVITBovis is publicly accessible at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis. Finally, a future second version is currently in progress to allow query of associated whole-genome sequencing data. Database URLhttp://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis

Bovine tuberculosis in Spain, is it really the final countdown?

“…This database is freely accessible and includes maps of those countries reporting new spoligotypes. Other widely used databases, such as SITVIT2, SITVITbovis [ 16 ] or MIRU-VNTRplus [ 17 ], contain data on MTBC isolates mostly obtained from clinical cases in humans. In Spain, mycoDB.es is of paramount importance: this database was established in 2008 thanks to collaboration between the MAPA and VISAVET-UCM, and contains epidemiological and molecular data concerning all MTBC isolates (mainly M. bovis and M. caprae ) obtained in Spain.…”

Bovine tuberculosis in Spain, is it really the final countdown?

“…This database is freely accessible and includes maps of those countries reporting new spoligotypes. Other widely used databases, such as SITVIT2, SITVITbovis [ 16 ] or MIRU-VNTRplus [ 17 ], contain data on MTBC isolates mostly obtained from clinical cases in humans. In Spain, mycoDB.es is of paramount importance: this database was established in 2008 thanks to collaboration between the MAPA and VISAVET-UCM, and contains epidemiological and molecular data concerning all MTBC isolates (mainly M. bovis and M. caprae ) obtained in Spain.…”

KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies)

“…The SITVIT databases and other resources ( Couvin et al , 2017 , 2022 , 2019 , 2020 ; Demay et al , 2012 ) developed by researchers at the Institut Pasteur de la Guadeloupe have provided a more complete global view of the molecular epidemiology of MTBC for public health surveillance. These resources are available online and may be of use to researchers working specifically on these bacterial organisms.…”

Recent progress in the genotyping of bovine tuberculosis and its rapid diagnosis via nanoparticle-based electrochemical biosensors

“…14 In the past, M. bovis genotyping methods have mostly relied on PCR-based assays to evaluate a few of the genetic markers. 15 Whole genome sequencing (WGS) of M. bovis will eventually substitute some challenging analyses as the cost per genome continues to drop, while also allowing for the required high resolution analysis of outbreaks. 16 These genetic techniques offer valuable insights into the causes of infection, the transmission routes, the geographic localization, and the preferred hosts, as well as the dynamics and risk factors of the disease, 17 thus promoting the reduction or elimination of the infection.…”

Bovine tuberculosis in Spain, is it really the final countdown?

“…This database is freely accessible and includes maps of those countries reporting new spoligotypes. Other widely used databases, such as SITVIT2, SITVITbovis [ 16 ] or MIRU-VNTRplus [ 17 ], contain data on MTBC isolates mostly obtained from clinical cases in humans. In Spain, mycoDB.es is of paramount importance: this database was established in 2008 thanks to collaboration between the MAPA and VISAVET-UCM, and contains epidemiological and molecular data concerning all MTBC isolates (mainly M. bovis and M. caprae ) obtained in Spain.…”

KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies)

“…The SITVIT databases and other resources ( Couvin et al , 2017 , 2022 , 2019 , 2020 ; Demay et al , 2012 ) developed by researchers at the Institut Pasteur de la Guadeloupe have provided a more complete global view of the molecular epidemiology of MTBC for public health surveillance. These resources are available online and may be of use to researchers working specifically on these bacterial organisms.…”

Recent progress in the genotyping of bovine tuberculosis and its rapid diagnosis via nanoparticle-based electrochemical biosensors

“…14 In the past, M. bovis genotyping methods have mostly relied on PCR-based assays to evaluate a few of the genetic markers. 15 Whole genome sequencing (WGS) of M. bovis will eventually substitute some challenging analyses as the cost per genome continues to drop, while also allowing for the required high resolution analysis of outbreaks. 16 These genetic techniques offer valuable insights into the causes of infection, the transmission routes, the geographic localization, and the preferred hosts, as well as the dynamics and risk factors of the disease, 17 thus promoting the reduction or elimination of the infection.…”

Bovine tuberculosis in Spain, is it really the final countdown?

“…This database is freely accessible and includes maps of those countries reporting new spoligotypes. Other widely used databases, such as SITVIT2, SITVITbovis [ 16 ] or MIRU-VNTRplus [ 17 ], contain data on MTBC isolates mostly obtained from clinical cases in humans. In Spain, mycoDB.es is of paramount importance: this database was established in 2008 thanks to collaboration between the MAPA and VISAVET-UCM, and contains epidemiological and molecular data concerning all MTBC isolates (mainly M. bovis and M. caprae ) obtained in Spain.…”

KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies)

“…The SITVIT databases and other resources ( Couvin et al , 2017 , 2022 , 2019 , 2020 ; Demay et al , 2012 ) developed by researchers at the Institut Pasteur de la Guadeloupe have provided a more complete global view of the molecular epidemiology of MTBC for public health surveillance. These resources are available online and may be of use to researchers working specifically on these bacterial organisms.…”

Recent progress in the genotyping of bovine tuberculosis and its rapid diagnosis via nanoparticle-based electrochemical biosensors

“…14 In the past, M. bovis genotyping methods have mostly relied on PCR-based assays to evaluate a few of the genetic markers. 15 Whole genome sequencing (WGS) of M. bovis will eventually substitute some challenging analyses as the cost per genome continues to drop, while also allowing for the required high resolution analysis of outbreaks. 16 These genetic techniques offer valuable insights into the causes of infection, the transmission routes, the geographic localization, and the preferred hosts, as well as the dynamics and risk factors of the disease, 17 thus promoting the reduction or elimination of the infection.…”