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Couvin D, Cervera-Marzal I, David A, Reynaud Y, Rastogi N. SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis. Database (Oxford) 2022; 2022:6506437. [PMID: 35028657 PMCID: PMC8962452 DOI: 10.1093/database/baab081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022]
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
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Iñaki Cervera-Marzal
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Audrey David
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Yann Reynaud
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
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Reis AC, Albuquerque T, Botelho A, Cunha MV. Polyclonal infection as a new scenario in Mycobacterium caprae epidemiology. Vet Microbiol 2019; 240:108533. [PMID: 31902500 DOI: 10.1016/j.vetmic.2019.108533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 11/30/2022]
Abstract
Portugal is one of the European Union countries with an ongoing eradication program for bovine tuberculosis (TB), which does not include systematic goat testing. However, surveillance in small ruminants is increasingly important, since goat and sheep can harbour Mycobacterium caprae and be an infection source to cattle with impact in the success of bovine TB control. Furthermore, the information regarding the epidemiology and biology of M. caprae is quite limited comparing to the cognate bovine-adapted ecotype, M. bovis. In this work, we applied spoligotyping and MIRU-VNTR (Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats) to M. caprae obtained between 2003 and 2014 from 55 animal hosts, including goat (n = 29), cattle (n = 21), sheep (n = 1) and wild boar (n = 4) from Portugal. The molecular analysis revealed a unique spoligotyping pattern (SB0157) and 24 MIRU types. Genotyping of serial M. caprae from herds with recurrent outbreaks enabled further discrimination of epidemiologically related isolates, supporting a clonal structure in Portugal and denoting the emergence of clonal diversity at the herd level, more apparent for MIRU4. Results suggest a founder effect and adaptive genotypic divergence, paving the way for sympatric speciation. Double allele findings at MIRU4 in over 20 % of infected animals indicates that co-infection and in vivo microevolution may be frequent in the goat-adapted ecotype. While polyclonal infection appears common in M. caprae epidemiology, the functional significance of subtle genotypic variations remains to be disclosed, namely at the interface with the host, to expand knowledge on the epidemiology and biology of this neglected ecotype.
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Affiliation(s)
- Ana C Reis
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, Edifício Principal, Piso 1, 2780 -157 Oeiras, Portugal; cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, 4º Piso, Campo Grande, 1749-016 Lisboa, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Teresa Albuquerque
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, Edifício Principal, Piso 1, 2780 -157 Oeiras, Portugal
| | - Ana Botelho
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, Edifício Principal, Piso 1, 2780 -157 Oeiras, Portugal
| | - Mónica V Cunha
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, Edifício Principal, Piso 1, 2780 -157 Oeiras, Portugal; cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, 4º Piso, Campo Grande, 1749-016 Lisboa, Portugal; BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
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Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea. PLoS Negl Trop Dis 2018; 12:e0006406. [PMID: 29664901 PMCID: PMC5922621 DOI: 10.1371/journal.pntd.0006406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 04/27/2018] [Accepted: 03/23/2018] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely. Spoligotyping, VNTR profiling, and whole genome sequencing (WGS) of M. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea’s largest slaughterhouse in the capital Asmara, were conducted.The 14 M. bovis isolates were classified into three different spoligotype patterns (SB0120, SB0134 and SB0948) and six VNTR profiles. WGS results matched those of the conventional genotyping methods and further discriminated the six VNTR profiles into 14 strains. Furthermore, phylogenetic analysis of the M. bovis isolates suggests two independent introductions of BTB into Eritrea possibly evolving from a common ancestral strain in Europe.This molecular study revealed the most important strains of M. bovis in Eritrea and their (dis)similarities with the strains generally present in East Africa and Europe, as well as potential routes of introduction of M. bovis. Though the sample size is small, the current study provides important information as well as platform for future in-depth molecular studies on isolates from both the dairy and the traditional livestock sectors in Eritrea and the region. This study provides information onthe origin of some of the M. bovis strains in Eritrea, its genetic diversity, evolution and patterns of spread between dairy herds. Such information is essential in the development and implementation of future BTB control strategy for Eritrea. The livestock sector plays a major role in poverty and hunger reduction in the vast majority of Africa, as a source of food, cash income, manure, draught power, transportation, savings, insurance and social status. However, for livestock to play this vital role, the impact of diseases of economic and zoonotic importance need to be reduced. Bovine tuberculosis, mainly caused by Mycobacterium bovis, is such an infectious disease. Slaughterhouse (gross pathology) surveillance, followed by bacterial culture and genotyping, are options to identify the disease-causing agents, their distribution, and enabling trace back of the sources of infections, in order to prevent their re-introduction and spread. Unfortunately, genotyping is by far not generally introduced in the continent. In the present study, tissues with tuberculosis-like lesions were collected from the Asmara municipal slaughterhouse, the largest slaughterhouse in Eritrea, and bacterial culture, classical Mycobacterium tuberculosis complex typing (Spoligotyping and VNTR profiling), as well as whole genome sequencing (WGS) were used to gain insight into the spatial and temporal distribution, genetic diversity and evolution of M. bovis strains circulating in Eritrean dairy cattle. The results revealed (dis)similarities of the Eritrean M. bovis strains with the strains generally present in Africa and Europe, potential routes of introduction to Eritrea and genetic diversity of the M. bovis strains. Future in-depth molecular studies including more samples from dairy cattle as well as cattle and goats from the traditional livestock sector are recommended.
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Armas F, Camperio C, Coltella L, Selvaggini S, Boniotti MB, Pacciarini ML, Di Marco Lo Presti V, Marianelli C. Comparison of semi-automated commercial rep-PCR fingerprinting, spoligotyping, 12-locus MIRU-VNTR typing and single nucleotide polymorphism analysis of the embB gene as molecular typing tools for Mycobacterium bovis. J Med Microbiol 2017; 66:1151-1157. [DOI: 10.1099/jmm.0.000536] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Federica Armas
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Cristina Camperio
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Luana Coltella
- Microbiology Laboratory, Bambino Gesù Paediatric Hospital, Rome, Italy
| | | | - Maria Beatrice Boniotti
- National Reference Centre for Mycobacterium Bovis Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Maria Lodovica Pacciarini
- National Reference Centre for Mycobacterium Bovis Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | | | - Cinzia Marianelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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Molecular and epidemiological population-based integrative analysis of human and animal Mycobacterium bovis infections in a low-prevalence setting. Vet Microbiol 2016; 195:30-36. [DOI: 10.1016/j.vetmic.2016.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/19/2016] [Accepted: 08/21/2016] [Indexed: 11/19/2022]
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Yang L, Wang C, Wang H, Meng Q, Wang Q. Evaluation of MIRU-VNTR for typing of Mycobacterium bovis isolated from Sika deer in Northeast China. BMC Vet Res 2015; 11:93. [PMID: 25889075 PMCID: PMC4399248 DOI: 10.1186/s12917-015-0402-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/20/2015] [Indexed: 11/29/2022] Open
Abstract
Background Bovine tuberculosis has led to serious economic losses for Sika Deer producers in China. Strategies for controlling the spread of Mycobacterium bovis are often hampered by a lack of epidemiological data. Specifically, tracing infections requires the ability to trace back infections, which, in turn, requires the ability to determine isolates with a common source. This study was planned to assess the discriminatory power of each mycobacterial interspersed repetitive unit (MIRU)-variable number tandem repeats (VNTR) locus and evaluate the most appropriate combination of MIRU-VNTR loci for molecular epidemiological studies on Sika Deer in China. Results The discriminatory power of MIRU-VNTR typing based on 22 known loci (12 MIRUs, 2 ETRs, 4 QUBs, and 4 Mtubs) were assessed in 96 Mycobacterium bovis strains collected sequentially from Sika Deer at a slaughterhouse in northeastern China. We defined four loci (MIRU4, ETRA, QUB11b, and Mtub4) as highly discriminative, eight loci (MIRU2, MIRU23, MIRU27, MIRU31, MIRU39, MIRU40, QUB26, and Mtub21) as moderately discriminative, and three loci (MIRU16, Mtub30, and Mtub34) as poorly discriminative. The final locus showed no polymorphism between strains. MIRU-VNTR typing as a whole was highly discriminative, with an overall allelic diversity of 0.897. Of the loci tested, the four highly discriminative loci and eight moderately discriminative loci proved to be most appropriate for first line typing of M. bovis from Sika Deer, with the same resolving ability as all 22 loci (H = 0.897). Conclusions MIRU-VNTR typing is quick and effective for typing bovine tuberculosis isolates from Sika Deer in China. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0402-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Yang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Xincheng Street No.2888, 130118, Changchun, China.
| | - Chunyu Wang
- Jilin Entry-Exit Inspection and Quadrant Bureau, Puyang Street No.1301, Changchun, 130062, China.
| | - Haijun Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Xincheng Street No.2888, 130118, Changchun, China.
| | - Qingfeng Meng
- Jilin Entry-Exit Inspection and Quadrant Bureau, Puyang Street No.1301, Changchun, 130062, China.
| | - Quankai Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Xincheng Street No.2888, 130118, Changchun, China. .,Jilin Sino-ROK Academy of Animal Sciences, Donghua Street No.1699, Changchun, 130600, China.
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Proposal of a Screening MIRU-VNTR Panel for the Preliminary Genotyping of Mycobacterium bovis in Mexico. BIOMED RESEARCH INTERNATIONAL 2015; 2015:416479. [PMID: 25945333 PMCID: PMC4402168 DOI: 10.1155/2015/416479] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/23/2014] [Indexed: 11/17/2022]
Abstract
Mycobacterium bovis is the major causative agent of bovine tuberculosis, one of the most relevant zoonoses in the world, and affects a wide range of wild and domesticated animals. Development of screening panels in mycobacterial genotyping, according to specific geographical regions, is strongly needed. The aim of this study is to select a panel, constituted by highly polymorphic MIRU-VNTR loci, to discriminate clinical isolates of M. bovis in Mexico. In this study, 65 isolates of M. bovis obtained from clinical bovine samples proceeding from different geographic regions of Mexico were identified by phenotypic and genotypic tests and subsequently genotyped by a 24-locus MIRU-VNTR panel. The most polymorphic loci were selected to build a panel with a high discriminatory power similar to the 24-locus panel results. A panel of seven elements (QUB 11a, MIRU 26, ETR-A, QUB 26, MIRU 16, MIRU 27, and MIRU 39) with the highest allelic diversity showed an appropriate differentiation. The selected MIRU-VNTR elements, according to the regional allelic variability, may be used in the preliminary genotyping of Mycobacterium bovis isolates in Mexico.
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Navarro Y, Romero B, Copano MF, Bouza E, Domínguez L, de Juan L, García-de-Viedma D. Multiple sampling and discriminatory fingerprinting reveals clonally complex and compartmentalized infections by M. bovis in cattle. Vet Microbiol 2014; 175:99-104. [PMID: 25439651 DOI: 10.1016/j.vetmic.2014.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/27/2014] [Accepted: 11/02/2014] [Indexed: 10/24/2022]
Abstract
The combination of new genotyping tools and a more exhaustive sampling policy in the analysis of infection by Mycobacterium tuberculosis has shown that infection by this pathogen is more complex than initially expected. Mixed infections, coexistence of clonal variants from a parental strain, and compartmentalized infections are all different modalities of this clonal complexity. Until recently, genotyping of Mycobacterium bovis in animal populations was based on spoligotyping and analysis of a single isolate per infection; therefore, clonal complexity is probably underdetected. We used multiple sampling combined with highly discriminatory MIRU-VNTR to study compartmentalized infections by M. bovis in a low-tuberculosis prevalence setting. We spoligotyped the M. bovis isolates from two or more anatomic locations sampled from 55 animals on 39 independent farms. Compartmentalized infections, with two different strains infecting independent lymph nodes in the same animal, were found in six cases (10.9%). MIRU-VNTR analysis confirmed that the compartmentalization was strict and that only one strain was present in each infected node. MIRU-VNTR analysis of additional infected animals on one of the farms confirmed that the compartmentalized infection was a consequence of superinfection, since the two strains were independently infecting other animals. This same analysis revealed the emergence of a microevolved clonal variant in one of the lymph nodes of the compartmentalized animal. Clonal complexity must also be taken into consideration in M. bovis infection, even in low-prevalence settings, and analyses must be adapted to detect it and increase the accuracy of molecular epidemiology studies.
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Affiliation(s)
- Yurena Navarro
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Beatriz Romero
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain
| | | | - Emilio Bouza
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucas Domínguez
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Lucía de Juan
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Darío García-de-Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain.
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