1
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:microorganisms10091845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host–pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host–pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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2
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Romano GE, Silva-Pereira TT, de Melo FM, Sisco MC, Banari AC, Zimpel CK, Soler-Camargo NC, Guimarães AMDS. Unraveling the metabolism of Mycobacterium caprae using comparative genomics. Tuberculosis (Edinb) 2022; 136:102254. [PMID: 36126496 DOI: 10.1016/j.tube.2022.102254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/01/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022]
Abstract
In our laboratory, Mycobacterium caprae has poor growth in standard medium (SM) 7H9-OADC supplemented with pyruvate and Tween-80. Our objectives were to identify mutations affecting M. caprae metabolism and use this information to design a culture medium to improve its growth. We selected 77 M. caprae genomes and sequenced M. caprae NLA000201913 used in our experiments. Mutations present in >95% of the strains compared to Mycobacterium tuberculosis H37Rv were analyzed in silico for their deleterious effects on proteins of metabolic pathways. Apart from the known defect in the pyruvate kinase, M. caprae has important lesions in enzymes of the TCA cycle, methylmalonyl cycle, B12 metabolism, and electron-transport chain. We provide evidence of enzymatic redundancy elimination and epistatic mutations, and possible production of toxic metabolites hindering M. caprae growth in vitro. A newly designed SM supplemented with l-glutamate allowed faster growth and increased final microbial mass of M. caprae. However, possible accumulation of metabolic waste-products and/or nutritional limitations halted M. caprae growth prior to a M. tuberculosis-like stationary phase. Our findings suggest that M. caprae relies on GABA and/or glyoxylate shunts for in vitro growth in routine media. The newly developed medium will improve experiments with this bacterium by allowing faster growth in vitro.
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Affiliation(s)
- Giovanni Emiddio Romano
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Filipe Menegatti de Melo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Maria Carolina Sisco
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil.
| | - Alexandre Campos Banari
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, 87 Prof Dr Orlando Marques de Paiva Avenue, São Paulo, SP, 05508-270, Brazil.
| | - Ana Marcia de Sá Guimarães
- Laboratory of Applied Research in Mycobacteria (LaPAM), Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 1374 Prof Lineu Prestes Avenue, Room 229, São Paulo, SP, 05508-000, Brazil; Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University. 625 Harrison Street, West Lafayette, IN, 47907, USA.
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3
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Zwyer M, Çavusoglu C, Ghielmetti G, Pacciarini ML, Scaltriti E, Van Soolingen D, Dötsch A, Reinhard M, Gagneux S, Brites D. A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics. OPEN RESEARCH EUROPE 2021; 1:100. [PMID: 37645186 PMCID: PMC10445919 DOI: 10.12688/openreseurope.14029.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 08/31/2023]
Abstract
Background: The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenetics with genomics. Accompanying the discovery of new genetic diversity, a body of operational nomenclature has evolved to assist comparative and molecular epidemiological studies of human TB. By contrast, for the livestock-associated MTBC members, Mycobacterium bovis, M. caprae and M. orygis, there has been a lack of comprehensive nomenclature to accommodate new genetic diversity uncovered by emerging phylogenomic studies. We propose to fill this gap by putting forward a new nomenclature covering the main phylogenetic groups within M. bovis, M. caprae and M. orygis. Methods: We gathered a total of 8,736 whole-genome sequences (WGS) from public sources and 39 newly sequenced strains, and selected a subset of 829 WGS, representative of the worldwide diversity of M. bovis, M. caprae and M. orygis. We used phylogenetics and genetic diversity patterns inferred from WGS to define groups. Results: We propose to divide M. bovis, M. caprae and M. orygis in three main phylogenetic lineages, which we named La1, La2 and La3, respectively. Within La1, we identified several monophyletic groups, which we propose to classify into eight sublineages (La1.1-La1.8). These sublineages differed in geographic distribution, with some being geographically restricted and others globally widespread, suggesting different expansion abilities. To ease molecular characterization of these MTBC groups by the community, we provide phylogenetically informed, single nucleotide polymorphisms that can be used as barcodes for genotyping. These markers were implemented in KvarQ and TB-Profiler, which are platform-independent, open-source tools. Conclusions: Our results contribute to an improved classification of the genetic diversity within the livestock-associated MTBC, which will benefit future molecular epidemiological and evolutionary studies.
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Affiliation(s)
- Michaela Zwyer
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cengiz Çavusoglu
- Department of Medical Microbiology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Dick Van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands Antilles
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Anna Dötsch
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Miriam Reinhard
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Sebastien Gagneux
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Daniela Brites
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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4
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Lombard JE, Patton EA, Gibbons-Burgener SN, Klos RF, Tans-Kersten JL, Carlson BW, Keller SJ, Pritschet DJ, Rollo S, Dutcher TV, Young CA, Hench WC, Thacker TC, Perea C, Lehmkuhl AD, Robbe-Austerman S. Human-to-Cattle Mycobacterium tuberculosis Complex Transmission in the United States. Front Vet Sci 2021; 8:691192. [PMID: 34322536 PMCID: PMC8311018 DOI: 10.3389/fvets.2021.691192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) species includes both M. tuberculosis, the primary cause of human tuberculosis (TB), and M. bovis, the primary cause of bovine tuberculosis (bTB), as well as other closely related Mycobacterium species. Zoonotic transmission of M. bovis from cattle to humans was recognized more than a century ago, but transmission of MTBC species from humans to cattle is less often recognized. Within the last decade, multiple published reports from around the world describe human-to-cattle transmission of MTBC. Three probable cases of human-to-cattle MTBC transmission have occurred in the United States since 2013. In the first case, detection of active TB disease (M. bovis) in a dairy employee in North Dakota prompted testing and ultimate detection of bTB infection in the dairy herd. Whole genome sequencing (WGS) demonstrated a match between the bTB strain in the employee and an infected cow. North Dakota animal and public health officials concluded that the employee's infection was the most likely source of disease introduction in the dairy. The second case involved a Wisconsin dairy herd with an employee diagnosed with TB disease in 2015. Subsequently, the herd was tested twice with no disease detected. Three years later, a cow originating from this herd was detected with bTB at slaughter. The strain in the slaughter case matched that of the past employee based on WGS. The third case was a 4-month-old heifer calf born in New Mexico and transported to Texas. The calf was TB tested per Texas entry requirements and found to have M. tuberculosis. Humans are the suspected source of M. tuberculosis in cattle; however, public health authorities were not able to identify an infected human associated with the cattle operation. These three cases provide strong evidence of human-to-cattle transmission of MTBC organisms and highlight human infection as a potential source of introduction of MTBC into dairy herds in the United States. To better understand and address the issue, a multisectoral One Health approach is needed, where industry, public health, and animal health work together to better understand the epidemiology and identify preventive measures to protect human and animal health.
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Affiliation(s)
- Jason E. Lombard
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, Field Epidemiologic Investigation Services, Fort Collins, CO, United States
| | - Elisabeth A. Patton
- Wisconsin Department of Agriculture, Trade and Consumer Protection, Madison, WI, United States
| | | | - Rachel F. Klos
- Wisconsin Department of Health Services, Division of Public Health, Madison, WI, United States
| | - Julie L. Tans-Kersten
- Wisconsin Department of Health Services, Division of Public Health, Madison, WI, United States
| | - Beth W. Carlson
- North Dakota Department of Agriculture, State Board of Animal Health, Bismarck, ND, United States
| | - Susan J. Keller
- North Dakota Department of Agriculture, State Board of Animal Health, Bismarck, ND, United States
| | | | - Susan Rollo
- Texas Animal Health Commission, Austin, TX, United States
| | - Tracey V. Dutcher
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, Field Epidemiologic Investigation Services, Fort Collins, CO, United States
| | - Cris A. Young
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, Field Epidemiologic Investigation Services, Fort Collins, CO, United States
| | - William C. Hench
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, Ruminant Health Center, Fort Collins, CO, United States
| | - Tyler C. Thacker
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, Ames, IA, United States
| | - Claudia Perea
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, Ames, IA, United States
| | - Aaron D. Lehmkuhl
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, Ames, IA, United States
| | - Suelee Robbe-Austerman
- United States Department of Agriculture: Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories, Ames, IA, United States
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5
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Bryant JM, Brown KP, Burbaud S, Everall I, Belardinelli JM, Rodriguez-Rincon D, Grogono DM, Peterson CM, Verma D, Evans IE, Ruis C, Weimann A, Arora D, Malhotra S, Bannerman B, Passemar C, Templeton K, MacGregor G, Jiwa K, Fisher AJ, Blundell TL, Ordway DJ, Jackson M, Parkhill J, Floto RA. Stepwise pathogenic evolution of Mycobacterium abscessus. Science 2021; 372:372/6541/eabb8699. [PMID: 33926925 DOI: 10.1126/science.abb8699] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria. We show that epigenetic modifiers, acquired through horizontal gene transfer, cause saltational increases in the pathogenic potential of specific environmental clones. Allopatric parallel evolution during chronic lung infection then promotes rapid increases in virulence through mutations in a discrete gene network; these mutations enhance growth within macrophages but impair fomite survival. As a consequence, we observe constrained pathogenic evolution while person-to-person transmission remains indirect, but postulate accelerated pathogenic adaptation once direct transmission is possible, as observed for M. tuberculosis Our findings indicate how key interventions, such as early treatment and cross-infection control, might restrict the spread of existing mycobacterial pathogens and prevent new, emergent ones.
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Affiliation(s)
- Josephine M Bryant
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Karen P Brown
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Sophie Burbaud
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Isobel Everall
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Wellcome Sanger Institute, Hinxton, UK
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Daniela Rodriguez-Rincon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Dorothy M Grogono
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Chelsea M Peterson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Deepshikha Verma
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Ieuan E Evans
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Divya Arora
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.,Scientific Computing Department, Science and Technology Facilities Council, Harwell, UK
| | - Bridget Bannerman
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Charlotte Passemar
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kerra Templeton
- Queen Elizabeth University Hospital, NHS Greater Glasgow & Clyde, Glasgow, Scotland, UK
| | - Gordon MacGregor
- Queen Elizabeth University Hospital, NHS Greater Glasgow & Clyde, Glasgow, Scotland, UK
| | - Kasim Jiwa
- Newcastle University Translational and Clinical Research Institute and Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Andrew J Fisher
- Newcastle University Translational and Clinical Research Institute and Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Diane J Ordway
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK. .,University of Cambridge Centre for AI in Medicine, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
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6
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Ciaravino G, Vidal E, Cortey M, Martín M, Sanz A, Mercader I, Perea C, Robbe-Austerman S, Allepuz A, Pérez de Val B. Phylogenetic relationships investigation of Mycobacterium caprae strains from sympatric wild boar and goats based on whole genome sequencing. Transbound Emerg Dis 2020; 68:1476-1486. [PMID: 32888386 PMCID: PMC8246549 DOI: 10.1111/tbed.13816] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/30/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022]
Abstract
Tuberculosis (TB) in wildlife challenges epidemiological surveillance and disease control. An outbreak of TB was detected in a free‐ranging wild boar population of a Natural Park in Catalonia (Spain) and the outbreak investigation was conducted in the area. During the study period (2015–2020), 278 wild boars were analysed by gross pathology, histopathology, mycobacterial culture and DVR‐spoligotyping. In addition, all cattle (49) and goat (47) herds of the area were tested with tuberculin skin test. TB compatible lesions were detected in 21 wild boars, and Mycobacterium caprae was isolated in 17 of them with two different spoligotypes: SB0415 (13) and SB1908 (4). Only two goat herds showed TB positive animals that were subsequently slaughtered. M. caprae with the spoligotypes SB0416 and SB0415 were isolated from these animals. To investigate the phylogenetic relationships and the transmission chain of the outbreak, nine strains isolated from six wild boars and three goats of the study area were analysed by whole genome sequencing (WGS) followed by single nucleotide polymorphism (SNP) analysis by maximum likelihood and median‐joining network inference methods. Results indicated that infected wild boars maintained M. caprae strains circulation in their own population and have likely transmitted the infection to goats, thus acting as TB reservoirs, compromising the success of livestock TB eradication campaigns and posing a risk for public health. The results also highlighted the usefulness of WGS followed by SNP analysis in providing relevant epidemiological information when detailed contact data are missing.
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Affiliation(s)
- Giovanna Ciaravino
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Enric Vidal
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Spain
| | - Martí Cortey
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Maite Martín
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Spain
| | - Albert Sanz
- Departament d'Agricultura, Ramaderia, Pesca i Alimentació de la Generalitat de Catalunya, Barcelona, Spain
| | - Irene Mercader
- Departament d'Agricultura, Ramaderia, Pesca i Alimentació de la Generalitat de Catalunya, Barcelona, Spain
| | - Claudia Perea
- National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA
| | - Alberto Allepuz
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Spain
| | - Bernat Pérez de Val
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Bellaterra, Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Spain
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7
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Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-Pereira TT, Camargo NCS, de Souza Filho AF, Ikuta CY, Neto JSF, Setubal JC, Heinemann MB, Guimaraes AMS. Global Distribution and Evolution of Mycobacterium bovis Lineages. Front Microbiol 2020; 11:843. [PMID: 32477295 PMCID: PMC7232559 DOI: 10.3389/fmicb.2020.00843] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3, and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis (South Siberian infected skeletons at ∼2,000 years before present) and indicates that extant M. bovis originated between 715 and 3,556 years BP, with later emergence in the New World and Oceania, likely influenced by trades among countries.
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Affiliation(s)
- Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Salvatore L Patané
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Cellular Cycle, Butantan Institute, São Paulo, Brazil
| | - Aureliano Coelho Proença Guedes
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Robson F de Souza
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana T Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila C Soler Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Antônio F de Souza Filho
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Soares Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sa Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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8
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Guimaraes AMS, Zimpel CK. Mycobacterium bovis: From Genotyping to Genome Sequencing. Microorganisms 2020; 8:E667. [PMID: 32375210 PMCID: PMC7285088 DOI: 10.3390/microorganisms8050667] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis. Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the disease remains a challenge for the veterinary and public health sectors, especially in developing countries and in high-income nations with wildlife reservoirs. Current bTB control programs are mostly based on test-and-slaughter, movement restrictions, and post-mortem inspection measures. In certain settings, contact tracing and surveillance has benefited from M. bovis genotyping techniques. More recently, whole-genome sequencing (WGS) has become the preferential technique to inform outbreak response through contact tracing and source identification for many infectious diseases. As the cost per genome decreases, the application of WGS to bTB control programs is inevitable moving forward. However, there are technical challenges in data analyses and interpretation that hinder the implementation of M. bovis WGS as a molecular epidemiology tool. Therefore, the aim of this review is to describe M. bovis genotyping techniques and discuss current standards and challenges of the use of M. bovis WGS for transmission investigation, surveillance, and global lineages distribution. We compiled a series of associated research gaps to be explored with the ultimate goal of implementing M. bovis WGS in a standardized manner in bTB control programs.
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Affiliation(s)
- Ana M. S. Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
| | - Cristina K. Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, São Paulo 01246-904, Brazil
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Loiseau C, Menardo F, Aseffa A, Hailu E, Gumi B, Ameni G, Berg S, Rigouts L, Robbe-Austerman S, Zinsstag J, Gagneux S, Brites D. An African origin for Mycobacterium bovis. Evol Med Public Health 2020; 2020:49-59. [PMID: 32211193 PMCID: PMC7081938 DOI: 10.1093/emph/eoaa005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. METHODOLOGY We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. RESULTS Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. CONCLUSIONS AND IMPLICATIONS Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. LAY SUMMARY During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.
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Affiliation(s)
- Chloé Loiseau
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Elena Hailu
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Balako Gumi
- Department of Animal Science and Range Management, Bule Hora University, Bule Hora Town, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Stefan Berg
- Bacteriology Department, Animal & Plant Health Agency (APHA), Weybridge, Surrey, UK
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Collection of Mycobacterial Cultures (BCCM/ITM), Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Suelee Robbe-Austerman
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA
| | - Jakob Zinsstag
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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Yoshida S, Suga S, Ishikawa S, Mukai Y, Tsuyuguchi K, Inoue Y, Yamamoto T, Wada T. Mycobacterium caprae Infection in Captive Borneo Elephant, Japan. Emerg Infect Dis 2019; 24:1937-1940. [PMID: 30226170 PMCID: PMC6154153 DOI: 10.3201/eid2410.180018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In 2016, disseminated tuberculosis caused by Mycobacterium caprae was diagnosed in a captive Borneo elephant in Japan. The bacterium was initially identified from clinical isolates. An isolate collected during a relapse showed isoniazid monoresistance and a codon 315 katG mutation.
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Leth C, Varadharajan A, Mester P, Fischaleck M, Rossmanith P, Schmoll F, Fink M. Matrixlysis, an improved sample preparation method for recovery of Mycobacteria from animal tissue material. PLoS One 2017; 12:e0181157. [PMID: 28723969 PMCID: PMC5517009 DOI: 10.1371/journal.pone.0181157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/27/2017] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, is the main causative agent of bovine tuberculosis in alpine regions. Bacterial culture is the gold standard in bovine tuberculosis diagnostic but takes up to twelve weeks. This increases the time and costs for stocks affected with bovine tuberculosis. Hence this study focused on the implementation of a fast and precise mycobacterial detection method and compared it with currently used methods. Matrix lysis is a chemical lysis using high concentrations of urea to solubilize bovine and red deer tissue and was used to detect even smallest amounts or non-visible lesions of mycobacteria. A total of 64 samples collected from 44 animals (37 red deer and 7 cattle) were tested by Matrix lysis. Forty-three of these samples were used for Mycobacterium tuberculosis complex detection by quantitative PCR and other 21 for subtyping the genetically different variants of M. caprae. Furthermore, three Matrix lysis samples were used for Next Generation Sequencing. Our results confirm that Matrix lysis is a fast and precise method for detecting Mycobacterium tuberculosis complex in native tissue samples. However, at the moment it reaches its limits when the samples were analyzed by Next Generation Sequencing and RD4 subtyping.
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Affiliation(s)
- Christoph Leth
- Austrian Agency for Health and Food Safety, Institute for Veterinary Disease Control, Moedling, Lower Austria, Austria
- University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Ashok Varadharajan
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Centre, LMU Munich, Munich, Germany
| | - Patrick Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Marlis Fischaleck
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Centre, LMU Munich, Munich, Germany
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Friedrich Schmoll
- Austrian Agency for Health and Food Safety, Institute for Veterinary Disease Control, Moedling, Lower Austria, Austria
| | - Maria Fink
- Austrian Agency for Health and Food Safety, Institute for Veterinary Disease Control, Moedling, Lower Austria, Austria
- * E-mail:
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