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Lorente-Leal V, Pozo P, Bezos J, Collado S, Vicente J, Stuber T, Álvarez J, de Juan L, Romero B. Revisiting Mycobacterium bovis SB0121 genetic diversity reflects the complexity behind bovine tuberculosis persistence in Spain. Prev Vet Med 2025; 239:106519. [PMID: 40215864 DOI: 10.1016/j.prevetmed.2025.106519] [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: 11/26/2024] [Revised: 03/12/2025] [Accepted: 03/23/2025] [Indexed: 04/29/2025]
Abstract
Identifying the causes of tuberculosis (TB) chronicity in cattle herds in Spain is a complex endeavour, mainly due to the multiple factors involved in persistence and the clonal population structure of the Mycobacterium tuberculosis complex. This study assessed the genomic diversity among M. bovis isolates belonging to SB0121, the most prevalent genotype in Spain, in chronically-infected herds. A total of 70 M. bovis isolates from 22 herds, located in six Spanish provinces, in which M. bovis SB0121 was isolated in at least three different sampling events were sequenced. Forty-three isolates from wildlife and cattle herds from the same or neighbouring municipalities to the problem herds were also included to identify putative local transmission events. The within-herd analysis revealed a highly complex scenario, in which the majority (95.45 %; n = 21) of the herds were affected by highly distant strains (> 12 SNP differences), probably as a result of separate introductions. Highly similar isolates (< 6 SNPs) were retrieved in different sampling events from 11 herds, likely indicating active transmission of the outbreak strain or continued exposure to the same source of infection. The between-herd and interspecies comparison suggested the occurrence of several putative epidemiological links between cattle and wildlife species from the same or neighbouring municipalities, reflecting the complex epidemiology of the disease in some of the studied areas. The findings of this study highlight the usefulness of whole genome sequencing to study bTB breakdowns and pinpoints its potential for unravelling possible sources of persistence in cattle herds.
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Affiliation(s)
- Víctor Lorente-Leal
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain.
| | - Pilar Pozo
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Javier Bezos
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain; Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Spain
| | - Soledad Collado
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de Sanidad de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, Madrid, Spain
| | - Joaquín Vicente
- Health and Biotechnology group (SaBio), Instituto de Investigaciones en Recursos Cinegéticos, Universidad de Castilla la Mancha, Spain
| | - Tod Stuber
- National Veterinary Services Laboratories (NVSL) Diagnostic Bacteriology and Pathology Laboratory, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA, USA
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain; Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Spain
| | - Lucía de Juan
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain; Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Spain
| | - Beatriz Romero
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain; Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Spain
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Thomas A, Halliday A, Clapp G, Symonds R, Hopewell‐Kelly N, McGrath C, Wheeler L, Dacey A, Noel N, Turner A, Oliver I, Wood J, Moran E, Virgo P, Tiller J, Upton P, Mitchell A, Goenka A, Brooks‐Pollock E. High Mycobacterium bovis Exposure but Low IGRA Positivity in UK Farm Workers. Zoonoses Public Health 2025; 72:369-378. [PMID: 40007044 PMCID: PMC12016005 DOI: 10.1111/zph.13214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 01/23/2025] [Accepted: 02/04/2025] [Indexed: 02/27/2025]
Abstract
BACKGROUND Between 1999 and 2021, 505 culture-confirmed cases of M. bovis disease in humans (zoonotic tuberculosis, TB) were diagnosed in England. We aimed to estimate the prevalence of M. bovis infection in persons exposed to TB-infected cattle in England and identify any risk factors associated with latent TB infection (LTBI) in this population. METHODS We co-developed a retrospective cohort study in Southwest England, a bovine TB high risk area, with members of the UK farming community. A questionnaire captured participant characteristics, behaviours and farming practices. Linkage with historical herd testing data was used to categorise participants as low, medium or high risk for TB exposure. Interferon gamma release assay (IGRA) positivity with Quantiferon was used to determine LTBI status and linked to questionnaire data. RESULTS We recruited 90 participants at agricultural shows and a standalone event. Participants were farmers/farm workers (76/90) and veterinary professionals (10/90). Median age was 45.5 years (IQR: 19-77); 63% were male; 67% reported BCG vaccination. M. bovis exposure was via direct contact with infected cattle and consumption of raw milk. One participant in the high-risk group was IGRA positive, all other participants were IGRA negative. Estimated IGRA positivity rate was 1.1% (95% CI 0.058%-7.0%) in all participants and 4.0% (95% CI 0.21%-22%) in participants with high exposure levels. CONCLUSIONS We found limited LTBI in individuals in contact with TB-infected cattle in England, despite high and prolonged exposure. We identified a high-risk group of farmers who should be prioritised for future engagement.
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Affiliation(s)
- Amy Thomas
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Alice Halliday
- Bristol Vaccine Centre, School of Cellular and Molecular MedicineUniversity of BristolBristolUK
| | - Genevieve Clapp
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Ross Symonds
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Carmel McGrath
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- The National Institute for Health and Care Research Applied Research Collaboration West (NIHR ARC West)University Hospitals Bristol and Weston NHS Foundation TrustBristolUK
- Faculty of Health and Applied Sciences, School of Health and Social WellbeingUniversity of West EnglandBristolUK
| | | | | | | | | | - Isabel Oliver
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- UK Health Security AgencyLondonUK
| | - James Wood
- Cambridge Veterinary SchoolUniversity of CambridgeCambridgeUK
| | - Ed Moran
- Department of Infectious DiseaseNorth Bristol NHS TrustBristolUK
| | | | | | - Paul Upton
- Animal and Plant Health AgencyAddlestoneUK
| | | | - Anu Goenka
- Bristol Vaccine Centre, School of Cellular and Molecular MedicineUniversity of BristolBristolUK
- Department of Paediatric Immunology and Infectious DiseasesBristol Royal Hospital for ChildrenBristolUK
| | - Ellen Brooks‐Pollock
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
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Carvalho CS, de Aquino VMS, Meyer R, Seyffert N, Castro TLP. Diagnosis of bacteria from the CMNR group in farm animals. Comp Immunol Microbiol Infect Dis 2024; 113:102230. [PMID: 39236397 DOI: 10.1016/j.cimid.2024.102230] [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: 03/03/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/07/2024]
Abstract
The CMNR group comprises bacteria of the genera Corynebacterium, Mycobacterium, Nocardia, and Rhodococcus and share cell wall and DNA content characteristics. Many pathogenic CMNR bacteria cause diseases such as mastitis, lymphadenitis, and pneumonia in farmed animals, which cause economic losses for breeders and represent a threat to public health. Traditional diagnosis in CMNR involves isolating target bacteria on general or selective media and conducting metabolic analyses with the assistance of laboratory biochemical identification systems. Advanced mass spectrometry may also support diagnosing these bacteria in the clinic's daily routine despite some challenges, such as the need for isolated bacteria. In difficult identification among some CMNR members, molecular methods using polymerase chain reaction (PCR) emerge as reliable options for correct specification that is sometimes achieved directly from clinical samples such as tracheobronchial aspirates and feces. On the other hand, immunological diagnostics such as the skin test or Enzyme-Linked Immunosorbent Assay (ELISA) for Mycobacterium tuberculosis yield promising results in subclinical infections with no bacterial growth involved. In this review, we present the methods most commonly used to diagnose pathogenic CMNR bacteria and discuss their advantages and limitations, as well as challenges and perspectives on adopting new technologies in diagnostics.
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Affiliation(s)
- Cintia Sena Carvalho
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Vitória M S de Aquino
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Roberto Meyer
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Núbia Seyffert
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Thiago L P Castro
- Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil.
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4
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Sunstrum J, Power LE, Fligiel HM, Lauter C, Kawam R, Dado C, Weatherhead M, Denbesten K, Bott J, Cinti S, Maxwell D, Signs K, Stobierski MG, Cosgrove M, Moriarty M, Vanderklok M, Meyerson J, Thacker T, Robbe-Austerman S. Human Disease due to Mycobacterium bovis Linked to Free-Ranging Deer in Michigan. Clin Infect Dis 2024; 78:637-645. [PMID: 38207126 DOI: 10.1093/cid/ciae009] [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: 09/07/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND A unique enzootic focus of Mycobacterium bovis in free-ranging deer was identified in northern lower Michigan in 1994, with subsequent evidence of transmission to local cattle herds. Between 2002 and 2017, 3 Michigan deer hunters with M. bovis disease were previously reported. We present 4 additional human cases linked to the zoonotic focus in deer, utilizing genomic epidemiology to confirm close molecular associations among human, deer and cattle M. bovis isolates. METHODS Identification of human tuberculosis (TB) cases with cultures of M. bovis was provided from the Michigan Department of Health and Human Services (MDHHS) tuberculosis database. Clinical review and interviews focused on risk factors for contact with wildlife and cattle. Whole genome sequences of human isolates were compared with a veterinary library of M. bovis strains to identify those linked to the enzootic focus. RESULTS Three confirmed and 1 probable human case with M. bovis disease were identified between 2019 and 2022, including cutaneous disease, 2 severe pulmonary disease cases, and human-to-human transmission. The 3 human isolates had 0-3 single-nucleotide polymorphisms (SNPs) with M. bovis strains circulating in wild deer and domestic cattle in Michigan. CONCLUSIONS Spillover of enzootic M. bovis from deer to humans and cattle continues to occur in Michigan. Future studies should examine the routes of transmission and degree of risk to humans through expanded epidemiological surveys. A One Health approach linking human, veterinary and environmental health should address screening for TB infection, public education, and mitigation of transmission.
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Affiliation(s)
- James Sunstrum
- Division of Infectious Disease, Corewell Health East, Westland, Michigan, USA
| | - Laura E Power
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Helene M Fligiel
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Carl Lauter
- Section of Infectious Diseases, Allergy and Immunology, William Beaumont University Hospital-Corewell Health East, Royal Oak, Michigan, USA
| | - Rayanah Kawam
- Section of Infectious Diseases, Allergy and Immunology, William Beaumont University Hospital-Corewell Health East, Royal Oak, Michigan, USA
| | - Christopher Dado
- Section of Pulmonary and Critical Care Medicine, William Beaumont University Hospital-Corewell Health East, Royal Oak, Michigan, USA
| | - Matthew Weatherhead
- Section of Pulmonary and Critical Care Medicine, William Beaumont University Hospital-Corewell Health East, Royal Oak, Michigan, USA
| | - Karen Denbesten
- Department of Internal Medicine, McLaren Northern Michigan Hospital, Petoskey, Michigan, USA
| | - Jonathan Bott
- Department of Medicine, Munson Medical Center, Traverse City, Michigan, USA
| | - Sandro Cinti
- Division of Infectious Disease, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Daniel Maxwell
- Department of Medicine, MyMichigan Medical Center, Alpena, Michigan, USA
| | - Kimberly Signs
- Michigan Department of Health and Human Services, Lansing, Michigan, USA
| | | | - Melinda Cosgrove
- Michigan Department of Natural Resources, Lansing, Michigan, USA
| | - Megan Moriarty
- Michigan Department of Natural Resources, Lansing, Michigan, USA
| | - Michael Vanderklok
- Michigan Department of Agriculture and Rural Development, Lansing, Michigan, USA
| | - Joshua Meyerson
- Health Department of Northwest Michigan, Charlevoix, Michigan, USA
| | - Tyler Thacker
- National Veterinary Services Laboratories, US Department of Agriculture, Ames, Iowa, USA
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, US Department of Agriculture, Ames, Iowa, USA
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5
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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: 7.0] [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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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: 27] [Impact Index Per Article: 5.4] [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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7
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Genomic Polymorphism Associated with the Emergence of Virulent Isolates of Mycobacterium bovis in the Nile Delta. Sci Rep 2019; 9:11657. [PMID: 31406159 PMCID: PMC6690966 DOI: 10.1038/s41598-019-48106-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium bovis is responsible for bovine tuberculosis in both animals and humans. Despite being one of the most important global zoonotic disease, data related to the ecology and pathogenicity of bovine tuberculosis is scarce, especially in developing countries. In this report, we examined the dynamics of M. bovis transmission among dairy cattle in the Nile Delta of Egypt. Animals belonging to 27 herds from 7 governorates were tested by the Single Intradermal Comparative Skin Tuberculin (SICST), as a preliminary screen for the presence of bovine tuberculosis. Positive SICST reactors were identified in 3% of the animals spread among 40% of the examined herds. Post-mortem examination of slaughtered reactors confirmed the presence of both pulmonary and/or digestive forms of tuberculosis in > 50% of the examined animals. Targeted and whole-genome analysis of M. bovis isolates indicated the emergences of a predominant spoligotype (SB0268) between 2013–2015, suggesting a recent clonal spread of this isolate within the Nile Delta. Surprisingly, 2 isolates belonged to M. bovis BCG group, which are not allowed for animal vaccination in Egypt, while the rest of isolates belonged to the virulent M. bovis clonal complex European 2 present in Latin America and several European countries. Analysis of strain virulence in the murine model of tuberculosis indicated the emergence of a more virulent strain (MBE4) with a specific genotype. More analysis is needed to understand the molecular basis for successful spread of virulent isolates of bovine tuberculosis among animals and to establish genotype/phenotype association.
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8
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Verteramo Chiu LJ, Tauer LW, Smith RL, Grohn YT. Assessment of the bovine tuberculosis elimination protocol in the United States. J Dairy Sci 2019; 102:2384-2400. [PMID: 30692003 DOI: 10.3168/jds.2018-14990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/07/2018] [Indexed: 12/27/2022]
Abstract
In this study, we analyzed the performance of the USDA's bovine tuberculosis (bTB) elimination protocol in a 1,000-cow closed dairy herd using an agent-based simulation model under different levels of initial bTB infection. We followed the bTB test sensitivity and specificity values used by the USDA in its model assessment. We estimated the net present value over a 20-yr horizon for a bTB-free milking herd and for bTB-infected herds following the USDA protocol. We estimated the expected time to identify the infection in the herd once it is introduced, its elimination time, the reproductive number (R0), and effective reproduction number (Re) under the USDA protocol. The optimal number of consecutive negative whole-herd tests (WHT) needed to declare a herd bTB-free with a 95% confidence under different bTB prevalence levels was derived. Our results support the minimum number of consecutive negative WHT required by the USDA protocol to declare a herd bTB-free; however, the number of consecutive negative WHT needed to eliminate bTB in a herd depends on the sensitivity and specificity of the tests. The robustness of the protocol was analyzed under conservative bTB test parameters from the literature. The cost of implementing the USDA protocol when 1 infected heifer is introduced in a 1,000-cow dairy herd is about $1,523,161. The average time until detection and the time required to eliminate bTB-infected animals from the herd, after 1 occult animal is introduced in the herd, were 735 and 119 d, respectively.
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Affiliation(s)
- Leslie J Verteramo Chiu
- Section of Epidemiology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
| | - Loren W Tauer
- Charles H. Dyson School of Applied Economics and Management, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
| | - Rebecca L Smith
- Department of Pathobiology, Cornell S. C. Johnson College of Business, University of Illinois, Urbana 61802
| | - Yrjo T Grohn
- Section of Epidemiology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
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9
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Price-Carter M, Brauning R, de Lisle GW, Livingstone P, Neill M, Sinclair J, Paterson B, Atkinson G, Knowles G, Crews K, Crispell J, Kao R, Robbe-Austerman S, Stuber T, Parkhill J, Wood J, Harris S, Collins DM. Whole Genome Sequencing for Determining the Source of Mycobacterium bovis Infections in Livestock Herds and Wildlife in New Zealand. Front Vet Sci 2018; 5:272. [PMID: 30425997 PMCID: PMC6218598 DOI: 10.3389/fvets.2018.00272] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/11/2018] [Indexed: 01/18/2023] Open
Abstract
The ability to DNA fingerprint Mycobacterium bovis isolates helped to define the role of wildlife in the persistence of bovine tuberculosis in New Zealand. DNA fingerprinting results currently help to guide wildlife control measures and also aid in tracing the source of infections that result from movement of livestock. During the last 5 years we have developed the ability to distinguish New Zealand (NZ) M. bovis isolates by comparing the sequences of whole genome sequenced (WGS) M. bovis samples. WGS provides much higher resolution than our other established typing methods and greatly improves the definition of the regional localization of NZ M. bovis types. Three outbreak investigations are described and results demonstrate how WGS analysis has led to the confirmation of epidemiological sourcing of infection, to better definition of new sources of infection by ruling out other possible sources, and has revealed probable wildlife infection in an area considered to be free of infected wildlife. The routine use of WGS analyses for sourcing new M. bovis infections will be an important component of the strategy employed to eradicate bovine TB from NZ livestock and wildlife.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Garry Knowles
- Aquaculture Veterinary Services Ltd., Clyde, New Zealand
| | | | - Joseph Crispell
- University College Dublin School of Veterinary Medicine, Dublin, Ireland
| | - Rowland Kao
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Suelee Robbe-Austerman
- Diagnostic Bacteriology Laboratory, National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Service, Ames, IA, United States
| | - Tod Stuber
- Diagnostic Bacteriology Laboratory, National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Service, Ames, IA, United States
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - James Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Simon Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Desmond M Collins
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
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10
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Orloski K, Robbe-Austerman S, Stuber T, Hench B, Schoenbaum M. Whole Genome Sequencing of Mycobacterium bovis Isolated From Livestock in the United States, 1989-2018. Front Vet Sci 2018; 5:253. [PMID: 30425994 PMCID: PMC6219248 DOI: 10.3389/fvets.2018.00253] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022] Open
Abstract
The United States official bovine tuberculosis (bTB) eradication program has utilized genotyping for Mycobacterium bovis isolates since 2000 and whole genome sequencing was implemented in 2013. The program has been highly successful, yet as bTB prevalence has reached historic lows, a small number of new bTB-affected cattle herds occur annually. Therefore, understanding the epidemiology of bTB transmission is critically important, in order to target limited resources for surveillance and achieve eradication. This evaluation described the diversity and epidemiology of M. bovis isolates identified in the USA livestock. Isolates from animals within the bTB endemic area of Michigan were excluded. Broad diversity was found among 1,248 isolates, collected from affected cattle and farmed cervids herds and fed cattle during 1989–2018. Nearly 70% of isolates from 109 herds/cases during 1999–2018 were European clonal complex 1 and 30% were European clonal complex 2. The sources of infection based on the herd investigation were known for 41% of herds/cases and 59% were not epidemiologically linked to another USA origin herd. Whole genome sequencing results were consistent with the investigation findings and previously unrecognized links between herds and cases were disclosed. For herds/cases with an unknown source of infection, WGS results suggested several possible sources, including undocumented cattle movement, imported cattle and humans. The use of WGS in new cases has reduced the time and costs associated with epidemiological investigations. Within herd SNP diversity was evaluated by examining 18 herds with 10 or more isolates sequenced. Forty percent of isolates had not diverged or accumulated any SNPs, and 86% of the isolates had accumulated 3 or fewer SNPs. The results of WGS does not support a bTB reservoir in USA cattle. The bTB eradication program appears to be highly effective as the majority of herds/cases in the USA are unique strains with limited herd to herd transmission.
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Affiliation(s)
- Kathy Orloski
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Centers for Epidemiology and Animal Health, Fort Collins, CO, United States
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA, United States
| | - Tod Stuber
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA, United States
| | - Bill Hench
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Fort Collins, CO, United States
| | - Mark Schoenbaum
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Fort Collins, CO, United States
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Andrievskaia O, Turcotte C, Berlie-Surujballi G, Battaion H, Lloyd D. Genotypes of Mycobacterium bovis strains isolated from domestic animals and wildlife in Canada in 1985-2015. Vet Microbiol 2017; 214:44-50. [PMID: 29408031 DOI: 10.1016/j.vetmic.2017.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/07/2017] [Indexed: 11/18/2022]
Abstract
Two internationally recognised and standardised genotyping methods, mycobacterial interspersed repetitive unit and variable number tandem repeat analysis (MIRU-VNTR) and spoligotyping, were applied to characterise genetic variations among 137 Mycobacterium bovis isolates recovered from Canadian domestic and wild animals during 1985-2015. Spoligotyping generated seven types that were discriminated further into12 MIRU-VNTR types. The discriminatory power indexes were estimated as 0.71 and 0.77 for spoligotyping and MIRU-VNTR typing approaches, respectively. In total, 6 prominent clusters of isolates were observed by the genotyping schemes. Four genotype clusters were exclusively observed in farmed animals. Three of these four clusters were affiliated with localised tuberculosis outbreaks, and each cluster corresponded to a single specific spoligotype (SB0140, SB0673, and SB1069) and a MIRU-VNTR profile. The fourth genotype cluster, with spoligotype SB0265 which segregated into two MIRU-VNTR types, was associated with bovine tuberculosis outbreaks in several farms across Canada during 1990-2002. Two genotype clusters of M. bovis stains were associated with wildlife reservoirs: a spoligotype SB0130 with 3 unique MIRU-VNTR profiles were observed in wood bison in Wood Buffalo National Park, and unique spoligotypes SB1070 and 1071 represented by four MIRU-VNTR profiles were recovered from cervidae species in and around the Riding Mountain National Park of Manitoba. Genotyping data confirmed M. bovis transmission between wildlife and livestock in Manitoba in 1990-2008. Overall, notwithstanding the low level of genetic diversity of Canadian M. bovis strains, the spoligotyping and MIRU-VNTR typing were useful tools in monitoring transmission of endemic strains and defining new introductions to Canada. The majority of genotypes were most likely introduced into domestic animals through live animal trade, and subsequently eliminated as a result of bovine tuberculosis outbreak investigation and eradication activities.
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Affiliation(s)
- Olga Andrievskaia
- Canadian Food Inspection Agency, Ottawa Laboratory (Fallowfield), 3851 Fallowfield Rd., Ottawa, Ontario K2H 8P9, Canada.
| | - Claude Turcotte
- Canadian Food Inspection Agency, Ottawa Laboratory (Fallowfield), 3851 Fallowfield Rd., Ottawa, Ontario K2H 8P9, Canada
| | - Gloria Berlie-Surujballi
- Canadian Food Inspection Agency, Ottawa Laboratory (Fallowfield), 3851 Fallowfield Rd., Ottawa, Ontario K2H 8P9, Canada
| | - Hannah Battaion
- Canadian Food Inspection Agency, Ottawa Laboratory (Fallowfield), 3851 Fallowfield Rd., Ottawa, Ontario K2H 8P9, Canada
| | - Dara Lloyd
- Canadian Food Inspection Agency, Ottawa Laboratory (Fallowfield), 3851 Fallowfield Rd., Ottawa, Ontario K2H 8P9, Canada
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