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Moens C, Bogaerts B, Lorente-Leal V, Vanneste K, De Keersmaecker SCJ, Roosens NHC, Mostin L, Fretin D, Marché S. Genomic comparison between Mycobacterium bovis and Mycobacterium microti and in silico analysis of peptide-based biomarkers for serodiagnosis. Front Vet Sci 2024; 11:1446930. [PMID: 39372902 PMCID: PMC11449866 DOI: 10.3389/fvets.2024.1446930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/28/2024] [Indexed: 10/08/2024] Open
Abstract
In recent years, there has been an increase in the number of reported cases of Mycobacterium microti infection in various animals, which can interfere with the ante-mortem diagnosis of animal tuberculosis caused by Mycobacterium bovis. In this study, whole genome sequencing (WGS) was used to search for protein-coding genes to distinguish M. microti from M. bovis. In addition, the population structure of the available M. microti genomic WGS datasets is described, including three novel Belgian isolates from infections in alpacas. Candidate genes were identified by examining the presence of the regions of difference and by a pan-genome analysis of the available WGS data. A total of 80 genes showed presence-absence variation between the two species, including genes encoding Proline-Glutamate (PE), Proline-Proline-Glutamate (PPE), and Polymorphic GC-Rich Sequence (PE-PGRS) proteins involved in virulence and host interaction. Filtering based on predicted subcellular localization, sequence homology and predicted antigenicity resulted in 28 proteins out of 80 that were predicted to be potential antigens. As synthetic peptides are less costly and variable than recombinant proteins, an in silico approach was performed to identify linear and discontinuous B-cell epitopes in the selected proteins. From the 28 proteins, 157 B-cell epitope-based peptides were identified that discriminated between M. bovis and M. microti species. Although confirmation by in vitro testing is still required, these candidate synthetic peptides containing B-cell epitopes could potentially be used in serological tests to differentiate cases of M. bovis from M. microti infection, thus reducing misdiagnosis in animal tuberculosis surveillance.
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Affiliation(s)
- Charlotte Moens
- Laboratory of Veterinary Bacteriology, Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
- Laboratory of Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Victor Lorente-Leal
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Laurent Mostin
- Experimental Center Machelen, Sciensano, Machelen, Belgium
| | - David Fretin
- Laboratory of Veterinary Bacteriology, Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Sylvie Marché
- Laboratory of Veterinary Bacteriology, Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
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Pereira AC, Pérez de Val B, Cunha MV. Phylogenetic analysis of Mycobacterium caprae highlights past and present epidemiological links at the Iberian Peninsula scale. Microbes Infect 2024:105405. [PMID: 39173900 DOI: 10.1016/j.micinf.2024.105405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/23/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
Mycobacterium caprae is linked to regular outbreaks of tuberculosis (TB) in geographically distinct caprine populations across Europe, namely Iberia where this ecovar may represent up to 8% of total animal TB cases, circulating in multi-host communities encompassing domestic ruminants and wildlife, representing severe financial losses. It also causes zoonotic human disease. In this work, we undertake the first phylodynamic and phylogeographic analyses of M. caprae to reconstruct past demography and transmission chains. First, we examined the worldwide diversity of M. caprae based on 229 unpublished and publicly available whole genome sequences, depicting Asian, Central-East European, and Iberian clades. Phylodynamic analyses of the SB0157 Iberian clade (n = 81) positioned the most recent common ancestor in goats, around 100 years ago. Host transition events were common between goats, wild boars, and humans, possibly resulting from mixed farming, extensive management, and close human proximity, facilitating interspecific transmission. We show the spread of M. caprae on multiple scales due to local and transnational animal trade, supporting historical and sustained cross-species transmission in Iberia. We highlight the value of intersecting genomic epidemiology with molecular ecology to resolve epidemiological links and show that an EU-official eradication program in goats is utterly needed to control TB in a multi-host scenario.
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Affiliation(s)
- André C Pereira
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Bernat Pérez de Val
- Unitat Mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la UAB, Bellaterra, Catalonia, Spain; WOAH collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Catalonia, Spain
| | - Mónica V Cunha
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; National Institute for Agrarian and Veterinary Research (INIAV IP), Av. da República, Quinta do Marquês, Edifício Principal, 2780-157 Oeiras, Portugal.
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Scaltriti E, Iyad K, Boniotti MB, Menozzi I, Bolzoni L, Ippolito D, Ciarello FP, Loda D, D’Incau M, Zanoni M, Presti VDML, Mazzone P, Gavaudan S, Pacciarini ML. Inside Mycobacterium bovis SB0120 spoligotype circulating in Italy: analysis of the most frequent genotypes by whole genome sequencing. Front Microbiol 2024; 15:1416605. [PMID: 39132144 PMCID: PMC11310128 DOI: 10.3389/fmicb.2024.1416605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Bovine tuberculosis (bTB) is a chronic inflammatory disease primarily caused by Mycobacterium bovis. The infection affects domestic animals and wildlife, posing a zoonotic risk to humans. To understand the dynamics of transmission and genetic diversity in Italy's M. bovis population, we conducted whole-genome sequencing (WGS) analysis on two prevalent genotypes, belonging to Spoligotype SB0120, identified in different geographical and temporal contexts. By comparing these genomes with international M. bovis isolates, we identified a distinct clade within the lineage La1.2, encompassing the Italian SB0120 isolates, indicating a genomic segregation of Italian M. bovis from other European isolates. Within Italy, a significant level of genetic variability emerged across regions, while isolates within epidemiologically linked outbreaks exhibited minimal genetic diversity. Additionally, isolates derived from cattle and wild boars within a tuberculosis hotspot in Central Italy and from cattle and black pigs in Sicily formed unified clonal clusters. This indicates the presence of persistent strains circulating in the examined regions. The genetic diversity within herds was limited, as specific clones endured over time within certain herds. This research enhances our comprehension of the epidemiology and transmission patterns of bTB in Italy, thereby aiding the development of precise control strategies and disease management. Using WGS and implementing standardized protocols and databases will be pivotal in combating bTB and promoting One-Health approaches to address this noteworthy public health concern.
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Affiliation(s)
- Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Karaman Iyad
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Maria Beatrice Boniotti
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Ilaria Menozzi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Luca Bolzoni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Dorotea Ippolito
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Flavia Pruiti Ciarello
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Daniela Loda
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Mario D’Incau
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Mariagrazia Zanoni
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Vincenzo Di Marco Lo Presti
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Piera Mazzone
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Perugia, Italy
| | - Stefano Gavaudan
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Ancona, Italy
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
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Pereira AC, Lourenço J, Themudo G, Botelho A, Cunha MV. Population structure and history of Mycobacterium bovis European 3 clonal complex reveal transmission across ecological corridors of unrecognized importance in Portugal. Microbiol Spectr 2024; 12:e0382923. [PMID: 38771094 PMCID: PMC11218495 DOI: 10.1128/spectrum.03829-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Mycobacterium bovis causes animal tuberculosis in livestock and wildlife, with an impact on animal health and production, wildlife management, and public health. In this work, we sampled a multi-host tuberculosis community from the official hotspot risk area of Portugal over 16 years, generating the largest available data set in the country. Using phylogenetic and ecological modeling, we aimed to reconstruct the history of circulating lineages across the livestock-wildlife interface to inform intervention and the implementation of genomic surveillance within the official eradication plan. We find evidence for the co-circulation of M. bovis European 1 (Eu1), Eu2, and Eu3 clonal complexes, with Eu3 providing sufficient temporal signal for further phylogenetic investigation. The Eu3 most recent common ancestor (bovine) was dated in the 1990s, subsequently transitioning to wildlife (red deer and wild boar). Isolate clustering based on sample metadata was used to inform phylogenetic inference, unravelng frequent transmission between two clusters that represent an ecological corridor of previously unrecognized importance in Portugal. The latter was associated with transmission at the livestock-wildlife interface toward locations with higher temperature and precipitation, lower agriculture and road density, and lower host densities. This is the first analysis of M. bovis Eu3 complex in Iberia, shedding light on background ecological factors underlying long-term transmission and informing where efforts could be focused within the larger hotspot risk area of Portugal. IMPORTANCE Efforts to strengthen surveillance and control of animal tuberculosis (TB) are ongoing worlwide. Here, we developed an eco-phylodynamic framework based on discrete phylogenetic approaches informed by M. bovis whole-genome sequence data representing a multi-host transmission system at the livestock-wildlife interface, within a rich ecological landscape in Portugal, to understand transmission processes and translate this knowledge into disease management benefits. We find evidence for the co-circulation of several M. bovis clades, with frequent transmission of the Eu3 lineage among cattle and wildlife populations. Most transition events between different ecological settings took place toward host, climate and land use gradients, underscoring animal TB expansion and a potential corridor of unrecognized importance for M. bovis maintenance. Results stress that animal TB is an established wildlife disease without ecological barriers, showing that control measures in place are insufficient to prevent long-distance transmission and spillover across multi-host communities, demanding new interventions targeting livestock-wildlife interactions.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Lourenço
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Gonçalo Themudo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Botelho
- INIAV, I.P.—National Institute for Agrarian and Veterinary Research, Oeiras, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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Bonilla-Aldana DK, Jiménez-Diaz SD, Lozada-Riascos C, Silva-Cajaleon K, Rodríguez-Morales AJ. Mapping Bovine Tuberculosis in Colombia, 2001-2019. Vet Sci 2024; 11:220. [PMID: 38787192 PMCID: PMC11125619 DOI: 10.3390/vetsci11050220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION Bovine tuberculosis is a zoonotic disease of significant impact, particularly in countries where a pastoral economy is predominant. Despite its importance, few studies have analysed the disease's behaviour in Colombia, and none have developed maps using geographic information systems (GIS) to characterise it; as such, we developed this study to describe the temporal-spatial distribution of bovine tuberculosis in Colombia over a period of 19 years. METHODS A retrospective cross-sectional descriptive study, based on reports by the Colombian Agricultural Institute (ICA), surveillance of tuberculosis on cattle farms in Colombia from 2001 to 2019 was carried out. The data were converted into databases using Microsoft Access 365®, and multiple epidemiological maps were generated with the QGIS® version 3.36 software coupled to shape files of all the country's departments. RESULTS During the study period, 5273 bovine tuberculosis cases were identified in multiple different departments of Colombia (with a mean of 278 cases/year). Regarding its temporal distribution, the number of cases varied from a maximum of 903 cases (17.12% of the total) in 2015 to a minimum of 0 between 2001 and 2004 and between 2017 and 2019 (between 2005 and 2016, the minimum was 46 cases, 0.87%). CONCLUSIONS GIS are essential for understanding the temporospatial behaviour of zoonotic diseases in Colombia, as is the case for bovine tuberculosis, with its potential implications for the Human and One Health approaches.
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Affiliation(s)
| | - S. Daniela Jiménez-Diaz
- Grupo Colaborativo de Investigación en Enfermedades Transmitidas por Vectores, Zoonóticas y Tropicales de Risaralda (GETZ), Pereira, Risaralda 660001, Colombia;
| | | | - Kenneth Silva-Cajaleon
- Faculty of Environmental Sciences and Health Sciences, Universidad Científica del Sur, Lima 15307, Peru; (K.S.-C.); (A.J.R.-M.)
| | - Alfonso J. Rodríguez-Morales
- Faculty of Environmental Sciences and Health Sciences, Universidad Científica del Sur, Lima 15307, Peru; (K.S.-C.); (A.J.R.-M.)
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas-Institución Universitaria Visión de las Américas, Pereira, Risaralda 660003, Colombia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36-5053, Lebanon
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Mabe L, Muthevhuli M, Thekisoe O, Suleman E. Accuracy of molecular diagnostic assays for detection of Mycobacterium bovis: A systematic review and meta-analysis. Prev Vet Med 2024; 226:106190. [PMID: 38574490 DOI: 10.1016/j.prevetmed.2024.106190] [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: 10/11/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024]
Abstract
Bovine tuberculosis (bovine TB) is a chronic wasting disease of cattle caused primarily by Mycobacterium bovis. Controlling bovine TB requires highly sensitive, specific, quick, and reliable diagnostic methods. This systematic review and meta-analysis evaluated molecular diagnostic tests for M. bovis detection to inform the selection of the most viable assay. On a per-test basis, loop-mediated isothermal amplification (LAMP) showed the highest overall sensitivity of 99.0% [95% CI: 86.2%-99.9%] and specificity of 99.8% [95% CI: 96.2%-100.00%]. Quantitative real-time polymerase chain reaction (qPCR) outperformed conventional PCR and nested PCR (nPCR) with a diagnostic specificity of 96.6% [95% CI: 88.9%-99.0%], while the diagnostic sensitivity of 70.8% [95% CI: 58.6-80.5%] was comparable to that of nPCR at 71.4% [95% CI: 60.7-80.2%]. Test sensitivity was higher with the input of milk samples (90.9% [95% CI: 56.0%-98.7%]), while specificity improved with tests based on major M. bovis antigens (97.8% [95% CI: 92.3%-99.4%]), the IS6110 insertion sequence (95.4% [95% CI: 87.6%-98.4%]), and the RD4 gene (90.7% [95% CI: 52.2%-98.9%]). The design of the currently available molecular diagnostic assays, while mostly based on nonspecific gene targets, prevents them from being accurate enough to diagnose M. bovis infections in cattle, despite their promise. Future assay development should focus on the RD4 region since it is the only target identified by genome sequence data as being distinctive for detecting M. bovis. The availability of a sufficiently accurate diagnostic test combined with the routine screening of milk samples can decrease the risk of zoonotic transmissions of M. bovis.
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Affiliation(s)
- Lerato Mabe
- NextGen Health Cluster, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa; Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Mpho Muthevhuli
- NextGen Health Cluster, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa
| | - Oriel Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Essa Suleman
- NextGen Health Cluster, Council for Scientific and Industrial Research, P.O. Box 395, Pretoria 0001, South Africa.
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Roos EO, Loubser J, Kerr TJ, Dippenaar A, Streicher E, Olea-Popelka F, Robbe-Austerman S, Stuber T, Buss P, de Klerk-Lorist LM, Warren RM, van Helden PD, Parsons SD, Miller MA. Whole genome sequencing improves the discrimination between Mycobacterium bovis strains on the southern border of Kruger National Park, South Africa. One Health 2023; 17:100654. [PMID: 38283183 PMCID: PMC10810834 DOI: 10.1016/j.onehlt.2023.100654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 11/08/2023] [Indexed: 01/30/2024] Open
Abstract
Background Mycobacterium bovis forms part of the Mycobacterium tuberculosis complex and has an extensive host range and zoonotic potential. Various genotyping methods (e.g., spoligotyping) have been used to describe the molecular epidemiology of M. bovis. Advances in whole genome sequencing (WGS) have increased resolution to enable detection of genomic variants to the level of single nucleotide polymorphisms. This is especially relevant to One Health research on tuberculosis which benefits by being able to use WGS to identify epidemiologically linked cases, especially recent transmission. The use of WGS in molecular epidemiology has been extensively used in humans and cattle but is limited in wildlife. This approach appears to overcome the limitations of conventional genotyping methods due to lack of genetic diversity in M. bovis. Methods This pilot study investigated the spoligotype and WGS of M. bovis isolates (n = 7) from wildlife in Marloth Park (MP) and compared these with WGS data from other South African M. bovis isolates. In addition, the greater resolution of WGS was used to explore the phylogenetic relatedness of M. bovis isolates in neighbouring wildlife populations. Results The phylogenetic analyses showed the closest relatives to the seven isolates from MP were isolates from wildlife in Kruger National Park (KNP), which shares a border with MP. However, WGS data indicated that the KNP and MP isolates formed two distinct clades, even though they had similar spoligotypes and identical in silico genetic regions of difference profiles. Conclusions Mycobacterium bovis isolates from MP were hypothesized to be directly linked to KNP wildlife, based on spoligotyping. However, WGS indicated more complex epidemiology. The presence of two distinct clades which were genetically distinct (SNP distance of 19-47) and suggested multiple transmission events. Therefore, WGS provided new insight into the molecular epidemiology of the M. bovis isolates from MP and their relationship to isolates from KNP. This approach will facilitate greater understanding of M. bovis transmission at wildlife-livestock-human interfaces and advances One Health research on tuberculosis, especially across different host species.
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Affiliation(s)
- Eduard O. Roos
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Johannes Loubser
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Tanya J. Kerr
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Elizma Streicher
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Francisco Olea-Popelka
- Department of Pathology and Laboratory Medicine, Schulich Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Private Bag X402, Skukuza, 1350, South Africa
| | - Lin-Mari de Klerk-Lorist
- Department of Agriculture Land Reform and Rural Development, Office of the State Veterinarian, Kruger National Park, PO Box 12, Skukuza, 1350, South Africa
| | - Robin M. Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Paul D. van Helden
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Sven D.C. Parsons
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Michele A. Miller
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
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Pereira AC, Reis AC, Cunha MV. Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal. Emerg Microbes Infect 2023; 12:2253340. [PMID: 37640285 PMCID: PMC10484045 DOI: 10.1080/22221751.2023.2253340] [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: 04/10/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
ABSTRACTAnimal tuberculosis (TB) remains a serious concern for animal and human health. Mycobacterium bovis circulates in multi-host systems, dominated by the European 2 clonal complex (Eu2) in Iberia. In this work, we use genomic epidemiology to infer the emergence, spread, and spatiotemporal patterns of Eu2 in the official epidemiological risk area of animal TB in Portugal. Phylogenetic analysis of 144 M. bovis whole-genome sequences from cattle, wild boar, and red deer, representing the 2002-2021 period, distinguished three Eu2 clades that evolved independently. The major Eu2 clade underwent phylodynamic inferences to estimate the time and location of outbreaks, host transitions, and spatial diffusion as well. The origin of this Eu2 clade was attributed to the red deer population in the Castelo Branco district, near the border with Spain. Most host transitions were intraspecific (80%), while interspecific transmissions between wildlife species (wild boar-red deer), and between wild boar and cattle, were highly supported. Phylogeographic reconstruction evidenced that most transitions (82%) occur within municipalities, highlighting local transmission corridors.Our study indicates that M. bovis continues to spread at the cattle-wildlife interface within the animal TB hotspot area, possibly driven by the foraging behaviour of wild boar near agricultural lands. Red deer seems to be an important driver of TB within wildlife hosts, while the wild boar links the multi-host wildlife community and livestock. This work highlights the value of combining genomic epidemiology with phylodynamic inference to resolve host jumps and spatial patterns of M. bovis, providing real-time clues about points of intervention.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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9
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Sawyer J, Rhodes S, Jones GJ, Hogarth PJ, Vordermeier HM. Mycobacterium bovis and its impact on human and animal tuberculosis. J Med Microbiol 2023; 72. [PMID: 37962183 DOI: 10.1099/jmm.0.001769] [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] [Indexed: 11/15/2023] Open
Abstract
Graphical abstract
Mycobacterium bovis
is a slow-growing (16–20 h generation time), Gram-positive and acid-fast bacterium member of the
Mycobacterium tuberculosis
complex pathogen group (MTBC). They are characterized by a complex, protective cell wall containing mycolic acids. The MTBCs are the causative agents of tuberculosis (TB). Following initial infection, subsequent pathological changes, and the progress of infection depend on the interplay between host defence mechanisms and mycobacterial virulence factors and the balance between the immunologic protective responses and the damaging inflammatory processes. Progression of the disease is characterized by the formation of typical caseous tuberculous granuloma (inflammatory mononuclear cell aggregates) because of the host's immune response to infection. The transmission and epidemiology of
Mycobacterium bovis
are complex and vary depending on the situation and ecosystem. In the UK, the spread of BTB in the UK cattle herd can occur by transmitting the disease from cattle to cattle and between badgers but also between badgers and cattle. The disease is thought to be primarily a respiratory disease with spread between individuals through mechanisms such as coughing or transfer of bacteria in respiratory secretions. It is also thought that environmental contamination may also lead to some transmission. The protective cell wall of the organism is believed to allow the organism to survive outside an animal host, which can then transfer to new hosts following subsequent environmental exposure. In some situations, ingestion of pathogens in food can lead to infection. The relative contribution of these routes and precise transmission mechanisms needs to be better understood.
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Affiliation(s)
- Jason Sawyer
- Animal and Plant Health Agency and WOAH Reference Laboratory for Mammalian TB, Addlestone, Surrey, UK
| | - Shelley Rhodes
- Animal and Plant Health Agency and WOAH Reference Laboratory for Mammalian TB, Addlestone, Surrey, UK
| | - Gareth J Jones
- Animal and Plant Health Agency and WOAH Reference Laboratory for Mammalian TB, Addlestone, Surrey, UK
| | - Philip J Hogarth
- Animal and Plant Health Agency and WOAH Reference Laboratory for Mammalian TB, Addlestone, Surrey, UK
| | - H Martin Vordermeier
- Animal and Plant Health Agency and WOAH Reference Laboratory for Mammalian TB, Addlestone, Surrey, UK
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10
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Zahran M, El-Shabasy RM, Elrashedy A, Mousa W, Nayel M, Salama A, Zaghawa A, Elsify A. Recent progress in the genotyping of bovine tuberculosis and its rapid diagnosis via nanoparticle-based electrochemical biosensors. RSC Adv 2023; 13:31795-31810. [PMID: 37908649 PMCID: PMC10613952 DOI: 10.1039/d3ra05606f] [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: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023] Open
Abstract
Bovine tuberculosis (bTB) is considered a worldwide infectious zoonotic disease. Mycobacterium bovis causes bTB disease. It is one of the Mycobacterium tuberculosis complex (MTBC) members. MTBC is a clonal complex of close relatives with approximately 99.95% similarity. M. bovis is a spillover pathogen that can transmit from animals to humans and rarely from humans to animals with contact. Genotyping techniques are important to discriminate and differentiate between MTBC species. Spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) are widely used but they have some limitations. As an alternative, whole genome sequencing approaches have been utilized due to their high-resolution power. They are employed in typing M. bovis and explain the evolutionary and phylogenetic relationships between isolates. The control of bTB disease has attracted a large amount of attention. Rapid and proper diagnosis is necessary for monitoring the disease as an initial step for its control and treatment. Nanotechnology has a potential impact on the rapid diagnosis and treatment of bTB through the use of nanocarrier and metal nanoparticles (NPs). Special attention has been paid to voltammetric and impedimetric electrochemical strategies as facile, sensitive, and selective methods for the efficient detection of tuberculosis. The efficacy of these sensors is enhanced in the presence of NPs, which act as recognition and/or redox probes. Gold, silver, copper, cobalt, graphene, and magnetic NPs, as well as polypyrrole nanowires and multiwalled carbon nanotubes have been employed for detecting tuberculosis. Overall, NP-based electrochemical sensors represent a promising tool for the diagnosis of bTB.
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Affiliation(s)
- Moustafa Zahran
- Department of Chemistry, Faculty of Science, Menoufia University Shebin El-Kom 32512 Egypt
- Menoufia Company for Water and Wastewater, Holding Company for Water and Wastewater Menoufia 32514 Egypt
| | - Rehan M El-Shabasy
- Department of Chemistry, Faculty of Science, Menoufia University Shebin El-Kom 32512 Egypt
- Chemistry Department, The American University in Cairo AUC Avenue New Cairo 11835 Egypt
| | - Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Walid Mousa
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Ahmed Zaghawa
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
| | - Ahmed Elsify
- Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City Egypt
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11
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Michelet L, Tambosco J, Biet F, Fach P, Delannoy S, Boschiroli ML. Deciphering the evolution of the temporal and geographic distribution of French Mycobacterium bovis genotypes using a high throughput SNP-targeted amplicon sequencing method. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 114:105497. [PMID: 37657678 DOI: 10.1016/j.meegid.2023.105497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Mycobacterium bovis, which belongs to the Mycobacterium tuberculosis complex, is a highly clonal pathogen. However, several lineages of M. bovis have been described worldwide and nine different clusters were identified in France. Targeted amplicon sequencing using next-generation sequencing technology of eighty-eight phylogenetically informative single nucleotide polymorphisms (SNPs) were used to infer the phylogenetic relationship of 630 strains of the National Reference Laboratory isolated between 1979 and 2018 from various animal species. This study allowed classifying 618 different genotypic profiles (combination of a spoligotype and 8 loci-MIRU-VNTR profiles) into the nine previously identified clusters. A global analysis of the entire collection of the National Reference Laboratory has made it possible to represent the evolution of clonal complexes and clusters in time and space for better assessing epidemiological changes of bovine tuberculosis in France.
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Affiliation(s)
- Lorraine Michelet
- Université Paris-Est, ANSES Animal Health Laboratory, National reference laboratory for Tuberculosis, 94706 Maisons-Alfort, France.
| | - Jennifer Tambosco
- Université Paris-Est, ANSES Animal Health Laboratory, National reference laboratory for Tuberculosis, 94706 Maisons-Alfort, France
| | | | - Patrick Fach
- IdentyPath Genomics Platform, Laboratory for Food Safety, Anses, 94706 Maisons-Alfort, France
| | - Sabine Delannoy
- IdentyPath Genomics Platform, Laboratory for Food Safety, Anses, 94706 Maisons-Alfort, France
| | - María Laura Boschiroli
- Université Paris-Est, ANSES Animal Health Laboratory, National reference laboratory for Tuberculosis, 94706 Maisons-Alfort, France
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12
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Appegren A, Boschiroli ML, De Cruz K, Michelet L, Héry-Arnaud G, Kempf M, Lanotte P, Bemer P, Peuchant O, Pestel-Caron M, Skalli S, Brasme L, Martin C, Enault C, Carricajo A, Guet-Revillet H, Ponsoda M, Jacomo V, Bourgoin A, Trombert-Paolantoni S, Carrière C, Dupont C, Conquet G, Galal L, Banuls AL, Godreuil S. Genetic Diversity and Population Structure of Mycobacterium bovis at the Human-Animal-Ecosystem Interface in France: “A One Health Approach”. Pathogens 2023; 12:pathogens12040548. [PMID: 37111434 PMCID: PMC10143977 DOI: 10.3390/pathogens12040548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Mycobacterium bovis infects cattle and wildlife, and also causes a small proportion of tuberculosis cases in humans. In most European countries, M. bovis infections in cattle have been drastically reduced, but not eradicated. Here, to determine the M. bovis circulation within and between the human, cattle, and wildlife compartments, we characterized by spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing the genetic diversity of M. bovis isolates collected from humans, cattle, and wildlife in France from 2000 to 2010. We also assessed their genetic structure within and among the different host groups, and across time and space. The M. bovis genetic structure and its spatiotemporal variations showed different dynamics in the human and animal compartments. Most genotypes detected in human isolates were absent in cattle and wildlife isolates, possibly because in patients, M. bovis infection was contracted abroad or was the reactivation of an old lesion. Therefore, they did not match the genetic pool present in France during the study period. However, some human-cattle exchanges occurred because some genotypes were common to both compartments. This study provides new elements for understanding M. bovis epidemiology in France, and calls for increased efforts to control this pathogen worldwide.
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Affiliation(s)
- Anaïs Appegren
- Laboratory of Bacteriology, CHU Montpellier, 34000 Montpellier, France
| | - Maria Laura Boschiroli
- ANSES Laboratory for Animal Health, Tuberculosis National Reference Laboratory, University Paris-Est, 94000 Maisons-Alfort, France
| | - Krystel De Cruz
- ANSES Laboratory for Animal Health, Tuberculosis National Reference Laboratory, University Paris-Est, 94000 Maisons-Alfort, France
| | - Lorraine Michelet
- ANSES Laboratory for Animal Health, Tuberculosis National Reference Laboratory, University Paris-Est, 94000 Maisons-Alfort, France
| | | | - Marie Kempf
- Laboratory of Bacteriology, CHU Angers, 49000 Angers, France
| | | | - Pascale Bemer
- Laboratory of Bacteriology, CHU Nantes, 44000 Nantes, France
| | - Olivia Peuchant
- Laboratory of Bacteriology, CHU Bordeaux, 33000 Bordeaux, France
| | | | - Soumaya Skalli
- Laboratory of Bacteriology, CHU Rouen, 76000 Rouen, France
| | - Lucien Brasme
- Laboratory of Bacteriology, CHU Reims, 51000 Reims, France
| | | | - Cecilia Enault
- Laboratory of Bacteriology, CHU Nîmes, 30000 Nîmes, France
| | - Anne Carricajo
- Laboratory of Bacteriology, CHU Saint-Etienne, 42000 Saint-Etienne, France
| | | | | | | | - Anne Bourgoin
- Laboratory of Bacteriology, CHU Poitiers, 86000 Poitiers, France
| | | | - Christian Carrière
- Laboratory of Bacteriology, CHU Montpellier, 34000 Montpellier, France
- UMR, MIVEGEC, IRD, CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Chloé Dupont
- Laboratory of Bacteriology, CHU Montpellier, 34000 Montpellier, France
| | - Guilhem Conquet
- Laboratory of Bacteriology, CHU Montpellier, 34000 Montpellier, France
| | - Lokman Galal
- UMR, MIVEGEC, IRD, CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Anne-Laure Banuls
- UMR, MIVEGEC, IRD, CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Sylvain Godreuil
- Laboratory of Bacteriology, CHU Montpellier, 34000 Montpellier, France
- UMR, MIVEGEC, IRD, CNRS, Université de Montpellier, 34000 Montpellier, France
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13
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Charles C, Conde C, Vorimore F, Cochard T, Michelet L, Boschiroli ML, Biet F. Features of Mycobacterium bovis Complete Genomes Belonging to 5 Different Lineages. Microorganisms 2023; 11:177. [PMID: 36677470 PMCID: PMC9865570 DOI: 10.3390/microorganisms11010177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Mammalian tuberculosis (TB) is a zoonotic disease mainly due to Mycobacterium bovis (M. bovis). A current challenge for its eradication is understanding its transmission within multi-host systems. Improvements in long-read sequencing technologies have made it possible to obtain complete bacterial genomes that provide a comprehensive view of species-specific genomic features. In the context of TB, new genomic references based on complete genomes genetically close to field strains are also essential to perform precise field molecular epidemiological studies. A total of 10 M. bovis strains representing each genetic lineage identified in France and in other countries were selected for performing complete assembly of their genomes. Pangenome analysis revealed a "closed" pangenome composed of 3900 core genes and only 96 accessory genes. Whole genomes-based alignment using progressive Mauve showed remarkable conservation of the genomic synteny except that the genomes have a variable number of copies of IS6110. Characteristic genomic traits of each lineage were identified through the discovery of specific indels. Altogether, these results provide new genetic features that improve the description of M. bovis lineages. The availability of new complete representative genomes of M. bovis will be useful to epidemiological studies and better understand the transmission of this clonal-evolving pathogen.
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Affiliation(s)
- Ciriac Charles
- Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), CEDEX, 94701 Maisons-Alfort, France
- Infectiologie et Santé Publique (ISP), Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Cyril Conde
- Infectiologie et Santé Publique (ISP), Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Fabien Vorimore
- Laboratory for Food Safety, Unit of ‘Pathogenic E. coli’ (COLiPATH) & Genomics Platform ‘IdentyPath’ (IDPA), ANSES, 94701 Maisons-Alfort, France
| | - Thierry Cochard
- Infectiologie et Santé Publique (ISP), Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Lorraine Michelet
- Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), CEDEX, 94701 Maisons-Alfort, France
| | - Maria Laura Boschiroli
- Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), CEDEX, 94701 Maisons-Alfort, France
| | - Franck Biet
- Infectiologie et Santé Publique (ISP), Institut National de Recherche pour L’agriculture, L’alimentation et L’environnement (INRAE), Université de Tours, UMR 1282, 37380 Nouzilly, France
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14
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Miranda-Velez M, Sarker GS, Ramisetty P, Geden S, Bartolomeu Halicki PC, Annamalai T, Tse-Dinh YC, Rohde KH, Moon JH. Proton Motive Force-Disrupting Antimycobacterial Guanylurea Polymer. Biomacromolecules 2022; 23:4668-4677. [DOI: 10.1021/acs.biomac.2c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Michelle Miranda-Velez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Golam Sabbir Sarker
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Priya Ramisetty
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Sandra Geden
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Priscila Cristina Bartolomeu Halicki
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Kyle H. Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Joong Ho Moon
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
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15
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Valcheva V, Perea C, Savova-Lalkovska T, Dimitrova A, Radulski L, Mokrousov I, Marinov K, Najdenski H, Bonovska M. Mycobacterium bovis and M. caprae in Bulgaria: insight into transmission and phylogeography gained through whole-genome sequencing. BMC Vet Res 2022; 18:148. [PMID: 35461250 PMCID: PMC9034630 DOI: 10.1186/s12917-022-03249-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/18/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND This study aimed to characterize recent Mycobacterium bovis/M. caprae isolates from Bulgaria by whole-genome sequencing (WGS) to gain a first insight into their molecular diversity, transmission, and position within the global phylogeography of this important zoonotic species. RESULTS The isolates were obtained from cattle in diverse locations of Bulgaria in 2015-2020 and were identified by microbiological and PCR assays. WGS data were used for phylogenetic analysis that also included M. bovis global dataset. Thirty-seven M. bovis/caprae isolates from Bulgaria were studied and 34 of them were SNP genotyped. The isolates were subdivided into 3 major phylogenetic groups. Type Mbovis-13 (Eu2 complex [western Europe and northern Africa]) included one isolate. Mbovis-37 type included 5 isolates outside of known clonal complexes. The Bulgarian M. caprae isolates formed a sub-group within the Mcaprae-27B cluster which also included 22 M. caprae isolates from Poland, Spain, Germany, and the Republic of Congo. The Bulgarian M. caprae isolates share their latest common ancestors with Spanish isolates. The Mbovis-37 group shares a distant common ancestor (pairwise distance 22-29 SNPs) with an isolate from Poland but was very distant (> 200 SNPs) from the rest of the tree. The Mbovis-13 group shares a common ancestor with two human isolates from Germany. Phylogeographically, both M. bovis clades had limited circulation in northeastern Bulgaria while the majority of the studied isolates (M. caprae) were from central and western provinces. A phylogenetic network-based analysis demonstrated that 11 Bulgarian isolates were separated by 1 to 6 SNPs within four clusters, mostly forming pairs of isolates. CONCLUSION The obtained WGS analysis positioned the Bulgarian isolates within the global phylogeography of M. bovis/M. caprae. Hypothetically, the observed phylogenetic diversity may not have resulted from livestock trade routes, but instead may reflect the deeply rooted M. bovis/M. caprae phylogeography of Europe. A high level of genetic divergence between the majority of the studied isolates suggests limited active transmission of bTB in Bulgaria during the survey period. At the same time, a possibility of the endemic presence of circulating bTB strains in the form of the latent persistent disease cannot be ruled out.
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Affiliation(s)
- Violeta Valcheva
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26, Acad. Georgi Bonchev str., 1113, Sofia, Bulgaria.
| | - Claudia Perea
- National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA
| | - Tanya Savova-Lalkovska
- National Diagnostic and Research Veterinary Medical Institute "Prof. Dr. G. Pavlov", Sofia, Bulgaria
| | - Albena Dimitrova
- National Diagnostic and Research Veterinary Medical Institute "Prof. Dr. G. Pavlov", Sofia, Bulgaria
| | | | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | | | - Hristo Najdenski
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26, Acad. Georgi Bonchev str., 1113, Sofia, Bulgaria
| | - Magdalena Bonovska
- Department of Infectious Microbiology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 26, Acad. Georgi Bonchev str., 1113, Sofia, Bulgaria
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16
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Mtetwa HN, Amoah ID, Kumari S, Bux F, Reddy P. The source and fate of Mycobacterium tuberculosis complex in wastewater and possible routes of transmission. BMC Public Health 2022; 22:145. [PMID: 35057793 PMCID: PMC8781043 DOI: 10.1186/s12889-022-12527-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 01/06/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The Mycobacterium tuberculosis complex (MTBC) consists of causative agents of both human and animal tuberculosis and is responsible for over 10 million annual infections globally. Infections occur mainly through airborne transmission, however, there are possible indirect transmissions through a faecal-oral route which is poorly reported. This faecal-oral transmission could be through the occurrence of the microbe in environments such as wastewater. This manuscript, therefore, reviews the source and fate of MTBC in the wastewater environment, including the current methods in use and the possible risks of infections. RESULTS The reviewed literature indicates that about 20% of patients with pulmonary TB may have extra-pulmonary manifestations such as GITB, resulting in shedding in feaces and urine. This could potentially be the reason for the detection of MTBC in wastewater. MTBC concentrations of up to 5.5 × 105 (±3.9 × 105) copies/L of untreated wastewater have been reported. Studies have indicated that wastewater may provide these bacteria with the required nutrients for their growth and could potentially result in environmental transmission. However, 98.6 (± 2.7) %, removal during wastewater treatment, through physical-chemical decantation (primary treatment) and biofiltration (secondary treatment) has been reported. Despite these reports, several studies observed the presence of MTBC in treated wastewater via both culture-dependent and molecular techniques. CONCLUSION The detection of viable MTBC cells in either treated or untreated wastewater, highlights the potential risks of infection for wastewater workers and communities close to these wastewater treatment plants. The generation of aerosols during wastewater treatment could be the main route of transmission. Additionally, direct exposure to the wastewater containing MTBC could potentially contribute to indirect transmissions which may lead to pulmonary or extra-pulmonary infections. This calls for the implementation of risk reduction measures aimed at protecting the exposed populations.
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Affiliation(s)
- Hlengiwe N Mtetwa
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Isaac D Amoah
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Poovendhree Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa.
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17
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Chan TH, Huang CS, Tu C, Jou R. Bovine tuberculosis in Taiwan, 2008-2019. Transbound Emerg Dis 2021; 69:e814-e822. [PMID: 34724711 DOI: 10.1111/tbed.14371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/22/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022]
Abstract
Bovine tuberculosis (bTB) is a zoonosis caused by Mycobacterium bovis. The impact of bTB on global TB control has been underestimated. We adopted the One Health approach to human bTB surveillance in Taiwan. Of 20,972 human TB cases, 202 (1.0%) were bTB, 78.2% were in males, 85.1% were new cases, 83.2% were pulmonary TB, and most were in Central (52.5%) and Southern (24.8%) Taiwan. Only 18.8% of bTB patients had known animal contact. Of the 202 human M. bovis strains, 100% were resistant to pyrazinamide (PZA), 30.2% were concurrently resistant to isoniazid (INH) and 2.0% were multidrug resistant, defined as being resistant to at least INH and rifampin. Whereas, of the 22 animal M. bovis strains, 100% and 22.7% were resistant to PZA and INH, respectively. Seven spoligotypes and 25 mycobacterial interspersed repetitive unit genotypes were identified. The predominant genotype, SB0265, was also prevalent in livestock. Notably, six animal-specific M. bovis genotypes were identified. bTB differential diagnosis and drug resistance detection are crucial for TB control. Comprehensive surveillance and human-animal interface investigations are needed.
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Affiliation(s)
- Tai-Hua Chan
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC.,Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chun-Sheng Huang
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, New Taipei City, Taiwan, ROC
| | - Chien Tu
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, New Taipei City, Taiwan, ROC
| | - Ruwen Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC.,Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Taipei, Taiwan, ROC.,Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
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18
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Lima DAR, Zimpel CK, Patané JS, Silva-Pereira TT, Etges RN, Rodrigues RA, Dávila AMR, Ikuta CY, Ferreira Neto JS, Guimarães AMS, Araújo FR. Genomic analysis of an outbreak of bovine tuberculosis in a man-made multi-host species system: A call for action on wildlife in Brazil. Transbound Emerg Dis 2021; 69:e580-e591. [PMID: 34633756 DOI: 10.1111/tbed.14343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022]
Abstract
We report on a 15-year-long outbreak of bovine tuberculosis (bTB) in wildlife from a Brazilian safari park. A timeline of diagnostic events and whole-genome sequencing (WGS) of 21 Mycobacterium bovis isolates from deer and llamas were analyzed. Accordingly, from 2003 to 2018, at least 16 animals, from eight species, died due to TB, which is likely an underestimated number. In three occasions since 2013, the deer presented positive tuberculin tests, leading to the park closure and culling of all deer. WGS indicated that multiple M. bovis strains were circulating, with at least three founding introductions since the park inauguration in 1977. Using a previously sequenced dataset of 71 M. bovis genomes from cattle, we found no recent transmission events between nearby farms and the park based on WGS. Lastly, by discussing socio-economic and environmental factors escaping current regulatory gaps that were determinant of this outbreak, we pledge for the development of a plan to report and control bTB in wildlife in Brazil.
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Affiliation(s)
- Daiane A R Lima
- Department of Veterinary Medicine, Graduate Program in Veterinary Sciences, School of Veterinary Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Cristina K Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 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, São Paulo, Brazil
| | - José S Patané
- Center for Bioinformatics and Computational Biology, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 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, São Paulo, Brazil
| | - Rodrigo N Etges
- Livestock and Rural Development, Secretary of Agriculture, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rudielle A Rodrigues
- Department of Veterinary Medicine, Graduate Program in Veterinary Sciences, School of Veterinary Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory and Graduate Program on Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, 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, São Paulo, Brazil
| | - José S Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Marcia S Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 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, São Paulo, Brazil
| | - Flábio R Araújo
- Embrapa Beef Cattle, Campo Grande, Mato Grosso do Sul, Brazil
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19
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Kim TW, Jang YH, Jeong MK, Seo Y, Park CH, Kang S, Lee YJ, Choi JS, Yoon SS, Kim JM. Single-nucleotide polymorphism-based epidemiological analysis of Korean Mycobacterium bovis isolates. J Vet Sci 2021; 22:e24. [PMID: 33774940 PMCID: PMC8007439 DOI: 10.4142/jvs.2021.22.e24] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background Bovine tuberculosis (TB) is caused by Mycobacterium bovis, a well-known cause of zoonotic tuberculosis in cattle and deer, and has been investigated in many physiological and molecular studies. However, detailed genome-level studies of M. bovis have not been performed in Korea. Objectives To survey whole genome-wide single-nucleotide polymorphism (SNP) variants in Korean M. bovis field isolates and to define M. bovis groups in Korea by comparing SNP typing with spoligotyping and variable number tandem repeat typing. Methods A total of 46 M. bovis field isolates, isolated from laryngopharyngeal lymph nodes and lungs of Korean cattle, wild boar, and Korean water deer, were used to identify SNPs by performing whole-genome sequencing. SNP sites were confirmed via polymerase chain reaction using 87 primer pairs. Results We identified 34 SNP sites with different frequencies across M. bovis isolates, and performed SNP typing and epidemiological analysis, which divided the 46 field isolates into 16 subtypes. Conclusions Through SNP analysis, detailed differences in samples with identical spoligotypes could be detected. SNP analysis is, therefore, a useful epidemiological tracing tool that could enable better management of bovine TB, thus preventing further outbreaks and reducing the impact of this disease.
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Affiliation(s)
- Tae Woon Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Yun Ho Jang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Min Kyu Jeong
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Yoonjeong Seo
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Chan Ho Park
- Gangwondo Livestock & Veterinary Service, Chuncheon 24203, Korea
| | - Sinseok Kang
- Chung Cheongbukdo Livestock & Veterinary Service, Jungbu-Branch, Chungju 27336, Korea
| | - Young Ju Lee
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Jeong Soo Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Soon Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Jae Myung Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
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20
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Sales ÉB, Fonseca AA, Gonçalves CM, Lage AP, Andrade GI, Suffys PN, Gomes HM, Dias NL, Ferreira Neto JS, Guimarães AMDS, Heinemann MB. Multispacer Sequence Typing for Mycobacterium bovis Genotyping. Front Vet Sci 2021; 8:666283. [PMID: 33981748 PMCID: PMC8107269 DOI: 10.3389/fvets.2021.666283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/30/2021] [Indexed: 11/13/2022] Open
Abstract
The molecular typing of Mycobacterium bovis, which causes bovine tuberculosis, can be accomplished by combining different polymorphic markers, contributing to its epidemiological investigation. Multispacer sequence typing (MST) is a sequencing-based method that employs intergenic regions susceptible to higher mutation rates given the low selection pressure. It has been applied to M. tuberculosis, but not to M. bovis. The aim of this study was to evaluate a MST for M. bovis. A total of 58 strains isolated from tissues with lesions suggestive of bovine tuberculosis, coming from cattle herds in six Brazilian states and four standard samples of M. bovis were typified employing the MST technique. Fourteen intergenic regions were used, and four types of genetic events were reported: single nucleotide mutation (SNP), insertion, deletion, and tandem repeat (TR). Seven loci were chosen for typing. Twenty-eight type sequences (ST) were identified, indicating type sequences (ST) were identified, indicating a 92.9% HGDI (Hunter Gaston Discriminatory Index). The data were used to analyze the evolutionary patterns of these isolates and correlate them to phylogeographic lineages based on the formation of clonal complexes generated from eBURST software. Later, we associated the MST with spoligotyping technique, currently considered the gold standard for classification of M. bovis. The results support the MST as an alternative method for genotyping of M. bovis. The method has the advantage of sequencing and the availability of sequences analyzed in public databases, which can be used by professionals around the world as a tool for further analysis. This was the first study to identify the variability of isolates of M. bovis by the MST method.
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Affiliation(s)
- Érica Bravo Sales
- Laboratório Federal de Defesa Agropecuária de Minas Gerais, Pedro Leopoldo, Minas Gerais, Brazil
| | - Antônio Augusto Fonseca
- Laboratório Federal de Defesa Agropecuária de Minas Gerais, Pedro Leopoldo, Minas Gerais, Brazil
| | | | - Andrey Pereira Lage
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Giovanna Ivo Andrade
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Natanael Lamas Dias
- Laboratório Federal de Defesa Agropecuária de Minas Gerais, Pedro Leopoldo, Minas Gerais, Brazil
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21
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Carneiro PA, Zimpel CK, Pasquatti TN, Silva-Pereira TT, Takatani H, Silva CBDG, Abramovitch RB, Sa Guimaraes AM, Davila AMR, Araujo FR, Kaneene JB. Genetic Diversity and Potential Paths of Transmission of Mycobacterium bovis in the Amazon: The Discovery of M. bovis Lineage Lb1 Circulating in South America. Front Vet Sci 2021; 8:630989. [PMID: 33665220 PMCID: PMC7921743 DOI: 10.3389/fvets.2021.630989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/15/2021] [Indexed: 11/13/2022] Open
Abstract
Bovine tuberculosis (bTB) has yet to be eradicated in Brazil. Herds of cattle and buffalo are important sources of revenue to people living in the banks of the Amazon River basin. A better understanding of Mycobacterium bovis (M. bovis) populational structure and transmission dynamics affecting these animals can significantly contribute in efforts to improve their sanitary status. Herein, we sequenced the whole genome of 22 M. bovis isolates (15 from buffalo and 7 from cattle) from 10 municipalities in the region of the Lower Amazon River Basin in Brazil and performed phylogenomic analysis and Single Nucleotide Polymorphism (SNP)-based transmission inference to evaluate population structure and transmission networks. Additionally, we compared these genomes to others obtained in unrelated studies in the Marajó Island (n = 15) and worldwide (n = 128) to understand strain diversity in the Amazon and to infer M. bovis lineages. Our results show a higher genomic diversity of M. bovis genomes obtained in the Lower Amazon River region when compared to the Marajó Island, while no significant difference was observed between M. bovis genomes obtained from cattle and buffalo (p ≥ 0.05). This high genetic diversity is reflected by the weak phylogenetic clustering of M. bovis from the Lower Amazon River region based on geographic proximity and in the detection of only two putative transmission clusters in the region. One of these clusters is the first description of inter-species transmission between cattle and buffalo in the Amazon, bringing implications to the bTB control program. Surprisingly, two M. bovis lineages were detected in our dataset, namely Lb1 and Lb3, constituting the first description of Lb1 in South America. Most of the strains of this study (13/22) and all 15 strains of the Marajó Island carried no clonal complex marker, suggesting that the recent lineage classification better describe the diversity of M. bovis in the Amazon.
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Affiliation(s)
- Paulo Alex Carneiro
- Center for Comparative Epidemiology, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- Amazonas State Federal Institute, Manaus, Brazil
| | - 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 Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | | | - Taiana T. Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Haruo Takatani
- Agência de Defesa Agropecuaria Do Amazonas, Manaus, Brazil
| | | | - Robert B. Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Ana Marcia Sa Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alberto M. R. Davila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute and Graduate Program in Biodiversity and Health, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - John B. Kaneene
- Center for Comparative Epidemiology, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
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22
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Vázquez-Chacón CA, Rodríguez-Gaxiola FDJ, López-Carrera CF, Cruz-Rivera M, Martínez-Guarneros A, Parra-Unda R, Arámbula-Meraz E, Fonseca-Coronado S, Vaughan G, López-Durán PA. Identification of drug resistance mutations among Mycobacterium bovis lineages in the Americas. PLoS Negl Trop Dis 2021; 15:e0009145. [PMID: 33591982 PMCID: PMC7886168 DOI: 10.1371/journal.pntd.0009145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/14/2021] [Indexed: 01/25/2023] Open
Abstract
Identifying the Mycobacterium tuberculosis resistance mutation patterns is of the utmost importance to assure proper patient's management and devising of control programs aimed to limit spread of disease. Zoonotic Mycobacterium bovis infection still represents a threat to human health, particularly in dairy production regions. Routinary, molecular characterization of M. bovis is performed primarily by spoligotyping and mycobacterial interspersed repetitive units (MIRU) while next generation sequencing (NGS) approaches are often performed by reference laboratories. However, spoligotyping and MIRU methodologies lack the resolution required for the fine characterization of tuberculosis isolates, particularly in outbreak settings. In conjunction with sophisticated bioinformatic algorithms, whole genome sequencing (WGS) analysis is becoming the method of choice for advanced genetic characterization of tuberculosis isolates. WGS provides valuable information on drug resistance and compensatory mutations that other technologies cannot assess. Here, we performed an analysis of the most frequently identified mutations associated with tuberculosis drug resistance and their genetic relationship among 2,074 Mycobacterium bovis WGS recovered primarily from non-human hosts. Full-length gene sequences harboring drug resistant associated mutations and their phylogenetic relationships were analyzed. The results showed that M. bovis isolates harbor mutations conferring resistance to both first- and second-line antibiotics. Mutations conferring resistance for isoniazid, fluoroquinolones, streptomycin, and aminoglycosides were identified among animal strains. Our findings highlight the importance of molecular surveillance to monitor the emergence of mutations associated with multi and extensive drug resistance in livestock and other non-human mammals.
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Affiliation(s)
- Carlos Arturo Vázquez-Chacón
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, México
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | | | | | - Mayra Cruz-Rivera
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Armando Martínez-Guarneros
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | - Ricardo Parra-Unda
- Unidad de Investigaciones en Salud Pública, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Eliakym Arámbula-Meraz
- Laboratorio de Genética y Biología Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Salvador Fonseca-Coronado
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
| | - Gilberto Vaughan
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
| | - Paúl Alexis López-Durán
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
- * E-mail:
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23
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Meiring C, Higgitt R, Dippenaar A, Roos E, Buss P, Hewlett J, Cooper D, Rogers P, Klerk‐Lorist L, Schalkwyk L, Hausler G, Helden P, Möller M, Warren R, Miller M. Characterizing epidemiological and genotypic features of
Mycobacterium bovis
infection in wild dogs (
Lycaon pictus
). Transbound Emerg Dis 2020. [DOI: 10.1111/tbed.13947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christina Meiring
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Roxanne Higgitt
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Anzaan Dippenaar
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Eduard Roos
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Peter Buss
- Veterinary Wildlife Services South African National Parks Skukuza South Africa
| | - Jennie Hewlett
- Veterinary Wildlife Services South African National Parks Skukuza South Africa
- Paraclinical Department Faculty of Veterinary Science University of Pretoria Onderstepoort South Africa
| | - Dave Cooper
- Ezemvelo KZN Wildlife Mtubatuba South Africa
| | - Peter Rogers
- Provet Wildlife Services & Companion Animal Hospital Hoedspruit South Africa
| | - Lin‐Mari Klerk‐Lorist
- Department of Agriculture, Forestry and FisheriesOffice of the State Veterinarian Skukuza South Africa
| | - Louis Schalkwyk
- Department of Agriculture, Forestry and FisheriesOffice of the State Veterinarian Skukuza South Africa
| | - Guy Hausler
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Paul Helden
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Marlo Möller
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Rob Warren
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Michele Miller
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
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24
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Dwyer RA, Witte C, Buss P, Goosen WJ, Miller M. Epidemiology of Tuberculosis in Multi-Host Wildlife Systems: Implications for Black ( Diceros bicornis) and White ( Ceratotherium simum) Rhinoceros. Front Vet Sci 2020; 7:580476. [PMID: 33330701 PMCID: PMC7672123 DOI: 10.3389/fvets.2020.580476] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Cases of tuberculosis (TB) resulting from infection with Mycobacterium tuberculosis complex (MTBC) have been recorded in captive white (Ceratotherium simum) and black (Diceros bicornis) rhinoceros. More recently, cases have been documented in free-ranging populations of both species in bovine tuberculosis (bTB) endemic areas of South Africa. There is limited information on risk factors and transmission patterns for MTBC infections in African rhinoceros, however, extrapolation from literature on MTBC infections in other species and multi-host systems provides a foundation for understanding TB epidemiology in rhinoceros species. Current diagnostic tests include blood-based immunoassays but distinguishing between subclinical and active infections remains challenging due to the lack of diagnostic techniques. In other species, demographic risk factors for MTBC infection include sex and age, where males and adults are generally at higher risk than females and younger individuals. Limited available historical information reflects similar age- and sex-associated patterns for TB in captive black and white rhinoceros, with more reports of MTBC-associated disease in black rhinoceros than in white rhinoceros. The degree of MTBC exposure in susceptible wildlife depends on their level of interaction, either directly with other infected individuals or indirectly through MTBC contaminated environments, which is dependent on the presence and abundance of infected reservoir hosts and the amount of MTBC shed in their excreta. Captive African rhinoceros have shown evidence of MTBC shedding, and although infection levels are low in free-ranging rhinoceros, there is a risk for intraspecies transmission. Free-ranging rhinoceros in bTB endemic areas may be exposed to MTBC from other infected host species, such as the African buffalo (Syncerus caffer) and greater kudu (Tragelaphus strepsiceros), through shared environmental niches, and resource co-utilization. This review describes current knowledge and information gaps regarding the epidemiology of TB in African rhinoceros.
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Affiliation(s)
- Rebecca A Dwyer
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Carmel Witte
- Disease Investigations, San Diego Zoo Global, San Diego, CA, United States
| | - Peter Buss
- Veterinary Wildlife Services, Kruger National Park, Skukuza, South Africa
| | - Wynand J Goosen
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Michele Miller
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
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