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Barandiaran S, Marfil MJ, La Sala LF, Tammone A, Condori WE, Winter M, Abate S, Rosas AC, Ponce L, Carpinetti B, Serena MS, Lozano Calderón LC, Zumárraga MJ. Tuberculosis in Wild Pigs from Argentina. ECOHEALTH 2024; 21:71-82. [PMID: 38727761 DOI: 10.1007/s10393-024-01681-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 03/19/2024] [Indexed: 05/26/2024]
Abstract
Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex (MTC) and non-tuberculous Mycobacteria (NTM), may infect wild and domestic mammals, including humans. Although cattle are the main hosts and spreaders of M. bovis, many wildlife hosts play an important role worldwide. In Argentina, wild boar and domestic pigs are considered important links in mammalian tuberculosis (mTB) transmission. The aim of this work was to investigate the presence of M. bovis in wild pigs from different regions of Argentina, to characterize isolates of M. bovis obtained, and to compare those with other previously found in vertebrate hosts. A total of 311 samples from wild pigs were obtained, and bacteriological culture, molecular identification and genotyping were performed, obtaining 63 isolates (34 MTC and 29 NTM). Twelve M. bovis spoligotypes were detected. Our findings suggest that wild pigs have a prominent role as reservoirs of mTB in Argentina, based on an estimated prevalence of 11.2 ± 1.8% (95% CI 8.0-14.8) for MTC and the frequency distribution of spoligotypes shared by cattle (75%), domestic pigs (58%) and wildlife (50%). Argentina has a typical scenario where cattle and pigs are farm-raised extensively, sharing the environment with wildlife, creating conditions for effective transmission of mTB in the wildlife-livestock-human interface.
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Affiliation(s)
- Soledad Barandiaran
- Instituto de Investigaciones en Producción Animal (INPA), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Av. Chorroarín 280, 1427, Buenos Aires, Argentina
| | - María Jimena Marfil
- Instituto de Investigaciones en Producción Animal (INPA), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Av. Chorroarín 280, 1427, Buenos Aires, Argentina.
| | | | - Agostina Tammone
- Centro de Investigación Veterinaria Tandil (CIVETAN) (UNCPBA-CICPBA-CONICET), Tandil, Argentina
| | - Walter Ezequiel Condori
- Centro de Investigación Veterinaria Tandil (CIVETAN) (UNCPBA-CICPBA-CONICET), Tandil, Argentina
| | - Marina Winter
- Sede Viedma del Centro de Investigaciones y Transferencia de Río Negro, Universidad Nacional de Río Negro, Viedma, Argentina
| | - Sergio Abate
- Sede Viedma del Centro de Investigaciones y Transferencia de Río Negro, Universidad Nacional de Río Negro, Viedma, Argentina
| | - Ana Carolina Rosas
- Programa Restauración de ambientes y especies amenazadas, Fundación Rewilding Argentina, Buenos Aires, Argentina
| | - Loredana Ponce
- Instituto de Investigaciones en Producción Animal (INPA), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Av. Chorroarín 280, 1427, Buenos Aires, Argentina
| | - Bruno Carpinetti
- Gestión Ambiental/Ecología, Instituto de Ciencias Sociales y Administración, Universidad Nacional Arturo Jauretche, Buenos Aires, Argentina
| | - María Soledad Serena
- Laboratorio de Virología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Martín José Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Buenos Aires, Argentina
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2
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Kapalamula TF, Chizimu JY, Akapelwa ML, Barnes DA, Toyting J, Bwalya P, Basikolo L, Squarre D, Chambaro HM, Gordon SV, Thapa J, Nakajima C, Suzuki Y. Insight into the genetic diversity of Mycobacterium bovis isolated from cattle in Malawi. Res Vet Sci 2023; 164:105030. [PMID: 37788548 DOI: 10.1016/j.rvsc.2023.105030] [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: 06/10/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
We describe the genetic diversity and phylogenetic relationships of Mycobacterium bovis, isolated from cattle in Malawi. Deletion analysis, spoligotyping, and MIRU-VNTR typing were used to genotype the isolates. Combined with a larger dataset from neighboring countries, the overall M. bovis diversity in Southern Africa was contextualized. From the southern and northern regions of Malawi, 24 isolates were confirmed as M. bovis. We pooled data for the central region (60 isolates) from our recent publication to conceptualize the genetic and phylogenetic relationships of M. bovis in Malawi. European 1 was the dominant M. bovis clonal complex, with 10 unique spoligotype patterns, and SB0131 was ubiquitous. High genetic diversity, a low clustering rate, and many singletons, coupled with a low mutation transmission index, infer a low level of recent transmission, and suggest an endemic status of bovine tuberculosis (bTB) in Malawi. M. bovis isolates from Zambia, Mozambique, and South Africa were genetically related to Malawian isolates, whereas Tanzanian isolates were distantly related. The diversity and phylogenetic analysis suggest earlier introductions and maintenance of M. bovis by constant reinfection from reservoir animals. These findings are fundamental to understanding the source and route of infection in order to establish alternative management strategies for bTB.
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Affiliation(s)
- Thoko Flav Kapalamula
- Faculty of Veterinary Medicine, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi; Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Joseph Yamweka Chizimu
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - Mwangala Lonah Akapelwa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - David Atomanyi Barnes
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Jirachaya Toyting
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Precious Bwalya
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; University Teaching Hospital, Ministry of Health, Lusaka, Zambia
| | - Linda Basikolo
- Department of Animal Health and Livestock Development, Ministry of Agriculture, Lilongwe, Malawi
| | - David Squarre
- Department of National Parks and Wildlife, Wildlife Veterinary Unit, Chilanga, Zambia
| | - Herman M Chambaro
- Division of Molecular Pathobiology, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; Department of National Parks and Wildlife, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan; Hokkaido University Institute for Vaccine Research and Development, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Hokkaido, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan; Hokkaido University Institute for Vaccine Research and Development, Sapporo, Hokkaido, Japan.
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3
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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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O'Brien DJ, Thacker TC, Salvador LCM, Duffiney AG, Robbe-Austerman S, Camacho MS, Lombard JE, Palmer MV. The devil you know and the devil you don't: current status and challenges of bovine tuberculosis eradication in the United States. Ir Vet J 2023; 76:16. [PMID: 37491296 PMCID: PMC10369704 DOI: 10.1186/s13620-023-00247-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 07/10/2023] [Indexed: 07/27/2023] Open
Abstract
Having entered into its second century, the eradication program for bovine tuberculosis (bTB, caused by Mycobacterium bovis) in the United States of America occupies a position both enviable and daunting. Excepting four counties in Michigan comprising only 6109 km2 (0.06% of US land area) classified as Modified Accredited, as of April 2022 the entire country was considered Accredited Free of bTB by the US Department of Agriculture for cattle and bison. On the surface, the now well-described circumstances of endemic bTB in Michigan, where white-tailed deer (Odocoileus virginianus) serve as a free-ranging wildlife maintenance host, may appear to be the principal remaining barrier to national eradication. However, the situation there is unique in the U.S., and far-removed from the broader issues of bTB control in the remainder of the country. In Michigan, extensive surveillance for bTB in deer over the last quarter century, and regulatory measures to maximize the harvest of publicly-owned wildlife, have been implemented and sustained. Prevalence of bTB in deer has remained at a low level, although not sufficiently low to eliminate cattle herd infections. Public attitudes towards bTB, cattle and deer, and their relative importance, have been more influential in the management of the disease than any limitations of biological science. However, profound changes in the demographics and social attitudes of Michigan's human population are underway, changes which are likely to force a critical reevaluation of the bTB control strategies thus far considered integral. In the rest of the U.S. where bTB is not self-sustaining in wildlife, changes in the scale of cattle production, coupled with both technical and non-technical issues have created their own substantial challenges. It is against this diverse backdrop that the evolution of whole genome sequencing of M. bovis has revolutionized understanding of the history and ecology of bTB in Michigan, resolved previously undiscernible epidemiological puzzles, provided insights into zoonotic transmission, and unified eradication efforts across species and agencies. We describe the current status of bTB eradication in the U.S., how circumstances and management have changed, what has been learned, and what remains more elusive than ever.
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Affiliation(s)
- Daniel J O'Brien
- Michigan Department of Natural Resources, Wildlife Disease Laboratory, 4125 Beaumont Road, Room 250, Lansing, MI, 48910-8106, USA.
- Retired. Current address: Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, MI, 48824, USA.
| | - Tyler C Thacker
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, 1920 Dayton Avenue, Ames, IA, 50010, USA
| | - Liliana C M Salvador
- Institute of Bioinformatics, Center for the Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- School of Animal & Comparative Biomedical Sciences, University of Arizona, Shantz Building, 1177 E 4th St, Tucson, AZ, 85719, USA
| | - Anthony G Duffiney
- United States Department of Agriculture, Animal and Plant Health Inspection Service-Wildlife Services, 2803 Jolly Road, Suite 100, Okemos, MI, 48864, USA
| | - Suelee Robbe-Austerman
- United States Department of Agriculture, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, 1920 Dayton Avenue, Ames, IA, 50010, USA
| | - Mark S Camacho
- United States Department of Agriculture, Cattle Health Center, Animal and Plant Health Inspection Service-Veterinary Services, Centennial Campus, Raleigh, NC, 27606, USA
| | - Jason E Lombard
- United States Department of Agriculture, Field Epidemiologic Investigation, Animal and Plant Health Inspection Service, Veterinary Services, 2150 Centre Avenue, Bldg. B, Fort Collins, CO, 80526, USA
| | - Mitchell V Palmer
- United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, 1920 Dayton Avenue, Ames, IA, 50010, USA
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Features of Mycobacterium bovis Complete Genomes Belonging to 5 Different Lineages. Microorganisms 2023; 11:microorganisms11010177. [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] [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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Edao BM, Ameni G, Berg S, Tekle M, Whatmore AM, Wood JLN, van Tonder AJ, Ashford RT. Whole genome sequencing of Ethiopian Brucella abortus isolates expands the known diversity of an early branching sub-Saharan African lineage. Front Microbiol 2023; 14:1128966. [PMID: 37213520 PMCID: PMC10192883 DOI: 10.3389/fmicb.2023.1128966] [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: 12/21/2022] [Accepted: 02/23/2023] [Indexed: 05/23/2023] Open
Abstract
Brucellosis remains one of the most significant zoonotic diseases globally, responsible for both considerable human morbidity and economic losses due to its impacts on livestock productivity. Despite this, there remain significant evidence gaps in many low- and middle-income countries, including those of sub-Saharan Africa. Here we report the first molecular characterisation of Brucella sp. from Ethiopia. Fifteen Brucella sp. isolates from an outbreak in cattle from a herd in central Ethiopia were identified as Brucella abortus, using bacterial culture and molecular methods. Sequencing of the Ethiopian B. abortus isolates allowed their phylogenetic comparison with 411 B. abortus strains of diverse geographical origins, using whole genome single nucleotide polymorphisms (wgSNP). The Ethiopian isolates belonged to an early-branching lineage (Lineage A) previously only represented by data from two strains, both of sub-Saharan African origin (Kenya and Mozambique). A second B. abortus lineage (Lineage B), also comprised solely of strains originating from sub-Saharan Africa, was identified. The majority of strains belonged to one of two lineages of strains originating from a much broader geographical range. Further analyses based on multi-locus sequence typing (MLST) and multi-locus variable-number tandem repeat analysis (MLVA) expanded the number of B. abortus strains available for comparison with the Ethiopian isolates and were consistent with the findings from wgSNP analysis. MLST profiles of the Ethiopian isolates expanded the sequence type (ST) diversity of the early branching lineage of B. abortus, equivalent to wgSNP Lineage A. A more diverse cluster of STs, equivalent to wgSNP Lineage B, was comprised solely of strains originating from sub-Saharan Africa. Similarly, analysis of B. abortus MLVA profiles (n = 1891) confirmed that the Ethiopian isolates formed a unique cluster, similar to only two existing strains, and distinct from the majority of other strains of sub-Saharan African origin. These findings expand the known diversity of an under-represented lineage of B. abortus and suggest a potential evolutionary origin for the species in East Africa. In addition to providing information concerning Brucella species extant within Ethiopia this work serves as the basis for further studies on the global population structure and evolutionary history of a major zoonotic pathogen.
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Affiliation(s)
- Bedaso Mammo Edao
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- College of Veterinary Medicine, Addis Ababa University, Bishoftu, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Stefan Berg
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muluken Tekle
- College of Veterinary Medicine, Addis Ababa University, Bishoftu, Ethiopia
| | - Adrian M. Whatmore
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - James L. N. Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andries J. van Tonder
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Roland T. Ashford
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- *Correspondence: Roland T. Ashford,
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Legall N, Salvador LCM. Selective sweep sites and SNP dense regions differentiate Mycobacterium bovis isolates across scales. Front Microbiol 2022; 13:787856. [PMID: 36160199 PMCID: PMC9489834 DOI: 10.3389/fmicb.2022.787856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 08/08/2022] [Indexed: 11/28/2022] Open
Abstract
Mycobacterium bovis, a bacterial zoonotic pathogen responsible for the economically and agriculturally important livestock disease bovine tuberculosis (bTB), infects a broad mammalian host range worldwide. This characteristic has led to bidirectional transmission events between livestock and wildlife species as well as the formation of wildlife reservoirs, impacting the success of bTB control measures. Next Generation Sequencing (NGS) has transformed our ability to understand disease transmission events by tracking variant sites, however the genomic signatures related to host adaptation following spillover, alongside the role of other genomic factors in the M. bovis transmission process are understudied problems. We analyzed publicly available M. bovis datasets collected from 700 hosts across three countries with bTB endemic regions (United Kingdom, United States, and New Zealand) to investigate if genomic regions with high SNP density and/or selective sweep sites play a role in Mycobacterium bovis adaptation to new environments (e.g., at the host-species, geographical, and/or sub-population levels). A simulated M. bovis alignment was created to generate null distributions for defining genomic regions with high SNP counts and regions with selective sweeps evidence. Random Forest (RF) models were used to investigate evolutionary metrics within the genomic regions of interest to determine which genomic processes were the best for classifying M. bovis across ecological scales. We identified in the M. bovis genomes 14 and 132 high SNP density and selective sweep regions, respectively. Selective sweep regions were ranked as the most important in classifying M. bovis across the different scales in all RF models. SNP dense regions were found to have high importance in the badger and cattle specific RF models in classifying badger derived isolates from livestock derived ones. Additionally, the genes detected within these genomic regions harbor various pathogenic functions such as virulence and immunogenicity, membrane structure, host survival, and mycobactin production. The results of this study demonstrate how comparative genomics alongside machine learning approaches are useful to investigate further the nature of M. bovis host-pathogen interactions.
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Affiliation(s)
- Noah Legall
- Interdisciplinary Disease Ecology Across Scales Research Traineeship Program, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Liliana C. M. Salvador
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Acquah SEK, Asare P, Danso EK, Tetteh P, Tetteh AY, Boateng D, Osei-Wusu S, Afum T, Ayamdooh YI, Akugre EA, Samad OA, Quaye L, Obiri-Danso K, Kock R, Asante-Poku A, Yeboah-Manu D. Molecular epidemiology of bovine tuberculosis in Northern Ghana identifies several uncharacterized bovine spoligotypes and suggests possible zoonotic transmission. PLoS Negl Trop Dis 2022; 16:e0010649. [PMID: 35951638 PMCID: PMC9398027 DOI: 10.1371/journal.pntd.0010649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/23/2022] [Accepted: 07/09/2022] [Indexed: 11/18/2022] Open
Abstract
Objective
We conducted an abattoir-based cross-sectional study in the five administrative regions of Northern Ghana to determine the distribution of bovine tuberculosis (BTB) among slaughtered carcasses and identify the possibility of zoonotic transmission.
Methods
Direct smear microscopy was done on 438 tuberculosis-like lesions from selected cattle organs and cultured on Lowenstein-Jensen media. Acid-fast bacilli (AFB) isolates were confirmed as members of the Mycobacterium tuberculosis complex (MTBC) by PCR amplification of IS6110 and rpoß. Characterization and assignment into MTBC lineage and sub-lineage were done by spoligotyping, with the aid of the SITVIT2, miruvntrplus and mbovis.org databases. Spoligotype data was compared to that of clinical M. bovis isolates from the same regions to identify similarities.
Results
A total of 319/438 (72.8%) lesion homogenates were smear positive out of which, 84.6% (270/319) had microscopic grade of at least 1+ for AFB. Two hundred and sixty-five samples (265/438; 60.5%) were culture positive, of which 212 (80.0%) were MTBC. Approximately 16.7% (34/203) of the isolates with correctly defined spoligotypes were negative for IS6110 PCR but were confirmed by rpoß. Spoligotyping characterized 203 isolates as M. bovis (198, 97.5%), M. caprae (3, 1.5%), M. tuberculosis (Mtbss) lineage (L) 4 Cameroon sub-lineage, (1, 0.5%), and M. africanum (Maf) L6 (1, 0.5%). A total of 53 unique spoligotype patterns were identified across the five administrative regions (33 and 28 were identified as orphan respectively by the SITVIT2 and mbovis.org databases), with the most dominant spoligotype being SIT1037/ SB0944 (77/203, 37.93%). Analysis of the bovine and human M. bovis isolates showed 75% (3/4) human M. bovis isolates sharing the same spoligotype pattern with the bovine isolates.
Conclusion
Our study identified that approximately 29% of M. bovis strains causing BTB in Northern Ghana are caused by uncharacterized spoligotypes. Our findings suggest possible zoonotic transmission and highlight the need for BTB disease control in Northern Ghana.
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Affiliation(s)
- Samuel Ekuban Kobina Acquah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- Department of Clinical Microbiology, School of Medicine and Health Sciences, University for Development Studies, Tamale, Ghana
- Department of Theoretical and Applied Biology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- * E-mail: (PA); (DYM)
| | - Emelia Konadu Danso
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Phillip Tetteh
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Amanda Yaa Tetteh
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Daniel Boateng
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Theophilus Afum
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | | | - Eric Agongo Akugre
- Veterinary Services Directorate, Ministry of Food and Agriculture, Bolgatanga, Ghana
| | - Omar Abdul Samad
- Veterinary Services Directorate, Ministry of Food and Agriculture, Wa, Ghana
| | - Lawrence Quaye
- Department of Biomedical Laboratory Sciences, School of Allied Health Sciences, University for Development Studies, Tamale, Ghana
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard Kock
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- * E-mail: (PA); (DYM)
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Spatial distribution of Mycobacterium bovis spoligotypes in cattle from the state of Minas Gerais, Brazil. Trop Anim Health Prod 2022; 54:238. [PMID: 35867201 DOI: 10.1007/s11250-022-03243-2] [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: 08/10/2021] [Accepted: 07/13/2022] [Indexed: 10/17/2022]
Abstract
Genotyping methods have led to a better understanding of the epidemiology of Mycobacterium bovis (M. bovis) infection, and its transmission dynamics, as well as the possible phylogenetic relationships between Mycobacterium strains, thus making bovine tuberculosis control programs more efficient. The goal of this study was to characterize the main spoligotypes of M. bovis isolated from cattle in the State of Minas Gerais, Brazil. It was carried out in 28 municipalities of "Triângulo Mineiro" and "Alto Paranaíba" regions of the state. Viscera samples were obtained from 58 bovines positive for tuberculosis according to comparative cervical tests, and from another 100 bovines with lesions suggestive of tuberculosis, which were donated by the National Agricultural Laboratory of Pedro Leopoldo, Minas Gerais. Microbiological isolation was performed in Stonebrink medium, and molecular identification of mycobacteria was performed by PCR. Genotyping was performed using the spoligotyping method at the Agrobiotechnology and Molecular Biology Institute of National Agricultural Technology Institute-National Scientific and Technical Research Council, Buenos Aires, Argentina. Among the 158 viscera samples, we obtained 40 (25%) isolates of M. bovis, and detected 11 spoligotype patterns, with a predominance of SB1142 (37.5%), SB0121 (25.0%), and SB1145 (10.0%). Other standards, SB0295, SB1050, SB0881, SB1144, SB1802, SB0140, SB0120, and SB0849, varied from 2.5 to 7.5%, heterogeneously distributed among the municipalities. The presence of spoligotypes shared with other Brazilian states and different countries indicates their possible exchange through epidemiological relationships, such as the transit of live animals and/or genetic similarity between strains that share a common ancestor.
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10
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Charles C, Conde C, Biet F, Boschiroli ML, Michelet L. IS6110 Copy Number in Multi-Host Mycobacterium bovis Strains Circulating in Bovine Tuberculosis Endemic French Regions. Front Microbiol 2022; 13:891902. [PMID: 35814675 PMCID: PMC9260277 DOI: 10.3389/fmicb.2022.891902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
IS6110 is an insertion sequence found in the Mycobacterium tuberculosis complex, to which Mycobacterium bovis belongs, which can play a role in genome plasticity and in bacterial evolution. In this study, the abundance and location of IS6110 on M. bovis genomic data of French animal field strains were studied. A first analysis was performed on a panel of 81 strains that reflect the national M. bovis population’s genetic diversity. The results show that more than one-third of them are IS6110 multicopy and that 10% have IS6110 in a high copy number (more than 6 copies). Multicopy strains are those circulating in the regions where prevalence was above the national average. Further study of 93 such strains, with an IS6110 copy number of 10-12, showed stability of IS6110 copy number and genome location over time and between host species. The correlation between M. bovis multicopy strains and high bovine tuberculosis (bTB) prevalence leads us to consider whether their epidemiological success could be partly due to genetic changes originated by IS6110 transposition.
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Affiliation(s)
- Ciriac Charles
- ANSES, Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, Paris, France
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Cyril Conde
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Maria Laura Boschiroli
- ANSES, Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, Paris, France
| | - Lorraine Michelet
- ANSES, Animal Health Laboratory, National Reference Laboratory for Tuberculosis, Paris-Est University, Paris, France
- *Correspondence: Lorraine Michelet,
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11
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Duault H, Michelet L, Boschiroli ML, Durand B, Canini L. A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France. Vet Res 2022; 53:28. [PMID: 35366933 PMCID: PMC8976416 DOI: 10.1186/s13567-022-01044-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/06/2022] [Indexed: 12/16/2022] Open
Abstract
In two “départements” in the South-West of France, bovine tuberculosis (bTB) outbreaks due to Mycobacterium bovis spoligotype SB0821 have been identified in cattle since 2002 and in wildlife since 2013. Using whole genome sequencing, the aim of our study was to clarify badger contribution to bTB transmission in this area. We used a Bayesian evolutionary model, to infer phylogenetic trees and migration rates between two pathogen populations defined by their host-species. In order to account for sampling bias, sub-population structure was inferred using the marginal approximation of the structured coalescent (Mascot) implemented in BEAST2. We included 167 SB0821 strains (21 isolated from badgers and 146 from cattle) and identified 171 single nucleotide polymorphisms. We selected a HKY model and a strict molecular clock. We estimated a badger-to-cattle transition rate (median: 2.2 transitions/lineage/year) 52 times superior to the cattle-to-badger rate (median: 0.042 transitions/lineage/year). Using the maximum clade credibility tree, we identified that over 75% of the lineages from 1989 to 2000 were present in badgers. In addition, we calculated a median of 64 transition events from badger-to-cattle (IQR: 10–91) and a median of zero transition event from cattle-to-badger (IQR: 0–3). Our model enabled us to infer inter-species transitions but not intra-population transmission as in previous epidemiological studies, where relevant units were farms and badger social groups. Thus, while we could not confirm badgers as possible intermediaries in farm-to-farm transmission, badger-to-cattle transition rate was high and we confirmed long-term presence of M.bovis in the badger population in the South-West of France.
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12
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Couvin D, Cervera-Marzal I, David A, Reynaud Y, Rastogi N. SITVITBovis—a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis. Database (Oxford) 2022; 2022:6506437. [PMID: 35028657 PMCID: PMC8962452 DOI: 10.1093/database/baab081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022]
Abstract
Limited data are available for bovine tuberculosis and the infections it can cause in humans and other mammals. We therefore constructed a publicly accessible SITVITBovis database that incorporates genotyping and epidemiological data on Mycobacterium bovis. It also includes limited data on Mycobacterium caprae (previously synonymous with the name M. bovis subsp. Caprae) that can infect both animals and humans. SITVITBovis incorporates data on 25,741 isolates corresponding to 60 countries of origin (75 countries of isolation). It reports a total of 1000 spoligotype patterns: 537 spoligotype international types (SITs, containing 25 278 clinical isolates) and 463 orphan patterns, allowing a wide overview of the geographic distribution of various phylogenetical sublineages (BOV_1, BOV_2, BOV_3 and BOV_4-CAPRAE). The SIT identifiers of the SITVITBovis were compared to the SB numbers of the Mbovis.org database to facilitate crosscheck among databases. Note that SITVITBovis also contains limited information on mycobacterial interspersed repetitive units-variable number of tandem repeats when available. Significant differences were observed when comparing age/gender of human isolates as well as various hosts. The database includes information on the regions where a strain was isolated as well as hosts involved, making it possible to see geographic trends. SITVITBovis is publicly accessible at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis. Finally, a future second version is currently in progress to allow query of associated whole-genome sequencing data. Database URLhttp://www.pasteur-guadeloupe.fr:8081/SITVIT_Bovis
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Affiliation(s)
- David Couvin
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Iñaki Cervera-Marzal
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Audrey David
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Yann Reynaud
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory–TB and Mycobacteria Unit, Institut Pasteur de Guadeloupe , Abymes 97183, Guadeloupe, France
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13
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Zwyer M, Çavusoglu C, Ghielmetti G, Pacciarini ML, Scaltriti E, Van Soolingen D, Dötsch A, Reinhard M, Gagneux S, Brites D. A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics. OPEN RESEARCH EUROPE 2021; 1:100. [PMID: 37645186 PMCID: PMC10445919 DOI: 10.12688/openreseurope.14029.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 08/31/2023]
Abstract
Background: The bacteria that compose the Mycobacterium tuberculosis complex (MTBC) cause tuberculosis (TB) in humans and in different animals, including livestock. Much progress has been made in understanding the population structure of the human-adapted members of the MTBC by combining phylogenetics with genomics. Accompanying the discovery of new genetic diversity, a body of operational nomenclature has evolved to assist comparative and molecular epidemiological studies of human TB. By contrast, for the livestock-associated MTBC members, Mycobacterium bovis, M. caprae and M. orygis, there has been a lack of comprehensive nomenclature to accommodate new genetic diversity uncovered by emerging phylogenomic studies. We propose to fill this gap by putting forward a new nomenclature covering the main phylogenetic groups within M. bovis, M. caprae and M. orygis. Methods: We gathered a total of 8,736 whole-genome sequences (WGS) from public sources and 39 newly sequenced strains, and selected a subset of 829 WGS, representative of the worldwide diversity of M. bovis, M. caprae and M. orygis. We used phylogenetics and genetic diversity patterns inferred from WGS to define groups. Results: We propose to divide M. bovis, M. caprae and M. orygis in three main phylogenetic lineages, which we named La1, La2 and La3, respectively. Within La1, we identified several monophyletic groups, which we propose to classify into eight sublineages (La1.1-La1.8). These sublineages differed in geographic distribution, with some being geographically restricted and others globally widespread, suggesting different expansion abilities. To ease molecular characterization of these MTBC groups by the community, we provide phylogenetically informed, single nucleotide polymorphisms that can be used as barcodes for genotyping. These markers were implemented in KvarQ and TB-Profiler, which are platform-independent, open-source tools. Conclusions: Our results contribute to an improved classification of the genetic diversity within the livestock-associated MTBC, which will benefit future molecular epidemiological and evolutionary studies.
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Affiliation(s)
- Michaela Zwyer
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cengiz Çavusoglu
- Department of Medical Microbiology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Parma, Italy
| | - Dick Van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands Antilles
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Anna Dötsch
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Miriam Reinhard
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Sebastien Gagneux
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Daniela Brites
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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14
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van Tonder AJ, Thornton MJ, Conlan AJK, Jolley KA, Goolding L, Mitchell AP, Dale J, Palkopoulou E, Hogarth PJ, Hewinson RG, Wood JLN, Parkhill J. Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial. PLoS Pathog 2021; 17:e1010075. [PMID: 34843579 PMCID: PMC8659364 DOI: 10.1371/journal.ppat.1010075] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/09/2021] [Accepted: 10/29/2021] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium bovis (M. bovis) is a causative agent of bovine tuberculosis, a significant source of morbidity and mortality in the global cattle industry. The Randomised Badger Culling Trial was a field experiment carried out between 1998 and 2005 in the South West of England. As part of this trial, M. bovis isolates were collected from contemporaneous and overlapping populations of badgers and cattle within ten defined trial areas. We combined whole genome sequences from 1,442 isolates with location and cattle movement data, identifying transmission clusters and inferred rates and routes of transmission of M. bovis. Most trial areas contained a single transmission cluster that had been established shortly before sampling, often contemporaneous with the expansion of bovine tuberculosis in the 1980s. The estimated rate of transmission from badger to cattle was approximately two times higher than from cattle to badger, and the rate of within-species transmission considerably exceeded these for both species. We identified long distance transmission events linked to cattle movement, recurrence of herd breakdown by infection within the same transmission clusters and superspreader events driven by cattle but not badgers. Overall, our data suggests that the transmission clusters in different parts of South West England that are still evident today were established by long-distance seeding events involving cattle movement, not by recrudescence from a long-established wildlife reservoir. Clusters are maintained primarily by within-species transmission, with less frequent spill-over both from badger to cattle and cattle to badger.
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Affiliation(s)
- Andries J. van Tonder
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mark J. Thornton
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew J. K. Conlan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Keith A. Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Lee Goolding
- Animal and Plant Health Agency, New Haw, United Kingdom
| | | | - James Dale
- Animal and Plant Health Agency, New Haw, United Kingdom
| | | | | | | | - James L. N. Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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15
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Abstract
Animal tuberculosis (TB) is an emergent disease caused by Mycobacterium bovis, one of the animal-adapted ecotypes of the Mycobacterium tuberculosis complex (MTC). In this work, whole-genome comparative analyses of 70 M. bovis were performed to gain insights into the pan-genome architecture. The comparison across M. bovis predicted genome composition enabled clustering into the core- and accessory-genome components, with 2736 CDS for the former, while the accessory moiety included 3897 CDS, of which 2656 are restricted to one/two genomes only. These analyses predicted an open pan-genome architecture, with an average of 32 CDS added by each genome and show the diversification of discrete M. bovis subpopulations supported by both core- and accessory-genome components. The functional annotation of the pan-genome classified each CDS into one or several COG (Clusters of Orthologous Groups) categories, revealing ‘transcription’ (total average CDSs, n=258), ‘lipid metabolism and transport’ (n=242), ‘energy production and conversion’ (n=214) and ‘unknown function’ (n=876) as the most represented. The closer analysis of polymorphisms in virulence-related genes in a restrict group of M. bovis from a multi-host system enabled the identification of clade-monomorphic non-synonymous SNPs, illustrating clade-specific virulence landscapes and correlating with disease severity. This first comparative pan-genome study of a diverse collection of M. bovis encompassing all clonal complexes indicates a high percentage of accessory genes and denotes an open, dynamic non-conservative pan-genome structure, with high evolutionary potential, defying the canons of MTC biology. Furthermore, it shows that M. bovis can shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion, adaptation and persistence.
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Affiliation(s)
- Ana C Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.,Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.,Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
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16
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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: 0] [Impact Index Per Article: 0] [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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17
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Reis AC, Cunha MV. Genome-wide estimation of recombination, mutation and positive selection enlightens diversification drivers of Mycobacterium bovis. Sci Rep 2021; 11:18789. [PMID: 34552144 PMCID: PMC8458382 DOI: 10.1038/s41598-021-98226-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/27/2021] [Indexed: 02/08/2023] Open
Abstract
Genome sequencing has reinvigorated the infectious disease research field, shedding light on disease epidemiology, pathogenesis, host-pathogen interactions and also evolutionary processes exerted upon pathogens. Mycobacterium tuberculosis complex (MTBC), enclosing M. bovis as one of its animal-adapted members causing tuberculosis (TB) in terrestrial mammals, is a paradigmatic model of bacterial evolution. As other MTBC members, M. bovis is postulated as a strictly clonal, slowly evolving pathogen, with apparently no signs of recombination or horizontal gene transfer. In this work, we applied comparative genomics to a whole genome sequence (WGS) dataset composed by 70 M. bovis from different lineages (European and African) to gain insights into the evolutionary forces that shape genetic diversification in M. bovis. Three distinct approaches were used to estimate signs of recombination. Globally, a small number of recombinant events was identified and confirmed by two independent methods with solid support. Still, recombination reveals a weaker effect on M. bovis diversity compared with mutation (overall r/m = 0.037). The differential r/m average values obtained across the clonal complexes of M. bovis in our dataset are consistent with the general notion that the extent of recombination may vary widely among lineages assigned to the same taxonomical species. Based on this work, recombination in M. bovis cannot be excluded and should thus be a topic of further effort in future comparative genomics studies for which WGS of large datasets from different epidemiological scenarios across the world is crucial. A smaller M. bovis dataset (n = 42) from a multi-host TB endemic scenario was then subjected to additional analyses, with the identification of more than 1,800 sites wherein at least one strain showed a single nucleotide polymorphism (SNP). The majority (87.1%) was located in coding regions, with the global ratio of non-synonymous upon synonymous alterations (dN/dS) exceeding 1.5, suggesting that positive selection is an important evolutionary force exerted upon M. bovis. A higher percentage of SNPs was detected in genes enriched into "lipid metabolism", "cell wall and cell processes" and "intermediary metabolism and respiration" functional categories, revealing their underlying importance in M. bovis biology and evolution. A closer look on genes prone to horizontal gene transfer in the MTBC ancestor and included in the 3R (DNA repair, replication and recombination) system revealed a global average negative value for Taijima's D neutrality test, suggesting that past selective sweeps and population expansion after a recent bottleneck remain as major evolutionary drivers of the obligatory pathogen M. bovis in its struggle with the host.
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Affiliation(s)
- Ana C Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Room 2.4.11, 1749-016, Lisbon, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, C2, Room 2.4.11, 1749-016, Lisbon, Portugal.
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal.
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18
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Perea C, Ciaravino G, Stuber T, Thacker TC, Robbe-Austerman S, Allepuz A, de Val BP. Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain. Microorganisms 2021; 9:microorganisms9081629. [PMID: 34442709 PMCID: PMC8401651 DOI: 10.3390/microorganisms9081629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (≤12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting.
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Affiliation(s)
- Claudia Perea
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
- Correspondence:
| | - Giovanna Ciaravino
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (G.C.); (A.A.)
| | - Tod Stuber
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Tyler C. Thacker
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, Ames, IA 50010, USA; (T.S.); (T.C.T.); (S.R.-A.)
| | - Alberto Allepuz
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (G.C.); (A.A.)
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), 08197 Bellaterra, Spain;
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - Bernat Pérez de Val
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), 08197 Bellaterra, Spain;
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
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Remot A, Carreras F, Coupé A, Doz-Deblauwe É, Boschiroli ML, Browne JA, Marquant Q, Descamps D, Archer F, Aseffa A, Germon P, Gordon SV, Winter N. Mycobacterial Infection of Precision-Cut Lung Slices Reveals Type 1 Interferon Pathway Is Locally Induced by Mycobacterium bovis but Not M. tuberculosis in a Cattle Breed. Front Vet Sci 2021; 8:696525. [PMID: 34307535 PMCID: PMC8299756 DOI: 10.3389/fvets.2021.696525] [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: 04/16/2021] [Accepted: 06/02/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis exacts a terrible toll on human and animal health. While Mycobacterium tuberculosis (Mtb) is restricted to humans, Mycobacterium bovis (Mb) is present in a large range of mammalian hosts. In cattle, bovine TB (bTB) is a noticeable disease responsible for important economic losses in developed countries and underestimated zoonosis in the developing world. Early interactions that take place between mycobacteria and the lung tissue early after aerosol infection govern the outcome of the disease. In cattle, these early steps remain poorly characterized. The precision-cut lung slice (PCLS) model preserves the structure and cell diversity of the lung. We developed this model in cattle in order to study the early lung response to mycobacterial infection. In situ imaging of PCLS infected with fluorescent Mb revealed bacilli in the alveolar compartment, in adjacent or inside alveolar macrophages, and in close contact with pneumocytes. We analyzed the global transcriptional lung inflammation signature following infection of PCLS with Mb and Mtb in two French beef breeds: Blonde d'Aquitaine and Charolaise. Whereas, lungs from the Blonde d'Aquitaine produced high levels of mediators of neutrophil and monocyte recruitment in response to infection, such signatures were not observed in the Charolaise in our study. In the Blonde d'Aquitaine lung, whereas the inflammatory response was highly induced by two Mb strains, AF2122 isolated from cattle in the UK and Mb3601 circulating in France, the response against two Mtb strains, H37Rv, the reference laboratory strain, and BTB1558, isolated from zebu in Ethiopia, was very low. Strikingly, the type I interferon pathway was only induced by Mb but not Mtb strains, indicating that this pathway may be involved in mycobacterial virulence and host tropism. Hence, the PCLS model in cattle is a valuable tool to deepen our understanding of early interactions between lung host cells and mycobacteria. It revealed striking differences between cattle breeds and mycobacterial strains. This model could help in deciphering biomarkers of resistance vs. susceptibility to bTB in cattle as such information is still critically needed for bovine genetic selection programs and would greatly help the global effort to eradicate bTB.
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Affiliation(s)
- Aude Remot
- INRAE, Université de Tours, Nouzilly, France
| | | | | | | | - Maria L Boschiroli
- Paris-Est University, National Reference Laboratory for Tuberculosis, Animal Health Laboratory, Anses, Maisons-Alfort, France
| | - John A Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | | | - Fabienne Archer
- INRAE, UMR754, Viral Infections and Comparative Pathology, IVPC, Univ Lyon, Université Claude Bernard Lyon 1, EPHE, Lyon, France
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Stephen V Gordon
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Dublin, Ireland
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20
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Rodrigues RDA, Ribeiro Araújo F, Rivera Dávila AM, Etges RN, Parkhill J, van Tonder AJ. Genomic and temporal analyses of Mycobacterium bovis in southern Brazil. Microb Genom 2021; 7. [PMID: 34016251 PMCID: PMC8209730 DOI: 10.1099/mgen.0.000569] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium bovis is a causal agent of bovine tuberculosis (bTB), one of the most important diseases currently facing the cattle industry worldwide. Tracing the source of M. bovis infections of livestock is an important tool for understanding the epidemiology of bTB and defining control/eradication strategies. In this study, whole genome sequencing (WGS) of 74 M. bovis isolates sourced from naturally infected cattle in the State of Rio Grande do Sul (RS), southern Brazil, was used to evaluate the population structure of M. bovis in the region, identify potential transmission events and date the introduction of clonal complex (CC) European 2 (Eu2). In silico spoligotyping identified 11 distinct patterns including four new profiles and two CCs, European 1 (Eu1) and Eu2. The analyses revealed a high level of genetic diversity in the majority of herds and identified putative transmission clusters that suggested that within- and between-herd transmission is occurring in RS. In addition, a comparison with other published M. bovis isolates from Argentina, Brazil, Paraguay and Uruguay demonstrated some evidence for a possible cross-border transmission of CC Eu1 into RS from Uruguay or Argentina. An estimated date for the introduction of CC Eu2 into RS in the middle of the 19th century correlated with the historical introduction of cattle into RS to improve existing local breeds. These findings contribute to the understanding of the population structure of M. bovis in southern Brazil and highlight the potential of WGS in surveillance and helping to identify bTB transmission.
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Affiliation(s)
- Rudielle de Arruda Rodrigues
- Postgraduate Program in Veterinary Science, Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | | | - Alberto Martín Rivera Dávila
- Computational and Systems Biology Laboratory, Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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21
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Almaw G, Mekonnen GA, Mihret A, Aseffa A, Taye H, Conlan AJK, Gumi B, Zewude A, Aliy A, Tamiru M, Olani A, Lakew M, Sombo M, Gebre S, Diguimbaye C, Hilty M, Fané A, Müller B, Hewinson RG, Ellis RJ, Nunez-Garcia J, Palkopoulou E, Abebe T, Ameni G, Parkhill J, Wood JLN, Berg S, van Tonder AJ. Population structure and transmission of Mycobacterium bovis in Ethiopia. Microb Genom 2021; 7:000539. [PMID: 33945462 PMCID: PMC8209724 DOI: 10.1099/mgen.0.000539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/02/2021] [Indexed: 12/03/2022] Open
Abstract
Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis, which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.
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Affiliation(s)
- Gizat Almaw
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Getnet Abie Mekonnen
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Hawult Taye
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abde Aliy
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Mekdes Tamiru
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Abebe Olani
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Matios Lakew
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Melaku Sombo
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Solomon Gebre
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Colette Diguimbaye
- Institut de Recherches en Elevage pour le Développement & Clinique Médico-Chirurgicale PROVIDENCE, N'Djaména, Chad
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Adama Fané
- Laboratoire Centrale Vétérinaire, Bamako, Mali
| | | | | | | | | | | | - Tamrat Abebe
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, UAE
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - James L. N. Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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22
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Kapalamula TF, Chizimu J, Belotindos L, Akapelwa M, Shrestha D, Nyenje ME, Munyeme M, Hang'ombe BM, Mkakosya RS, Gordon SV, Nakajima C, Suzuki Y. Molecular epidemiology of Mycobacterium bovis in central parts of Malawi. Transbound Emerg Dis 2021; 69:1577-1588. [PMID: 33900039 DOI: 10.1111/tbed.14127] [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: 01/06/2021] [Revised: 03/13/2021] [Accepted: 04/21/2021] [Indexed: 11/28/2022]
Abstract
Bovine tuberculosis (bTB) is a neglected disease that affects cattle and humans. The burden of bTB is higher in developing countries as compared to industrialized countries. The reasons behind this discrepancy include the fact that bTB control measures, such as testing and slaughter of infected cattle and pasteurization of milk, are not usually practised in developing countries largely because of their high cost. To improve our understanding of bTB in developing countries, molecular typing studies are essential, in particular in terms of transmission dynamics, infection sources and knowledge of circulating strains of the principal causative agent, Mycobacterium bovis. In this study, we applied a suite of molecular typing techniques encompassing deletion analysis, spoligotyping and MIRU-VNTR to isolates recovered from samples collected during the routine post-mortem of cattle at the cold storage abattoir in Lilongwe, Malawi. Out of 63 isolates, 51 (81%) belonged to the European 1. M. bovis clonal complex. Spoligotyping identified 8 profiles, with SB0131 being the predominant type (56% of isolates). Spoligotypes SB0273 and SB0425 were identified in 14% and 13%, respectively, of the isolates. MIRU-VNTR showed a high discriminatory power of 0.959 and differentiated the 8 spoligotypes to 31 genotypes. The high diversity of M. bovis within the study area suggests the infection has been circulating in the area for a considerable period of time, likely facilitated by the lack of effective control measures. We also observed genetic similarities between isolates from Malawi (this study) to isolates described in previous studies in Zambia and Mozambique, suggesting transmission links in this region. The information provided by this study provides much needed evidence for the formulation of improved bTB control strategies.
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Affiliation(s)
- Thoko Flav Kapalamula
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Joseph Chizimu
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Lawrence Belotindos
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mwangala Akapelwa
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Dipti Shrestha
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mirriam Ethel Nyenje
- Community Health Sciences Unit, National Tuberculosis Reference Laboratory, Lilongwe, Malawi
| | - Musso Munyeme
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | - Bernard Mudenda Hang'ombe
- School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, University of Zambia, Lusaka, Zambia
| | | | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Chie Nakajima
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
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23
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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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24
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Long-term molecular surveillance provides clues on a cattle origin for Mycobacterium bovis in Portugal. Sci Rep 2020; 10:20856. [PMID: 33257726 PMCID: PMC7705689 DOI: 10.1038/s41598-020-77713-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/17/2020] [Indexed: 11/08/2022] Open
Abstract
Animal tuberculosis (TB), caused by Mycobacterium bovis, is maintained in Portugal in a multi-host system, with cattle, red deer and wild boar, playing a central role. However, the ecological processes driving transmission are not understood. The main aim of this study was thus to contribute to the reconstruction of the spatiotemporal history of animal TB and to refine knowledge on M. bovis population structure in order to inform novel intervention strategies. A collection of 948 M. bovis isolates obtained during long-term surveillance (2002–2016, 15 years) of cattle (n = 384), red deer (n = 303) and wild boar (n = 261), from the main TB hotspot areas, was characterized by spoligotyping and 8 to 12-loci MIRU-VNTR. Spoligotyping identified 64 profiles and MIRU-VNTR distinguished 2 to 36 subtypes within each spoligotype, enabling differentiation of mixed or clonal populations. Common genotypic profiles within and among livestock and wildlife in the same spatiotemporal context highlighted epidemiological links across hosts and regions, as for example the SB0119-M205 genotype shared by cattle in Beja district or SB0121-M34 shared by the three hosts in Castelo Branco and Beja districts. These genomic data, together with metadata, were integrated in a Bayesian inference framework, identifying five ancestral M. bovis populations. The phylogeographic segregation of M. bovis in specific areas of Portugal where the disease persists locally is postulated. Concurrently, robust statistics indicates an association of the most probable ancient population with cattle and Beja, providing a clue on the origin of animal TB epidemics. This relationship was further confirmed through a multinomial probability model that assessed the influence of host species on spatiotemporal clustering. Two significant clusters were identified, one that persisted between 2004 and 2010, in Beja district, with Barrancos county at the centre, overlapping the central TB core area of the Iberian Peninsula, and highlighting a significant higher risk associated to cattle. The second cluster was predominant in the 2012–2016 period, holding the county Rosmaninhal at the centre, in Castelo Branco district, for which wild boar contributed the most in relative risk. These results provide novel quantitative insights beyond empirical perceptions, that may inform adaptive TB control choices in different regions.
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25
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Mekonnen GA, Mihret A, Tamiru M, Hailu E, Olani A, Aliy A, Sombo M, Lakew M, Gumi B, Ameni G, Wood JLN, Berg S. Genotype Diversity of Mycobacterium bovis and Pathology of Bovine Tuberculosis in Selected Emerging Dairy Regions of Ethiopia. Front Vet Sci 2020; 7:553940. [PMID: 33195524 PMCID: PMC7554335 DOI: 10.3389/fvets.2020.553940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/14/2020] [Indexed: 11/26/2022] Open
Abstract
Bovine tuberculosis (bTB) is endemic in Ethiopia with higher prevalence in cattle, particularly in the central parts. Spread of Mycobacterium bovis (M. bovis) to wider regions is inevitable in uncontrolled conditions. This study was conducted to explore the pathology, characterize M. bovis strains, and describe genotypic diversity to demonstrate possible epidemiological links in emerging dairy areas of Ethiopia, namely, Mekelle and Gondar. Twenty-seven bTB positive cattle identified by the Single Intradermal Comparative Cervical Tuberculin (SICCT) test were subjected to post-mortem inspection to determine lesion distribution and pathological score. Samples from tissues with visible tuberculous or suspected non-visible lesions were processed and cultured following a standard protocol. Isolates identified as M. bovis by Region of Difference (RD)-based Polymerase Chain Reaction (PCR) were also spoligotyped to determine their spoligotype patterns. Post-mortem inspection of visceral organs indicated bTB suggestive lesions in 41% of the animals, with 25% being in the lungs. Lymph nodes from 77% of the animals had lesions. Fifty-five isolates identified from 24 of the slaughtered animals were confirmed as M. bovis. No other mycobacterial species were isolated. Spoligotyping classified strains from 21 of these animals into seven spoligotype patterns: SB0133, SB0134, SB1176, SB2233, SB2290, SB2467, and SB2520. More than one spoligotype were identified from five of these animals, and none of the last four spoligotypes had been reported in Ethiopia before. SB0134 was the most predominant type (47%) followed by SB0133 (25.5%). SB0133, SB2290, SB2467, and SB1176 are spoligotypes lacking spacers 3–7, characteristics of M. bovis strains of the African 2 (Af2) clonal complex, while SB0134, SB2233, and SB2520 do not belong to any of the established clonal complexes and likely to have a different evolutionary history. Despite a small sample size, the present study showed strain diversity with multiple genotypes identified in a single herd and even within a single animal, and the genotypes showed no sign of geographical localization, which could be a consequence of significant movement of bTB diseased cattle around the country, spreading the disease. Therefore, any future control programme of bTB in Ethiopia needs to address the risks of cattle movement.
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Affiliation(s)
- Getnet Abie Mekonnen
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia.,Animal Health and Zoonotic Research Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Bacterial and Viral Diseases Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Mekdes Tamiru
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Elena Hailu
- Bacterial and Viral Diseases Research Directorate, Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abebe Olani
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Abde Aliy
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Melaku Sombo
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Matios Lakew
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Balako Gumi
- Animal Health and Zoonotic Research Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Animal Health and Zoonotic Research Unit, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.,Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - James L N Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Berg
- Animal and Plant Health Agency, Weybridge, United Kingdom
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26
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Lekko YM, Ooi PT, Omar S, Mazlan M, Ramanoon SZ, Jasni S, Jesse FFA, Che-Amat A. Mycobacterium tuberculosis complex in wildlife: Review of current applications of antemortem and postmortem diagnosis. Vet World 2020; 13:1822-1836. [PMID: 33132593 PMCID: PMC7566238 DOI: 10.14202/vetworld.2020.1822-1836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a chronic inflammatory and zoonotic disease caused by Mycobacterium tuberculosis complex (MTBC) members, which affects various domestic animals, wildlife, and humans. Some wild animals serve as reservoir hosts in the transmission and epidemiology of the disease. Therefore, the monitoring and surveillance of both wild and domestic hosts are critical for prevention and control strategies. For TB diagnosis, the single intradermal tuberculin test or the single comparative intradermal tuberculin test, and the gamma-interferon test, which is regarded as an ancillary test, are used. Postmortem examination can identify granulomatous lesions compatible with a diagnosis of TB. In contrast, smears of the lesions can be stained for acid-fast bacilli, and samples of the affected organs can be subjected to histopathological analyses. Culture is the gold standard test for isolating mycobacterial bacilli because it has high sensitivity and specificity compared with other methods. Serology for antibody detection allows the testing of many samples simply, rapidly, and inexpensively, and the protocol can be standardized in different laboratories. Molecular biological analyses are also applicable to trace the epidemiology of the disease. In conclusion, reviewing the various techniques used in MTBC diagnosis can help establish guidelines for researchers when choosing a particular diagnostic method depending on the situation at hand, be it disease outbreaks in wildlife or for epidemiological studies. This is because a good understanding of various diagnostic techniques will aid in monitoring and managing emerging pandemic threats of infectious diseases from wildlife and also preventing the potential spread of zoonotic TB to livestock and humans. This review aimed to provide up-to-date information on different techniques used for diagnosing TB at the interfaces between wildlife, livestock, and humans.
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Affiliation(s)
- Yusuf Madaki Lekko
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Maiduguri, 1069 PMB, Maiduguri, Borno State, Nigeria
| | - Peck Toung Ooi
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sharina Omar
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mazlina Mazlan
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Zubaidah Ramanoon
- Department of Farm and Exotic Animal Medicine and Surgery, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Sabri Jasni
- Department of Paraclinical, Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, Malaysia
| | - Faez Firdaus Abdullah Jesse
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Azlan Che-Amat
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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27
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Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-Pereira TT, Camargo NCS, de Souza Filho AF, Ikuta CY, Neto JSF, Setubal JC, Heinemann MB, Guimaraes AMS. Global Distribution and Evolution of Mycobacterium bovis Lineages. Front Microbiol 2020; 11:843. [PMID: 32477295 PMCID: PMC7232559 DOI: 10.3389/fmicb.2020.00843] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3, and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis (South Siberian infected skeletons at ∼2,000 years before present) and indicates that extant M. bovis originated between 715 and 3,556 years BP, with later emergence in the New World and Oceania, likely influenced by trades among countries.
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Affiliation(s)
- Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Salvatore L Patané
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Cellular Cycle, Butantan Institute, São Paulo, Brazil
| | - Aureliano Coelho Proença Guedes
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Robson F de Souza
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana T Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila C Soler Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Antônio F de Souza Filho
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Soares Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sa Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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28
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Guimaraes AMS, Zimpel CK. Mycobacterium bovis: From Genotyping to Genome Sequencing. Microorganisms 2020; 8:E667. [PMID: 32375210 PMCID: PMC7285088 DOI: 10.3390/microorganisms8050667] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis. Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the disease remains a challenge for the veterinary and public health sectors, especially in developing countries and in high-income nations with wildlife reservoirs. Current bTB control programs are mostly based on test-and-slaughter, movement restrictions, and post-mortem inspection measures. In certain settings, contact tracing and surveillance has benefited from M. bovis genotyping techniques. More recently, whole-genome sequencing (WGS) has become the preferential technique to inform outbreak response through contact tracing and source identification for many infectious diseases. As the cost per genome decreases, the application of WGS to bTB control programs is inevitable moving forward. However, there are technical challenges in data analyses and interpretation that hinder the implementation of M. bovis WGS as a molecular epidemiology tool. Therefore, the aim of this review is to describe M. bovis genotyping techniques and discuss current standards and challenges of the use of M. bovis WGS for transmission investigation, surveillance, and global lineages distribution. We compiled a series of associated research gaps to be explored with the ultimate goal of implementing M. bovis WGS in a standardized manner in bTB control programs.
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Affiliation(s)
- Ana M. S. Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
| | - Cristina K. Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, São Paulo 01246-904, Brazil
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29
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Branger M, Loux V, Cochard T, Boschiroli ML, Biet F, Michelet L. The complete genome sequence of Mycobacterium bovis Mb3601, a SB0120 spoligotype strain representative of a new clonal group. INFECTION GENETICS AND EVOLUTION 2020; 82:104309. [PMID: 32240800 DOI: 10.1016/j.meegid.2020.104309] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 11/29/2022]
Abstract
Mycobacterium bovis strain Mb3601 was isolated from the lymph node of an infected bovine in a bovine tuberculosis highly enzoonotic area of Burgundy, France. It was selected to obtain a complete genome for a new clonal complex, mainly constituted by SB0120-spoligotype strains that we propose to name "European 3". It was recently described as "clonal group I" based on whole-genome SNP analysis of 87 French strains. Here we describe the 4,365,068 bp complete genome obtained by the combination of PacBio and Illumina technologies. This genome of 65.64% G + C content includes 4024 predicted protein-coding genes, 52 tRNA, 3 rRNA and 11 copies of IS6110.
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Affiliation(s)
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
| | | | - Maria Laura Boschiroli
- Paris-Est University, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Animal Health Laboratory, National reference Laboratory for Tuberculosis, 94701 Maisons-Alfort cedex, France
| | - Franck Biet
- INRAE, Université de Tours, ISP, 37380 Nouzilly, France.
| | - Lorraine Michelet
- Paris-Est University, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Animal Health Laboratory, National reference Laboratory for Tuberculosis, 94701 Maisons-Alfort cedex, France.
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30
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Arnot LF, Michel A. Challenges for controlling bovine tuberculosis in South Africa. ACTA ACUST UNITED AC 2020; 87:e1-e8. [PMID: 32129639 PMCID: PMC7059242 DOI: 10.4102/ojvr.v87i1.1690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/04/2019] [Accepted: 10/18/2019] [Indexed: 01/19/2023]
Abstract
All effects taken together, bovine tuberculosis (bTB) has a long-term detrimental effect on bovine herds and many wildlife species in South Africa. The disease is not only found in domestic cattle but also in African buffaloes and has to date been diagnosed in 21 wildlife species, including several rare and endangered species, thus having a potentially serious effect on conservation and biodiversity. In cattle, bTB is mostly characterised by sporadic outbreaks, but bovine herds chronically infected with the clinical disease are not uncommon. Presently, the recognised bTB control strategy in South Africa is based on 'test and slaughter', using the intradermal tuberculin test, followed by the slaughter of animals that have tested positive. Affected herds are placed under veterinary quarantine with movement restrictions until the outbreak is eradicated; this can take several years or last indefinitely if the outbreak cannot be eradicated. The same measures apply to infected buffalo populations, often with no prospect of ever being eradicated. This strategy is neither practical nor viable in the context of a communal farming system and becomes unethical when dealing with valuable wildlife reservoir hosts. Transmission of bTB between wildlife and cattle has been demonstrated and emphasises the need for an effective, affordable and culturally acceptable control strategy to curb the spread of bTB in South Africa. In countries with similar challenges, vaccination has been used and found to be promising for treating wild and domestic reservoir species and may hence be of value as a complementary tool for bTB control in South Africa.
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Affiliation(s)
- Luke F Arnot
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa; and, Bovine Tuberculosis and Brucellosis Research Programme, Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria.
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31
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Phylogenomic Perspective on a Unique Mycobacterium bovis Clade Dominating Bovine Tuberculosis Infections among Cattle and Buffalos in Northern Brazil. Sci Rep 2020; 10:1747. [PMID: 32019968 PMCID: PMC7000724 DOI: 10.1038/s41598-020-58398-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/13/2020] [Indexed: 11/08/2022] Open
Abstract
Lack of routine surveillance in countries endemic for bovine tuberculosis (TB) and limited laboratory support contributes to the inability to differentiate the Mycobacterium tuberculosis Complex species, leading to an underestimated burden of the disease. Here, Whole-Genome Sequencing of Mycobacterium bovis isolated from tissues with TB-like lesions obtained from cattle and buffalos at Marajó Island, Brazil, demonstrates that recent transmission of M. bovis is ongoing at distinct sites. Moreover, the M. bovis epidemiology in this setting is herein found to be dominated by an endemic and unique clade composed of strains evolved from a common ancestor that are now genetically differentiated from other M. bovis clades. Additionally, envisioning a rapid strain differentiation and tracing across multiple settings, 28 globally validated strain-specific SNPs were identified, three of which considered as robust markers for the M. bovis Marajó strain. In conclusion, this study contributes with data regarding the identification of a novel M. bovis phylogenetic clade responsible for ongoing transmission events in both cattle and buffalo species in Brazil, provides a framework to investigate the dissemination of this highly prevalent strain and, holds the potential to inform TB control strategies that may help to prevent the spread of bovine and zoonotic TB.
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32
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Loiseau C, Menardo F, Aseffa A, Hailu E, Gumi B, Ameni G, Berg S, Rigouts L, Robbe-Austerman S, Zinsstag J, Gagneux S, Brites D. An African origin for Mycobacterium bovis. EVOLUTION MEDICINE AND PUBLIC HEALTH 2020; 2020:49-59. [PMID: 32211193 PMCID: PMC7081938 DOI: 10.1093/emph/eoaa005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 12/20/2022]
Abstract
Background and objectives Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. Methodology We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. Results Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. Conclusions and implications Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. Lay summary During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.
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Affiliation(s)
- Chloé Loiseau
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Elena Hailu
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Balako Gumi
- Department of Animal Science and Range Management, Bule Hora University, Bule Hora Town, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Stefan Berg
- Bacteriology Department, Animal & Plant Health Agency (APHA), Weybridge, Surrey, UK
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Collection of Mycobacterial Cultures (BCCM/ITM), Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Suelee Robbe-Austerman
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA
| | - Jakob Zinsstag
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Daniela Brites
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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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: 2.4] [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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Sales ÉB, de Alencar AP, Hodon MA, Soares Filho PM, de Souza-Filho AF, Lage AP, Heinemann MB, Fonseca Júnior AA. Identification of clonal complexes of Mycobacterium bovis in Brazil. Arch Microbiol 2019; 201:1047-1051. [PMID: 31111186 DOI: 10.1007/s00203-019-01674-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/04/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022]
Abstract
Bovine tuberculosis is a disease that is widely distributed around the world. Its causative agent, Mycobacterium bovis, has characteristics of a microorganism with clonal multiplication in populations with no evidence of genetic exchange between strains, and, consequently, a group of strains can be identified as descending from a common ancestor. The aim of this study was to investigate the clonal complexes of M. bovis isolated from samples of lesions suggestive of bovine tuberculosis collected from slaughterhouses in various states of Brazil between 2006 and 2012. Ninety samples were analyzed, and it was found that 14.4% belonged to the clonal complex European1 and 81.1% to the clonal complex European2, while 4.65% were not identified as any of the four known complexes.
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Affiliation(s)
- Érica Bravo Sales
- Laboratório Nacional Agropecuário de Minas Gerais, Pedro Leopoldo, Minas Gerais, Brazil
| | | | - Mikael Arrais Hodon
- Laboratório Nacional Agropecuário de Minas Gerais, Pedro Leopoldo, Minas Gerais, Brazil
| | | | - Antonio Francisco de Souza-Filho
- Laboratório de Zoonoses Bacterianas, Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Andrey Pereira Lage
- Laboratório de Bacteriologia Aplicada, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcos Bryan Heinemann
- Laboratório de Zoonoses Bacterianas, Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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35
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Otchere ID, van Tonder AJ, Asante-Poku A, Sánchez-Busó L, Coscollá M, Osei-Wusu S, Asare P, Aboagye SY, Ekuban SA, Yahayah AI, Forson A, Baddoo A, Laryea C, Parkhill J, Harris SR, Gagneux S, Yeboah-Manu D. Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana. PLoS One 2019; 14:e0209395. [PMID: 30830912 PMCID: PMC6398925 DOI: 10.1371/journal.pone.0209395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
Background Bovine tuberculosis (bTB) caused by Mycobacterium bovis is a re-emerging problem in both livestock and humans. The association of some M. bovis strains with hyper-virulence, MDR-TB and disseminated disease makes it imperative to understand the biology of the pathogen. Methods Mycobacterium bovis (15) among 1755 M. tuberculosis complex (MTBC) isolated between 2012 and 2014 were characterized and analyzed for associated patient demography and other risk factors. Five of the M. bovis isolates were whole-genome sequenced and comparatively analyzed against a global collection of published M. bovis genomes. Results Mycobacterium bovis was isolated from 3/560(0.5%) females and 12/1195(1.0%) males with pulmonary TB. The average age of M. bovis infected cases was 46.8 years (7-72years). TB patients from the Northern region of Ghana (1.9%;4/212) had a higher rate of infection with M. bovis (OR = 2.7,p = 0.0968) compared to those from the Greater Accra region (0.7%;11/1543). Among TB patients with available HIV status, the odds of isolating M. bovis from HIV patients (2/119) was 3.3 higher relative to non-HIV patients (4/774). Direct contact with livestock or their unpasteurized products was significantly associated with bTB (p<0.0001, OR = 124.4,95% CI = 30.1–508.3). Two (13.3%) of the M. bovis isolates were INH resistant due to the S315T mutation in katG whereas one (6.7%) was RIF resistant with Q432P and I1491S mutations in rpoB. M. bovis from Ghana resolved as mono-phyletic branch among mostly M. bovis from Africa irrespective of the host and were closest to the root of the global M. bovis phylogeny. M. bovis-specific amino acid mutations were detected among MTBC core genes such as mce1A, mmpL1, pks6, phoT, pstB, glgP and Rv2955c. Additional mutations P6T in chaA, G187E in mgtC, T35A in Rv1979c, S387A in narK1, L400F in fas and A563T in eccA1 were restricted to the 5 clinical M. bovis from Ghana. Conclusion Our data indicate potential zoonotic transmission of bTB in Ghana and hence calls for intensified public education on bTB, especially among risk groups.
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Affiliation(s)
- Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | | | - Mireia Coscollá
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Samuel Yaw Aboagye
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | | | | | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Akosua Baddoo
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Clement Laryea
- Public Health Department, 37 Military Hospital, Accra, Ghana
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Simon R. Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
- * E-mail:
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36
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Gormley E, Corner LAL. Wild Animal Tuberculosis: Stakeholder Value Systems and Management of Disease. Front Vet Sci 2018; 5:327. [PMID: 30622951 PMCID: PMC6308382 DOI: 10.3389/fvets.2018.00327] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/10/2018] [Indexed: 11/13/2022] Open
Abstract
When human health is put at risk from the transmission of animal diseases, the options for intervention often require input from stakeholders whose differing values systems contribute to decisions on disease management. Animal tuberculosis (TB), caused principally by Mycobacterium bovis is an archetypical zoonotic pathogen in that it can be transmitted from animals to humans and vice versa. Although elimination of zoonotic transmission of TB to humans is frequently promoted as the raison d'être for TB management in livestock, in many countries the control strategies are more likely based on minimizing the impact of sustained infection on the agricultural industry. Where wild animals are implicated in the epidemiology of the disease, the options for control and eradication can require involvement of additional stakeholder groups. Conflict can arise when different monetary and/or societal values are assigned to the affected animals. This may impose practical and ethical dilemmas for decision makers where one or more species of wild animal is seen by some stakeholders to have a greater value than the affected livestock. Here we assess the role of stakeholder values in influencing TB eradication strategies in a number of countries including Ireland, the UK, the USA, Spain, France, Australia, New Zealand and South Africa. What it reveals is that the level of stakeholder involvement increases with the complexity of the epidemiology, and that similar groups of stakeholders may agree to a set of control and eradication measures in one region only to disagree with applying the same measures in another. The level of consensus depends on the considerations of the reservoir status of the infected host, the societal values assigned to each species, the type of interventions proposed, ethical issues raised by culling of sentient wild animals, and the economic cost benefit effectiveness of dealing with the problem in one or more species over a long time frame. While there is a societal benefit from controlling TB, the means to achieve this requires identification and long-term engagement with all key stakeholders in order to reach agreement on ethical frameworks that prioritize and justify control options, particularly where culling of wild animals is concerned.
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Affiliation(s)
- Eamonn Gormley
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Leigh A L Corner
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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37
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Allen AR, Skuce RA, Byrne AW. Bovine Tuberculosis in Britain and Ireland - A Perfect Storm? the Confluence of Potential Ecological and Epidemiological Impediments to Controlling a Chronic Infectious Disease. Front Vet Sci 2018; 5:109. [PMID: 29951489 PMCID: PMC6008655 DOI: 10.3389/fvets.2018.00109] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/03/2018] [Indexed: 12/17/2022] Open
Abstract
Successful eradication schemes for bovine tuberculosis (bTB) have been implemented in a number of European and other countries over the last 50 years. However, the islands of Britain and Ireland remain a significant aberration to this trend, with the recent exception of Scotland. Why have eradication schemes failed within these countries, while apparently similar programs have been successful elsewhere? While significant socio-economic and political factors have been discussed elsewhere as key determinants of disease eradication, here we review some of the potential ecological and epidemiological constraints that are present in these islands relative to other parts of Europe. We argue that the convergence of these potential factors may interact additively to diminish the potential of the present control programs to achieve eradication. Issues identified include heterogeneity of diagnostic testing approaches, the presence of an abundant wildlife reservoir of infection and the challenge of sustainably managing this risk effectively; the nature, size, density and network structure of cattle farming; potential effects of Mycobacterium bovis strain heterogeneity on disease transmission dynamics; possible impacts of concurrent endemic infections on the disclosure of truly infected animals; climatological differences and change coupled with environmental contamination. We further argue that control and eradication of this complex disease may benefit from an ecosystem level approach to management. We hope that this perspective can stimulate a new conversation about the many factors potentially impacting bTB eradication schemes in Britain and Ireland and possibly stimulate new research in the areas identified.
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Affiliation(s)
| | - R. A. Skuce
- Veterinary Science Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
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Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea. PLoS Negl Trop Dis 2018; 12:e0006406. [PMID: 29664901 PMCID: PMC5922621 DOI: 10.1371/journal.pntd.0006406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 04/27/2018] [Accepted: 03/23/2018] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely. Spoligotyping, VNTR profiling, and whole genome sequencing (WGS) of M. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea’s largest slaughterhouse in the capital Asmara, were conducted.The 14 M. bovis isolates were classified into three different spoligotype patterns (SB0120, SB0134 and SB0948) and six VNTR profiles. WGS results matched those of the conventional genotyping methods and further discriminated the six VNTR profiles into 14 strains. Furthermore, phylogenetic analysis of the M. bovis isolates suggests two independent introductions of BTB into Eritrea possibly evolving from a common ancestral strain in Europe.This molecular study revealed the most important strains of M. bovis in Eritrea and their (dis)similarities with the strains generally present in East Africa and Europe, as well as potential routes of introduction of M. bovis. Though the sample size is small, the current study provides important information as well as platform for future in-depth molecular studies on isolates from both the dairy and the traditional livestock sectors in Eritrea and the region. This study provides information onthe origin of some of the M. bovis strains in Eritrea, its genetic diversity, evolution and patterns of spread between dairy herds. Such information is essential in the development and implementation of future BTB control strategy for Eritrea. The livestock sector plays a major role in poverty and hunger reduction in the vast majority of Africa, as a source of food, cash income, manure, draught power, transportation, savings, insurance and social status. However, for livestock to play this vital role, the impact of diseases of economic and zoonotic importance need to be reduced. Bovine tuberculosis, mainly caused by Mycobacterium bovis, is such an infectious disease. Slaughterhouse (gross pathology) surveillance, followed by bacterial culture and genotyping, are options to identify the disease-causing agents, their distribution, and enabling trace back of the sources of infections, in order to prevent their re-introduction and spread. Unfortunately, genotyping is by far not generally introduced in the continent. In the present study, tissues with tuberculosis-like lesions were collected from the Asmara municipal slaughterhouse, the largest slaughterhouse in Eritrea, and bacterial culture, classical Mycobacterium tuberculosis complex typing (Spoligotyping and VNTR profiling), as well as whole genome sequencing (WGS) were used to gain insight into the spatial and temporal distribution, genetic diversity and evolution of M. bovis strains circulating in Eritrean dairy cattle. The results revealed (dis)similarities of the Eritrean M. bovis strains with the strains generally present in Africa and Europe, potential routes of introduction to Eritrea and genetic diversity of the M. bovis strains. Future in-depth molecular studies including more samples from dairy cattle as well as cattle and goats from the traditional livestock sector are recommended.
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Genetic diversity and potential routes of transmission of Mycobacterium bovis in Mozambique. PLoS Negl Trop Dis 2018; 12:e0006147. [PMID: 29346413 PMCID: PMC5772998 DOI: 10.1371/journal.pntd.0006147] [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: 08/21/2017] [Accepted: 12/01/2017] [Indexed: 11/18/2022] Open
Abstract
Bovine tuberculosis is a zoonotic disease with largely unknown impact in Africa, with risk factors such as HIV and direct contact with animals or consumption of Mycobacterium bovis infected animal products. In order to understand and quantify this risk and design intervention strategies, good epidemiological studies are needed. Such studies can include molecular typing of M. bovis isolates. The aim of this study was to apply these tools to provide novel information concerning the distribution of bovine tuberculosis in cattle in Mozambique and thereby provide relevant information to guide policy development and strategies to contain the disease in livestock, and reduce the risk associated with transmission to humans. A collection of 178 M. bovis isolates was obtained from cattle in Mozambique. Using spoligotyping and regions of difference analysis, we classified the isolates into clonal complexes, thus reporting the first characterisation of M. bovis strains in this region. Data from MIRU-VNTR typing was used to compare isolates from a number of African countries, revealing a deeply geographically structured diversity of M. bovis. Eastern Africa appears to show high diversity, suggesting deep evolution in that region. The diversity of M. bovis in Africa does not seem to be a function of recent importation of animals, but is probably maintained within each particular region by constant reinfection from reservoir animals. Understanding the transmission routes of M. bovis in Mozambique and elsewhere is essential in order to focus public health and veterinary resources to contain bovine tuberculosis. Bovine tuberculosis is a rather neglected zoonotic disease caused by Mycobacterium bovis that is of global concern owing to the persistence of the bacillus in reservoirs that can spread bovine tuberculosis between animals and humans. Africa remains understudied regarding this pathogen, and should be an area of concern given that in many regions the consumption of raw milk or meat from infected animals persists and the presence of HIV infection renders the population more susceptible. In order to control the disease, we need to understand M. bovis epidemiology, which includes the sources of infection. The important conclusion drawn from the work presented here is that there is a strong association between M. bovis genetic characteristics and geography. This implies that the diversity of M. bovis isolates in Mozambique does not seem to be caused by recent introductions to the territory, but is probably maintained within reservoirs in each particular region.
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Lasserre M, Fresia P, Greif G, Iraola G, Castro-Ramos M, Juambeltz A, Nuñez Á, Naya H, Robello C, Berná L. Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates. BMC Genomics 2018; 19:2. [PMID: 29291727 PMCID: PMC5748942 DOI: 10.1186/s12864-017-4249-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background Bovine tuberculosis (bTB) poses serious risks to animal welfare and economy, as well as to public health as a zoonosis. Its etiological agent, Mycobacterium bovis, belongs to the Mycobacterium tuberculosis complex (MTBC), a group of genetically monomorphic organisms featured by a remarkably high overall nucleotide identity (99.9%). Indeed, this characteristic is of major concern for correct typing and determination of strain-specific traits based on sequence diversity. Due to its historical economic dependence on cattle production, Uruguay is deeply affected by the prevailing incidence of Mycobacterium bovis. With the world’s highest number of cattle per human, and its intensive cattle production, Uruguay represents a particularly suited setting to evaluate genomic variability among isolates, and the diversity traits associated to this pathogen. Results We compared 186 genomes from MTBC strains isolated worldwide, and found a highly structured population in M. bovis. The analysis of 23 new M. bovis genomes, belonging to strains isolated in Uruguay evidenced three groups present in the country. Despite presenting an expected highly conserved genomic structure and sequence, these strains segregate into a clustered manner within the worldwide phylogeny. Analysis of the non-pe/ppe differential areas against a reference genome defined four main sources of variability, namely: regions of difference (RD), variable genes, duplications and novel genes. RDs and variant analysis segregated the strains into clusters that are concordant with their spoligotype identities. Due to its high homoplasy rate, spoligotyping failed to reflect the true genomic diversity among worldwide representative strains, however, it remains a good indicator for closely related populations. Conclusions This study introduces a comprehensive population structure analysis of worldwide M. bovis isolates. The incorporation and analysis of 23 novel Uruguayan M. bovis genomes, sheds light onto the genomic diversity of this pathogen, evidencing the existence of greater genetic variability among strains than previously contemplated. Electronic supplementary material The online version of this article (10.1186/s12864-017-4249-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moira Lasserre
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Fresia
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gonzalo Greif
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gregorio Iraola
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Miguel Castro-Ramos
- Departamento de Bacteriología, División de Laboratorios Veterinarios (DI.LA.VE.) "Miguel C. Rubino", Montevideo, Uruguay
| | - Arturo Juambeltz
- Departamento de Bacteriología, División de Laboratorios Veterinarios (DI.LA.VE.) "Miguel C. Rubino", Montevideo, Uruguay
| | - Álvaro Nuñez
- Departamento de Bacteriología, División de Laboratorios Veterinarios (DI.LA.VE.) "Miguel C. Rubino", Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Carlos Robello
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay. .,Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
| | - Luisa Berná
- Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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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: 1.1] [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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42
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Zimpel CK, Brandão PE, de Souza Filho AF, de Souza RF, Ikuta CY, Ferreira Neto JS, Camargo NCS, Heinemann MB, Guimarães AMS. Complete Genome Sequencing of Mycobacterium bovis SP38 and Comparative Genomics of Mycobacterium bovis and M. tuberculosis Strains. Front Microbiol 2017; 8:2389. [PMID: 29259589 PMCID: PMC5723337 DOI: 10.3389/fmicb.2017.02389] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium bovis causes bovine tuberculosis and is the main organism responsible for zoonotic tuberculosis in humans. We performed the sequencing, assembly and annotation of a Brazilian strain of M. bovis named SP38, and performed comparative genomics of M. bovis genomes deposited in GenBank. M. bovis SP38 has a traditional tuberculous mycobacterium genome of 4,347,648 bp, with 65.5% GC, and 4,216 genes. The majority of CDSs (2,805, 69.3%) have predictive function, while 1,206 (30.07%) are hypothetical. For comparative analysis, 31 M. bovis, 32 M. bovis BCG, and 23 Mycobacterium tuberculosis genomes available in GenBank were selected. M. bovis RDs (regions of difference) and Clonal Complexes (CC) were identified in silico. Genome dynamics of bacterial groups were analyzed by gene orthology and polymorphic sites identification. M. bovis polymorphic sites were used to construct a phylogenetic tree. Our RD analyses resulted in the exclusion of three genomes, mistakenly annotated as virulent M. bovis. M. bovis SP38 along with strain 35 represent the first report of CC European 2 in Brazil, whereas two other M. bovis strains failed to be classified within current CC. Results of M. bovis orthologous genes analysis suggest a process of genome remodeling through genomic decay and gene duplication. Quantification, pairwise comparisons and distribution analyses of polymorphic sites demonstrate greater genetic variability of M. tuberculosis when compared to M. bovis and M. bovis BCG (p ≤ 0.05), indicating that currently defined M. tuberculosis lineages are more genetically diverse than M. bovis CC and animal-adapted MTC (M. tuberculosis Complex) species. As expected, polymorphic sites annotation shows that M. bovis BCG are subjected to different evolutionary pressures when compared to virulent mycobacteria. Lastly, M. bovis phylogeny indicates that polymorphic sites may be used as markers of M. bovis lineages in association with CC. Our findings highlight the need to better understand host-pathogen co-evolution in genetically homogeneous and/or diverse host populations, considering the fact that M. bovis has a broader host range when compared to M. tuberculosis. Also, the identification of M. bovis genomes not classified within CC indicates that the diversity of M. bovis lineages may be larger than previously thought or that current classification should be reviewed.
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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
| | - Paulo E Brandão
- 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
| | - Robson F de Souza
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical 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
| | - Naila C Soler Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - 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 M S Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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43
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Egbe NF, Muwonge A, Ndip L, Kelly RF, Sander M, Tanya V, Ngwa VN, Handel IG, Novak A, Ngandalo R, Mazeri S, Morgan KL, Asuquo A, de C Bronsvoort BM. Molecular epidemiology of Mycobacterium bovis in Cameroon. Sci Rep 2017; 7:4652. [PMID: 28680043 PMCID: PMC5498612 DOI: 10.1038/s41598-017-04230-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/11/2017] [Indexed: 11/28/2022] Open
Abstract
We describe the largest molecular epidemiological study of Bovine Tuberculosis (bTB) in a sub-Saharan African country with higher spatial resolution providing new insights into bTB. Four hundred and ninety-nine samples were collected for culture from 201 and 179 cattle with and without bTB-like lesions respectively out of 2,346 cattle slaughtered at Bamenda, Ngaoundere, Garoua and Maroua abattoirs between 2012–2013. Two hundred and fifty-five M. bovis were isolated, identified and genotyped using deletion analysis, Hain® Genotype MTBC, spoligotyping and MIRU-VNTR. African 1 was the dominant M. bovis clonal complex, with 97 unique genotypes including 19 novel spoligotypes representing the highest M. bovis genetic diversity observed in Africa to date. SB0944 and SB0953 dominated (63%) the observed spoligotypes. A third of animals with multiple lesions had multiple strain infections. Higher diversity but little evidence of recent transmission of M. bovis was more common in Adamawa compared to the North-West Region. The Adamawa was characterised by a high frequency of singletons possibly due to constant additions from an active livestock movement network compared to the North-West Region where a local expansion was more evident. The latter combined with population-based inferences suggest an unstable and stable bTB-endemic status in the North-West and Adamawa Regions respectively.
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Affiliation(s)
- N F Egbe
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Microbiology and Parasitology Unit, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | - A Muwonge
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - L Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon.,Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - R F Kelly
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Farm Animal Clinical Sciences, School of Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK
| | - M Sander
- Tuberculosis Reference Laboratory, Bamenda, P.O. Box 586, Cameroon
| | - V Tanya
- Cameroon Academy of Sciences, P.O. Box 1457, Yaoundé, Cameroon
| | - V Ngu Ngwa
- School of Veterinary Medicine and Sciences, University of Ngaoundere, B.P. 454, Ngaoundere, Cameroon
| | - I G Handel
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - A Novak
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - R Ngandalo
- Laboratoire de Recherches Vétérinaires et Zootechniques de Farcha, N'Djaména, Chad
| | - S Mazeri
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - K L Morgan
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst Campus, Neston, Wirral, CH64 7TE, UK
| | - A Asuquo
- Microbiology and Parasitology Unit, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | - B M de C Bronsvoort
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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44
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Allen AR. One bacillus to rule them all? - Investigating broad range host adaptation in Mycobacterium bovis. INFECTION GENETICS AND EVOLUTION 2017; 53:68-76. [PMID: 28434972 DOI: 10.1016/j.meegid.2017.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/11/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Adrian R Allen
- Agri-Food and Biosciences Institute, AFBI Stormont, Department of Bacteriology, Lamont Building, Stoney Road, Belfast BT4 3SD, United Kingdom.
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45
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Rahim Z, Thapa J, Fukushima Y, van der Zanden AGM, Gordon SV, Suzuki Y, Nakajima C. Tuberculosis Caused by Mycobacterium orygis in Dairy Cattle and Captured Monkeys in Bangladesh: a New Scenario of Tuberculosis in South Asia. Transbound Emerg Dis 2016; 64:1965-1969. [PMID: 27888587 DOI: 10.1111/tbed.12596] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Mycobacterium orygis, commonly known as the oryx bacillus and a newly proposed Mycobacterium tuberculosis complex subspecies, was isolated from 18 cattle in a dairy farm and two captured rhesus monkeys in a zoo in Bangladesh. All the infected animals had tuberculosis lesions in their lungs, suggesting transmission and infection with M. orygis by an airborne route. The 20 isolates were analysed using a range of conventional and molecular typing methods, and RD-deletion typing and sequencing of selected genes confirmed the isolates as M. orygis. Multiple-locus variable-number tandem repeat analysis (MLVA) allowed the isolates to be divided into three clusters based on the relatedness of their MLVA profiles. The two monkey isolates shared the same MLVA pattern with 15 of the cattle isolates, whereas the remaining three cattle isolates had different patterns, even though the latter animals had been kept in the same dairy farm. The diversity observed among isolates may suggest the bacteria have been established in this area for a long period. This study along with other recent findings that report the detection of M. orygis from animals as well as humans originating from South Asia potentially indicate endemic distribution of M. orygis in South Asia.
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Affiliation(s)
- Z Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - J Thapa
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Y Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - A G M van der Zanden
- Laboratory for Medical Microbiology and Public Health, Enschede, The Netherlands
| | - S V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Y Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - C Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
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46
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Milian-Suazo F, Garcia-Casanova L, Robbe-Austerman S, Canto-Alarcon GJ, Barcenas-Reyes I, Stuber T, Rodriguez-Hernandez E, Flores-Villalva S. Molecular Relationship between Strains of M. bovis from Mexico and Those from Countries with Free Trade of Cattle with Mexico. PLoS One 2016; 11:e0155207. [PMID: 27171239 PMCID: PMC4865116 DOI: 10.1371/journal.pone.0155207] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/26/2016] [Indexed: 12/02/2022] Open
Abstract
The purpose of this study was to identify relationships between spoligotypes of M. bovis from cattle in Mexico and those reported in countries with free trade of cattle with Mexico: Australia, Canada, New Zealand and the United States of America. Mexican spoligotypes were obtained from isolates collected from cattle in different parts of the country. Spoligotypes from Canada and New Zealand were obtained from different reports in the literature. Those from the United States were obtained from the database of the National Veterinary Services Laboratory in APHIS-USDA. In order to perform the analysis in a single data set, spoligotypes were all converted to binary data and classified according to www.mbovis.org or www.pasteur-guadeloupe.fr:8081. Epidemiologic information included country and species infected. From 3,198 isolates, 174 different spoligotypes were obtained, 95 were orphans. Ninety one percent of the isolates came from the Unites States (n = 1,609) and Mexico (n = 1,323). Spoligotype SB0265 is shared between Canada and the United States in cattle and wildlife. Six spoligotypes, SB0673, SB0121, SB0145, SB0971, SB0140 and SB1165, were frequent in cattle and wildlife in the United States and cattle in Mexico, suggesting wide exchange of strains. Spoligotype SB0669 was found only in Mexico. Spoligotype SB0140 was the most common in Australia and the sixth in the United States and Mexico. In a phylogenetic analysis, spoligotype SB0140 appears as the oldest spoligotype in the data set, suggesting this as the ancestral spoligotype for all spoligotypes in the five countries. Some spoligotypes are shared by animals and humans, corroborating the zoonotic importance of M. bovis.
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Affiliation(s)
- Feliciano Milian-Suazo
- Facultad de Ciencias Naturales-Universidad Autónoma de Querétaro, Querétaro, Querétaro, México
| | - Leticia Garcia-Casanova
- Facultad de Ciencias Naturales-Universidad Autónoma de Querétaro, Querétaro, Querétaro, México
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratory-APHIS, United States Department of Agriculture, Ames, Iowa, United States of America
| | | | - Isabel Barcenas-Reyes
- Facultad de Ciencias Naturales-Universidad Autónoma de Querétaro, Querétaro, Querétaro, México
| | - Tod Stuber
- National Veterinary Services Laboratory-APHIS, United States Department of Agriculture, Ames, Iowa, United States of America
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Gioffré A, Correa Muñoz M, Alvarado Pinedo MF, Vaca R, Morsella C, Fiorentino MA, Paolicchi F, Ruybal P, Zumárraga M, Travería GE, Romano MI. Molecular typing of Argentinian Mycobacterium avium subsp. paratuberculosis isolates by multiple-locus variable number-tandem repeat analysis. Braz J Microbiol 2015; 46:557-64. [PMID: 26273274 PMCID: PMC4507551 DOI: 10.1590/s1517-838246220140283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 11/16/2014] [Indexed: 11/24/2022] Open
Abstract
Multiple-locus variable number-tandem repeat analysis (MLVA) of
Mycobacterium avium subspecies
paratuberculosis (MAP) isolates may contribute to the
knowledge of strain diversity in Argentina. Although the diversity of MAP has
been previously investigated in Argentina using IS900-RFLP, a
small number of isolates were employed, and a low discriminative power was
reached. The aim of the present study was to test the genetic diversity among
MAP isolates using an MLVA approach based on 8 repetitive loci. We studied 97
isolates from cattle, goat and sheep and could describe 7 different patterns:
INMV1, INMV2, INMV11, INMV13, INMV16, INMV33 and one incomplete pattern. INMV1
and INMV2 were the most frequent patterns, grouping 76.3% of the isolates. We
were also able to demonstrate the coexistence of genotypes in herds and
co-infection at the organism level. This study shows that all the patterns
described are common to those described in Europe, suggesting an epidemiological
link between the continents.
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Affiliation(s)
- Andrea Gioffré
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Magnolia Correa Muñoz
- Universidad Autónoma de Baja California, Universidad Autónoma de Baja California, Mexicali, México, Universidad Autónoma de Baja California, Mexicali, México
| | - María F Alvarado Pinedo
- Universidad Nacional de La Plata, Centro de Diagnóstico e Investigaciones Veterinarias, Faculdad de Ciencias Veterinarias, Universidad Nacional de La Plata, Chascomús, Argentina, Centro de Diagnóstico e Investigaciones Veterinarias, Faculdad de Ciencias Veterinarias, Universidad Nacional de La Plata, Chascomús, Argentina
| | - Roberto Vaca
- Universidad Nacional de La Plata, Cátedra de Zootecnia Especial II, Faculdad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina, Cátedra de Zootecnia Especial II, Faculdad de Ciencias Veterinarias, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Claudia Morsella
- Instituto Nacional de Tecnología Agropecuaria, Laboratorio de Bacteriología, Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina, Laboratorio de Bacteriología, Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina
| | - María Andrea Fiorentino
- Instituto Nacional de Tecnología Agropecuaria, Laboratorio de Bacteriología, Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina, Laboratorio de Bacteriología, Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina
| | - Fernando Paolicchi
- Instituto Nacional de Tecnología Agropecuaria, Laboratorio de Bacteriología, Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina, Laboratorio de Bacteriología, Estación Experimental Agropecuaria, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina
| | - Paula Ruybal
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Martín Zumárraga
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Gabriel E Travería
- Universidad Nacional de La Plata, Centro de Diagnóstico e Investigaciones Veterinarias, Faculdad de Ciencias Veterinarias, Universidad Nacional de La Plata, Chascomús, Argentina, Centro de Diagnóstico e Investigaciones Veterinarias, Faculdad de Ciencias Veterinarias, Universidad Nacional de La Plata, Chascomús, Argentina
| | - María Isabel Romano
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina, Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
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48
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Hauer A, De Cruz K, Cochard T, Godreuil S, Karoui C, Henault S, Bulach T, Bañuls AL, Biet F, Boschiroli ML. Genetic evolution of Mycobacterium bovis causing tuberculosis in livestock and wildlife in France since 1978. PLoS One 2015; 10:e0117103. [PMID: 25658691 PMCID: PMC4319773 DOI: 10.1371/journal.pone.0117103] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/18/2014] [Indexed: 11/18/2022] Open
Abstract
To study the dynamics of bovine tuberculosis (bTB) in France, 4,654 M. bovis strains isolated mainly from livestock and wildlife since 1978 were characterized by spoligotyping and MLVA based on MIRU-VNTR. In our study spoligotyping allowed the discrimination of 176 types although 3 spoligotypes are predominant and account for more than half of the total strain population: SB0120 (26%), SB0134 (11%) and SB0121 (6%). In addition, 11% of the isolates, principally from Southern France, showing close spoligotypes and MIRU-VNTR types have been gathered in a family designated as the "F4-family". MLVA typing allowed extensive discrimination, particularly for strains with predominant spoligotypes, with a total of 498 genotypes, several of which were highly regionalized. The similarity of the strains' genetic relationships based on spoligotyping and MIRU-VNTR markers supports the co-existence of different clonal populations within the French M. bovis population. A genetic evolution of the strains was observed both geographically and in time. Indeed, as a result of the reduction of bTB due to the national control campaigns, a large reduction of the strains' genetic variability took place in the last ten years. However, in the regions were bTB is highly prevalent at present, cases in both livestock and in wildlife are due to the spread of unique local genotype profiles. Our results show that the highly discriminating genotyping tools used in this study for molecular studies of bTB are useful for addressing pending questions, which would lead to a better insight into the epidemiology of the disease, and for finding proper solutions for its sustainable control in France.
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Affiliation(s)
- Amandine Hauer
- Université Paris-Est, Laboratoire National de Référence de la Tuberculose, Unité de Zoonoses Bactériennes, Laboratoire de Santé Animale, ANSES, Maisons-Alfort Cedex, France
- INRA, UMR1282, Infectiologie et Santé Publique (ISP-311), Nouzilly, France
| | - Krystel De Cruz
- Université Paris-Est, Laboratoire National de Référence de la Tuberculose, Unité de Zoonoses Bactériennes, Laboratoire de Santé Animale, ANSES, Maisons-Alfort Cedex, France
| | - Thierry Cochard
- INRA, UMR1282, Infectiologie et Santé Publique (ISP-311), Nouzilly, France
| | - Sylvain Godreuil
- INSERM U1058 Infection par le VIH et par agents à tropisme cutanéo-muqueux: de la pathogenèse à la prévention, Montpellier, France
- Centre Hospitalier Régional Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Département de Bactériologie-Virologie, Montpellier, France
| | - Claudine Karoui
- Université Paris-Est, Laboratoire National de Référence de la Tuberculose, Unité de Zoonoses Bactériennes, Laboratoire de Santé Animale, ANSES, Maisons-Alfort Cedex, France
| | - Sylvie Henault
- Université Paris-Est, Laboratoire National de Référence de la Tuberculose, Unité de Zoonoses Bactériennes, Laboratoire de Santé Animale, ANSES, Maisons-Alfort Cedex, France
| | - Tabatha Bulach
- Université Paris-Est, Laboratoire National de Référence de la Tuberculose, Unité de Zoonoses Bactériennes, Laboratoire de Santé Animale, ANSES, Maisons-Alfort Cedex, France
| | - Anne-Laure Bañuls
- MIVEGEC, UMR IRD 224-CNRS 5290-Universités Montpellier 1 et 2, Centre IRD, Montpellier, France
| | - Franck Biet
- INRA, UMR1282, Infectiologie et Santé Publique (ISP-311), Nouzilly, France
| | - María Laura Boschiroli
- Université Paris-Est, Laboratoire National de Référence de la Tuberculose, Unité de Zoonoses Bactériennes, Laboratoire de Santé Animale, ANSES, Maisons-Alfort Cedex, France
- * E-mail:
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49
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de la Cruz ML, Perez A, Bezos J, Pages E, Casal C, Carpintero J, Romero B, Dominguez L, Barker CM, Diaz R, Alvarez J. Spatial dynamics of bovine tuberculosis in the Autonomous Community of Madrid, Spain (2010-2012). PLoS One 2014; 9:e115632. [PMID: 25536514 PMCID: PMC4275235 DOI: 10.1371/journal.pone.0115632] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 11/05/2014] [Indexed: 12/31/2022] Open
Abstract
Progress in control of bovine tuberculosis (bTB) is often not uniform, usually due to the effect of one or more sometimes unknown epidemiological factors impairing the success of eradication programs. Use of spatial analysis can help to identify clusters of persistence of disease, leading to the identification of these factors thus allowing the implementation of targeted control measures, and may provide some insights of disease transmission, particularly when combined with molecular typing techniques. Here, the spatial dynamics of bTB in a high prevalence region of Spain were assessed during a three year period (2010-2012) using data from the eradication campaigns to detect clusters of positive bTB herds and of those infected with certain Mycobacterium bovis strains (characterized using spoligotyping and VNTR typing). In addition, the within-herd transmission coefficient (β) was estimated in infected herds and its spatial distribution and association with other potential outbreak and herd variables was evaluated. Significant clustering of positive herds was identified in the three years of the study in the same location ("high risk area"). Three spoligotypes (SB0339, SB0121 and SB1142) accounted for >70% of the outbreaks detected in the three years. VNTR subtyping revealed the presence of few but highly prevalent strains within the high risk area, suggesting maintained transmission in the area. The spatial autocorrelation found in the distribution of the estimated within-herd transmission coefficients in herds located within distances <14 km and the results of the spatial regression analysis, support the hypothesis of shared local factors affecting disease transmission in farms located at a close proximity.
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Affiliation(s)
- Maria Luisa de la Cruz
- Centro de Vigilancia Sanitaria Veterinaria VISAVET, Universidad Complutense, Madrid, Spain
| | - Andres Perez
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Javier Bezos
- Centro de Vigilancia Sanitaria Veterinaria VISAVET, Universidad Complutense, Madrid, Spain
- MAEVA SERVET SL, Alameda del Valle, Madrid, Spain
| | - Enrique Pages
- Área de Ganadería, Dirección General de Medio Ambiente, Consejería de Medio Ambiente, Vivienda y Ordenación del Territorio de la Comunidad de Madrid, Madrid, Spain
| | - Carmen Casal
- Centro de Vigilancia Sanitaria Veterinaria VISAVET, Universidad Complutense, Madrid, Spain
| | - Jesus Carpintero
- Área de Ganadería, Dirección General de Medio Ambiente, Consejería de Medio Ambiente, Vivienda y Ordenación del Territorio de la Comunidad de Madrid, Madrid, Spain
| | - Beatriz Romero
- Centro de Vigilancia Sanitaria Veterinaria VISAVET, Universidad Complutense, Madrid, Spain
| | - Lucas Dominguez
- Área de Ganadería, Dirección General de Medio Ambiente, Consejería de Medio Ambiente, Vivienda y Ordenación del Territorio de la Comunidad de Madrid, Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Christopher M. Barker
- Center for Vectorborne Diseases and Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Rosa Diaz
- Área de Ganadería, Dirección General de Medio Ambiente, Consejería de Medio Ambiente, Vivienda y Ordenación del Territorio de la Comunidad de Madrid, Madrid, Spain
| | - Julio Alvarez
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
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50
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Tsao K, Robbe-Austerman S, Miller RS, Portacci K, Grear DA, Webb C. Sources of bovine tuberculosis in the United States. INFECTION GENETICS AND EVOLUTION 2014; 28:137-43. [DOI: 10.1016/j.meegid.2014.09.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 11/30/2022]
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