1
|
Pereira AC, Lourenço J, Themudo G, Botelho A, Cunha MV. Population structure and history of Mycobacterium bovis European 3 clonal complex reveal transmission across ecological corridors of unrecognized importance in Portugal. Microbiol Spectr 2024; 12:e0382923. [PMID: 38771094 PMCID: PMC11218495 DOI: 10.1128/spectrum.03829-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Mycobacterium bovis causes animal tuberculosis in livestock and wildlife, with an impact on animal health and production, wildlife management, and public health. In this work, we sampled a multi-host tuberculosis community from the official hotspot risk area of Portugal over 16 years, generating the largest available data set in the country. Using phylogenetic and ecological modeling, we aimed to reconstruct the history of circulating lineages across the livestock-wildlife interface to inform intervention and the implementation of genomic surveillance within the official eradication plan. We find evidence for the co-circulation of M. bovis European 1 (Eu1), Eu2, and Eu3 clonal complexes, with Eu3 providing sufficient temporal signal for further phylogenetic investigation. The Eu3 most recent common ancestor (bovine) was dated in the 1990s, subsequently transitioning to wildlife (red deer and wild boar). Isolate clustering based on sample metadata was used to inform phylogenetic inference, unravelng frequent transmission between two clusters that represent an ecological corridor of previously unrecognized importance in Portugal. The latter was associated with transmission at the livestock-wildlife interface toward locations with higher temperature and precipitation, lower agriculture and road density, and lower host densities. This is the first analysis of M. bovis Eu3 complex in Iberia, shedding light on background ecological factors underlying long-term transmission and informing where efforts could be focused within the larger hotspot risk area of Portugal. IMPORTANCE Efforts to strengthen surveillance and control of animal tuberculosis (TB) are ongoing worlwide. Here, we developed an eco-phylodynamic framework based on discrete phylogenetic approaches informed by M. bovis whole-genome sequence data representing a multi-host transmission system at the livestock-wildlife interface, within a rich ecological landscape in Portugal, to understand transmission processes and translate this knowledge into disease management benefits. We find evidence for the co-circulation of several M. bovis clades, with frequent transmission of the Eu3 lineage among cattle and wildlife populations. Most transition events between different ecological settings took place toward host, climate and land use gradients, underscoring animal TB expansion and a potential corridor of unrecognized importance for M. bovis maintenance. Results stress that animal TB is an established wildlife disease without ecological barriers, showing that control measures in place are insufficient to prevent long-distance transmission and spillover across multi-host communities, demanding new interventions targeting livestock-wildlife interactions.
Collapse
Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Lourenço
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Gonçalo Themudo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Botelho
- INIAV, I.P.—National Institute for Agrarian and Veterinary Research, Oeiras, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
2
|
Pinto D, Themudo G, Pereira AC, Botelho A, Cunha MV. Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation. Int J Mol Sci 2024; 25:3869. [PMID: 38612679 PMCID: PMC11011339 DOI: 10.3390/ijms25073869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Epidemiological surveillance of animal tuberculosis (TB) based on whole genome sequencing (WGS) of Mycobacterium bovis has recently gained track due to its high resolution to identify infection sources, characterize the pathogen population structure, and facilitate contact tracing. However, the workflow from bacterial isolation to sequence data analysis has several technical challenges that may severely impact the power to understand the epidemiological scenario and inform outbreak response. While trying to use archived DNA from cultured samples obtained during routine official surveillance of animal TB in Portugal, we struggled against three major challenges: the low amount of M. bovis DNA obtained from routinely processed animal samples; the lack of purity of M. bovis DNA, i.e., high levels of contamination with DNA from other organisms; and the co-occurrence of more than one M. bovis strain per sample (within-host mixed infection). The loss of isolated genomes generates missed links in transmission chain reconstruction, hampering the biological and epidemiological interpretation of data as a whole. Upon identification of these challenges, we implemented an integrated solution framework based on whole genome amplification and a dedicated computational pipeline to minimize their effects and recover as many genomes as possible. With the approaches described herein, we were able to recover 62 out of 100 samples that would have otherwise been lost. Based on these results, we discuss adjustments that should be made in official and research laboratories to facilitate the sequential implementation of bacteriological culture, PCR, downstream genomics, and computational-based methods. All of this in a time frame supporting data-driven intervention.
Collapse
Affiliation(s)
- Daniela Pinto
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Gonçalo Themudo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
| | - André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana Botelho
- National Institute for Agrarian and Veterinary Research (INIAV IP), Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal;
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; (D.P.); (A.C.P.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Pereira AC, Reis AC, Cunha MV. Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal. Emerg Microbes Infect 2023; 12:2253340. [PMID: 37640285 PMCID: PMC10484045 DOI: 10.1080/22221751.2023.2253340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
ABSTRACTAnimal tuberculosis (TB) remains a serious concern for animal and human health. Mycobacterium bovis circulates in multi-host systems, dominated by the European 2 clonal complex (Eu2) in Iberia. In this work, we use genomic epidemiology to infer the emergence, spread, and spatiotemporal patterns of Eu2 in the official epidemiological risk area of animal TB in Portugal. Phylogenetic analysis of 144 M. bovis whole-genome sequences from cattle, wild boar, and red deer, representing the 2002-2021 period, distinguished three Eu2 clades that evolved independently. The major Eu2 clade underwent phylodynamic inferences to estimate the time and location of outbreaks, host transitions, and spatial diffusion as well. The origin of this Eu2 clade was attributed to the red deer population in the Castelo Branco district, near the border with Spain. Most host transitions were intraspecific (80%), while interspecific transmissions between wildlife species (wild boar-red deer), and between wild boar and cattle, were highly supported. Phylogeographic reconstruction evidenced that most transitions (82%) occur within municipalities, highlighting local transmission corridors.Our study indicates that M. bovis continues to spread at the cattle-wildlife interface within the animal TB hotspot area, possibly driven by the foraging behaviour of wild boar near agricultural lands. Red deer seems to be an important driver of TB within wildlife hosts, while the wild boar links the multi-host wildlife community and livestock. This work highlights the value of combining genomic epidemiology with phylodynamic inference to resolve host jumps and spatial patterns of M. bovis, providing real-time clues about points of intervention.
Collapse
Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE – Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
5
|
Boschiroli ML. Animal tuberculosis control in a disease-free country, France: does the long and winding road really lead to eradication? Ir Vet J 2023; 76:25. [PMID: 37752587 PMCID: PMC10521394 DOI: 10.1186/s13620-023-00258-5] [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: 12/09/2022] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
It took France almost fifty years to attain its officially animal tuberculosis (TB) free status in 2000, granting the country a favourable position for international live animal trading. The initial TB control program has been adapted at different times in its history in order to suit changing epidemiological contexts: it was first focused on detection and elimination of infected animals while later on protecting TB free herds became a priority.In spite of all the efforts put into the program, final eradication has still not been achieved. Instead, the eradication process has stalled, most probably due to changes in breeding practices in the last 30 years. Indeed, the beef industry has overtaken the milk industry, which has led to the occurrence of new TB risks. Novel epidemiological situations in some regions of extensive beef cattle farming, where wildlife species (wild boar, badger) are also infected, have emerged. More adapted measures have thus been implemented, progressively evaluated and improved in order to reinforce prevention of infection, to follow up with the eradication goal and to strengthen, coordinate and re-motivate field resources. These include, among others, introduction of biosecurity measures in the herd, risk based surveillance and management of wildlife and cattle, improvement of screening in the field and at the abattoir, better diagnosis, but also improvement of communication, awareness, training activities of the main field actors. Very importantly, this new plan has been established through the participation of the majority of involved stakeholders -the farmer industry, hunter associations, veterinarians, scientists and the government-, through coordinated specific steering committees and ad hoc working groups.Without doubt, the main challenge for the next few years is reinforcing communication to encourage and strengthen the program in an already faltering agro-social system. In addition, it will be essential to continue sustaining national research and international collaborations to feed the program with relevant scientific data enabling the authorities to undertake the most pertinent measures for tackling the disease in the short term.
Collapse
Affiliation(s)
- María Laura Boschiroli
- Tuberculosis National Reference Laboratory, Animal Health Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), 94701, Maisons-Alfort, France.
| |
Collapse
|
6
|
Rossi G, Shih BBJ, Egbe NF, Motta P, Duchatel F, Kelly RF, Ndip L, Sander M, Tanya VN, Lycett SJ, Bronsvoort BM, Muwonge A. Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data. Front Vet Sci 2023; 10:1086001. [PMID: 37266384 PMCID: PMC10230100 DOI: 10.3389/fvets.2023.1086001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/14/2023] [Indexed: 06/03/2023] Open
Abstract
When studying the dynamics of a pathogen in a host population, one crucial question is whether it transitioned from an epidemic (i.e., the pathogen population and the number of infected hosts are increasing) to an endemic stable state (i.e., the pathogen population reached an equilibrium). For slow-growing and slow-evolving clonal pathogens such as Mycobacterium bovis, the causative agent of bovine (or animal) and zoonotic tuberculosis, it can be challenging to discriminate between these two states. This is a result of the combination of suboptimal detection tests so that the actual extent of the pathogen prevalence is often unknown, as well as of the low genetic diversity, which can hide the temporal signal provided by the accumulation of mutations in the bacterial DNA. In recent years, the increased availability, efficiency, and reliability of genomic reading techniques, such as whole-genome sequencing (WGS), have significantly increased the amount of information we can use to study infectious diseases, and therefore, it has improved the precision of epidemiological inferences for pathogens such as M. bovis. In this study, we use WGS to gain insights into the epidemiology of M. bovis in Cameroon, a developing country where the pathogen has been reported for decades. A total of 91 high-quality sequences were obtained from tissue samples collected in four abattoirs, 64 of which were with complete metadata. We combined these with environmental, demographic, ecological, and cattle movement data to generate inferences using phylodynamic models. Our findings suggest M. bovis in Cameroon is slowly expanding its epidemiological range over time; therefore, endemic stability is unlikely. This suggests that animal movement plays an important role in transmission. The simultaneous prevalence of M. bovis in co-located cattle and humans highlights the risk of such transmission being zoonotic. Therefore, using genomic tools as part of surveillance would vastly improve our understanding of disease ecology and control strategies.
Collapse
Affiliation(s)
- Gianluigi Rossi
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barbara Bo-Ju Shih
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Nkongho Franklyn Egbe
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Paolo Motta
- The Food and Agriculture Organization of the United Nations, Regional Office for Asia and the Pacific, Bangkok, Thailand
| | - Florian Duchatel
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| | - Robert Francis Kelly
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Lucy Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | | | | | - Samantha J. Lycett
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Barend Mark Bronsvoort
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
- Centre of Expertise on Animal Diseases Outbreaks, EPIC, Edinburgh, United Kingdom
| | - Adrian Muwonge
- The Roslin Institute, R(D)SVS, University of Edinburgh – Easter Bush Campus, Midlothian, United Kingdom
| |
Collapse
|
7
|
Bouchez-Zacria M, Ruette S, Richomme C, Lesellier S, Payne A, Boschiroli ML, Courcoul A, Durand B. Analysis of a multi-type resurgence of Mycobacterium bovis in cattle and badgers in Southwest France, 2007-2019. Vet Res 2023; 54:41. [PMID: 37138355 PMCID: PMC10158257 DOI: 10.1186/s13567-023-01168-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Although control measures to tackle bovine tuberculosis (bTB) in cattle have been successful in many parts of Europe, this disease has not been eradicated in areas where Mycobacterium bovis circulates in multi-host systems. Here we analyzed the resurgence of 11 M. bovis genotypes (defined based on spoligotyping and MIRU-VNTR) detected in 141 farms between 2007 and 2019, in an area of Southwestern France where wildlife infection was also detected from 2012 in 65 badgers. We used a spatially-explicit model to reconstruct the simultaneous diffusion of the 11 genotypes in cattle farms and badger populations. Effective reproduction number R was estimated to be 1.34 in 2007-2011 indicating a self-sustained M. bovis transmission by a maintenance community although within-species Rs were both < 1, indicating that neither cattle nor badger populations acted as separate reservoir hosts. From 2012, control measures were implemented, and we observed a decrease of R below 1. Spatial contrasts of the basic reproduction ratio suggested that local field conditions may favor (or penalize) local spread of bTB upon introduction into a new farm. Calculation of generation time distributions showed that the spread of M. bovis has been more rapid from cattle farms (0.5-0.7 year) than from badger groups (1.3-2.4 years). Although eradication of bTB appears possible in the study area (since R < 1), the model suggests it is a long-term prospect, because of the prolonged persistence of infection in badger groups (2.9-5.7 years). Supplementary tools and efforts to better control bTB infection in badgers (including vaccination for instance) appear necessary.
Collapse
Affiliation(s)
- Malika Bouchez-Zacria
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), University Paris-Est, 14 Rue Pierre Et Marie Curie, 94700, Maisons-Alfort, France
- Independent Researcher, Audincthun, France
| | - Sandrine Ruette
- French Office for Biodiversity (OFB), Research and Scientific Support Direction, Vincennes, France
| | - Céline Richomme
- Nancy Laboratory for Rabies and Wildlife, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Malzéville, France
| | - Sandrine Lesellier
- Nancy Laboratory for Rabies and Wildlife, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Malzéville, France
| | - Ariane Payne
- French Office for Biodiversity (OFB), Research and Scientific Support Direction, Vincennes, France
| | - Maria-Laura Boschiroli
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), University Paris-Est, 14 Rue Pierre Et Marie Curie, 94700, Maisons-Alfort, France
- Tuberculosis Reference Laboratory, Bacterial Zoonosis Unit, Laboratory for Animal Health, Paris-Est University, ANSES, 94700, Maisons‑Alfort, France
| | - Aurélie Courcoul
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), University Paris-Est, 14 Rue Pierre Et Marie Curie, 94700, Maisons-Alfort, France
- Oniris, Nantes, France
| | - Benoit Durand
- Laboratory for Animal Health, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), University Paris-Est, 14 Rue Pierre Et Marie Curie, 94700, Maisons-Alfort, France.
| |
Collapse
|
8
|
Deciphering the role of host species for two
Mycobacterium bovis
genotypes from the European 3 clonal complex circulation within a cattle‐badger‐wild boar multihost system. Microbiologyopen 2023. [DOI: 10.1002/mbo3.1331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
9
|
Santos N, Colino EF, Arnal MC, de Luco DF, Sevilla I, Garrido JM, Fonseca E, Valente AM, Balseiro A, Queirós J, Almeida V, Vicente J, Gortázar C, Alves PC. Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities. Epidemics 2022; 41:100633. [PMID: 36174428 DOI: 10.1016/j.epidem.2022.100633] [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: 02/06/2022] [Revised: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 12/29/2022] Open
Abstract
The contribution of wildlife species to pathogen maintenance in multi-host communities has seldom been quantified. To assess the relative contribution of the main wildlife hosts of animal tuberculosis (TB) to its maintenance, we estimated the basic reproduction number (R0) of Mycobacterium tuberculosis complex in wild boar and red deer at 29 sites in the Iberian Peninsula. Host abundance and true TB prevalence were estimated for each species at each site by sampling from distributions incorporating the uncertainty in the proportion of the population harvested each year, sensitivity, and specificity of the diagnostic methods, while excretion of mycobacteria was estimated using site-occupancy models. The distributions of these parameters were then used to estimate, at each site, the R0,wild boar (range 0.1 - 55.9, average 8.7, standard deviation 11.8), and the R0,red deer (0.1 - 18.9, 2.2, 3.9). Animal TB is maintained in epidemiological scenarios ranging from any single species acting as a maintenance host (the wild boar in 18 sites and the red deer in 5), to facultative multi-host disease (6 sites). The prevalence of TB in the red deer is likely an important driver of the epidemiology in multi-host communities. The wild boar was the main maintenance host of TB in most of the study sites and could have an epidemiological role linking the wildlife multi-host community and livestock.
Collapse
Affiliation(s)
- Nuno Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal.
| | - Elisa Ferreras Colino
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - María Cruz Arnal
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Daniel Fernández de Luco
- Departamento de Patología Animal, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | - Iker Sevilla
- Animal Health Department. NEIKER-Basque Institute for Agricultural Research and Development. Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Joseba M Garrido
- Animal Health Department. NEIKER-Basque Institute for Agricultural Research and Development. Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Eliana Fonseca
- Instituto de Conservação da Natureza e das Florestas, I.P., Braga, Portugal
| | - Ana M Valente
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Ana Balseiro
- Animal Health Department, Instituto de Ganadería de Montaña (IGM, CSIC-ULE), León, Spain; Animal Health Department, Facultad de Veterinaria, Universidad de León, León, Spain, Instituto de Ganadería de Montaña (IGM, CSIC-ULE), León, Spain
| | - João Queirós
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Virgílio Almeida
- Faculty of Veterinary Medicine, University of Lisbon, Campus da Ajuda, Lisboa, Portugal; CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Campus da Ajuda, Lisboa, Portugal
| | - Joaquín Vicente
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Christian Gortázar
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Paulo Célio Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal; Estação Biológica de Mértola (EBM), CIBIO, Mértola, Portugal
| |
Collapse
|
10
|
Pozo P, Lorente-Leal V, Robbe-Austerman S, Hicks J, Stuber T, Bezos J, de Juan L, Saez JL, Romero B, Alvarez J. Use of Whole-Genome Sequencing to Unravel the Genetic Diversity of a Prevalent Mycobacterium bovis Spoligotype in a Multi-Host Scenario in Spain. Front Microbiol 2022; 13:915843. [PMID: 35898917 PMCID: PMC9309649 DOI: 10.3389/fmicb.2022.915843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
Despite the efforts invested in the eradication of bovine tuberculosis in Spain, herd prevalence has remained constant in the country during the last 15 years (~1.5–1.9%) due to a combination of epidemiological factors impairing disease control, including between-species transmission. Here, our aim was to investigate the molecular diversity of Mycobacterium bovis isolates belonging to the highly prevalent SB0339 spoligotype in the cattle-wildlife interface in different regions of Spain using whole-genome sequencing (WGS). Genomic data of 136 M. bovis isolates recovered from different animal species (cattle, wild boar, fallow deer, and red deer) and locations between 2005 and 2018 were analyzed to investigate between- and within-species transmission, as well as within-herds. All sequenced isolates differed by 49–88 single nucleotide polymorphisms from their most recent common ancestor. Genetic heterogeneity was geographic rather than host species-specific, as isolates recovered from both cattle and wildlife from a given region were more closely related compared to isolates from the same species but geographically distant. In fact, a strong association between the geographic and the genetic distances separating pairs of M. bovis isolates was found, with a significantly stronger effect when cattle isolates were compared with wildlife or cattle-wildlife isolates in Spain. The same results were obtained in Madrid, the region with the largest number of sequenced isolates, but no differences depending on the host were observed. Within-herd genetic diversity was limited despite the considerable time elapsed between isolations. The detection of closely related strains in different hosts demonstrates the complex between-host transmission dynamics present in endemic areas in Spain. In conclusion, WGS results a valuable tool to track bTB infection at a high resolution and may contribute to achieve its eradication in Spain.
Collapse
Affiliation(s)
- Pilar Pozo
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Pilar Pozo,
| | - Victor Lorente-Leal
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, Department of Agriculture, Ames, IA, United States
| | - Jessica Hicks
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, Department of Agriculture, Ames, IA, United States
| | - Tod Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, Department of Agriculture, Ames, IA, United States
| | - Javier Bezos
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucia de Juan
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose Luis Saez
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de Sanidad de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación, Madrid, Spain
| | - Beatriz Romero
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Julio Alvarez
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | | |
Collapse
|