Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal

References

• Pereira AC, Reis AC, Ramos B, et al. Animal tuberculosis: impact of disease heterogeneity in transmission, diagnosis and control. Transbound Emerg Dis. 2020;67(5):1828–1846. doi:10.1111/tbed.13539
   PubMed Web of Science ®Google Scholar
• Ramos B, Pereira AC, Reis AC, et al. Estimates of the global and continental burden of animal tuberculosis in key livestock species worldwide: a meta-analysis study. One Health. 2020;10:100169, doi:10.1016/j.onehlt.2020.100169
   PubMed Web of Science ®Google Scholar
• Reis AC, Ramos B, Pereira AC, et al. The hard numbers of tuberculosis epidemiology in wildlife: a meta-regression and systematic review. Transbound Emerg Dis. 2021. doi:10.1111/tbed.13948
   Web of Science ®Google Scholar
• Reis AC, Ramos B, Pereira AC, et al. Global trends of epidemiological research in livestock tuberculosis for the last four decades. Transbound Emerg Dis. 2021. doi:10.1111/tbed.13763
   Web of Science ®Google Scholar
• Reis AC, Tenreiro R, Albuquerque T, et al. Long-term molecular surveillance provides clues on a cattle origin for Mycobacterium bovis in Portugal. Sci Rep. 2020;10(1):20856, doi:10.1038/s41598-020-77713-8
   PubMed Web of Science ®Google Scholar
• Cunha MV, Matos F, Canto A, et al. Implications and challenges of tuberculosis in wildlife ungulates in Portugal: a molecular epidemiology perspective. Res Vet Sci. 2012;92(2):225–235. doi:10.1016/j.rvsc.2011.03.009.
   PubMed Web of Science ®Google Scholar
• Direcção Geral de Alimentação e Veterinária (DGAV). Programme for the eradication of bovine tuberculosis, bovine brucellosis or sheep and goat brucellosis. Programmes for eradication, control and surveillance of animal diseases and zoonoses submitted for obtaining EU financial contribution; 2019.
   Google Scholar
• Direcção Geral de Veterinária (DGV). [Plano de controlo e erradicação de Tuberculose bovina em caça maior]. Ministério da Agricultura, Mar, Ambiente e Ordenamento do Território; 2011.
   Google Scholar
• Rodriguez-Campos S, Schürch AC, Dale J, et al. DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing. Infect Genet Evol. 2012;12(4):602–609. doi:10.1016/j.meegid.2011.08.032
   PubMed Web of Science ®Google Scholar
• Crispell J, Zadoks RN, Harris SR, et al. Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand. BMC Genomics. 2017;18(1):180, doi:10.1186/s12864-017-3569-x
   PubMedGoogle Scholar
• Crispell J, Benton CH, Balaz D, et al. Fog signaling has diverse roles in epithelial morphogenesis in insects. eLife. 2019;8:e45833, doi:10.7554/eLife.47346
   PubMed Web of Science ®Google Scholar
• Trewby H, Wright D, Breadon EL, et al. Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis. Epidemics. 2016;14:26–35. doi:10.1016/j.epidem.2015.08.003
   PubMed Web of Science ®Google Scholar
• Duault H, Michelet L, Boschiroli M-L, et al. A Bayesian evolutionary model towards understanding wildlife contribution to F4-family Mycobacterium bovis transmission in the South-West of France. Vet Res 2022;53(1):28, doi:10.1186/s13567-022-01044-x
   PubMed Web of Science ®Google Scholar
• Salvador LCM, O’Brien DJ, Cosgrove MK, et al. Disease management at the wildlife-livestock interface: using whole-genome sequencing to study the role of elk in Mycobacterium bovis transmission in Michigan, USA. Mol Ecol. 2019;28(9):2192–2205. doi:10.1111/mec.15061
   PubMed Web of Science ®Google Scholar
• Canini L, Modenesi G, Courcoul A, et al. 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. Microbiol Open. 2023;12(1):e1331, doi:10.1002/mbo3.1331
   Google Scholar
• Reis AC, Salvador LCM, Robbe-Austerman S, et al. Whole genome sequencing refines knowledge on the population structure of mycobacterium bovis from a multi-host tuberculosis system. Microorganisms. 2021;9(8). doi:10.3390/microorganisms9081585
   Web of Science ®Google Scholar
• Guimaraes AMS, Zimpel CK. Mycobacterium bovis: from genotyping to genome sequencing. Microorganisms. 2020; 8(5). doi:10.3390/microorganisms8050667
   Web of Science ®Google Scholar
• Chen S, Zhou Y, Chen Y, et al. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i890. doi:10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMCPMC6129281. eng.
   PubMed Web of Science ®Google Scholar
• Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20(1):257, doi:10.1186/s13059-019-1891-0
   PubMed Web of Science ®Google Scholar
• Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinf. 2013;14(2):178–192. doi:10.1093/bib/bbs017. PubMed PMID: 22517427; PubMed Central PMCID: PMCPMC3603213. eng.
   PubMed Web of Science ®Google Scholar
• Gabbassov E, Moreno-Molina M, Comas I, et al. SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data. Microb Genom. 2021;7(6). doi:10.1099/mgen.0.000607. PubMed PMID: 34165419; PubMed Central PMCID: PMCPMC8461467. eng.
   PubMedGoogle Scholar
• Pinto D, Themudo G, Pereira AC, et al. Rescue of Mycobacterium bovis DNA obtained through routine analysis of animal samples: key steps for robust whole genome sequence data generation and interpretation. Submitted.
   Google Scholar
• Steiner A, Stucki D, Coscolla M, et al. Kvar Q: targeted and direct variant calling from fastq reads of bacterial genomes. BMC Genomics. 2014;15(1):881, doi:10.1186/1471-2164-15-881
   PubMedGoogle Scholar
• Zwyer M, Çavusoglu C, Ghielmetti G, et al. A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics. Open Res Europe. 2021;1(100). doi:10.12688/openreseurope.14029.2
   PubMedGoogle Scholar
• Kumar S, Stecher G, Li M, et al. Mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018;35(6):1547–1549. doi:10.1093/molbev/msy096. PubMed PMID: 29722887; PubMed Central PMCID: PMCPMC5967553. eng.
   PubMed Web of Science ®Google Scholar
• Rambaut A, Lam TT, Max Carvalho L, et al. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2(1):vew007, doi:10.1093/ve/vew007
   PubMed Web of Science ®Google Scholar
• To T-H, Jung M, Lycett S, et al. Fast dating using least-squares criteria and algorithms. Syst Biol 2016;65(1):82–97. doi:10.1093/sysbio/syv068
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, et al. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9(8):772–772. doi:10.1038/nmeth.2109
   PubMed Web of Science ®Google Scholar
• Bouckaert R, Vaughan TG, Barido-Sottani J, et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 2019;15(4):e1006650, doi:10.1371/journal.pcbi.1006650
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Ho SYW, Phillips MJ, et al. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4(5):e88, doi:10.1371/journal.pbio.0040088
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A, Shapiro B, et al. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005;22(5):1185–1192. doi:10.1093/molbev/msi103
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Nicholls GK, Rodrigo AG, et al. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002;161(3):1307–1320. doi:10.1093/genetics/161.3.1307
   PubMed Web of Science ®Google Scholar
• Ferreira MAR, Suchard MA. Bayesian analysis of elapsed times in continuous-time Markov chains. Can J Stat. 2008;36(3):355–368. doi:https://doi.org/10.1002/cjs.5550360302.
   Web of Science ®Google Scholar
• Rambaut A, Drummond AJ, Xie D, et al. Posterior summarization in Bayesian phylogenetics using tracer 1.7. Syst Biol 2018;67(5):901–904. doi:10.1093/sysbio/syy032
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007;7(1):214, doi:10.1186/1471-2148-7-214
   PubMed Web of Science ®Google Scholar
• Lartillot N, Philippe H. Computing Bayes factors using thermodynamic integration. Syst Biol. 2006;55(2):195–207. doi:10.1080/10635150500433722. PubMed PMID: 16522570; eng.
   PubMed Web of Science ®Google Scholar
• Kass RE, Raftery AE. Bayes factors. J Am Stat Assoc. 1995;90(430):773–795. doi:10.1080/01621459.1995.10476572
   Web of Science ®Google Scholar
• Santos N, Richomme C, Nunes T, et al. Quantification of the animal tuberculosis multi-host community offers insights for control. Pathogens. 2020. doi:10.3390/pathogens9060421.
   Web of Science ®Google Scholar
• Lemey P, Rambaut A, Drummond AJ, et al. Bayesian phylogeography finds its roots. PLoS Comput Biol 2009;5(9):e1000520, doi:10.1371/journal.pcbi.1000520
   PubMed Web of Science ®Google Scholar
• Pagel M, Meade A, Barker D. Bayesian estimation of ancestral character states on phylogenies. Syst Biol 2004;53(5):673–684. doi:10.1080/10635150490522232
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003;13(11):2498–2504. doi:10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Menardo F, Duchêne S, Brites D, et al. The molecular clock of Mycobacterium tuberculosis. PLoS Pathog 2019;15(9):e1008067, doi:10.1371/journal.ppat.1008067
   PubMed Web of Science ®Google Scholar
• Zimpel CK, Patané JSL, Guedes ACP, et al. Global distribution and evolution of mycobacterium bovis lineages. Front Microbiol. 2020;11; doi:10.3389/fmicb.2020.00843. English.
   PubMed Web of Science ®Google Scholar
• 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 [hypothesis and theory]. Front Vet Sci. 2018;5:109.
   PubMed Web of Science ®Google Scholar
• Cox DR, Donnelly CA, Bourne FJ, et al. Simple model for tuberculosis in cattle and badgers. Proc Natl Acad Sci USA. 2005;102(49):17588–17593. doi:10.1073/pnas.0509003102. PubMed PMID: 16306260; PubMed Central PMCID: PMCPMC1292989. eng.
   PubMed Web of Science ®Google Scholar
• Brooks-Pollock E, Wood JL. Eliminating bovine tuberculosis in cattle and badgers: insight from a dynamic model. Proc Biol Sci. 2015;282(1808):20150374, doi:10.1098/rspb.2015.0374. PubMed PMID: 25972466; PubMed Central PMCID: PMCPMC4455805. eng.
   PubMed Web of Science ®Google Scholar
• Delahay RJ, Walker N, Smith GC, et al. Long-term temporal trends and estimated transmission rates for Mycobacterium bovis infection in an undisturbed high-density badger (Meles meles) population. Epidemiol Infect. 2013;141(7):1445–1456. doi:10.1017/S0950268813000721. PubMed PMID: 23537573; PubMed Central PMCID: PMCPMC9151602. eng.
   PubMed Web of Science ®Google Scholar
• Santos N, Colino EF, Arnal MC, et al. Complementary roles of wild boar and red deer to animal tuberculosis maintenance in multi-host communities. Epidemics. 2022;41:100633, doi:10.1016/j.epidem.2022.100633.
   PubMed Web of Science ®Google Scholar
• Veličković N, Ferreira E, Djan M, et al. Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe. Heredity (Edinb). 2016;117(5):348–357. doi:10.1038/hdy.2016.53
   PubMed Web of Science ®Google Scholar
• Carvalho J, Torres RT, Acevedo P, et al. Propagule pressure and land cover changes as main drivers of red and roe deer expansion in mainland Portugal. Divers Distrib. 2018;24(4):551–564. doi:https://doi.org/10.1111/ddi.12703.
   Web of Science ®Google Scholar
• Vieira-Pinto M, Alberto J, Aranha J, et al. Combined evaluation of bovine tuberculosis in wild boar (Sus scrofa) and red deer (Cervus elaphus) from Central-East Portugal. Eur J Wildlife Res. 2011;57(6):1189–1201. doi:10.1007/s10344-011-0532-z
   Web of Science ®Google Scholar
• Santos N, Almeida V, Gortázar C, et al. Patterns of Mycobacterium tuberculosis-complex excretion and characterization of super-shedders in naturally-infected wild boar and red deer. Vet Res 2015;46(1):129, doi:10.1186/s13567-015-0271-3
   PubMedGoogle Scholar
• Rosalino LM, Teixeira D, Camarinha C, et al. Even generalist and resilient species are affected by anthropic disturbance: evidence from wild boar activity patterns in a Mediterranean landscape. Mammal Res. 2022;67(3):317–325. doi:10.1007/s13364-022-00632-8
   Web of Science ®Google Scholar
• Ares-Pereira G, Rosalino LM, Teixeira D, et al. Eucalyptus plantations alter spatiotemporal relationships of wild ungulates. Agric Ecosyst Environ. 2022;340:108174, doi:https://doi.org/10.1016/j.agee.2022.108174.
   Web of Science ®Google Scholar
• Pozo P, VanderWaal K, Grau A, et al. Analysis of the cattle movement network and its association with the risk of bovine tuberculosis at the farm level in Castilla y Leon, Spain. Transbound Emerg Dis. 2019;66(1):327–340. doi:https://doi.org/10.1111/tbed.13025.
   PubMed Web of Science ®Google Scholar
• Palisson A, Courcoul A, Durand B. Role of cattle movements in bovine tuberculosis spread in France between 2005 and 2014. PLoS ONE. 2016;11(3):e0152578, doi:10.1371/journal.pone.0152578
   PubMed Web of Science ®Google Scholar
• Gilbert M, Mitchell A, Bourn D, et al. Cattle movements and bovine tuberculosis in Great Britain. Nature. 2005;435(7041):491–496. doi:10.1038/nature03548. PubMed PMID: 15917808; eng.
   PubMed Web of Science ®Google Scholar
• Charles C, Conde C, Vorimore F, et al. Features of mycobacterium bovis complete genomes belonging to 5 different lineages. Microorganisms. 2023. doi:10.3390/microorganisms11010177
   Web of Science ®Google Scholar