Genome-wide diversity and phylogeography of Mycobacterium avium subsp. paratuberculosis in Canadian dairy cattle

PLoS ONE

Volumn 11, Issue 2, 2016, Pages

  Ahlstrom, Christina ^a   Barkema, Herman W ^a   Stevenson, Karen ^b   Zadoks, Ruth N ^b,c   Biek, Roman ^c   Kao, Rowland ^c   Trewby, Hannah ^c   Haupstein, Deb ^d   Kelton, David F ^e   Fecteau, Gilles ^f   Labrecque, Olivia ^g   Keefe, Greg P ^h   McKenna, Shawn L B ^h   Tahlan, Kapil ⁱ   De Buck, Jeroen ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b MOREDUN RESEARCH INSTITUTE   (United Kingdom)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

^d SaskMilk   (Canada)

^e UNIVERSITY OF GUELPH   (Canada)

^f UNIVERSITÉ DE MONTRÉAL   (Canada)

^g Laboratoire d'Epidemiosurveillance Animale du Quebec   (Canada)

^h UNIVERSITY OF PRINCE EDWARD ISLAND   (Canada)

ⁱ MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL TRANSMISSION; BACTERIUM ISOLATE; CANADA; CLADISTICS; DAIRY CATTLE; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ALBERTA; ANIMAL; BOVINE; BOVINE TUBERCULOSIS; DNA SEQUENCE; FECES; FEMALE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PARATUBERCULOSIS;

BACTERIAL DNA;

ALBERTA; ANIMALS; CATTLE; DNA, BACTERIAL; FECES; FEMALE; GENOME, BACTERIAL; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS; PARATUBERCULOSIS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; TUBERCULOSIS, BOVINE;

EID: 84960510279     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0149017     Document Type: Article

References (44)

1. Barkema H. Global prevalence and economics of infection with Mycobacterium avium subsp. paratuberculosisin ruminants. Paratuberculosis: Organism, Disease, Control. 2010; Edited by Behr MA and Collins DM. Cambridge, MA: CAB International.
2. Behr MA. The path to Crohn's disease: is mucosal pathology a secondary event? Inflamm Bowel Dis. 2010;16:896-902. doi: 10.1002/ibd.21171 PMID: 19924803
3. Barkema HW, Hendrick S, Buck JM de, Ghosh S, Kaplan GG, Rioux KP, et al. Zoonotic pathogens in the food chain. Wallingford: CABI; 2010. doi: 10.1079/9781845936815.0000
4. McKenna SLB, Keefe GP, Tiwari A, Van Leeuwen J, Barkema HW. Johne's disease in Canada part II: disease impacts, riskfactors, and control programs for dairy producers. Can Vet J. 2006;47:1089-99. PMID: 17147140
5. Wolf R, Barkema HW, De Buck J, Slomp M, Flaig J, Haupstein D, etal. High herd-level prevalence of Mycobacterium avium subspecies paratuberculosis in Western Canadian dairy farms, based on environmental sampling. J Dairy Sci. 2014;97:6250-9. doi: 10.3168/jds.2014-8101 PMID: 25151881
6. Collins DM, Gabric DM, de Lisle GW. Identification of two groups of Mycobacterium paratuberculosis strains by restriction endonuclease analysis and DNA hybridization. J Clin Microbiol. 1990;28:1591-6. PMID: 2166089
7. Alexander DC, Turenne CY, Behr MA. Insertion and deletion events that define the pathogen Mycobacterium avium subsp. paratuberculosis. J Bacteriol. 2009;191:1018-25. doi: 10.1128/JB.01340-08 PMID: 19028885
8. Ahlstrom C, Barkema HW, Stevenson K, Zadoks RN, Biek R, Kao R, et al. Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level. BMC Genomics. 2015;16:161. doi: 10.1186/s12864-015-1387-6 PMID: 25765045
9. Amonsin A, Li LL, Zhang Q, Bannantine JP, Motiwala AS, Sreevatsan S, etal. Multilocus short sequence repeat sequencing approach for differentiating among Mycobacterium avium subsp. paratuberculosis strains. J Clin Microbiol. 2004;42:1694-702. doi: 10.1128/JCM.42.4.1694-1702.2004 PMID: 15071027
10. Thibault VC, Grayon M, Boschiroli ML, Hubbans C, Overduin P, Stevenson K, etal. New variable-number tandem-repeat markers for typing Mycobacterium avium subsp. paratuberculosis and M. avium strains: comparison with IS900 and IS1245 restriction fragment length polymorphism typing. J Clin Microbiol. 2007;45:2404-10. doi: 10.1128/JCM.00476-07 PMID: 17537942
11. Collins DM, Gabric DM de LG. Strain characterization of Mycobacterium avium subsp. paratuberculosis. Paratuberculosis: Organism, Disease, Control. 2010; Edited by Behr MA and Collins DM. Cambridge, MA: CAB International.
12. Sohal JS, Arsenault J, Labrecque O, Fairbrother J-H, Roy J-P, Fecteau G, etal. Genetic structure of Mycobacterium avium subsp. paratuberculosis population in cattle herds in Quebec as revealed by using a combination of multilocus genomic analyses. J Clin Microbiol. 2014;52:2764-75. doi: 10.1128/JCM.00386-14 PMID: 24829229
13. Keim P, Van Ert MN, Pearson T, Vogler AJ, Huynh LY, Wagner DM. Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infect Genet Evol. 2004;4:205-13. doi: 10.1016/j.meegid.2004.02.005 PMID: 15450200
14. Biek R, O'Hare A, Wright D, Mallon T, McCormick C, Orton RJ, etal. Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathog. 2012;8:e1003008. doi: 10.1371/journal.ppat.1003008 PMID: 23209404
15. Coscolla M, Gagneux S. Does M.tuberculosis genomic diversity explain disease diversity? Drug DiscovToday Dis Mech. 2010;7:e43-e59. doi: 10.1016/j.ddmec.2010.09.004 PMID: 21076640
16. Gollnick NS, Mitchell RM, Baumgart M, Janagama HK, Sreevatsan S, Schukken YH. Survival of Mycobacterium avium subsp. paratuberculosis in bovine monocyte-derived macrophages is not affected by host infection status but depends on the infecting bacterial genotype. Vet Immunol Immunopathol. 2007;120:93-105. doi: 10.1016/j.vetimm.2007.07.017 PMID: 17825427
17. Janagama HK, Jeong Kil, Kapur V, Coussens P, Sreevatsan S. Cytokine responses of bovine macrophages to diverse clinical Mycobacterium avium subspecies paratuberculosis strains. BMC Microbiol. 2006;6:10. doi: 10.1186/1471-2180-6-10 PMID: 16478544
18. Motiwala AS, Janagama HK, Paustian ML, Zhu X, Bannantine JP, Kapur V, etal. Comparative transcriptional analysis of human macrophages exposed to animal and human isolates of Mycobacterium avium subspecies paratuberculosis with diverse genotypes. Infect Immun. 2006;74:6046-56. doi: 10. 1128/IAI.00326-06 PMID: 17057086
19. Borrmann E, Möbius P, Diller R, Köhler H. Divergent cytokine responses of macrophages to Mycobacterium avium subsp. paratuberculosis strains of Types II and III in a standardized in vitro model. Vet Microbiol. 2011;152:101-11. doi: 10.1016/j.vetmic.2011.04.002 PMID: 21555192
20. Lavers CJ, McKenna SLB, Dohoo IR, Barkema HW, Keefe GP. Evaluation of environmental fecal culture for Mycobacterium avium subspecies paratuberculosis detection in dairy herds and association with apparent within-herd prevalence. Can Vet J. 2013;54:1053-60. PMID: 24179240
21. Vary PH, Andersen PR, Green E, Hermon-Taylor J, McFadden JJ. Use of highly specific DNA probes and the polymerase chain reaction to detect Mycobacterium paratuberculosis in Johne's disease. J Clin Microbiol. 1990;28:933-7. PMID: 2351737
22. Ahlstrom C, Barkema HW, De Buck J. Improved short-sequence-repeat genotyping of Mycobacterium avium subsp. paratuberculosis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol. 2014;80:534-9. doi: 10.1128/AEM.03212-13 PMID: 24212568
23. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60. doi: 10.1093/bioinformatics/btp324 PMID: 19451168
24. Li L, Bannantine JP, Zhang Q, Amonsin A, May BJ, Alt D, et al. The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc Natl Acad Sci USA. 2005;102:12344-9. doi: 10.1073/pnas.0505662102 PMID: 16116077
25. Wynne JW, Seemann T, Bulach DM, Coutts SA, Talaat AM, Michalski WP. Resequencing the Mycobacterium avium subsp. paratuberculosis K10 genome: improved annotation and revised genome sequence. J Bacteriol. 2010;192:6319-20. doi: 10.1128/JB.00972-10 PMID: 20870759
26. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, etal. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
27. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696-704. PMID: 14530136
28. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9:772. doi: 10.1038/nmeth.2109
29. Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39:W475-8. doi: 10.1093/nar/gkr201 PMID: 21470960
30. Schmidt HA, Strimmer K, Vingron M, von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002;18:502-4. doi: 10.1093/bioinformatics/18.3.502 PMID: 11934758
31. Strimmer K, von Haeseler A. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci USA. 1997;94:6815-9. PMID: 9192648
32. Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics. 2006;172:2665-81. doi: 10.1534/genetics.105.048975 PMID: 16489234
33. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254-67. doi: 10.1093/molbev/msj030 PMID: 16221896
34. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available: http://www. R-project.org/.
35. Parker J, Rambaut A, Pybus OG. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect Genet Evol. 2008;8:239-46. doi: 10.1016/j.meegid.2007.08.001 PMID: 17921073
36. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29:1969-73. doi: 10.1093/molbev/mss075 PMID: 22367748
37. Whittington RJ, Marsh IB, Whitlock RH. Typing of IS 1311 polymorphisms confirms that bison (Bison bison) with paratuberculosis in Montana are infected with a strain of Mycobacterium avium subsp. paratuberculosis distinct from that occurring in cattle and other domesticated livestock. Mol Cell Probes. 2001;15:139-45. doi: 10.1006/mcpr.2001.0346 PMID: 11352594
38. Animal Industry Market Information System dairy genetics database. 2015. Available: http://www.dairyinfo.gc.ca/index e.php?s1=dff-fcil&s2=farm-ferme&s3=nb. Accessed 6 June 2015.
39. Atlantic Johnes Disease Initiative. 2015. Available: http://www.atlanticjohnes.ca. Accessed 6 June 2015.
40. Dubé C, Ribble C, Kelton D, McNab B. Comparing network analysis measures to determine potential epidemic size of highly contagious exotic diseases in fragmented monthly networks of dairy cattle movements in Ontario, Canada. Transbound Emerg Dis. 2008;55:382-92. doi: 10.1111/j.1865-1682. 2008.01053.x PMID: 18840200
41. Donnelly CA, Nouvellet P. The contribution of badgers to confirmed tuberculosis in cattle in high-incidence areas in England. PLoSCurr. 2013;5. doi: 10.1371/currents.outbreaks. 097a904d3f3619db2fe78d24bc776098
42. Green DM, Kiss IZ, Mitchell AP, Kao RR. Estimates for local and movement-based transmission of bovine tuberculosis in British cattle. Proc Biol Sci. The Royal Society; 2008;275:1001-5. doi: 10.1098/rspb.2007.1601 PMID: 18252669
43. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, etal. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011;364:730-9. doi: 10.1056/NEJMoa1003176 PMID: 21345102
44. Animal Industry Market Information System trade database. 2013. Available: http://www.dairyinfo.gc. ca/index e.php?s1=dff-fcil&s2=imp-exp&s3=gen. Accessed 6 June 2015.