Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis

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• 作者：Josephine M. Bryant ; Virginie C. Thibault ; David G. E. Smith…
• 关键词：Mycobacterium avium subspecies paratuberculosis ; Johne’s disease ; Genome wide sequencing ; Phylogenomics ; Genotyping
• 刊名：BMC Genomics
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：17
• 期：1
• 全文大小：1,655 KB
• 参考文献：1.Barkema HW, Hesselink JW, McKenna SLB, Benedictus G, Groenendaal H. Global prevalence and economics of infection with Mycobacterium avium subsp. paratuberculosis in ruminants. In: Behr MA, Collins DM, editors. Paratuberculosis: organism, disease, control. Cambridge: CAB International; 2010. p. 10–21.CrossRef
  2.Motiwala AS, Amonsin A, Strother M, Manning EJ, Kapur V, Sreevatsan S. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolates recovered from wild animal species. J Clin Microbiol. 2004;42:1703–12.PubMedCentral CrossRef PubMed
  3.Hutchings MR, Stevenson K, Greig A, Davidson R, Marion G, Judge J. Infection of non-ruminant wildlife by Mycobacterium avium subsp. paratuberculosis. In: Behr MA, Collins DM, editors. Paratuberculosis: organism, disease, control. Cambridge: CAB International; 2010. p. 188–200.CrossRef
  4.Ghadiali AH, Strother M, Naser SA, Manning EJ, Sreevatsan S. Mycobacterium avium subsp. paratuberculosis strains isolated from Crohn’s disease patients and animal species exhibit similar polymorphic locus patterns. J Clin Microbiol. 2004;42:5345–8.PubMedCentral CrossRef PubMed
  5.Clarke CJ. The pathology and pathogenesis of paratuberculosis in ruminants and other species. J Comp Pathol. 1997;116:217–61.CrossRef PubMed
  6.Ghosh P, Hsu C, Alyamani EJ, Shehata MM, Al-Dubaib MA, Al-Naeem A, et al. Genome-wide analysis of the emerging infection with Mycobacterium avium subspecies paratuberculosis in the Arabian camels (Camelus dromedarius). PLoS One. 2012;7:e31947.PubMedCentral CrossRef PubMed
  7.Mackintosh C, Griffin JF. Paratuberculosis in deer, camelids and other ruminants. In: Behr MA, Collins DM, editors. Paratuberculosis: organism, disease, control. Cambridge: CAB International; 2010. p. 179–87.CrossRef
  8.Beard PM, Rhind S, Buxton D, Daniels MJ, Henderson D, Pirie A, et al. Natural paratuberculosis infection in rabbits in Scotland. J Comp Pathol. 2001;124:290–9.CrossRef PubMed
  9.Salgado M, Monti G, Sevilla I, Manning E. Association between cattle herd Mycobacterium avium subsp. paratuberculosis (MAP) infection and infection of a hare population. Trop Anim Health Prod. 2014;46:1313–6.CrossRef PubMed
  10.Naser SA, Sagramsingh SR, Naser AS, Thanigachalam S. Mycobacterium avium subspecies paratuberculosis causes Crohn’s disease in some inflammatory bowel disease patients. World J Gastroenterol. 2014;20:7403–15.PubMedCentral CrossRef PubMed
  11.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.PubMedCentral CrossRef PubMed
  12.Collins DM. Strain characterization of Mycobacterium avium subsp. paratuberculosis. In: Behr MA, Collins DM, editors. Paratuberculosis: organism, disease, control. Cambridge: CAB International; 2010. p. 294–305.CrossRef
  13.Stevenson K. Comparative differences between strains of Mycobacterium avium subsp. paratuberculosis. In: Behr MA, Collins DM, editors. Paratuberculosis: organism, disease, control. Cambridge: CAB International; 2010. p. 126–37.CrossRef
  14.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.PubMedCentral PubMed
  15.Stevenson K, Hughes VM, de Juan L, Inglis NF, Wright F, Sharp JM. Molecular characterization of pigmented and non-pigmented isolates of Mycobacterium avium subspecies paratuberculosis. J Clin Microbiol. 2002;40:1798–804.PubMedCentral CrossRef PubMed
  16.Stevenson K. Genetic diversity of Mycobacterium avium subspecies paratuberculosis and the influence of strain type on infection and pathogenesis: a review. Vet Res. 2015;46:64.PubMedCentral CrossRef PubMed
  17.de Juan L, Mateos A, Domínguez L, Sharp JM, Stevenson K. Genetic diversity of Mycobacterium avium subspecies paratuberculosis isolates from goats detected by pulsed-field gel electrophoresis. Vet Microbiol. 2005;106:249–57.CrossRef PubMed
  18.Castellanos E, Alvarez J, Aranaz A, Romero B, De Juan L, Bezos J, et al. Use of Single Nucleotide Polymorphisms in inh-A gene to characterize Mycobacterium avium subsp. paratuberculosis into Types I, II and III. In: Nielsen SS, editor. Proceedings of the Ninth International Colloquium on Paratuberculosis: 29 October - 2 November 2007; Tsukuba. Tsukuba: International Association for Paratuberculosis; 2007. p. 6–8.
  19.Castellanos E, Aranaz A, Romero B, de Juan L, Àlvarez J, Bezos J, et al. Polymorphisms in gyrA and gyrB genes among Mycobacterium avium subsp. paratuberculosis Type I, II, and III isolates. J Clin Microbiol. 2007;45:3439–42.PubMedCentral CrossRef PubMed
  20.Whittington RJ, Marsh IB, Whitlock RH. Typing of IS1311 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.CrossRef PubMed
  21.Sevilla I, Singh SV, Garrido JM, Aduriz G, Rodríguez S, Geijo MV, et al. Molecular typing of Mycobacterium avium subsp. paratuberculosis strains from different hosts and regions. Sci Tech Rev (OIE). 2005;24:1061–6.
  22.Sohal JS, Singh SV, Singh PK, Singh AV, Kumar N. A new marker IS1311 L2 PCR-REA for identification of ‘Indian Bison’ type Mycobacterium avium subspecies paratuberculosis. Indian J Biotechnol. 2013;12:204–7.
  23.Biet F, Sevilla IA, Cochard T, Lefrançois LH, Garrido JM, Heron I, et al. Inter and intra-subtype genotypic differences that differentiate Mycobacterium avium subsp. paratuberculosis strains. BMC Microbiol. 2012;12:264.PubMedCentral CrossRef PubMed
  24.Thibault VC, Grayon M, Boschiroli ML, Hubbans C, Overduin P, Stevenson K, et al. New variable number tandem repeat markers for typing Mycobacterium avium subsp. paratuberculosis and Mycobacterium avium strains: comparison with IS900 RFLP and IS1245 RFLP typing. J Clin Microbiol. 2007;45:2404–10.PubMedCentral CrossRef PubMed
  25.Mac INMV database. [http://​mac-inmv.​tours.​inra.​fr ].
  26.Semret M, Turenne CY, de Haas P, Collins DM, Behr MA. Differentiating host-associated variants of Mycobacterium avium by PCR for detection of large sequence polymorphisms. J Clin Microbiol. 2006;44:881–7.PubMedCentral CrossRef PubMed
  27.Wynne JW, Seeman T, Bulach D, Coutts SA, Talaat AM, Michalski WP. Re-sequencing the Mycobacterium avium subspecies paratuberculosis K10 genome: improved annotation and revised genome sequence. J Bacteriol. 2010;192:6319–20.PubMedCentral CrossRef PubMed
  28.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.PubMedCentral CrossRef PubMed
  29.Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science. 2010;327:469–74.PubMedCentral CrossRef PubMed
  30.Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688–90.CrossRef PubMed
  31.Drummond AJ, Rambaut A. BEAST: Bayesian Evolutionary Analysis by Sampling Trees. BMC Evol Biol. 2007;7:214.PubMedCentral CrossRef PubMed
  32.Verdugo C, Pleydell E, Price-Carter M, Prattley D, Collins D, de Lisle G, et al. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms. Prev Vet Med. 2014;117:436–46.CrossRef PubMed
  33.Moloney BJ, Whittington RJ. Cross species transmission of ovine Johne’s disease from sheep to cattle: an estimate of prevalence in exposed susceptible cattle. Aust Vet J. 2008;86:117–23.CrossRef PubMed
  34.Wynne JW, Bull TJ, Seeman T, Bulach DM, Wagner J, Kirkwood CD, et al. Exploring the zoonotic potential of Mycobacterium avium subspecies paratuberculosis through comparative genomics. PLoS One. 2011;6:e22171.PubMedCentral CrossRef PubMed
  35.Hsu C-Y, Wu C-W, Talaat AM. Genome-wide sequence variation among Mycobacterium avium subspecies paratuberculosis isolates: a better understanding of Johne’s disease transmission dynamics. Front Microbiol. 2011;2:236.PubMedCentral CrossRef PubMed
  36.Singh SV, Kumar N, Singh SN, Bhattacharya T, Sohal JS, Singh PK, et al. Genome sequence of the “Indian Bison Type” biotype of Mycobacterium avium subsp. paratuberculosis strain S5. Genome Announc. 2013;1(1):e00005–13.PubMedCentral CrossRef PubMed
  37.Bannantine JP, Wu C-W, Hsu C, Zhou S, Schwartz DC, Bayles DO, et al. Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association. BMC Genomics. 2012;13:89.PubMedCentral CrossRef PubMed
  38.Stevenson K, Àlvarez J, Bakker D, Biet F, de Juan L, Denham S, et al. Occurrence of Mycobacterium avium subspecies paratuberculosis across host species and European countries with evidence for transmission between wildlife and domestic ruminants. BMC Microbiol. 2009;9:212.PubMedCentral CrossRef PubMed
  39.Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems - an application of Simpson's index of diversity. J Clin Microbiol. 1988;26:2465–6.PubMedCentral PubMed
  40.Comas I, Homolka S, Niemann S, Gagneux S. Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies. PLoS One. 2009;4(11):e7815.PubMedCentral CrossRef PubMed
  41.Reyes J, Chan CHS, Tanaka MM. Impact of homoplasy on variable numbers of tandem repeats and spoligotypes in Mycobacterium tuberculosis. Infect Genet Evol. 2012;12:811–8.CrossRef PubMed
  42.Newsholme P, Procopio J, Lima MM, Pithon-Curi TC, Curi R. Glutamine and glutamate –their central role in cell metabolism and function. Cell Biochem Funct. 2003;21:1–9.CrossRef PubMed
  43.Carroll P, Pashley CA, Parish T. Functional analysis of GlnE, an essential adenylyl transferase in Mycobacterium tuberculosis. J Bacteriol. 2008;190:4894–902.PubMedCentral CrossRef PubMed
  44.Parish T, Stoker NG. glnE is an essential gene in Mycobacterium tuberculosis. J Bacteriol. 2000;182:5715–20.PubMedCentral CrossRef PubMed
  45.Malhotra V, Tyagi JS, Clark-Curtiss JE. DevR-mediated adaptive response in Mycobacterium tuberculosis H37Ra: links to asparagine metabolism. Tuberculosis (Edinb). 2009;89:169–74.CrossRef
  46.Bull TJ, Schock A, Sharp JM, Greene M, McKendrick IJ, Sales J, et al. Genomic variations associated with attenuation in Mycobacterium avium subsp. paratuberculosis vaccine strains. BMC Microbiol. 2013;13:11.PubMedCentral CrossRef PubMed
  47.Domenech P, Reed MB, Barry 3rd CE. Contribution of the Mycobacterium tuberculosis MmpL protein family to virulence and drug resistance. Infect Immun. 2005;73:3492–501.PubMedCentral CrossRef PubMed
  48.Betts JC, Lukey PT, Rob LC, McAdam RA, Duncan K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol. 2002;43:717–31.CrossRef PubMed
  49.Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, et al. Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis. 2013;13:100.CrossRef
  50.Bannantine JP, Zhang Q, Li LL, Kapur V. Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates. BMC Microbiol. 2003;3:10.PubMedCentral CrossRef PubMed
  51.Beste DJ, Espasa M, Bonde B, Kierzek AM, Stewart GR, McFadden J. The genetic requirements for fast and slow growth in mycobacteria. PLoS One. 2009;4(4):e5349.PubMedCentral CrossRef PubMed
  52.Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26:1641–50.PubMedCentral CrossRef PubMed
  53.Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol. 2010;27:2038–51.PubMedCentral CrossRef PubMed
  
• 作者单位：Josephine M. Bryant (1) (2)
  Virginie C. Thibault (3)
  David G. E. Smith (3) (4)
  Joyce McLuckie (3)
  Ian Heron (3)
  Iker A. Sevilla (5)
  Franck Biet (6)
  Simon R. Harris (1)
  Duncan J. Maskell (7)
  Stephen D. Bentley (1)
  Julian Parkhill (1)
  Karen Stevenson (3)
  
  1. Wellcome Trust Sanger Institute, Genome Campus, Cambridge, UK
  2. Division of Infection and Immunity, University College London, London, UK
  3. Moredun Research Institute, Pentlands Science Park, Penicuik, EH26 0PZ, UK
  4. Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, G12 8QQ, UK
  5. Neiker-tecnalia, Dpto. de Producción y Sanidad Animal, Berreaga 1, 48160, Derio, Bizkaia, Spain
  6. INRA, UMR1282, Infectiologie Santé Publique (ISP-311), F-37380, Nouzilly, France
  7. Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne’s disease in livestock. Determining genetic diversity is prerequisite to understanding the epidemiology and biology of Map. We performed the first whole genome sequencing (WGS) of 141 global Map isolates that encompass the main molecular strain types currently reported. We investigated the phylogeny of the Map strains, the diversity of the genome and the limitations of commonly used genotyping methods.