Veterinary Research Communications

, Volume 41, Issue 2, pp 113–128 | Cite as

Investigation of intra-herd spread of Mycobacterium caprae in cattle by generation and use of a whole-genome sequence

  • S. Broeckl
  • S. Krebs
  • A. Varadharajan
  • R. K. Straubinger
  • H. Blum
  • M. Buettner
Original Article

Abstract

Single nucleotide polymorphisms (SNPs) calculated from whole genome sequencing (WGS) are ideally suited to study evolutionary relationships of pathogens and their epidemiology. Mycobacterium caprae infections have been documented frequently in cattle and red deer along the Bavarian and Austrian Alps during the last decade. However, little is still known about the transmission within cattle holdings and possible alterations of the genomes of M. caprae during such events. The aim of this study was to study the molecular epidemiology of bovine tuberculosis (bTB) in selected herds based on isolate-specific genome-wide SNPs and to perform a phylogenetic network analysis. In total, 61 M. caprae isolates were collected originating from eight cattle farms over a period of twelve years between 2004 and 2015. Analysis of their sequence data revealed that the M. caprae isolates of an affected farm differ at all in a few SNPs. In contrast, many more SNPs were found when comparing the M. caprae genomes originating from different herds. The results demonstrated that the spread of bTB in the affected farms occurred by direct transmission between the members of each herd rather than between herds and a M. caprae introduction in farms after contact events e. g. on summer pastures can readily be traced by WGS analysis. Furthermore, we assembled a nearly complete whole genome sequence of M. caprae derived from several cattle isolates originating from bTB cases in the Bavarian Alpine region.

Keywords

Mycobacterium caprae Bovine tuberculosis (bTB) Whole genome sequencing (WGS) Molecular epidemiology Single nucleotide polymorphism (SNP) Cattle 

Supplementary material

11259_2017_9679_MOESM1_ESM.pdf (204 kb)
ESM 1(PDF 204 kb)
11259_2017_9679_MOESM2_ESM.xlsx (19 kb)
ESM 2(XLSX 19 kb)
11259_2017_9679_MOESM3_ESM.xlsx (15 kb)
ESM 3(XLSX 15 kb)
11259_2017_9679_MOESM4_ESM.pdf (268 kb)
ESM 4(PDF 268 kb)

References

  1. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061–1073. doi:10.1038/nature09534 CrossRefPubMedGoogle Scholar
  2. Alam I, Antunes A, Kamau AA, Ba alawi W, Kalkatawi M, Stingl U, Bajic VB, Hernandez-Lemus E (2013) INDIGO – INtegrated data warehouse of MIcrobial GenOmes with examples from the Red Sea extremophiles. PLoS One 8(12):e82210. doi:10.1371/journal.pone.0082210 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Aranaz A, Cousins D, Mateos A, Domínguez L (2003) Elevation of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to species rank as Mycobacterium caprae comb. Nov., sp. nov. Int J Syst Evol Microbiol 53(Pt 6):1785–1789. doi:10.1099/ijs.0.02532-0 CrossRefPubMedGoogle Scholar
  4. Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16(1):37–48CrossRefPubMedGoogle Scholar
  5. Barlow ND, Kean JM, Hickling G, Livingstone PG, Robson AB (1997) A simulation model for the spread of bovine tuberculosis within New Zealand cattle herds. Prev Vet Med 32(1–2):57–75. doi:10.1016/S0167-5877(97)00002-0 CrossRefPubMedGoogle Scholar
  6. Biek R, O'Hare A, Wright D, Mallon T, McCormick C, Orton RJ, McDowell S, Trewby H, Skuce RA, Kao RR (2012) Whole genome sequencing reveals local transmission patterns of Mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathog 8(11):e1003008. doi:10.1371/journal.ppat.1003008 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Brooks-Pollock E, Roberts GO, Keeling MJ (2014) A dynamic model of bovine tuberculosis spread and control in great Britain. Nature 511(7508):228–231. doi:10.1038/nature13529 CrossRefPubMedGoogle Scholar
  8. Bryant JM, Harris SR, Parkhill J, Dawson R, Diacon AH, van Helden P, Pym A, Mahayiddin AA, Chuchottaworn C, Sanne IM, Louw C, Boeree MJ, Hoelscher M, McHugh TD, Bateson ALC, Hunt RD, Mwaigwisya S, Wright L, Gillespie SH, Bentley SD (2013a) Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study. Lancet Respir Med 1(10):786–792. doi:10.1016/S2213-2600(13)70231-5 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Bryant JM, Schurch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, Kremer K, van Hijum SA, Siezen RJ, Borgdorff M, Bentley SD, Parkhill J, van Soolingen D (2013b) Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data. BMC Infect Dis 13:110. doi:10.1186/1471-2334-13-110 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA (2012) Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28(4):464–469. doi:10.1093/bioinformatics/btr703 CrossRefPubMedGoogle Scholar
  11. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393(6685):537–544. doi:10.1038/31159 CrossRefPubMedGoogle Scholar
  12. Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, Harris SR, Niemann S, Diel R, Aseffa A, Gao Q, Young D, Gagneux S (2013) Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet 45(10):1176–1182. doi:10.1038/ng.2744 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Conlan AJK, McKinley TJ, Karolemeas K, Pollock EB, Goodchild AV, Mitchell AP, Birch CPD, Clifton-Hadley RS, Wood JLN (2012) Estimating the hidden burden of bovine tuberculosis in great Britain. PLoS Comput Biol 8(10):e1002730. doi:10.1371/journal.pcbi.1002730 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Copin R, Coscollá M, Seiffert SN, Bothamley G, Sutherland J, Mbayo G, Gagneux S, Ernst JD (2014) Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. MBio 5(1):13. doi:10.1128/mBio.00960-13 CrossRefGoogle Scholar
  15. de La Fuente J, Díez-Delgado I, Contreras M, Vicente J, Cabezas-Cruz A, Manrique M, Tobes R, López V, Romero B, Domínguez L, Garrido JM, Juste R, Gortazar C (2015) Complete genome sequences of field isolates of Mycobacterium bovis and Mycobacterium caprae. Genome Announc 3(3). doi:10.1128/genomeA.00247-15
  16. de La Rua-Domenech R, Goodchild AT, Vordermeier HM, Hewinson RG, Christiansen KH, Clifton-Hadley RS (2006) Ante mortem diagnosis of tuberculosis in cattle: a review of the tuberculin tests, gamma-interferon assay and other ancillary diagnostic techniques. Res Vet Sci 81(2):190–210. doi:10.1016/j.rvsc.2005.11.005 CrossRefPubMedGoogle Scholar
  17. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43(5):491–498. doi:10.1038/ng.806 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Domogalla J, Prodinger WM, Blum H, Krebs S, Gellert S, Müller M, Neuendorf E, Sedlmaier F, Büttner M (2013) Region of difference 4 in alpine Mycobacterium caprae isolates indicates three variants. J Clin Microbiol 51(5):1381–1388. doi:10.1128/JCM.02966-12 CrossRefPubMedPubMedCentralGoogle Scholar
  19. Eisenberg T, Nesseler A, Sauerwald C, Kling U, Riße K, Kaim U, Althoff G, Fiege N, Schlez K, Hamann H-P, Fawzy A, Moser I, Riße R, Kraft G, Zschöck M, Menge C (2015) Mycobacterium tuberculosis exposure of livestock in a German dairy farm: implications for intra vitam diagnosis of bovine tuberculosis in an officially tuberculosis-free country. Epidemiol Infect:1–8. doi:10.1017/S0950268815001995
  20. European Commission (1996) 97/76/EC: Commission Decision of 17 December 1996 laying down the methods of control for maintaining the officially tuberculosis free status of bovine herds in certain Member States and regions of Member States (Text with EEA relevance). CELEX number: 31997D0076. Official Journal L 019, 22/01/1997:34–36Google Scholar
  21. Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred II error probabilities. Genome Res 8(3):186–194. doi:10.1101/gr.8.3.186 CrossRefPubMedGoogle Scholar
  22. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces UsingPhred I. Accuracy assessment. Genome Res 8(3):175–185. doi:10.1101/gr.8.3.175 CrossRefPubMedGoogle Scholar
  23. Federal Research Institute for Animal Health (2016) Official collection of methods for the sampling and investigation of materials of animal origin for notifiable animal diseases (method collection). pp. 1–22. https://openagrar.bmel-forschung.de/receive/openagrar_mods_00005698
  24. Fink M, Schleicher C, Gonano M, Prodinger WM, Pacciarini M, Glawischnig W, Ryser-Degiorgis M-P, Walzer C, Stalder GL, Lombardo D, Schobesberger H, Winter P, Büttner M (2015) Red deer as maintenance host for bovine tuberculosis, alpine region. Emerg Infect Dis 21(3):464–467. doi:10.3201/eid2103.141119 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Fischer EAJ, van Roermund HJW, Hemerik L, van Asseldonk MAPM, de Jong MCM (2005) Evaluation of surveillance strategies for bovine tuberculosis (Mycobacterium bovis) using an individual based epidemiological model. Prev Vet Med 67(4):283–301. doi:10.1016/j.prevetmed.2004.12.002 CrossRefPubMedGoogle Scholar
  26. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJM, Brinkman FSL, Brunham RC, Tang P (2011) Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 364(8):730–739. doi:10.1056/NEJMoa1003176 CrossRefPubMedGoogle Scholar
  27. Gilbert M, Mitchell A, Bourn D, Mawdsley J, Clifton-Hadley R, Wint W (2005) Cattle movements and bovine tuberculosis in great Britain. Nature 435(7041):491–496. doi:10.1038/nature03548 CrossRefPubMedGoogle Scholar
  28. Goodchild AV, Clifton-Hadley RS (2001) Cattle-to-cattle transmission of Mycobacterium bovis. Tuberculosis (Edinb) 81(1–2):23–41. doi:10.1054/tube.2000.0256 CrossRefGoogle Scholar
  29. Groenen PM, Bunschoten AE, van Soolingen D, van Embden JD (1993) Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method. Mol Microbiol 10(5):1057–1065CrossRefPubMedGoogle Scholar
  30. Guerra-Assunção JA, Crampin AC, Houben R, Mzembe T, Mallard K, Coll F, Khan P, Banda L, Chiwaya A, Pereira RP, McNerney R, Fine PE, Parkhill J, Clark TG, Glynn, JR (2015) Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. eLife 4:110. doi: 10.7554/eLife.05166
  31. Hall LMC (2006) Hypermutable bacteria isolated from humans - a critical analysis. Microbiology 152(9):2505–2514. doi:10.1099/mic.0.29079-0 CrossRefPubMedGoogle Scholar
  32. Henkle E, Winthrop KL (2015) Nontuberculous mycobacteria infections in immunosuppressed hosts. Clin Chest Med 36(1):91–99. doi:10.1016/j.ccm.2014.11.002 CrossRefPubMedGoogle Scholar
  33. Hermans PW, van Soolingen D, Bik EM, de Haas PE, Dale JW, van Embden JD (1991) Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect Immun 59(8):2695–2705PubMedPubMedCentralGoogle Scholar
  34. Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S, Blaser MJ (2008) High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 6(12):e311. doi:10.1371/journal.pbio.0060311 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Humblet MF, Boschiroli ML, Saegerman C (2009) Classification of worldwide bovine tuberculosis risk factors in cattle: a stratified approach. Vet Res 40(5). doi:10.1051/vetres/2009033
  36. James BW, Williams A, Marsh PD (2000) The physiology and pathogenicity of Mycobacterium tuberculosis grown under controlled conditions in a defined medium. J Appl Microbiol 88(4):669–677. doi:10.1046/j.1365-2672.2000.01020.x CrossRefPubMedGoogle Scholar
  37. Jarzembowski, Young (2008) Nontuberculous Mycobacterial Infections. Archives of Pathology & Laboratory Medicine (No. 8):1333–1341Google Scholar
  38. Johnston WT, Gettinby G, Cox DR, Donnelly CA, Bourne J, Clifton-Hadley R, Le Fevre AM, McInerney JP, Mitchell A, Morrison WI, Woodroffe R (2005) Herd-level risk factors associated with tuberculosis breakdowns among cattle herds in England before the 2001 foot-and-mouth disease epidemic. Biol Lett 1(1):53–56. doi:10.1098/rsbl.2004.0249 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Kalkatawi M, Alam I, Bajic VB (2015) BEACON: automated tool for bacterial GEnome annotation ComparisON. BMC Genomics 16(1):493. doi:10.1186/s12864-015-1826-4 CrossRefGoogle Scholar
  40. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J (1997) Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 35(4):907–914PubMedPubMedCentralGoogle Scholar
  41. King HC, Murphy A, James P, Travis E, Porter D, Hung YJ, Sawyer J, Cork J, Delahay RJ, Gaze W, Courtenay O, Wellington EM (2015) The variability and seasonality of the environmental reservoir of Mycobacterium Bovis shed by wild European badgers. Sci Report 5:12318. doi:10.1038/srep12318 CrossRefGoogle Scholar
  42. Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23(10):1289–1291. doi:10.1093/bioinformatics/btm091 CrossRefPubMedGoogle Scholar
  43. Lin S-H, Liao Y-C, Watson M (2013) CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 8(3):e60843. doi:10.1371/journal.pone.0060843 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Magdalena J, Supply P, Locht C (1998) Specific differentiation between Mycobacterium bovis BCG and virulent strains of the Mycobacterium tuberculosis complex. J Clin Microbiol 36(9):2471–2476PubMedPubMedCentralGoogle Scholar
  45. Namouchi A, Didelot X, Schöck U, Gicquel B, Rocha EPC (2012) After the bottleneck: genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res 22(4):721–734. doi:10.1101/gr.129544.111 CrossRefPubMedPubMedCentralGoogle Scholar
  46. O'brien DJ, Schmitt SM, Fitzgerald SD, Berry DE, Hickling GJ (2006) Managing the wildlife reservoir of Mycobacterium bovis: the Michigan, USA, experience. Vet Microbiol 112(2–4):313–323. doi:10.1016/j.vetmic.2005.11.014 CrossRefPubMedGoogle Scholar
  47. OIE - World Organisation for Animal Health (2012) Manual of diagnostic tests and vaccines for terrestrial animals, 7.ed. OIE, ParisGoogle Scholar
  48. Otto TD, Dillon GP, Degrave WS, Berriman M (2011) RATT: rapid annotation transfer tool. Nucleic Acids Res 39(9):e57–e57. doi:10.1093/nar/gkq1268 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Palisson A, Courcoul A, Durand B, Cunha MV (2016) Role of cattle movements in bovine tuberculosis spread in France between 2005 and 2014. PLoS One 11(3):e0152578. doi:10.1371/journal.pone.0152578 CrossRefPubMedPubMedCentralGoogle Scholar
  50. Pérez-Lago L, Comas I, Navarro Y, González-Candelas F, Herranz M, Bouza E, García-de-Viedma D (2014) Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis transmission. J Infect Dis 209(1):98–108. doi:10.1093/infdis/jit439 CrossRefPubMedGoogle Scholar
  51. Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K, Chauhan DS, Sivasubbu S, Scaria V (2015) Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome. PLoS One 10(4):e0122979. doi:10.1371/journal.pone.0122979 CrossRefPubMedPubMedCentralGoogle Scholar
  52. Phillips C, Foster C, Morris P, Teverson R (2003) The transmission of Mycobacterium bovis infection to cattle. Res Vet Sci 74(1):1–15. doi:10.1016/S0034-5288(02)00145-5 CrossRefPubMedGoogle Scholar
  53. Price MN, Dehal PS, Arkin AP (2010) FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490. doi:10.1371/journal.pone.0009490 CrossRefPubMedPubMedCentralGoogle Scholar
  54. Prodinger WM, Brandstatter A, Naumann L, Pacciarini M, Kubica T, Boschiroli ML, Aranaz A, Nagy G, Cvetnic Z, Ocepek M, Skrypnyk A, Erler W, Niemann S, Pavlik I, Moser I (2005) Characterization of Mycobacterium caprae isolates from Europe by mycobacterial interspersed repetitive unit genotyping. J Clin Microbiol 43(10):4984–4992. doi:10.1128/JCM.43.10.4984-4992.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  55. Prodinger WM, Indra A, Koksalan OK, Kilicaslan Z, Richter E (2014) Mycobacterium caprae infection in humans. Expert Rev Anti-Infect Ther 12(12):1501–1513. doi:10.1586/14787210.2014.974560 CrossRefPubMedGoogle Scholar
  56. Rettinger A, Broeckl S, Fink M, Prodinger WM, Blum H, Krebs S, Domogalla J, Just F, Gellert S, Straubinger RK, Büttner M (2015) The region of difference four is a robust genetic marker for subtyping Mycobacterium caprae isolates and is linked to spatial distribution of three subtypes. Transbound Emerg Dis. doi:10.1111/tbed.12438 PubMedGoogle Scholar
  57. Rhyan JC, Spraker TR (2010) Emergence of diseases from wildlife reservoirs. Vet Pathol 47(1):34–39. doi:10.1177/0300985809354466 CrossRefPubMedGoogle Scholar
  58. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B (2000) Artemis: sequence visualization and annotation. Bioinformatics 16(10):944–945. doi:10.1093/bioinformatics/16.10.944 CrossRefPubMedGoogle Scholar
  59. Schellner H (1956) Risk of infection incattle grazing pastures contaminated with tubercle bacilli. Rindertuberkulose 5 1956(5):179–188Google Scholar
  60. Schoepf K, Prodinger WM, Glawischnig W, Hofer E, Revilla-Fernandez S, Hofrichter J, Fritz J, Köfer J, Schmoll F (2012) A two-Years' survey on the prevalence of tuberculosis caused by Mycobacterium caprae in red deer (Cervus elaphus) in the Tyrol, Austria. ISRN Vet Sci 2012(15):1–7. doi:10.5402/2012/245138 CrossRefGoogle Scholar
  61. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069. doi:10.1093/bioinformatics/btu153 CrossRefPubMedGoogle Scholar
  62. Stein RA (2011) Super-spreaders in infectious diseases. Int J Infect Dis 15(8):e510–e513. doi:10.1016/j.ijid.2010.06.020 CrossRefPubMedGoogle Scholar
  63. Stucki D, Ballif M, Bodmer T, Coscolla M, Maurer A-M, Droz S, Butz C, Borrell S, Längle C, Feldmann J, Furrer H, Mordasini C, Helbling P, Rieder HL, Egger M, Gagneux S, Fenner L (2015) Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing. J Infect Dis 211(8):1306–1316. doi:10.1093/infdis/jiu601 CrossRefPubMedGoogle Scholar
  64. Supply P, Lesjean S, Savine E, Kremer K, van Soolingen D, Locht C (2001) Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units. J Clin Microbiol 39(10):3563–3571. doi:10.1128/JCM.39.10.3563-3571.2001 CrossRefPubMedPubMedCentralGoogle Scholar
  65. Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD (2012) A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 7(7):1260–1284. doi:10.1038/nprot.2012.068 CrossRefPubMedPubMedCentralGoogle Scholar
  66. Tortoli E (2009) Clinical manifestations of nontuberculous mycobacteria infections. Clin Microbiol Infect 15(10):906–910. doi:10.1111/j.1469-0691.2009.03014.x CrossRefPubMedGoogle Scholar
  67. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3--new capabilities and interfaces. Nucleic Acids Res 40(15):e115. doi:10.1093/nar/gks596 CrossRefPubMedPubMedCentralGoogle Scholar
  68. Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TE (2013) Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis 13(2):137–146. doi:10.1016/S1473-3099(12)70277-3 CrossRefPubMedPubMedCentralGoogle Scholar
  69. Woolley SM, Posada D, Crandall KA, Stajich JE (2008) A comparison of phylogenetic network methods using computer simulation. PLoS One 3(4):e1913. doi:10.1371/journal.pone.0001913 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • S. Broeckl
    • 1
  • S. Krebs
    • 2
  • A. Varadharajan
    • 2
  • R. K. Straubinger
    • 3
  • H. Blum
    • 2
  • M. Buettner
    • 1
  1. 1.Bavarian Health and Food Safety AuthorityOberschleissheimGermany
  2. 2.Laboratory for Functional Genome Analysis (LAFUGA), Gene CenterLudwig-Maximilians-University (LMU) MunichMunichGermany
  3. 3.Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary MedicineLudwig-Maximilians-University (LMU) MunichMunichGermany

Personalised recommendations