Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing

BMC Microbiology

Volumn 13, Issue 1, 2013, Pages

  Underwood, Anthony P ^a   Jones, Garan ^a,b   Mentasti, Massimo ^a   Fry, Norman K ^a   Harrison, Timothy G ^a  

^a PUBLIC HEALTH ENGLAND   (United Kingdom)

^b UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

Clustering; Legionella pneumophila; Population structure; Recombination; Sequence based typing; Whole genome sequencing

Indexed keywords

ARTICLE; BACTERIAL MUTATION; BACTERIAL STRAIN; BACTERIUM ISOLATE; DISEASE SEVERITY; GENE FREQUENCY; GENE MAPPING; GENE SEQUENCE; HELICOBACTER PYLORI; HORIZONTAL GENE TRANSFER; INTERMETHOD COMPARISON; LEGIONELLA PNEUMOPHILA; LEGIONNAIRE DISEASE; MOLECULAR EVOLUTION; NEISSERIA MENINGITIDIS; NONHUMAN; PHYLOGENY; POPULATION STRUCTURE; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE;

LEGIONELLA PNEUMOPHILA;

DNA, BACTERIAL; GENETIC VARIATION; GENOME, BACTERIAL; HUMANS; LEGIONELLA PNEUMOPHILA; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; MOLECULAR TYPING; SEQUENCE ANALYSIS, DNA;

EID: 84890837667     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-13-302     Document Type: Article

References (54)

1. Taxonomy and typing of legionellae. Harrison TG, Saunders NA, Reviews in Medical Microbiology 1994 5 79 10.1097/00013542-199404000-00001
2. A multicenter evaluation of genotypic methods for the epidemiologic typing of Legionella pneumophila serogroup 1: results of a pan-European study. Fry NK, Alexiou-Daniel S, Bangsborg JM, Bernander S, Castellani Pastoris M, Etienne J, Forsblom B, Gaia V, Helbig JH, Lindsay D, Christian Lück P, Pelaz C, Uldum SA, Harrison TG, Clin Microbiol Infect 1999 5 462 477 10.1111/j.1469-0691.1999.tb00176.x 11856290
3. Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation. Gaia V, Fry NK, Harrison TG, Peduzzi R, J Clin Microbiol 2003 41 2932 2939 10.1128/JCM.41.7.2932-2939.2003 12843023
4. Consensus sequence-based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila. Gaia V, Fry NK, Afshar B, Lück PC, Meugnier H, Etienne J, Peduzzi R, Harrison TG, J Clin Microbiol 2005 43 2047 2052 10.1128/JCM.43.5.2047-2052.2005 15872220
5. Multilocus sequence typing for global surveillance of meningococcal disease. Brehony C, Jolley KA, Maiden MCJ, FEMS Microbiol Rev 2007 31 15 26 10.1111/j.1574-6976.2006.00056.x 17168997
6. Distribution of Legionella pneumophila serogroups, monoclonal antibody subgroups and DNA sequence types in recent clinical and environmental isolates from England and Wales (2000-2008). Harrison TG, Afshar B, Doshi N, Fry NK, Lee JV, Eur J Clin Microbiol Infect Dis 2009 28 781 791 10.1007/s10096-009-0705-9 19156453
7. Sequence-based typing of Legionella pneumophila serogroup 1 clinical isolates from Belgium between 2000 and 2010. Vekens E, Soetens O, De Mendonça R, Echahidi F, Roisin S, Deplano A, Eeckhout L, Achtergael W, Piérard D, Denis O, Wybo I, Euro Surveill 2012 17 20302 23137466
8. Sequences, sequence clusters and bacterial species. Hanage WP, Fraser C, Spratt BG, Philos Trans R Soc Lond B Biol Sci 2006 361 1917 1927 10.1098/rstb.2006.1917 17062411
9. Genetic structure of populations of Legionella pneumophila. Selander RK, McKinney RM, Whittam TS, Bibb WF, Brenner DJ, Nolte FS, Pattison PE, J Bacteriol 1985 163 1021 1037 4030689
10. Mosaic structure of pathogenicity islands in Legionella pneumophila. Ko KS, Lee HK, Park M-Y, Kook Y-H, J Mol Evol 2003 57 63 72 10.1007/s00239-002- 2452-8 12962307
11. Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain). Coscollá M, Gosalbes MJ, Catalán V, González-Candelas F, Environ Microbiol 2006 8 1056 1063 10.1111/j.1462-2920.2006.00997.x 16689726
12. Clonal population structure of Legionella pneumophila inferred from allelic profiling. Edwards MT, Fry NK, Harrison TG, Microbiology (Reading, Engl) 2008 154 852 864 10.1099/mic.0.2007/012336-0
13. Population structure and recombination in environmental isolates of Legionella pneumophila. Coscollá M, González-Candelas F, Environ Microbiol 2007 9 643 656 10.1111/j.1462-2920.2006.01184.x 17298365
14. Comparison of clinical and environmental samples of Legionella pneumophila at the nucleotide sequence level. Coscollá M, González-Candelas F, Infect Genet Evol 2009 9 882 888 10.1016/j.meegid.2009.05.013 19465160
15. Molecular evolution of key genes for type II secretion in Legionella pneumophila. Costa J, d'Avó AF, da Costa MS, Veríssimo A, Environ Microbiol 2012 14 2017 2033 10.1111/j.1462-2920.2011.02646.x 22118294
16. Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Coscollá M, Comas I, González-Candelas F, Mol Biol Evol 2011 28 985 1001 10.1093/molbev/msq278 20961962
17. Legionella pneumophila: population genetics, phylogeny and genomics. Gomez-Valero L, Rusniok C, Buchrieser C, Infect Genet Evol 2009 9 727 739 10.1016/j.meegid.2009.05.004 19450709
18. Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence-based scheme for typing Legionella pneumophila serogroup 1 strains. Ratzow S, Gaia V, Helbig JH, Fry NK, Lück PC, J Clin Microbiol 2007 45 1965 1968 10.1128/JCM.00261-07 17409215
19. The impact of homologous recombination on the generation of diversity in bacteria. Hanage WP, Fraser C, Spratt BG, J Theor Biol 2006 239 210 219 10.1016/j.jtbi.2005.08.035 16236325
20. How clonal are bacteria? Smith JM, Smith NH, O'Rourke M, Spratt BG, Proc Natl Acad Sci USA 1993 90 4384 4388 10.1073/pnas.90.10.4384 8506277
21. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H, Tuanyok A, Price EP, Glass MB, Leadem B, Beckstrom-Sternberg JS, Allan GJ, Foster JT, Wagner DM, Okinaka RT, Sim SH, Pearson O, Wu Z, Chang J, Kaul R, Hoffmaster AR, Brettin TS, Robison RA, Mayo M, Gee JE, Tan P, Currie BJ, Keim P, BMC Biol 2009 7 78 10.1186/1741-7007-7-78 19922616
22. An African origin for the intimate association between humans and Helicobacter pylori. Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, Falush D, Stamer C, Prugnolle F, van der Merwe SW, Yamaoka Y, Graham DY, Perez-Trallero E, Wadstrom T, Suerbaum S, Achtman M, Nature 2007 445 915 918 10.1038/nature05562 17287725
23. Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes. Gomez-Valero L, Rusniok C, Jarraud S, Vacherie B, Rouy Z, Barbe V, Médigue C, Etienne J, Buchrieser C, BMC Genomics 2011 12 536 10.1186/1471-2164-12-536 22044686
24. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Stamatakis A, Ludwig T, Meier H, Bioinformatics 2005 21 456 463 10.1093/bioinformatics/bti191 15608047
25. FastTree 2-approximately maximum-likelihood trees for large alignments. Price MN, Dehal PS, Arkin AP, PLoS ONE 2010 5 9490 10.1371/journal.pone.0009490 20224823
26. Displaying the relatedness among isolates of bacterial species-the eBURST approach. Spratt BG, Hanage WP, Li B, Aanensen DM, Feil EJ, FEMS Microbiol Lett 2004 241 129 134 10.1016/j.femsle.2004.11.015 15598523
27. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. Corander J, Marttinen P, Sirén J, Tang J, BMC Bioinformatics 2008 9 539 10.1186/1471-2105-9-539 19087322
28. Bayesian identification of admixture events using multilocus molecular markers. Corander J, Marttinen P, Mol Ecol 2006 15 2833 2843 10.1111/j.1365-294X.2006.02994.x 16911204
29. Identifying currents in the gene pool for bacterial populations using an integrative approach. Tang J, Hanage WP, Fraser C, Corander J, PLoS Comput Biol 2009 5 1000455 10.1371/journal.pcbi.1000455 19662158
30. Dendroscope: An interactive viewer for large phylogenetic trees. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R, BMC Bioinformatics 2007 8 460 10.1186/1471-2105-8-460 18034891
31. Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity. Cazalet C, Rusniok C, Brüggemann H, Zidane N, Magnier A, Ma L, Tichit M, Jarraud S, Bouchier C, Vandenesch F, Kunst F, Etienne J, Glaser P, Buchrieser C, Nat Genet 2004 36 1165 1173 10.1038/ng1447 15467720
32. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. Reuter S, Harrison TG, Köser CU, Ellington MJ, Smith GP, Parkhill J, Peacock SJ, Bentley SD, Török ME, BMJ Open 2013 3 002175 23306006
33. Legionella pneumophila strain 130b possesses a unique combination of type IV secretion systems and novel Dot/Icm secretion system effector proteins. Schroeder GN, Petty NK, Mousnier A, Harding CR, Vogrin AJ, Wee B, Fry NK, Harrison TG, Newton HJ, Thomson NR, Beatson SA, Dougan G, Hartland EL, Frankel G, J Bacteriol 2010 192 6001 6016 10.1128/JB.00778-10 20833813
34. Identification and characterization of a new conjugation/type IVA secretion system (trb/tra) of Legionella pneumophila Corby localized on two mobile genomic islands. Glöckner G, Albert-Weissenberger C, Weinmann E, Jacobi S, Schunder E, Steinert M, Hacker J, Heuner K, Int J Med Microbiol 2008 298 411 428 10.1016/j.ijmm.2007.07.012 17888731
35. Legionella pneumophila pangenome reveals strain-specific virulence factors. D'Auria G, Jiménez-Hernández N, Peris-Bondia F, Moya A, Latorre A, BMC Genomics 2010 11 181 10.1186/1471-2164-11-181 20236513
36. The genomic sequence of the accidental pathogen Legionella pneumophila. Chien M, Morozova I, Shi S, Sheng H, Chen J, Gomez SM, Asamani G, Hill K, Nuara J, Feder M, Rineer J, Greenberg JJ, Steshenko V, Park SH, Zhao B, Teplitskaya E, Edwards JR, Pampou S, Georghiou A, Chou I-C, Iannuccilli W, Ulz ME, Kim DH, Geringer-Sameth A, Goldsberry C, Morozov P, Fischer SG, Segal G, Qu X, Rzhetsky A, et al. Science 2004 305 1966 1968 10.1126/science.1099776 15448271
37. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. Alikhan N-F, Petty NK, Ben Zakour NL, Beatson SA, BMC Genomics 2011 12 402 10.1186/1471-2164-12-402 21824423
38. A comparison of virulence of two strains of Legionella pneumophila based on experimental aerosol infection of guinea-pigs. Jepras RI, Fitzgeorge RB, Baskerville A, J Hyg (Lond) 1985 95 29 38 10.1017/S0022172400062252 4020112
39. When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum. Osborn AM, Böltner D, Plasmid 2002 48 202 212 10.1016/S0147-619X(02)00117-8 12460536
40. Sequence type analysis and recombinational tests (START). Jolley KA, Feil EJ, Chan MS, Maiden MC, Bioinformatics 2001 17 1230 1231 10.1093/ bioinformatics/17.12.1230 11751234
41. Inference of bacterial microevolution using multilocus sequence data. Didelot X, Falush D, Genetics 2007 175 1251 1266 17151252
42. A comparison of homologous recombination rates in bacteria and archaea. Vos M, Didelot X, ISME J 2009 3 199 208 10.1038/ismej.2008.93 18830278
43. RDP3: a flexible and fast computer program for analyzing recombination. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P, Bioinformatics 2010 26 2462 2463 10.1093/bioinformatics/btq467 20798170
44. R Core Team, R: a Language and Environment for Statistical Computing Vienna, Austria: R Foundation for Statistical Computing 2013
45. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino DR, Birney E, Genome Res 2008 18 821 829 10.1101/gr.074492.107 18349386
46. Scaffolding pre-assembled contigs using SSPACE. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W, Bioinformatics 2011 27 578 579 10.1093/bioinformatics/btq683 21149342
47. The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup, Bioinformatics 2009 25 2078 2079 10.1093/bioinformatics/btp352 19505943
48. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Langmead B, Trapnell C, Pop M, Salzberg SL, Genome Biol 2009 10 25 10.1186/gb-2009-10-3-r25 19261174
49. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Li W, Godzik A, Bioinformatics 2006 22 1658 1659 10.1093/bioinformatics/btl158 16731699
50. Identifying bacterial genes and endosymbiont DNA with Glimmer. Delcher AL, Bratke KA, Powers EC, Salzberg SL, Bioinformatics 2007 23 673 679 10.1093/bioinformatics/btm009 17237039
51. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
52. PHYLIP-Phylogeny Inference Package (Version 3.2). Felsenstein J, Cladistics 1989 5 164 166
53. a Python library for phylogenetic computing. Sukumaran J, Holder MT, Dendro P, Bioinformatics 2010 26 1569 1571 10.1093/bioinformatics/btq228 20421198
54. BioRuby: bioinformatics software for the Ruby programming language. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T, Bioinformatics 2010 26 2617 2619 10.1093/bioinformatics/btq475 20739307