SuperPhy: Predictive genomics for the bacterial pathogen Escherichia coli

BMC Microbiology

Volumn 16, Issue 1, 2016, Pages

  Whiteside, Matthew D ^a   Laing, Chad R ^a   Manji, Akiff ^a   Kruczkiewicz, Peter ^a   Taboada, Eduardo N ^a   Gannon, Victor P J ^a  

^a PUBLIC HEALTH AGENCY OF CANADA   (Canada)

Author keywords

Anti microbial resistance; Bioinformatics; Comparative genomics; Epidemiology; Population genomics; Software; Virulence factors

Indexed keywords

BIOLOGICAL MARKER; VIRULENCE FACTOR;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; CLADISTICS; CONTROLLED STUDY; DATA ANALYSIS; ESCHERICHIA COLI; GENETIC DATABASE; GENOME ANALYSIS; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HOST PATHOGEN INTERACTION; MOLECULAR PHYLOGENY; NONHUMAN; PREDICTION; PROMOTER REGION; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SUPERPHY DATABASE; DNA SEQUENCE; GENETICS; GENOMICS; NUCLEIC ACID DATABASE; PHENOTYPE; PROCEDURES; SOFTWARE;

DATABASES, NUCLEIC ACID; DRUG RESISTANCE, BACTERIAL; ESCHERICHIA COLI; GENOME, BACTERIAL; GENOMICS; PHENOTYPE; SEQUENCE ANALYSIS, DNA; SOFTWARE; VIRULENCE FACTORS;

EID: 84964968206     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/s12866-016-0680-0     Document Type: Article

References (47)

1. Jones B. Technology: nanopore sequencing for clinical diagnostics. Nat Rev Genet. 2015;16:68.
2. Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev. 2015;28:541-63.
3. Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016 Feb 11;530(7589):228.
4. Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, Nair S, Neal K, Nye K, Peters T, Pinna ED, Robinson E, Struthers K, Webber M, Catto A, Dallman TJ, Hawkey P, Loman NJ. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 2015;16:114.
5. Graham RMA, Doyle CJ, Jennison AV. Real-time investigation of a legionella pneumophila outbreak using whole genome sequencing. Epidemiol Infect. 2014;142:2347-51.
6. Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O, Larsen MV, Aarestrup FM. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother. 2013;68:771-7.
7. Cody AJ, McCarthy ND, Jansen van Rensburg M, Isinkaye T, Bentley SD, Parkhill J, et al. Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing. J Clin Microbiol. 2013 Aug;51(8):2526-34.
8. Andreevskaya M, Johansson P, Laine P, Smolander O-P, Sonck M, Rahkila R, Jääskeläinen E, Paulin L, Auvinen P, Björkroth J. Genome sequence and transcriptome analysis of meat-spoilage-associated lactic acid bacterium lactococcus piscium MKFS47. Appl Environ Microbiol. 2015;81:3800-11.
9. Mazzaglia A, Studholme DJ, Taratufolo MC, Cai R, Almeida NF, Goodman T, Guttman DS, Vinatzer BA, Balestra GM. Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS ONE. 2012;7:e36518.
10. Nasser W, Beres SB, Olsen RJ, Dean MA, Rice KA, Long SW, Kristinsson KG, Gottfredsson M, Vuopio J, Raisanen K, Caugant DA, Steinbakk M, Low DE, McGeer A, Darenberg J, Henriques-Normark B, Beneden CAV, Hoffmann S, Musser JM. Evolutionary pathway to increased virulence and epidemic group A streptococcus disease derived from 3,615 genome sequences. Proc Natl Acad Sci. 2014;111:E1768-76.
11. Kopac S, Wang Z, Wiedenbeck J, Sherry J, Wu M, Cohan FM. Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis. Appl Environ Microbiol. 2014 Aug;80(16):4842-53.
12. Zhang S, Yin Y, Jones MB, Zhang Z, Kaiser BLD, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol. 2015;53:1685-92.
13. Halachev MR, Chan JZ, Constantinidou CI, Cumley N, Bradley C, Smith-Banks M, Oppenheim B, Pallen MJ. Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant acinetobacter baumannii in Birmingham, England. Genome Med. 2014;6:70.
14. Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol. 2014;15:538.
15. Jr WMD, Westblade LF, Ford B. Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis. 2012;31:1719-26.
16. Biek R, O'Hare A, Wright D, Mallon T, McCormick C, Orton RJ, McDowell S, Trewby H, Skuce RA, Kao RR. Whole genome sequencing reveals local transmission patterns of mycobacterium bovis in sympatric cattle and badger populations. PLoS Pathog. 2012;8, e1003008.
17. Lemke AA, Harris-Wai JN. Stakeholder engagement in policy development: challenges and opportunities for human genomics. Genet Med. 2015 Dec; 17(12):949-57.
18. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJC, Yoo HS, Zhang C, Zhang Y, Sobral BW. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2013;42:D581-91.
19. Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fevre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Medigue C. MicroScope-an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res. 2012;41:D636-47.
20. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2013;42:D560-7.
21. Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11:595.
22. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15(11):524.
23. Riley DR, Angiuoli SV, Crabtree J, Hotopp JCD, Tettelin H. Using Sybil for interactive comparative genomics of microbes on the web. Bioinformatics. 2012;28:160-6.
24. Fricke WF, Rasko DA. Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions. Nat Rev Genet. 2014;15:49-55.
25. Sherry NL, Porter JL, Seemann T, Watkins A, Stinear TP, Howden BP. Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory. J Clin Microbiol. 2013;51:1396-401.
26. Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VPJ. Pan-genome sequence analysis using panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics. 2010;11:461.
27. Mungall CJ, Emmert DB. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics. 2007;23:i337-46.
28. Racine JS. RStudio: a platform-independent IDE for r and sweave. J Appl Econ. 2012;27:167-72.
29. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-7.
30. Price MN, Dehal PS, Arkin AP. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5, e9490.
31. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, Pascale GD, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O'Brien JS, Pawlowski AC, Piddock LJV, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother. 2013;57:3348-57.
32. Chen L, Xiong Z, Sun L, Yang J, Jin Q. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 2011;40:D641-5.
33. Donnenberg M, editor. Escherichia Coli: Pathotypes and Principles of Pathogenesis. 2nd edition. Amsterdam: Academic Press; 2013.
34. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
35. Statistical Computing RF. R: A language and environment for statistical computing. Vienna: R Development Core Team; 2005.
36. Scheutz F, Teel LD, Beutin L, Piérard D, Buvens G, Karch H, Mellmann A, Caprioli A, Tozzoli R, Morabito S, Strockbine NA, Melton-Celsa AR, Sanchez M, Persson S, O'Brien AD. Multicenter evaluation of a sequence-based protocol for subtyping Shiga toxins and standardizing Stx nomenclature. J Clin Microbiol. 2012;50:2951-63.
37. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.
38. Tenaillon O, Skurnik D, Picard B, Denamur E. The population genetics of commensal escherichia coli. Nat Rev Microbiol. 2010;8:207-17.
39. Selander RK, Caugant DA, Ochman H, Musser JM, Gilmour MN, Whittam TS. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol. 1986;51:873-84.
40. Goullet P, Picard B. Comparative electrophoretic polymorphism of esterases and other enzymes in escherichia coli. J Gen Microbiol. 1989;135:135-43.
41. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev. 2005;15:589-94.
42. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced escherichia coli genomes. Microb Ecol. 2010;60:708-20.
43. Gordienko EN, Kazanov MD, Gelfand MS. Evolution of pan-genomes of escherichia coli, shigella spp. and salmonella enterica. J Bacteriol. 2013;195:2786-92.
44. Pupo GM, Lan R, Reeves PR. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci U S A. 2000;97:10567-72.
45. Sahl JW, Morris CR, Emberger J, Fraser CM, Ochieng JB, Juma J, Fields B, Breiman RF, Gilmour M, Nataro JP, Rasko DA. Defining the phylogenomics of Shigella species: a pathway to diagnostics. J Clin Microbiol. 2015;53:951-60.
46. Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M, Finlay BB. Recent advances in understanding enteric pathogenic escherichia coli. Clin Microbiol Rev. 2013;26:822-80.
47. Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, McLaughlin SF, Henkhaus JK, Leopold B, Bielaszewska M, Prager R, Brzoska PM, Moore RL, Guenther S, Rothberg JM, Karch H. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS ONE. 2011;6, e22751.