Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic

Emerging Microbes and Infections

Volumn 2, Issue , 2013, Pages

  Fittipaldi, Nahuel ^a,f   Tyrrell, Gregory J ^b   Low, Donald E ^c   Martin, Irene ^d   Lin, David ^e   Hari, Kumar L ^e   Musser, James M ^a  

^a HOUSTON METHODIST HOSPITAL   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

^c MOUNT SINAI HOSPITAL   (Canada)

^d PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^e cBio Inc   (United States)

^f PUBLIC HEALTH ONTARIO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL INFECTION; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM ISOLATION; BIOINFORMATICS; CANADA; CLONING; EPIDEMIC; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOME; HUMAN; NONHUMAN; PRIORITY JOURNAL; STREPTOCOCCUS GROUP A; UNITED STATES;

BACTERIA (MICROORGANISMS); STREPTOCOCCUS SP. 'GROUP A';

EID: 84879384151     PISSN: None     EISSN: 22221751     Source Type: Journal    
DOI: 10.1038/emi.2013.13     Document Type: Article

References (38)

1. Dasgupta A, Banerjee R, Das S, Basak S. Evolutionary perspective on the origin of Haitian cholera outbreak strain. J Biomol Struct Dyn 2012; 30: 338-346.
2. Chin CS, Sorenson J, Harris JB et al. The origin of the Haitian cholera outbreak strain. N Engl J Med 2011; 364: 33-42.
3. Gardy JL, Johnston JC, Ho Sui SJ et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011; 364: 730-739.
4. Gilmour MW, Graham M, van Domselaar G et al. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 2010; 11: 120.
5. Rasko DA, Webster DR, Sahl JW et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011; 365: 709-717.
6. Rohde H, Qin J, Cui Y et al. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011; 365: 718-724.
7. Beres SB, Carroll RK, Shea PR et al. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci USA 2010; 107: 4371-4376.
8. Fittipaldi N, Beres SB, Olsen RJ et al. Full-genome dissection of an epidemic of severe invasive disease caused by a hypervirulent, recently emerged clone of group A Streptococcus. Am J Pathol 2012; 180: 1522-1534.
9. Shea PR, Beres SB, Flores AR et al. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations. Proc Natl Acad Sci USA 2011; 108: 5039-5044.
10. Loman NJ, Constantinidou C, Chan JZ et al. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 2012; 10: 599-606.
11. Otto TD. Real-time sequencing. Nat Rev Microbiol 2011; 9: 633.
12. Baldry S. Attack of the clones. Nat Rev Microbiol 2010; 8: 390.
13. Olsen RJ, Long SW, Musser JM. Bacterial genomics in infectious disease and the clinical pathology laboratory. Arch Pathol Lab Med 2012; 136: 1414-1422.
14. Olsen RJ, Shelburne SA, Musser JM. Molecular mechanisms underlying group A streptococcal pathogenesis. Cell Microbiol 2009; 11: 1-12.
15. Lancefield RC. The antigenic complex of Streptococcus haemolyticus: I. Demonstration of a type-specific substance in extracts of Streptococcus haemolyticus. J Exp Med 1928; 47: 91-103.
16. Scott JR, Pulliam WM, Hollingshead SK, Fischetti VA. Relationship of M protein genes in group A streptococci. Proc Natl Acad Sci USA 1985; 82: 1822-1826.
17. Manjula BN, Acharya AS, Fairwell T, Fischetti VA. Antigenic domains of the streptococcal Pep M5 protein. Localization of epitopes crossreactive with type 6 M protein and identification of a hypervariable region of the M molecule. J Exp Med1986; 163: 129-138.
18. Tyrrell GJ, Lovgren M, St Jean T et al. Epidemic of group A Streptococcus M/emm59 causing invasive disease in Canada. Clin Infect Dis 2010; 51: 1290-1297.
19. Fittipaldi N, Olsen RJ, Beres SB, van Beneden C, Musser JM. Genomic analysis of emm59 group A Streptococcus invasive strains, United States. Emerg Infect Dis 2012; 18: 650-652.
20. Blankenberg D, von Kuster G, Coraor N et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010; Chapter 19: Unit 19.10.1-21.
21. Giardine B, Riemer C, Hardison RC et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005; 15: 1451-1455.
22. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010; 11: R86.
23. Lassmann T, Hayashizaki Y, Daub CO. TagDust - a program to eliminate artifacts from next generation sequencing data. Bioinformatics 2009; 25: 2839-2840.
24. Nusbaum C, Ohsumi TK, Gomez J et al. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat Methods 2009; 6: 67-69.
25. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18: 821-829.
26. Altschul SF, Madden TL, Schaffer AA et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic AcidsRes 1997; 25: 3389-3402.
27. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673-4680.
28. Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006; 23: 254-267.
29. Chevenet F, Brun C, Banuls AL, Jacq B, Christen R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 2006; 7: 439.
30. Mutreja A, Kim DW, Thomson NR et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 2011; 477: 462-465.
31. Beres SB, Musser JM. Contribution of exogenous genetic elements to the group A Streptococcus metagenome. PLoS ONE 2007; 2: e800.
32. Churchward G. The two faces of Janus: virulence gene regulation by CovR/S in group A streptococci. Mol Microbiol 2007; 64: 34-41.
33. Luo F, Lizano S, Banik S, Zhang H, Bessen DE. Role of Mga in group A streptococcal infection at the skin epithelium. Microb Pathog 2008; 45: 217-224.
34. Hondorp ER, McIver KS. The Mga virulence regulon: infection where the grass is greener. Mol Microbiol 2007; 66: 1056-1065.
35. Koser CU, Holden MT, Ellington MJ et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med 2012; 366: 2267-2275.
36. Georgiades K. Genomics of epidemic pathogens. Clin Microbiol Infect 2012; 18: 213-217.
37. Dettman JR, Rodrigue N, Melnyk AH, Wong A, Bailey SF, Kassen R. Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol Ecol 2012; 21: 2058-2077.
38. Musser JM, Shelburne SA 3rd. A decade of molecular pathogenomic analysis of group A Streptococcus. J Clin Invest 2009; 119: 2455-2463.