Using single-nucleotide polymorphisms to discriminate disease-associated from carried genomes of Neisseria meningitidis

Journal of Bacteriology

Volumn 193, Issue 14, 2011, Pages 3633-3641

  Katz, Lee S ^a,b   Sharma, Nitya V ^a   Harcourt, Brian H ^b   Wang, Jennifer Dolan Thomas ^b   Mayer, Leonard W ^b   Jordan, I King ^a,c  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^c PanAmerican Bioinformatics Institute   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM ISOLATE; COMPARATIVE STUDY; CONTROLLED STUDY; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; NEISSERIA MENINGITIDIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SYMBIOSIS;

BASE SEQUENCE; CARRIER STATE; GENETIC VARIATION; GENOME, BACTERIAL; HUMANS; MENINGOCOCCAL INFECTIONS; MOLECULAR SEQUENCE DATA; NEISSERIA MENINGITIDIS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; VIRULENCE;

BACTERIA (MICROORGANISMS); NEISSERIA MENINGITIDIS;

EID: 79960394176     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01198-10     Document Type: Article

References (52)

1. Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Angellotti, M. C., S. B. Bhuiyan, G. Chen, and X. F. Wan. 2007. CodonO: codon usage bias analysis within and across genomes. Nucleic Acids Res. 35:W132-W136.
3. Benjamin, W. H., Jr., J. Yother, P. Hall, and D. E. Briles. 1991. The Salmonella typhimurium locus mviA regulates virulence in Itys but not Ityr mice: functional mviA results in avirulence; mutant (nonfunctional) mviA results in virulence. J. Exp. Med. 174:1073-1083.
4. Bentley, S. D., et al. 2007. Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18. PLoS Genet. 3:e23.
5. Bille, E., et al. 2005. A chromosomally integrated bacteriophage in invasive meningococci. J. Exp. Med. 201:1905-1913.
6. Castillo-Davis, C. I., and D. L. Hartl. 2003. GeneMerge-post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 19:891-892.
7. Chen, L., et al. 2005. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 33:D325-D328.
8. Claus, H., M. C. Maiden, R. Maag, M. Frosch, and U. Vogel. 2002. Many carried meningococci lack the genes required for capsule synthesis and transport. Microbiology 148:1813-1819.
9. Claus, H., et al. 2005. Genetic analysis of meningococci carried by children and young adults. J. Infect. Dis. 191:1263-1271.
10. Darling, A. C., B. Mau, F. R. Blattner, and N. T. Perna. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394-1403.
11. Davila, S., et al. 2010. Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease. Nat. Genet. 42:772-776.
12. Dolan-Livengood, J. M., Y. K. Miller, L. E. Martin, R. Urwin, and D. S. Stephens. 2003. Genetic basis for nongroupable Neisseria meningitidis. J. Infect. Dis. 187:1616-1628.
13. Dull, P. M., et al. 2005. Neisseria meningitidis serogroup W-135 carriage among US travelers to the 2001 Hajj. J. Infect. Dis. 191:33-39.
14. Emanuelsson, O., S. Brunak, G. von Heijne, and H. Nielsen. 2007. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2:953-971.
15. Holmes, E. C., R. Urwin, and M. C. Maiden. 1999. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol. Biol. Evol. 16:741-749.
16. Hotopp, J. C., et al. 2006. Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes. Microbiology 152:3733-3749.
17. Hudson, R. R., M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589.
18. Inoue, A., et al. 2008. Involvement of an essential gene, mviN, in murein synthesis in Escherichia coli. J. Bacteriol. 190:7298-7301.
19. Jolley, K. A., D. J. Wilson, P. Kriz, G. McVean, and M. C. Maiden. 2005. The influence of mutation, recombination, population history, and selection on patterns of genetic diversity in Neisseria meningitidis. Mol. Biol. Evol. 22: 562-569.
20. Joseph, B., et al. 2010. Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence. J. Bacteriol. 192:5363-5377.
21. Juncker, A. S., et al. 2003. Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci. 12:1652-1662.
22. Kingsford, C. L., K. Ayanbule, and S. L. Salzberg. 2007. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol. 8:R22.
23. Kislyuk, A. O., et al. 2010. A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics 26:1819-1826.
24. Kumar, S., M. Nei, J. Dudley, and K. Tamura. 2008. MEGA: a biologistcentric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 9:299-306.
25. Lingappa, J. R., et al. 2003. Serogroup W-135 meningococcal disease during the Hajj, 2000. Emerg. Infect. Dis. 9:665-671.
26. Maiden, M. C., et al. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U. S. A. 95:3140-3145.
27. Maiden, M. C. J., and D. A. Caugant. 2006. The population biology of Neisseria meningitidis: implications for meningococcal disease, epidemiology and control, p. 17-35. In M. Frosch and M. C. J. Maiden (ed.), Handbook of meningococcal disease: infection biology, vaccination, clinical management. Wiley-VCH Verlag GmbH & Co., Weinheim, Germany.
28. Margulies, M., et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376-380.
29. Mayer, L. W., et al. 2002. Outbreak of W135 meningococcal disease in 2000: not emergence of a new W135 strain but clonal expansion within the electophoretic type-37 complex. J. Infect. Dis. 185:1596-1605.
30. Meyers, L. A., B. R. Levin, A. R. Richardson, and I. Stojiljkovic. 2003. Epidemiology, hypermutation, within-host evolution and the virulence of Neisseria meningitidis. Proc. Biol. Sci. 270:1667-1677.
31. Parkhill, J., et al. 2000. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404:502-506.
32. Peng, J., et al. 2008. Characterization of ST-4821 complex, a unique Neisseria meningitidis clone. Genomics 91:78-87.
33. Perrin, A., et al. 2002. Comparative genomics identifies the genetic islands that distinguish Neisseria meningitidis, the agent of cerebrospinal meningitis, from other Neisseria species. Infect. Immun. 70:7063-7072.
34. Pop, M., A. Phillippy, A. L. Delcher, and S. L. Salzberg. 2004. Comparative genome assembly. Brief. Bioinform. 5:237-248.
35. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
36. Pruitt, K. D., T. Tatusova, and D. R. Maglott. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61-D65.
37. Rangannan, V., and M. Bansal. 2010. High-quality annotation of promoter regions for 913 bacterial genomes. Bioinformatics 26:3043-3050.
38. Rosenstein, N. E., B. A. Perkins, D. S. Stephens, T. Popovic, and J. M. Hughes. 2001. Meningococcal disease. N. Engl. J. Med. 344:1378-1388.
39. Rusniok, C., et al. 2009. NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis. Genome Biol. 10:R110.
40. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
41. Scarselli, M., et al. 2006. Neisseria meningitidis NhhA is a multifunctional trimeric autotransporter adhesin. Mol. Microbiol. 61:631-644.
42. Schoen, C., et al. 2008. Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. Proc. Natl. Acad. Sci. U. S. A. 105:3473-3478.
43. Reference deleted.
44. Sjolinder, H., J. Eriksson, L. Maudsdotter, H. Aro, and A. B. Jonsson. 2008. Meningococcal outer membrane protein NhhA is essential for colonization and disease by preventing phagocytosis and complement attack. Infect. Immun. 76:5412-5420.
45. Snyder, L. A., and N. J. Saunders. 2006. The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated 'virulence genes.' BMC Genomics 7:128.
46. Stabler, R. A., et al. 2005. Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species. Microbiology 151:2907-2922.
47. Stein, L. D., et al. 2002. The generic genome browser: a building block for a model organism system database. Genome Res. 12:1599-1610.
48. Tettelin, H., et al. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287:1809-1815.
49. Thompson, J. D., T. J. Gibson, and D. G. Higgins. 2002. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinform. 2:2.3.
50. Vernikos, G. S., and J. Parkhill. 2006. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22:2196-2203.
51. Yang, J., L. Chen, L. Sun, J. Yu, and Q. Jin. 2008. VFDB 2008 release: an enhanced Web-based resource for comparative pathogenomics. Nucleic Acids Res. 36:D539-D542.
52. Zdobnov, E. M., and R. Apweiler. 2001. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.