BacWGSTdb, a database for genotyping and source tracking bacterial pathogens

Nucleic Acids Research

Volumn 44, Issue D1, 2016, Pages D682-D687

  Ruan, Zhi ^a   Feng, Ye ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIUM ISOLATION; DATA ANALYSIS; GENE SEQUENCE; GENOTYPE; GEOGRAPHY; MICROBIOLOGICAL EXAMINATION; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; TIME; BACTERIUM; CLASSIFICATION; GENOMICS; GENOTYPING TECHNIQUE; ISOLATION AND PURIFICATION; NUCLEIC ACID DATABASE; PROCEDURES;

BACTERIA; DATABASES, NUCLEIC ACID; GENOME, BACTERIAL; GENOMICS; GENOTYPING TECHNIQUES; MULTILOCUS SEQUENCE TYPING;

EID: 84976877713     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1004     Document Type: Article

References (30)

1. Maiden, M.C., Bygraves, J.A., Feil, E., Morelli, G., Russell, J.E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D.A. 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.
2. Perez-Losada, M., Cabezas, P., Castro-Nallar, E. and Crandall, K.A. (2013) Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect. Genet. Evol., 16, 38-53.
3. Aanensen, D.M. and Spratt, B.G. (2005) The multilocus sequence typing network: mlst.net. Nucleic Acids Res., 33, W728-W733.
4. Maiden, M.C. (2006) Multilocus sequence typing of bacteria. Annu. Rev. Microbiol., 60, 561-588.
5. Forde, B.M. and O'Toole, P.W. (2013) Next-generation sequencing technologies and their impact on microbial genomics. Brief. Funct. Genomics, 12, 440-453.
6. Sabat, A.J., Budimir, A., Nashev, D., Sa-Leao, R., van Dijl, J., Laurent, F., Grundmann, H. and Friedrich, A.W. (2013) Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro. Surveill., 18, 20380.
7. Bertelli, C. and Greub, G. (2013) Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin. Microbiol. Infect., 19, 803-813.
8. Torok, M.E. and Peacock, S.J. (2012) Rapid whole-genome sequencing of bacterial pathogens in the clinical microbiology laboratory-pipe dream or reality? J. Antimicrob. Chemother., 67, 2307-2308.
9. Didelot, X., Bowden, R., Wilson, D.J., Peto, T.E. and Crook, D.W. (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet., 13, 601-612.
10. Kodama, Y., Shumway, M., Leinonen, R. and International Nucleotide Sequence Database Collaboration. (2012) The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res., 40, D54-D56.
11. Silvester, N., Alako, B., Amid, C., Cerdeno-Tarraga, A., Cleland, I., Gibson, R., Goodgame, N., Ten Hoopen, P., Kay, S., Leinonen, R. et al. (2015) Content discovery and retrieval services at the European Nucleotide Archive. Nucleic Acids Res., 43, D23-D29.
12. Maiden, M.C., Jansen van Rensburg, M.J., Bray, J.E., Earle, S.G., Ford, S.A., Jolley, K.A. and McCarthy, N.D. (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nat. Rev. Microbiol., 11, 728-736.
13. Jolley, K.A. and Maiden, M.C. (2014) Using multilocus sequence typing to study bacterial variation: prospects in the genomic era. Future Microbiol., 9, 623-630.
14. Jolley, K.A. and Maiden, M.C. (2013) Automated extraction of typing information for bacterial pathogens from whole genome sequence data: Neisseria meningitidis as an exemplar. Euro. Surveill., 18, 20379.
15. Jolley, K.A. and Maiden, M.C. (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinform., 11, 595.
16. Sheppard, S.K., Jolley, K.A. and Maiden, M.C. (2012) A gene-by-gene approach to bacterial population genomics: whole genome MLST of campylobacter. Genes (Basel), 3, 261-277.
17. Tamura, K., Nei, M. and Kumar, S. (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. U.S.A., 101, 11030-11035.
18. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
19. Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S. and Madden, T.L. (2008) NCBI BLAST: a better web interface. Nucleic Acids Res., 36, W5-W9.
20. Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C. and Salzberg, S.L. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12.
21. Sheneman, L., Evans, J. and Foster, J.A. (2006) Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics, 22, 2823-2824.
22. Pethica, R., Barker, G., Kovacs, T. and Gough, J. (2010) TreeVector: scalable, interactive, phylogenetic trees for the web. PLoS One, 5, e8934.
23. Benson, D.A., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2015) GenBank. Nucleic Acids Res., 43, D30-D35.
24. Wattam, A.R., Abraham, D., Dalay, O., Disz, T.L., Driscoll, T., Gabbard, J.L., Gillespie, J.J., Gough, R., Hix, D., Kenyon, R. et al. (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res., 42, D581-D591.
25. Adams-Haduch, J.M., Onuoha, E.O., Bogdanovich, T., Tian, G.B., Marschall, J., Urban, C.M., Spellberg, B.J., Rhee, D., Halstead, D.C., Pasculle, A.W. et al. (2011) Molecular epidemiology of carbapenem-nonsusceptible Acinetobacter baumannii in the United States. J. Clin. Microbiol., 49, 3849-3854.
26. Wright, M.S., Haft, D.H., Harkins, D.M., Perez, F., Hujer, K.M., Bajaksouzian, S., Benard, M.F., Jacobs, M.R., Bonomo, R.A. and Adams, M.D. (2014) New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. Mbio, 5, doi:10.1128/mBio.00963-13.
27. Ruan, Z., Chen, Y., Jiang, Y., Zhou, H., Zhou, Z., Fu, Y., Wang, H., Wang, Y. and Yu, Y. (2013) Wide distribution of CC92 carbapenem-resistant and OXA-23-producing Acinetobacter baumannii in multiple provinces of China. Int. J. Antimicrob. Agents, 42, 322-328.
28. Lee, H.Y., Chen, C.L., Wu, S.R., Huang, C.W. and Chiu, C.H. (2014) Risk factors and outcome analysis of acinetobacter baumannii complex bacteremia in critical patients. Crit. Care Med., 42, 1081-1088.
29. Wang, N., Ozer, E.A., Mandel, M.J. and Hauser, A.R. (2014) Genome-wide identification of Acinetobacter baumannii genes necessary for persistence in the lung. Mbio, 5, doi:10.1128/mBio.01163-14.
30. Wen, H., Wang, K., Liu, Y., Tay, M., Lauro, F.M., Huang, H., Wu, H., Liang, H., Ding, Y., Givskov, M. et al. (2014) Population dynamics of an Acinetobacter baumannii clonal complex during colonization of patients. J. Clin. Microbiol., 52, 3200-3208.