PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Liu, Yen Yi ^a   Chiou, Chien Shun ^a   Chen, Chih Chieh ^b  

^a CENTER FOR DISEASE CONTROL   (Taiwan)

^b NATIONAL SUN YAT SEN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; GENETIC DATABASE; GENETICS; INTERNET; MULTILOCUS SEQUENCE TYPING; PROCEDURES; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; WHOLE GENOME SEQUENCING;

ALLELES; BACTERIAL TYPING TECHNIQUES; DATABASES, GENETIC; GENOME, BACTERIAL; INTERNET; MULTILOCUS SEQUENCE TYPING; SALMONELLA TYPHIMURIUM; WHOLE GENOME SEQUENCING;

EID: 84994750616     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep36213     Document Type: Article

References (25)

1. Swaminathan, B., Barrett, T. J., Hunter, S. B., Tauxe, R. V. & Force, C. D. C. P. T. PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis 7, 382-389, doi: 10.3201/eid0703.010303 (2001).
2. Chiou, C. S. Multilocus variable-number tandem repeat analysis as a molecular tool for subtyping and phylogenetic analysis of bacterial pathogens. Expert Review of Molecular Diagnostics 10, 5-7, doi: 10.1586/Erm.09.76 (2010).
3. Chiou, C. S. et al. A simple approach to obtain comparable Shigella sonnei MLVA results across laboratories. International Journal of Medical Microbiology 303, 678-684, doi: 10.1016/j. ijmm.2013.09.008 (2013).
4. Jonathan, S. B., Michael, G. & Adam, M. Whole-genome sequencing detection of ongoing contamination at a restaurant, Rhode Island, USA, 2014. Emerg Infect Dis 22, 1474, doi: 10.3201/eid2208.151917 (2016).
5. Jackson, B. R. et al. Implementation of nationwide real-time whole-genome sequencing to enhance Listeriosis outbreak detection and investigation. Clin. Infect. Dis. 63, 380-386, doi: 10.1093/cid/ciw242 (2016).
6. Zerbino, D. R. & Birney, E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18, 821-829, doi: 10.1101/gr.074492.107 (2008).
7. Bankevich, A. et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology 19, 455-477, doi: 10.1089/cmb.2012.0021 (2012).
8. Luo, R. B. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, doi: Artn 1810.1186/2047-217x-1-18 (2012).
9. Leekitcharoenphon, P. et al. snpTree-a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics 13 Suppl 7, S6, doi: 10.1186/1471-2164-13-S7-S6 (2012).
10. Taylor, A. J. et al. Characterization of foodborne outbreaks of Salmonella enterica serovar Enteritidis with whole-genome sequencing single nucleotide polymorphism-based analysis for surveillance and outbreak detection. J. Clin. Microbiol. 53, 3334-3340, doi: 10.1128/JCM.01280-15 (2015).
11. de Been, M. et al. A core genome MLST scheme for high-resolution typing of Enterococcus faecium. J Clin Microbiol, doi: 10.1128/ JCM.01946-15 (2015).
12. Cheng, J., Cao, F. & Liu, Z. AGP: a multimethods web server for alignment-free genome phylogeny. Mol Biol Evol 30, 1032-1037, doi: 10.1093/molbev/mst021 (2013).
13. Snipen, L. & Ussery, D. W. Standard operating procedure for computing pangenome trees. Stand Genomic Sci 2, 135-141, doi: 10.4056/sigs.38923 (2010).
14. Jolley, K. A. & Maiden, M. C. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC bioinformatics 11, 595, doi: 10.1186/1471-2105-11-595 (2010).
15. Pang, S. et al. Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella enterica Serovar Typhimurium. J Clin Microbiol 50, 727-734, doi: 10.1128/JCM.01284-11 (2012).
16. Schork, N. J., Fallin, D. & Lanchbury, J. S. Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet 58, 250-264 (2000).
17. Collins, A., Lonjou, C. & Morton, N. E. Genetic epidemiology of single-nucleotide polymorphisms. Proceedings of the National Academy of Sciences of the United States of America 96, 15173-15177, doi: 10.1073/pnas.96.26.15173 (1999).
18. Maiden, M. C. et al. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 11, 728-736, doi: 10.1038/ nrmicro3093 (2013).
19. Aanensen, D. M. & Spratt, B. G. The multilocus sequence typing network: mlst. net. Nucleic Acids Res 33, W728-W733, doi: 10.1093/ nar/gki415 (2005).
20. Leekitcharoenphon, P., Nielsen, E. M., Kaas, R. S., Lund, O. & Aarestrup, F. M. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PloS one 9, e87991, doi: 10.1371/journal. pone.0087991 (2014).
21. Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069, doi: 10.1093/bioinformatics/btu153 (2014).
22. Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691-3693, doi: 10.1093/bioinformatics/ btv421 (2015).
23. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410, doi: 10.1016/S0022-2836(05)80360-2 (1990).
24. Huerta-Cepas, J., Dopazo, J. & Gabaldon, T. ETE: a python Environment for Tree Exploration. BMC bioinformatics 11, 24, doi: 10.1186/1471-2105-11-24 (2010).
25. Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368-376 (1981).