1887

Abstract

Whole-genome sequencing (WGS) provides the highest resolution analysis for comparison of bacterial isolates in public health microbiology. However, although increasingly being used routinely for some pathogens such as Listeria monocytogenes and Salmonella enterica, the use of WGS is still limited for other organisms, such as Neisseria gonorrhoeae. Multi-antigen sequence typing (NG-MAST) is the most widely performed typing method for epidemiological surveillance of gonorrhoea. Here, we present NGMASTER, a command-line software tool for performing in silico NG-MAST on assembled genome data. NGMASTER rapidly and accurately determined the NG-MAST of 630 assembled genomes, facilitating comparisons between WGS and previously published gonorrhoea epidemiological studies. The source code and user documentation are available at https://github.com/MDU-PHL/ngmaster.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000076
2016-08-25
2019-09-18
Loading full text...

Full text loading...

/deliver/fulltext/mgen/2/8/mgen000076.html?itemId=/content/journal/mgen/10.1099/mgen.0.000076&mimeType=html&fmt=ahah

References

  1. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S. et al. 2012; SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  2. Bolger A. M., Lohse M., Usadel B.. 2014; Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  3. CDC 2013; Antibiotic Resistance Threats in the United States, 2013 Atlanta, GA, USA: Centers for Disease Control and Prevention, US Department of Health and Human Services;
    [Google Scholar]
  4. Chung G. T., Yoo J. S., Oh H. B., Lee Y. S., Cha S. H., Kim S. J., Yoo C. K.. 2008; Complete genome sequence of Neisseria gonorrhoeae NCCP11945. J Bacteriol190:6035–6036 [CrossRef][PubMed]
    [Google Scholar]
  5. Cock P. J., Antao T., Chang J. T., Chapman B. A., Cox C. J., Dalke A., Friedberg I., Hamelryck T., Kauff F. et al. 2009; Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics25:1422–1423 [CrossRef][PubMed]
    [Google Scholar]
  6. Demczuk W., Lynch T., Martin I., Van Domselaar G., Graham M., Bharat A., Allen V., Hoang L., Lefebvre B. et al. 2015; Whole-genome phylogenomic heterogeneity of Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in Canada between 1989 and 2013. J Clin Microbiol53:191–200 [CrossRef][PubMed]
    [Google Scholar]
  7. Demczuk W., Martin I., Peterson S., Bharat A., Van Domselaar G., Graham M., Lefebvre B., Allen V., Hoang L. et al. 2016; Genomic epidemiology and molecular resistance mechanisms of Azithromycin-resistant Neisseria gonorrhoeae in Canada from 1997 to 2014. J Clin Microbiol54:1304–1313 [CrossRef][PubMed]
    [Google Scholar]
  8. Ezewudo M. N., Joseph S. J., Castillo-Ramirez S., Dean D., Del Rio C., Didelot X., Dillon J. A., Selden R. F., Shafer W. M. et al. 2015; Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. Peer J3:e806 [CrossRef][PubMed]
    [Google Scholar]
  9. Grad Y. H., Kirkcaldy R. D., Trees D., Dordel J., Harris S. R., Goldstein E., Weinstock H., Parkhill J., Hanage W. P. et al. 2014; Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. Lancet Infect Dis14:220–226 [CrossRef][PubMed]
    [Google Scholar]
  10. Heymans R., Golparian D., Bruisten S. M., Schouls L. M., Unemo M.. 2012; Evaluation of Neisseria gonorrhoeae multiple-locus variable-number tandem-repeat analysis, N. gonorrhoeae multiantigen sequence typing, and full-length porB gene sequence analysis for molecular epidemiological typing. J Clin Microbiol50:180–183 [CrossRef][PubMed]
    [Google Scholar]
  11. Li D., Liu C. M., Luo R., Sadakane K., Lam T. W.. 2015; MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics31:1674–1676 [CrossRef][PubMed]
    [Google Scholar]
  12. Martin I. M., Ison C. A., Aanensen D. M., Fenton K. A., Spratt B. G.. 2004; Rapid sequence-based identification of gonococcal transmission clusters in a large metropolitan area. J Infect Dis189:1497–1505 [CrossRef][PubMed]
    [Google Scholar]
  13. Unemo M., Dillon J. A.. 2011; Review and international recommendation of methods for typing Neisseria gonorrhoeae isolates and their implications for improved knowledge of gonococcal epidemiology, treatment, and biology. Clin Microbiol Rev24:447–458 [CrossRef][PubMed]
    [Google Scholar]
  14. WHO 2014; Antimicrobial resistance: global report on surveillance 2014. Geneva, Switzerland: : World Health Organization;
    [Google Scholar]
  15. Walker B. J., Abeel T., Shea T., Priest M., Abouelliel A., Sakthikumar S., Cuomo C. A., Zeng Q., Wortman J. et al. 2014; Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One9:e112963 [CrossRef][PubMed]
    [Google Scholar]
  16. Chung, G. T., Yoo, J. S., Oh, H. B., Lee, Y. S., Cha, S. H., Kim, S. J. & Yoo, C. K. ENA BioProject accession PRJNA29335 2008
  17. Demczuk, W., Lynch, T., Martin, I., Van Domselaar, G., Graham, M., Bharat, A., Allen, V., Hoang, L., Lefebvre, B., Tyrrell, G., Horsman, G., Haldane, D., Garceau, R., Wylie, J., Wong, T. & Mulvey, M. R. ENA BioProject accession PRJNA266539 2015
  18. Demczuk, W., Martin, I., Peterson, S., Bharat, A., Van Domselaar, G., Graham, M., Lefebvre, B., Allen, V., Hoang, L., Tyrrell, G., Horsman, G., Wylie, J., Haldane, D., Archibald, C., Wong, T., Unemo, M. & Mulvey, M. R. ENA BioProject accession PRJNA298332 2016
  19. Grad, Y. H., Kirkcaldy, R. D., Trees, D., Dordel, J., Harris, S. R., Goldstein, E., Weinstock, H., Parkhill, J., Hanage, W. P., Bentley, S. & Lipsitch, M. ENA BioProject accession PRJEB2999 2014
  20. Kwong, J. C., Gonçalves da Silva, A., Dyet, K., Williamson, D. W., Stinear, T. P., Howden, B. P. & Seemann, T. ENA BioProject PRJEB14168 2016
  21. Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B. & de Hoon, M. J. Biopython.http://biopython.org/ 2009
  22. Aanensen, D. NG-MAST database.http://www.ng-mast.net/ 2004
  23. Kwong, J. C., Gonçalves da Silva, A., & Seemann, T. NGMASTER (v0.3).https://github.com/MDU-PHL/ngmaster 2016
  24. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic (v0.35).http://www.usadellab.org/cms/?page=trimmomatic 2014
  25. Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT (v1.0.3).https://github.com/voutcn/megahit 2015
  26. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A. & Pevzner, P. A. SPAdes (vvvvvvvv3.7.1).http://bioinf.spbau.ru/spades 2012
  27. Seemann, T. Snippy (v3.1).https://github.com/tseemann/snippy 2016
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000076
Loading
/content/journal/mgen/10.1099/mgen.0.000076
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error