NGMASTER:in silico multi-antigen sequence typing for Neisseria gonorrhoeae

Jason C Kwong; Anders Gonçalves da Silva; Kristin Dyet; Deborah A Williamson; Timothy P Stinear; Benjamin P Howden; Torsten Seemann

doi:10.1099/mgen.0.000076

NGMASTER:in silico multi-antigen sequence typing for Neisseria gonorrhoeae

Microb Genom. 2016 Aug 25;2(8):e000076. doi: 10.1099/mgen.0.000076. eCollection 2016 Aug.

Authors

Jason C Kwong^{1

2

3}, Anders Gonçalves da Silva^{2

3}, Kristin Dyet⁴, Deborah A Williamson³, Timothy P Stinear^{2

1}, Benjamin P Howden^{2

1

3}, Torsten Seemann^{2

5}

Affiliations

¹ 2Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia.
² 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia.
³ 3Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia.
⁴ 4Institute of Environmental Science and Research, Wellington, New Zealand.
⁵ 5Victorian Life Sciences Computation Initiative, University of Melbourne, Carlton, Australia.

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.

Keywords: In silico typing; Multi-antigen sequence typing; NG-MAST; Neisseria gonorrhoeae; Whole-genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Typing Techniques / methods*
Genome, Bacterial / genetics*
Neisseria gonorrhoeae / genetics*
Sequence Analysis, DNA*
Software*