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Volume 10, Issue 1

pyngoST: fast, simultaneous and accurate multiple sequence typing of genome collections Open Access

Abstract

Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), multi-antigen sequence typing (NG-MAST) and sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.

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Keyword(s): genome assemblies , Neisseria gonorrhoeae , population structure and sequence typing
Funding
This study was supported by the:
  • Ministerio de Ciencia e Innovación (Award PRE2021-098199)
    • Principle Award Recipient: AndreaSanchez-Serrano
  • Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital, Generalitat Valenciana (Award CISEJI/2022/66)
    • Principle Award Recipient: LeonorSanchez-Buso
  • Conselleria de Sanitat Universal i Salut Pública (Award CDEI-06/20-B)
    • Principle Award Recipient: LeonorSanchez-Buso
  • Ministerio de Ciencia e Innovación (Award PID2020-120113RA-I00/AEI/10.13039/501100011033)
    • Principle Award Recipient: LeonorSanchez-Buso
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-01-30
2024-12-05
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pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections
M Gen 10, 001189 (2024); https://doi.org/10.1099/mgen.0.001189
/content/journal/mgen/10.1099/mgen.0.001189
/content/journal/mgen/10.1099/mgen.0.001189
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