stringMLST: a fast k-mer based tool for multilocus sequence typing

Bioinformatics
Anuj GuptaLavanya Rishishwar

Abstract

Rapid and accurate identification of the sequence type (ST) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. Cheaper and faster next-generation sequencing (NGS) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (MLST). But data generated by NGS platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate's ST can be determined. These are computationally intensive and time consuming steps, which are not ideally suited for real-time molecular epidemiology. Here, we present stringMLST, an assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. The program implements a simple hash table data structure to find exact matches between short sequence strings (k-mers) and an MLST allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools. The source code and documentations are available at http://jordan.biology.gatech.edu/page/software/stringMLST CONTACT: lavanya.rishishwar@gatech.eduSupplementary information: ...Continue Reading

References

Apr 18, 1998·Proceedings of the National Academy of Sciences of the United States of America·M C MaidenB G Spratt
Jan 16, 2007·International Journal of Systematic and Evolutionary Microbiology·Johan GorisJames M Tiedje
Jul 31, 2007·Future Microbiology·Eija K Hyytiä-TreesPeter Gerner-Smidt
Dec 15, 2010·BMC Bioinformatics·Keith A Jolley, Martin C J Maiden
Jan 13, 2012·Journal of Clinical Microbiology·Mette V LarsenOle Lund
Jul 13, 2012·Journal of Clinical Microbiology·Keith A JolleyMartin C J Maiden
Jul 26, 2012·BMC Genomics·Michael InouyeKathryn E Holt
Aug 28, 2013·Nature Reviews. Microbiology·Martin C J MaidenNoel D McCarthy
Nov 26, 2014·Genome Medicine·Michael InouyeKathryn E Holt

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Citations

Jan 27, 2019·Genome Research·John A LeesNicholas J Croucher
Feb 3, 2019·Applied and Environmental Microbiology·Yun WuJustin Payne
Jan 11, 2018·Microbial Genomics·Pedro FeijaoLeonid Chindelevitch
Sep 19, 2019·Proceedings of the National Academy of Sciences of the United States of America·Felix Mba MedieUNKNOWN MRSA Systems Immunobiology Group
Sep 22, 2019·Applied and Environmental Microbiology·Shaokang ZhangXiangyu Deng
Nov 24, 2019·BMC Bioinformatics·Mattia DalsassAlessandro Brozzi
Jul 4, 2020·Nucleic Acids Research·Hector F Espitia-NavarroLavanya Rishishwar
Jun 1, 2019·Critical Reviews in Microbiology·Fernando Hayashi Sant'AnnaLuciane M P Passaglia
Jun 21, 2018·PeerJ·Ignacio Ferrés, Gregorio Iraola
Oct 5, 2017·Genome Biology·Andrzej ZielezinskiWojciech M Karlowski
Jan 17, 2020·BMC Bioinformatics·Yichen HeXianming Shi
Nov 7, 2019·Parasites & Vectors·Abdulazeem Abdulsalam Ibrahim AlkhidirHarry Pickering
Feb 1, 2020·Nature Communications·Ilse M BoekhoudWiep Klaas Smits
Nov 10, 2020·Infection Control and Hospital Epidemiology : the Official Journal of the Society of Hospital Epidemiologists of America·Satoru MitsuboshiMasami Tsugita
May 4, 2020·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·N Hassoun-KheirM Paul
Jun 23, 2021·Nature Communications·Jesse C ThomasUNKNOWN Antimicrobial Resistant Neisseria gonorrhoeae Working Group

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