MentaLiST - A fast MLST caller for large MLST schemes

Microb Genom. 2018 Feb;4(2):e000146. doi: 10.1099/mgen.0.000146. Epub 2018 Jan 10.

Abstract

MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.

Keywords: multi-locus sequence typing; next-generation sequencing; pathogen surveillance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Bacterial Typing Techniques / methods*
  • Disease Outbreaks
  • Enterococcus faecium / genetics
  • Epidemiological Monitoring
  • Foodborne Diseases / microbiology
  • Genes, Essential
  • Genome, Bacterial
  • Humans
  • Molecular Epidemiology / methods
  • Multilocus Sequence Typing / instrumentation*
  • Multilocus Sequence Typing / methods*
  • Mycobacterium tuberculosis / genetics
  • Salmonella / genetics
  • Software
  • Time Factors
  • Whole Genome Sequencing