Systems-Based Approach for Optimization of Assembly-Free Bacterial MLST Mapping

Natasha Pavlovikj, Joao Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson

Research output: Contribution to journalArticlepeer-review


Epidemiological surveillance of bacterial pathogens requires real-time data analysis with a fast turnaround, while aiming at generating two main outcomes: (1) species-level identification and (2) variant mapping at different levels of genotypic resolution for population-based tracking and surveillance, in addition to predicting traits such as antimicrobial resistance (AMR). Multi-locus sequence typing (MLST) aids this process by identifying sequence types (ST) based on seven ubiquitous genome-scattered loci. In this paper, we selected one assembly-dependent and one assembly-free method for ST mapping and applied them with the default settings and ST schemes they are distributed with, and systematically assessed their accuracy and scalability across a wide array of phylogenetically divergent Public Health-relevant bacterial pathogens with available MLST databases. Our data show that the optimal k-mer length for stringMLST is species-specific and that genome-intrinsic and-extrinsic features can affect the performance and accuracy of the program. Although suitable parameters could be identified for most organisms, there were instances where this program may not be directly deployable in its current format. Next, we integrated stringMLST into our freely available and scalable hierarchical-based population genomics platform, ProkEvo, and further demonstrated how the implementation facilitates automated, reproducible bacterial population analysis.

Original languageEnglish (US)
Article number670
Issue number5
StatePublished - May 2022


  • MLST
  • ProkEvo
  • genomic epidemiology
  • k-mer lengths
  • multi-locus sequence typing
  • parameter-tunning
  • public health
  • stringMLST
  • surveillance
  • whole-genome sequencing
  • zoonotic pathogens

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • General Biochemistry, Genetics and Molecular Biology
  • Space and Planetary Science
  • Palaeontology


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