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

ABSTRACT: 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 divergen

SUBMITTER: Pavlovikj N 

PROVIDER: S-EPMC9147691 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature