SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.

SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. Appl Environ Microbiol. 2019 Sep 20;: Authors: Zhang S, Den-Bakker HC, Li S, Chen J, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X Abstract SeqSero, launched in 2015, is a software tool for Salmonella serotype determination from whole genome sequencing (WGS) data. Despite its routine use in public health and food safety laboratories in the United States and other countries, the original SeqSero pipeline is relatively slow (minutes per genome using sequencing reads), is not optimized for draft genome assemblies, and may assign multiple serotypes for a strain. Here we present SeqSero2 (github.com/denglab/SeqSero2; denglab.info/SeqSero2), an algorithmic transformation and functional update of the original SeqSero. Major improvements include: 1) additional sequence markers for identification of Salmonella species and subspecies and certain serotypes; 2) a k-mer based algorithm for rapid serotype prediction from raw reads (seconds per genome) and improved serotype prediction from assemblies; and 3) a targeted assembly approach for specific retrieval of serotype determinants from WGS for serotype prediction, new allele discovery, and prediction troubleshooting. Evaluated using 5,794 genomes representing 364 common US serotypes, including 2,280 human isolates of 117 serotypes from the National Antimicrobial Resistance Monitoring System, Seq...
Source: Applied and Environmental Microbiology - Category: Microbiology Authors: Tags: Appl Environ Microbiol Source Type: research