Short read sequence typing (SRST): multi-locus sequence types from short reads
Open Access
- 24 July 2012
- journal article
- Published by Springer Science and Business Media LLC in BMC Genomics
- Vol. 13 (1), 338
- https://doi.org/10.1186/1471-2164-13-338
Abstract
Background Multi-locus sequence typing (MLST) has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven) to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation, host or niche, serotype and even clinical or drug resistance profiles. Recent advances in sequencing technology mean it is increasingly feasible to perform bacterial population analysis at the whole genome level. This offers massive gains in resolving power and genetic profiling compared to MLST, and will eventually replace MLST for bacterial typing and population analysis. However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context. Results We present a software tool, SRST, for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST uses read mapping and an allele assignment score incorporating sequence coverage and variability, to determine the most likely allele at each MLST locus. Analysis of over 3,500 loci in more than 500 publicly accessible Illumina read sets showed SRST to be highly accurate at allele assignment. SRST output is compatible with common analysis tools such as eBURST, Clonal Frame or PhyloViz, allowing easy comparison between novel genome data and MLST data. Alignment, fastq and pileup files can also be generated for novel alleles. Conclusions SRST is a novel software tool for accurate assignment of sequence types using short read data. Several uses for the tool are demonstrated, including quality control for high-throughput sequencing projects, plasmid MLST and analysis of genomic data during outbreak investigation. SRST is open-source, requires Python, BWA and SamTools, and is available from http://srst.sourceforge.net.This publication has 30 references indexed in Scilit:
- Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from EuropeNature Genetics, 2012
- Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strainMicrobiology, 2012
- Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011Proceedings of the National Academy of Sciences of the United States of America, 2012
- Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmissionOpen Biology, 2011
- Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in GermanyNew England Journal of Medicine, 2011
- Open-Source Genomic Analysis of Shiga-Toxin-Producing E. coli O104:H4New England Journal of Medicine, 2011
- Navigating the future of bacterial molecular epidemiologyCurrent Opinion in Microbiology, 2010
- Fast and accurate long-read alignment with Burrows–Wheeler transformBioinformatics, 2010
- Phylogenetic understanding of clonal populations in an era of whole genome sequencingInfection, Genetics and Evolution, 2009
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009