ArticleGenome medicine2014
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs.
Article in Genome medicine, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 686 papers, 1 of them a synthesis that pooled it.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
686 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Diversity, functional classification and genotyping of SHV β-lactamases inMicrobial genomics · 2024Pooled it
- A Simplified Guide to Whole-Genome Sequence Analysis of Salmonella on the Command Line.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Comparative performance of portable DNA extraction protocols and bioinformatics workflows for rapid detection of gram-negative bacteria and antimicrobial resistance using Oxford Nanopore sequencing.Microbiology spectrum · 2026Article
- Whole-Genome Sequencing ofMicroorganisms · 2026Article
- Whole-Genome Sequencing-Based Characterisation ofMicroorganisms · 2026Article
- K-MARVEL: K-Mer-based antimicrobial resistance virtual exploration lab.Nature communications · 2026Article
- Computational Genomics for Resistome Characterization: Current Advancements and Future Challenges Under a One Health Perspective.Antibiotics (Basel, Switzerland) · 2026Review
- A posttranslational modification of fimbriae drives pathogenicity inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Evaluation of Short Versus Long Course of Tobramycin Combined with Piperacillin/Tazobactam Against Antibiotic-ResistantAntibiotics (Basel, Switzerland) · 2026Article
- Stabilizing features of cefotaximase harbouring plasmids enable persistence in UK livestock.Microbial genomics · 2026Article
- Group B streptococcal disease in infants 0-3 months in The Netherlands, 1987-2023: a nationwide genomic and epidemiological surveillance study.The Lancet regional health. Europe · 2026Article
- Evidence for Genotype-Associated Differences in Disease Severity and Limitations of Serotype-Based Classification inPathogens (Basel, Switzerland) · 2026Article
- Genomic characterization of invasiveMicrobial genomics · 2026Article
- Prevalence and activity of class II microcins inApplied and environmental microbiology · 2026Article
- Genetic and Phenotypic Characteristics of FiveAnimals : an open access journal from MDPI · 2026Article
- Dominance of the ST20Microorganisms · 2026Article
- Genome on the move: emergence of hybrid atypical enteropathogenic/enteroaggregativeMicrobiology spectrum · 2026Article
- Integrated genomic and phenotypic characterization of antimicrobial resistance in Shiga toxin-producing Escherichia coli from asymptomatic carriers in Japan.Scientific reports · 2026Article
- Closely RelatedVeterinary sciences · 2026Article
- Gelatinase regulates the egress of intracellular replicating populations during Enterococcus faecalis infection.PLoS pathogens · 2026Article
626 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. We include validation of SRST2 within a public health laboratory, and demonstrate its use for microbial genome surveillance in the hospital setting. In the face of rising threats of antimicrobial resistance and emerging virulence among bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.