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SRST specifications


Unique identifier OMICS_12777
Alternative names Short Read Sequence Typing, SRST2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequences flanking each locus, Illumina read data
Input format FASTQ
Output data Locus variants, scores and coverage statistics for each locus and readset
Operating system Unix/Linux, Mac OS
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.2.0
Stability Stable
SAMtools, Scipy, Numpy, bowtie
Maintained Yes




No version available



  • person_outline Kathryn Holt

Publications for Short Read Sequence Typing

SRST citations


Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] phylogenetic resolution of the 25 most closely related isolates. In silico phylotyping, based on the Clermont et al. typing scheme, was performed using a previously described methodology. The program SRST2 (v0.2.0) was used to identify MLST types by matching reads to the Escherichia coli #1 database downloaded from […]


Alkaline Peptone Water Based Enrichment Method for mcr 3 From Acute Diarrheic Outpatient Gut Samples

PMCID: 5943531
PMID: 29774212
DOI: 10.3389/fmed.2018.00099
call_split See protocol

[…] oroad, Beijing, China). The raw Illumina reads were assembled into a draft genome sequence using CLC Genomics Workbench 9.0 (CLC Bio, Aarhus, Denmark). Antibiotic resistance genes were analyzed using SRST2 (), with reference sequences for the antibiotic resistance genes obtained from the ARG-ANNOT database (). […]


Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole Genome Phylogenetic Analysis

PMCID: 5932376
PMID: 29720527
DOI: 10.1128/mSphere.00464-17
call_split See protocol

[…] ence types (MLSTs) and spa types were determined by the traditional Sanger sequencing analysis or, when typing had not been performed and genomic sequence data were available, MLST was performed with SRST2 (). SCCmec cassette typing using conventional methods was performed on a subset of isolates depending on the time of their collection (, ). To determine SCCmec types for isolates that did not ha […]


Invasive Methicillin Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages

PMCID: 5932375
PMID: 29720528
DOI: 10.1128/mSphere.00571-17
call_split See protocol

[…] r each strain based on the methods of Gordon et al. (). Roary () was used to estimate a pan-genome from de novo-assembled contigs of the strains sequenced in the study. The MLST was ascertained using SRST2 (). Two strains were excluded because pangenome content suggested they were not S. aureus, and 8 strains fell outside CC8 based on MLST patterns. […]


Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

Antimicrob Agents Chemother
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] 015]) () for antibiotic resistance genes and to a database for mainly plasmid-borne heavy metal resistance genes that have been described thoroughly (see Table S1 in the supplemental material), using srst2 (v0.2.0) ().The isolates were assigned to the main E. coli phylogenetic groups on the basis of their clustering in a neighbor-joining tree created from rMLST alleles. Sequences were assembled us […]


Environmental colonization and onward clonal transmission of carbapenem resistant Acinetobacter baumannii (CRAB) in a medical intensive care unit: the case for environmental hygiene

PMCID: 5891964
PMID: 29644052
DOI: 10.1186/s13756-018-0343-z

[…] to the GenBank database. De novo assembly of the Illumina reads was performed using SPAdes Genome Assembler []. Bacterial species were identified using Kraken []. Multilocus STs were identified using SRST2 []. Isolates with species discordance comparing phenotypic with genotypic speciation were excluded from further analysis. […]


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SRST institution(s)
Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia
SRST funding source(s)
This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant #VR0082.

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