The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

PloS One
Catherine E YoshidaEduardo N Taboada


For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploa...Continue Reading


Sep 1, 1993·Journal of Bacteriology·B J Masten, T M Joys
Apr 18, 1998·Proceedings of the National Academy of Sciences of the United States of America·M C MaidenB G Spratt
Apr 4, 2001·The Journal of Clinical Investigation·J Fierer, D G Guiney
Jun 1, 2001·Emerging Infectious Diseases·B SwaminathanUNKNOWN CDC PulseNet Task Force
May 8, 2004·Journal of Clinical Microbiology·J R McQuistonP I Fields
Jul 3, 2004·BMC Bioinformatics·Keith A JolleyMartin C J Maiden
Nov 17, 2006·Journal of Clinical Microbiology·Karin BallmerHerbert Hächler
Jan 26, 2007·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Chloe K B MortimerCatherine Arnold
Jun 9, 2007·Journal of Microbiological Methods·Catherine YoshidaKris Rahn
Jul 20, 2007·Journal of Clinical Microbiology·Collette FitzgeraldPatricia Fields
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Feb 19, 2010·Journal of Clinical Microbiology·Elloulu Ben-DarifMathew Upton
Mar 10, 2010·BMC Bioinformatics·Doug HyattLoren J Hauser
Dec 17, 2010·Journal of Clinical Microbiology·John R McQuistonPatricia I Fields
Nov 1, 2008·Microbial Biotechnology·B Tankouo-SandjongL Bodrossy
Jun 24, 2011·Journal of Clinical Microbiology·Kristyn FranklinMohamed A Karmali
Jul 19, 2011·Veterinary Microbiology·Chad R LaingVictor P J Gannon
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Jun 9, 2012·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·W M DunneB Ford
Jun 28, 2012·PLoS Pathogens·Mark AchtmanUNKNOWN S. Enterica MLST Study Group
Aug 10, 2012·PLoS Pathogens·Claudio U KöserSharon J Peacock
Oct 13, 2012·Bioinformatics·Limin FuWeizhong Li
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Feb 2, 2013·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·M J Struelens, S Brisse
Feb 21, 2013·Bioinformatics·Alexey GurevichGlenn Tesler
Apr 4, 2013·Public Health Genomics·M W GilmourG Van Domselaar
Aug 28, 2013·Nature Reviews. Microbiology·Martin C J MaidenNoel D McCarthy
Sep 16, 2014·Diagnostic Microbiology and Infectious Disease·Catherine YoshidaRoderick M Card
Nov 26, 2014·Genome Medicine·Michael InouyeKathryn E Holt
Mar 13, 2015·Journal of Clinical Microbiology·Shaokang ZhangXiangyu Deng
May 15, 2015·Journal of Clinical Microbiology·Katrine G JoensenFlemming Scheutz

❮ Previous
Next ❯


Mar 5, 2016·Genome Announcements·Catherine YoshidaJohn H E Nash
Feb 6, 2017·American Journal of Infection Control·Patrick TangLinda M Hoang
Jan 20, 2018·Genome Announcements·James RobertsonJohn H E Nash
Apr 5, 2018·Journal of Medical Microbiology·Bilal DjeghoutSamir K Saha
Apr 6, 2018·PLoS Genetics·Nabil-Fareed AlikhanMark Achtman
Jun 24, 2017·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·F Tagini, G Greub
Feb 17, 2017·Journal of Clinical Microbiology·Benjamin M HetmanEduardo N Taboada
Aug 26, 2016·Clinical Microbiology Reviews·J RonholmFranco Pagotto
Jun 8, 2017·Clinical Microbiology Reviews·Tarah LynchGary Van Domselaar
Nov 30, 2018·Clinical Microbiology Reviews·Ohad Gal-Mor
May 1, 2019·Antimicrobial Agents and Chemotherapy·Chand S MangatUNKNOWN Canadian Integrated Program for Antimicrobial Resistance Surveillance Public Health Partnership
Jan 11, 2018·Microbial Genomics·Pedro FeijaoLeonid Chindelevitch
Jun 5, 2019·PLoS Neglected Tropical Diseases·Caisey V PulfordJay C D Hinton
Sep 22, 2019·Applied and Environmental Microbiology·Shaokang ZhangXiangyu Deng
Dec 12, 2018·Microbiology Resource Announcements·Kyrylo BessonovJohn H E Nash
May 30, 2019·BMC Genomics·Alexey V RakovDieter M Schifferli
Jul 3, 2020·Veterinary Medicine and Science·Kevin J CummingsLaura B Goodman
Sep 24, 2020·PloS One·Abdurrahman Hassan JibrilJohn Elmerdahl Olsen
Aug 11, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·John A CrumpRuth N Zadoks

❮ Previous
Next ❯

Methods Mentioned


Software Mentioned

Salmonella In Silico Typing Resource ( SISTR )
Microbial In silico Typing ” ( MIST )

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.