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Can genome-based analysis be the new gold-standard for routine Salmonella serotyping?

https://doi.org/10.1101/806208
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.fm.2017.08.017openalex-snapshot
Evaluation of WGS based approaches for investigating a food-borne outbreak caused by Salmonella enterica serovar Derby in Germany
inferredcites →https://doi.org/10.1016/j.fm.2017.12.009openalex-snapshot
International Symposium on Salmonella and salmonellosis
inferredcites →https://doi.org/10.1038/nbt.2522openalex-snapshot
Updating benchtop sequencing performance comparison
inferredcites →https://doi.org/10.1038/s41598-018-33266-5openalex-snapshot
Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:-
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1089/fpd.2011.1038openalex-snapshot
Clonal Dissemination of Salmonella enterica Serovar Infantis in Germany
inferredcites →https://doi.org/10.1089/fpd.2013.1714openalex-snapshot
Molecular Characterization of “Inconsistent” Variants of Salmonella Typhimurium Isolated in Italy
inferredcites →https://doi.org/10.1101/613554openalex-snapshot
The user’s guide to comparative genomics with EnteroBase, including case studies on transmissions of micro-clades of Salmonella , the phylogeny of ancient and modern Yersinia pestis genomes, and the core genomic diversity of all Escherichia
inferredcites →https://doi.org/10.1128/aem.02991-09openalex-snapshot
Pork Contaminated with Salmonella enterica Serovar 4,[5],12:i:−, an Emerging Health Risk for Humans
inferredcites →https://doi.org/10.1128/jb.186.5.1518-1530.2004openalex-snapshot
eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data
inferredcites →https://doi.org/10.1128/jcm.00323-15openalex-snapshot
Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data
inferredcites →https://doi.org/10.1128/jcm.01229-08openalex-snapshot
Rapid Multiplex PCR and Real-Time TaqMan PCR Assays for Detection of Salmonella enterica and the Highly Virulent Serovars Choleraesuis and Paratyphi C
inferredcites →https://doi.org/10.1128/jcm.02437-08openalex-snapshot
WHO Global Salm-Surv External Quality Assurance System for Serotyping of Salmonella Isolates from 2000 to 2007
inferredcites →https://doi.org/10.1186/1471-2164-13-338openalex-snapshot
Short read sequence typing (SRST): multi-locus sequence types from short reads
inferredcites →https://doi.org/10.1371/journal.pgen.1007261openalex-snapshot
A genomic overview of the population structure of Salmonella
inferredcites →https://doi.org/10.1371/journal.pone.0042304openalex-snapshot
An Integrated Pipeline for de Novo Assembly of Microbial Genomes
inferredcites →https://doi.org/10.1371/journal.pone.0128349openalex-snapshot
Outbreak of Uncommon O4 Non-Agglutinating Salmonella Typhimurium Linked to Minced Pork, Saxony-Anhalt, Germany, January to April 2013
inferredcites →https://doi.org/10.1371/journal.pone.0147101openalex-snapshot
The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies
inferredcites →https://doi.org/10.1371/journal.ppat.1002776openalex-snapshot
Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica
inferredcites →https://doi.org/10.2807/1560-7917.es.2019.24.36.1800543openalex-snapshot
Salmonellosis outbreak with novel Salmonella enterica subspecies enterica serotype (11:z41:e,n,z15) attributable to sesame products in five European countries, 2016 to 2017
inferredcites →https://doi.org/10.3201/eid2204.150531openalex-snapshot
Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005–2010
inferredcites →https://doi.org/10.3389/fmicb.2017.01044openalex-snapshot
The Validation and Implications of Using Whole Genome Sequencing as a Replacement for Traditional Serotyping for a National Salmonella Reference Laboratory
inferredcites →https://doi.org/10.3389/fmicb.2018.00715openalex-snapshot
A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:-
inferredcites →https://doi.org/10.3389/fmicb.2018.00775openalex-snapshot
Challenges and Promises for Planning Future Clinical Research Into Bacteriophage Therapy Against Pseudomonas aeruginosa in Cystic Fibrosis. An Argumentative Review
inferredcites →https://doi.org/10.3389/fmicb.2018.02993openalex-snapshot
Salmonella Serotyping Using Whole Genome Sequencing
inferredcites →https://doi.org/10.7717/peerj.2308openalex-snapshot
MOST: a modified MLST typing tool based on short read sequencing
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