Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

By M. Larsen, Salvatore Cosentino, Simon Rasmussen, Carsten Friis, Henrik Hasman, R. Marvig, L. Jelsbak, Thomas Sicheritz-Pontén, David Wayne Ussery, Frank Moller Aarestrup and 1 more. Journal of Clinical Microbiology, 2012

2,085 citations recorded by the source corpus.

Subfields: Clinical Biochemistry, Microbiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dad0232ff530b7a58430a0b61ea413bc030145a3

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Clinical Biochemistry

1. Ole Lund
2. Frank Moller Aarestrup
3. Kathryn E. Holt

In Microbiology

1. Michael Inouye
2. Justin Zobel
3. Lesley-Ann Raven
4. Harriet Dashnow
5. Mark B. Schultz
6. Bernard J. Pope
7. T. Tomita
8. Kathryn E. Holt

In Molecular Biology

1. Ole Lund
2. Frank Moller Aarestrup
3. Thomas Sicheritz-Pontén
4. Michael Inouye
5. Justin Zobel
6. Rick L. Stevens
7. David Wayne Ussery
8. Lesley-Ann Raven

Citations in the corpus

• PATRIC, the bacterial bioinformatics database and analysis resource (2013, methodology): “The PATRIC Multi-Locus Sequence Typing (MLST) pipeline extracts MLST sequence types from bacterial genomes using the PubMLST API for reference MLST profiles (24).”
• In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing (2014, methodology): “If raw sequence reads are uploaded, they are first assembled (after the sequencing platform is given by the user) as described previously (16).”
• Insights from 20 years of bacterial genome sequencing (2015, methodology): “The first tool developed at CGEwas a method for MLSTof bacteria using the raw reads (or assembled genomes) as input (Larsen et al. 2012).”
• Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli (2014, methodology): “Sequence data can be submitted either as assembled genomes or raw reads from various sequencing technologies, since assembly of raw sequence reads is incorporated into the tool, as described previously for other CGE tools (23, 24).”
• Benchmarking of Methods for Genomic Taxonomy (2014, methodology): “For the short reads of the SRA reads set, the optimal k -mer length was estimated and used for de novo assembly as described previously (23) using Velvet, version 1.1.04 (24).”
• SRST2: Rapid genomic surveillance for public health and hospital microbiology labs (2014, methodology): “Currently available methods rely on assembling short reads into longer contiguous sequences (contigs), which can be interrogated using BLAST or other search algorithms to identify genes or alleles of interest (for example, ARG-Annot [18]; ResFinder, PlasmidFinder and MLST typer [19-21]; BIGSdb [22,2”