Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

Publication: Research - peer-reviewJournal article – Annual report year: 2012

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@article{eb703606a1f54453ac8eb07fa3bfc426,
title = "Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria",
publisher = "American Society for Microbiology",
author = "Larsen, {Mette Voldby} and Salvatore Cosentino and Simon Rasmussen and Rundsten, {Carsten Friis} and Henrik Hasman and Marvig, {Rasmus Lykke} and Lars Jelsbak and Thomas Sicheritz-Pontén and Ussery, {David W.} and Aarestrup, {Frank M.} and Ole Lund",
year = "2012",
doi = "10.1128/JCM.06094-11",
volume = "50",
number = "4",
pages = "1355--1361",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",

}

RIS

TY - JOUR

T1 - Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

A1 - Larsen,Mette Voldby

A1 - Cosentino,Salvatore

A1 - Rasmussen,Simon

A1 - Rundsten,Carsten Friis

A1 - Hasman,Henrik

A1 - Marvig,Rasmus Lykke

A1 - Jelsbak,Lars

A1 - Sicheritz-Pontén,Thomas

A1 - Ussery,David W.

A1 - Aarestrup,Frank M.

A1 - Lund,Ole

AU - Larsen,Mette Voldby

AU - Cosentino,Salvatore

AU - Rasmussen,Simon

AU - Rundsten,Carsten Friis

AU - Hasman,Henrik

AU - Marvig,Rasmus Lykke

AU - Jelsbak,Lars

AU - Sicheritz-Pontén,Thomas

AU - Ussery,David W.

AU - Aarestrup,Frank M.

AU - Lund,Ole

PB - American Society for Microbiology

PY - 2012

Y1 - 2012

N2 - Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

AB - Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

U2 - 10.1128/JCM.06094-11

DO - 10.1128/JCM.06094-11

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 0095-1137

IS - 4

VL - 50

SP - 1355

EP - 1361

ER -