Multilocus sequence typing of total-genome-sequenced bacteria

TY - JOUR

T1 - Multilocus sequence typing of total-genome-sequenced bacteria

AU - Larsen, Mette V

AU - Cosentino, Salvatore

AU - Rasmussen, Simon

AU - Friis, Carsten

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

PY - 2012/4

Y1 - 2012/4

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.

KW - Bacteria/classification

KW - Bacterial Typing Techniques

KW - Contig Mapping

KW - Databases, Genetic

KW - Genes, Bacterial

KW - Genome, Bacterial

KW - High-Throughput Nucleotide Sequencing

KW - Multilocus Sequence Typing

U2 - 10.1128/jcm.06094-11

DO - 10.1128/jcm.06094-11

M3 - Journal article

C2 - 22238442

SN - 0095-1137

VL - 50

SP - 1355

EP - 1361

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

IS - 4

ER -