Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
Top Cited Papers
- 1 April 2012
- journal article
- research article
- Published by American Society for Microbiology in Journal of Clinical Microbiology
- Vol. 50 (4), 1355-1361
- https://doi.org/10.1128/jcm.06094-11
Abstract
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 .Keywords
This publication has 34 references indexed in Scilit:
- Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing TechnologyPLOS ONE, 2011
- Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis OutbreakThe New England Journal of Medicine, 2011
- BIGSdb: Scalable analysis of bacterial genome variation at the population levelBMC Bioinformatics, 2010
- Development of a multi-locus sequence typing scheme for avian isolates of Pasteurella multocidaVeterinary Microbiology, 2010
- Phylogenetic and genomic diversity of human bacteremic Escherichia coli strainsBMC Genomics, 2008
- Velvet: Algorithms for de novo short read assembly using de Bruijn graphsGenome Research, 2008
- mlstdbNet – distributed multi-locus sequence typing (MLST) databasesBMC Bioinformatics, 2004
- Multilocus sequence typing (MLST) shows that the 'Iberian' clone of methicillin-resistant Staphylococcusaureus has spread to France and acquired reduced susceptibility to teicoplaninJournal of Antimicrobial Chemotherapy, 2002
- Secrets of success of a human pathogen: molecular evolution of pandemic clones of meticillin-resistant Staphylococcus aureusThe Lancet Infectious Diseases, 2002
- Mutation frequency and biological cost of antibiotic resistance in Helicobacter pyloriProceedings of the National Academy of Sciences of the United States of America, 2001