High-throughput multilocus sequence typing: bringing molecular typing to the next level.
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TLDR
A high-throughput MLST (HiMLST) method that employs next-generation sequencing (NGS) technology (Roche 454), to generate large quantities of high-quality MLST data at low costs is introduced.Abstract:
Multilocus sequence typing (MLST) is a widely used system for typing microorganisms by sequence analysis of housekeeping genes. The main advantage of MLST in comparison to other typing techniques is the unambiguity and transferability of sequence data. However, a main disadvantage is the high cost of DNA sequencing. Here we introduce a high-throughput MLST (HiMLST) method that employs next-generation sequencing (NGS) technology (Roche 454), to generate large quantities of high-quality MLST data at low costs. The HiMLST protocol consists of two steps. In the first step MLST target genes are amplified by PCR in multi-well plates. During this PCR the amplicons of each bacterial isolate are provided with a unique DNA barcode, the multiplex identifier (MID). In the second step all amplicons are pooled and sequenced in a single NGS-run. The MLST profile of each individual isolate can be retrieved easily using its unique MID. With HiMLST we have profiled 575 isolates of Legionella pneumophila, Staphylococcus aureus, Pseudomonas aeruginosa and Streptococcus pneumoniae in mixed species HiMLST experiments. In conclusion, the introduction of HiMLST paves the way for a broad employment of the MLST as a high-quality and cost-effective method for typing microbial species.read more
Citations
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DNA sequence-based identification of Fusarium : Current status and future directions
TL;DR: This mini-review is to provide a contemporary guide to the following three web-accessible resources for DNA sequence-based identifications of Fusarium : FUSARIUM-ID (http://isolate.fusariumdb.org/; Geiser et al. 2004; Park and O’Donnell 2010; and NCBI GenBank ( http://www.ncbi.nlm.nih.gov/).
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Pathogen typing in the genomics era: MLST and the future of molecular epidemiology.
Marcos Pérez-Losada,Patricia Cabezas,Patricia Cabezas,Eduardo Castro-Nallar,Keith A. Crandall +4 more
TL;DR: The literature is simply too vast to make this review comprehensive, nevertheless, it is attempted to include enough references in a variety of key areas to introduce the reader to the broad applications and complications of MLST data.
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Next-generation sequencing (NGS) in the microbiological world : how to make the most of your money
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Streptococcus agalactiae in the environment of bovine dairy herds – rewriting the textbooks?
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So, You Want to Use Next Generation Sequencing In Marine Systems? Insight from the Pan Pacific Advanced Studies Institute
Demian A. Willette,Fred W. Allendorf,Paul H. Barber,Daniel J. Barshis,Kent E. Carpenter,Eric D. Crandall,William A. Cresko,Iria Fernandez-Silva,Mikhail V. Matz,Eli Meyer,Mudjekeewis D. Santos,Lisa W. Seeb,James E. Seeb +12 more
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References
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Journal ArticleDOI
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
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TL;DR: Multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms, can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate.
Journal ArticleDOI
Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus.
Mark C. Enright,Nicholas P. J. Day,Catrin E. Davies,Sharon J Peacock,Sharon J Peacock,Brian G. Spratt +5 more
TL;DR: A multilocus sequence typing (MLST) scheme has been developed for Staphylococcus aureus and provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet.
Journal ArticleDOI
A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease
Mark C. Enright,Brian G. Spratt +1 more
TL;DR: A pneumococcal multilocus sequence typing scheme and database is developed by sequencing approximately 450 bp fragments of seven housekeeping loci from 295 isolates to provide an allelic profile, or sequence type (ST), and the relatedness between isolates was obtained by constructing a dendrogram from the matrix of pairwise differences between STs.
Journal ArticleDOI
Evaluation of Protein A Gene Polymorphic Region DNA Sequencing for Typing of Staphylococcus aureus Strains
Bo Shopsin,Bo Shopsin,Manuel Gómez,S. O. Montgomery,Douglas H. Smith,Michael Waddington,Deborah E. Dodge,D. A. Bost,M. Riehman,S. Naidich,Barry N. Kreiswirth +10 more
TL;DR: In the NYC collection, spa typing provided a clonal assignment for 185 of 195 strains within the five major groups previously described, and spa sequencing appears to be a highly effective rapid typing tool for S. aureus that, despite some expense of specificity, has significant advantages in terms of speed, ease of use, easy of interpretation, and standardization among laboratories.