Keywords
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribers receive full online access to your subscription and archive of back issues up to and including 2002.
Content published before 2002 is available via pay-per-view purchase only.
Subscribe:
Subscribe to Clinics in Laboratory MedicineAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- Guidelines for the validation and application of typing methods for use in bacterial epidemiology.Clin Microbiol Infect. 2007; 13: 1-46
- Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology.J Clin Microbiol. 1997; 35: 907-914
- DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting.Nucleic Acids Res. 1992; 20: 5137-5142
- Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes.Nucleic Acids Res. 1991; 19: 6823-6831
- Development of a new PCR-ribotyping method for Clostridium difficile based on ribosomal RNA gene sequencing.FEMS Microbiol Lett. 1999; 175: 261-266
- Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA).FEMS Immunol Med Microbiol. 2007; 49: 22-27
- Diversity of CRISPR loci in Escherichia coli.Microbiology. 2010; 156: 1351-1361
- Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex.Methods Mol Biol. 2009; 551: 117-128
- Scalable SNP analyses of 100+ bacterial or viral genomes.J Forensic Res. 2010; 1: 107
- DNA microarray technology: a new tool for the epidemiological typing of bacterial pathogens?.FEMS Immunol Med Microbiol. 2006; 47: 178-189
- Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms.Proc Natl Acad Sci U S A. 1998; 95: 3140-3145
- Visualization of comparative genomic analyses by BLAST score ratio.BMC Bioinformatics. 2005; 6: 2
- Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis.Cell. 1984; 37: 67-75
- Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard.J Clin Microbiol. 2005; 43: 1045-1050
- Pulsed-field gel electrophoresis.Nat Protoc. 2007; 2: 677-684
- PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States.Emerg Infect Dis. 2001; 7: 382-389
- Pulsenet: a program to detect and track food contamination events. Wiley Handbook of Science and Technology for Homeland Security.([Internet]) John Wiley & Sons, Inc, 2008 (Available at:) (Accessed November 15, 2012)
- Development and validation of a PulseNet standardized protocol for subtyping isolates of Cronobacter species.Foodborne Pathog Dis. 2012; 9: 861-867
- Standardization and international multicenter validation of a PulseNet pulsed-field gel electrophoresis protocol for subtyping Shigella flexneri isolates.Foodborne Pathog Dis. 2012; 9: 418-424
- Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet.Foodborne Pathog Dis. 2006; 3: 59-67
- Cohort study of molecular identification and typing of Mycobacterium abscessus, Mycobacterium massiliense, and Mycobacterium bolletii.J Clin Microbiol. 2009; 47: 1985-1995
- In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction.Bioinformatics. 2004; 20: 798-799
MLVA - Multiple Loci VNTR Analysis databases and software [Internet]. Available at: http://minisatellites.u-psud.fr/. Accessed January 14, 2013.
- Vibrio cholerae strain typing and phylogeny study based on simple sequence repeats.J Clin Microbiol. 2007; 45: 736-746
- Multiple-locus variable-number tandem-repeats analysis of Salmonella enterica subsp. enterica serovar Typhimurium using PCR multiplexing and multicolor capillary electrophoresis.J Microbiol Methods. 2004; 59: 163-172
- PCR targeted to the 16S-23S rRNA gene intergenic spacer region of Clostridium difficile and construction of a library consisting of 116 different PCR ribotypes.J Clin Microbiol. 1999; 37: 461-463
- Study of polymorphic variable-number of tandem repeats loci in the ECOR collection and in a set of pathogenic Escherichia coli and Shigella isolates for use in a genotyping assay.J Microbiol Methods. 2007; 69: 197-205
- Molecular typing of methicillin-resistant Staphylococcus aureus on the basis of protein A gene polymorphism.Eur J Clin Microbiol Infect Dis. 1996; 15: 60-64
- Comparison of protein A gene sequencing with pulsed-field gel electrophoresis and epidemiologic data for molecular typing of methicillin-resistant Staphylococcus aureus.J Clin Microbiol. 2000; 38: 1347-1351
- A preliminary guideline for the assignment of methicillin-resistant Staphylococcus aureus to a Canadian pulsed-field gel electrophoresis epidemic type using spa typing.Can J Infect Dis Med Microbiol. 2008; 19: 273-281
- spa typing method for discriminating among Staphylococcus aureus isolates: implications for use of a single marker to detect genetic micro- and macrovariation.J Clin Microbiol. 2004; 42: 792-799
- Current knowledge of type-specific M antigens of group A streptococci.J Immunol. 1962; 89: 307-313
- Multilocus sequence typing of Streptococcus pyogenes representing most known emm types and distinctions among subpopulation genetic structures.J Bacteriol. 2004; 186: 4285-4294
- Global emm type distribution of group A streptococci: systematic review and implications for vaccine development.Lancet Infect Dis. 2009; 9: 611-616
Streptococcus pyogenes emm sequence database [Internet]. Available at: http://www.cdc.gov/ncidod/biotech/strep/strepblast.htm. Accessed January 14, 2013.
PubMLST.org [Internet]. Available at: http://pubmlst.org/. Accessed January 14, 2013.
MLST.NET [Internet]. Available at: http://www.mlst.net. Accessed January 14, 2013.
- Database-driven multi locus sequence typing (MLST) of bacterial pathogens.Bioinformatics. 2001; 17: 1077-1083
- mlstdbNet - distributed multi-locus sequence typing (MLST) databases.BMC Bioinformatics. 2004; 5: 86
- The multilocus sequence typing network: mlst.net.Nucleic Acids Res. 2005; 33: W728-W733
- Genetic variation analysis of Vibrio cholerae using multilocus sequencing typing and multi-virulence locus sequencing typing.Infect Genet Evol. 2011; 11: 1121-1128
- Multi-virulence-locus sequence typing of Listeria monocytogenes.Appl Environ Microbiol. 2004; 70: 913-920
- Preliminary phylogenetic identification of virulent Chlamydophila pecorum strains.Infect Genet Evol. 2008; 8: 764-771
- Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data.Nucleic Acids Res. 2009; 37: W606-W611
Meningococcus Genome Informatics Platform [Internet]. Available at: http://mgip.biology.gatech.edu/home.php. Accessed January 14, 2013.
- High-throughput multilocus sequence typing: bringing molecular typing to the next level.PLoS One. 2012; 7: e39630
- Multilocus sequence typing of total-genome-sequenced bacteria.J Clin Microbiol. 2012; 50: 1355-1361
- Novel epidemic clones of Listeria monocytogenes, United States, 2011.Emerg Infect Dis. 2013; 19: 147-150
- BIGSdb: scalable analysis of bacterial genome variation at the population level.BMC Bioinformatics. 2010; 11: 595
- High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.Nat Rev Microbiol. 2012; 10: 599-606
- Genome sequencing in clinical microbiology.Nat Biotechnol. 2012; 30: 1068-1071
- Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages.PLoS One. 2012; 7 ([Internet]) (Available at:) (Accessed January 14, 2013)
- Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock.MBio. 2012; 3 (pii:e00305–11)
- SNP-based typing: a useful tool to study Bordetella pertussis populations.PLoS One. 2011; 6 ([Internet]) (Available at:) (Accessed January 14, 2013)
- Small CRISPR RNAs guide antiviral defense in prokaryotes.Science. 2008; 321: 960-964
- CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA.Science. 2008; 322: 1843-1845
- CRISPR provides acquired resistance against viruses in prokaryotes.Science. 2007; 315: 1709-1712
- Evolution and classification of the CRISPR-Cas systems.Nat Rev Microbiol. 2011; 9: 467-477
- Resolving lineage assignation on Mycobacterium tuberculosis clinical isolates classified by spoligotyping with a new high-throughput 3R SNPs based method.Infect Genet Evol. 2010; 10: 1066-1074
- Subtyping Salmonella enterica serovar enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs).Appl Environ Microbiol. 2011; 77: 4520-4526
- Specific detection of enteroaggregative hemorrhagic Escherichia coli O104:H4 strains by use of the CRISPR locus as a target for a diagnostic real-time PCR.J Clin Microbiol. 2012; 50: 3485-3492
- A framework for assessing the concordance of molecular typing methods and the true strain phylogeny of Campylobacter jejuni and C. coli using draft genome sequence data.Front Cell Infect Microbiol. 2012; 2 ([Internet]) (Available at:) (Accessed January 14, 2013)
Bacterial Isolate Genome Sequence Database (BIGSdb) [Internet]. Available at: http://pubmlst.org/software/database/bigsdb/. Accessed January 14, 2013.
ARDB - Antibiotic Resistance Genes Database [Internet]. Available at: http://ardb.cbcb.umd.edu/. Accessed January 14, 2013.
The Comprehensive Antibiotic Resistance Database [Internet]. Available at: http://arpcard.mcmaster.ca/. Accessed January 14, 2013.
VFDB: Virulence Factors Database [Internet]. Available at: http://www.mgc.ac.cn/VFs/. Accessed January 14, 2013.
- Integrating genome-based informatics to modernize global disease monitoring, information sharing, and response.Emerg Infect Dis. 2012; 18: e1
- Impacts of culture-independent diagnostic practices on public health surveillance for bacterial enteric pathogens.Clin Infect Dis. 2012; 54: S432-S439
Article info
Footnotes
The author has no disclosures.
The findings and conclusions in this report are those of the author, and do not necessarily represent the views of the Centers for Disease Control and Prevention.
Identification
Copyright
Published by Elsevier Inc.
