High-throughput multilocus sequence typing: Bringing molecular typing to the next level

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Boers, Stefan A ^a   van der Reijden, Wil A ^a   Jansen, Ruud ^a  

^a Laboratory of Public Health Haarlem   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

AMPLICON; ARTICLE; BACTERIUM ISOLATE; COST CONTROL; COST EFFECTIVENESS ANALYSIS; DNA BARCODING; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE TARGETING; GENETIC PROCEDURES; HIGH THROUGHPUT MULTILOCUS SEQUENCE TYPING; HIGH THROUGHPUT SEQUENCING; LEGIONELLA PNEUMOPHILA; MULTILOCUS SEQUENCE TYPING; MULTIPLEX IDENTIFIER; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PSEUDOMONAS AERUGINOSA; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE;

ALLELES; BACTERIA; GENES, BACTERIAL; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR TYPING; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); LEGIONELLA PNEUMOPHILA; PSEUDOMONAS AERUGINOSA; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE;

EID: 84864013926     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039630     Document Type: Article

References (31)

1. Van Belkum A, (2002) Molecular typing of micro-organisms: at the centre of diagnostics, genomics and pathogenesis of infectious diseases? J Med Microbiol 51: 7-10.
2. Mohr O'Hara C, Brenner FW, Miller M, (2000) Classification, identification, and clinical significance of Proteus, Providencia, and Morganella. Clin Microbiol Rev 13: 534-546.
3. Carriço JA, Silva-Costa C, Melo-Cristino J, Pinto FR, de Lencastre H, et al. (2006) Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. J Clin Microbiol 44: 2524-2532.
4. Van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, et al. (2007) Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Infect 13: 1-46.
5. Melles DC, Gorkink RFJ, Boelens HAM, Snijders SV, Peeters JK, et al. (2004) Natural population dynamics and expansion of pathogenic clones of Staphylococcus aureus. J Clin Invest 114: 1732-1740.
6. Franco A, Hendriksen RS, Lorenzetti S, Onorati R, Gentile G, et al. (2011) Characterization of Salmonella occurring at high prevalence in a population of the land iguana Conolophus subcristatus in Galápagos Islands, Equador. PLoS One 6: e23147.
7. Sobral D, Le Cann P, Gerard A, Jarraud S, Lebeau B, et al. (2011) High-throughput typing method to identify a non-outbreak-involved Legionella pneumophila strain colonizing the entire water supply system in the town of Rennes, France. Appl Environ Microbiol 77: 6899-6907.
8. Gaia V, Fry NK, Harrison TG, Peduzzi R, (2003) Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation. J Clin Microbiol 41: 2932-2939.
9. Frénay HM, Bunschoten AE, Schouls LM, van Leeuwen WJ, Vandenbroucke-Grauls CM, et al. (1996) Molecular typing of methicillin-resistant Staphylococcus aureus on the basis of protein A gene polymorphism. Eur J Clin Microbiol Infect Dis 15: 60-64.
10. Shopsin B, Gomez M, Montgomery SO, Smith DH, Waddington M, et al. (1999) Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J Clin Microbiol 37: 3556-3563.
11. Facklam R, Beall B, Efstratiou A, Fischetti V, Johnson D, et al. (1999) Emm typing and validation of provisional M types for group A streptococci. Emerg Infect Dis 5: 247-253.
12. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, et al. (1998) Multilocus sequence tying: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95: 3140-3145.
13. Maiden MCJ, (2006) Multilocus sequence tying of bacteria. Annu Rev Microbiol 60: 561-588.
14. Haas J, Katus HA, Meder B, (2011) Next-generation sequencing entering the clinical arena. Mol Cell Probes 25: 206-211.
15. Hall TA, Sampath R, Blyn LB, Ranken R, Ivy C, et al. (2009) Rapid molecular genotyping and clonal complex assignment of Staphylococcus aureus isolates by PCR coupled to electrospray ionization-mass spectrometry. J Clin Microbiol 47: 1733-1741.
16. Dunne EM, Ong EK, Moser RJ, Siba PM, Phuanukoonnon S, et al. (2011) Multilocus sequence typing of Streptococcus pneumoniae by use of mass spectrometry. J Clin Microbiol 49: 3756-3760.
17. Pareek CS, Smoczynski R, Tretyn A, (2011) Sequencing technologies and genome sequencing. J Appl Genetics 52: 413-435.
18. Jiang Q, Turner T, Sosa MX, Rakha A, Arnold S, et al. (2012) Rapid and efficient human mutation detection using a bench-top next-generation DNA sequencer. Hum Mutat 33: 281-289.
19. Singh P, Foley SL, Nayak R, Kwon YM, (2012) Multilocus sequence typing of Salmonella strains by high-throughput sequencing of selectively amplified target genes. J Microbiol Methods 88: 127-133.
20. Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5: 887-893.
21. Smith AM, Heisler LE, St. Onge RP, Farias-Hesson E, Wallace IM, et al. (2010) Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38: e142.
22. Neiman M, Lundin S, Savolainen P, Ahmadian A, (2011) Decoding a substantial set of samples in parallel by massive sequencing. PLoS One 6: e17785.
23. Ratzow S, Gaia V, Helbig JH, Fry NK, Lück PC, (2007) Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence-based scheme for typing Legionella pneumophila serogroup 1 strains. J Clin Microbiol 45: 1965-1968.
24. Enright MC, Day NPJ, Davies CE, Peacock SJ, Spratt BG, (2000) Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 38: 1008-1015.
25. Curran B, Jonas D, Grundmann H, Pitt T, Dowson CG, (2004) Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa. J Clin Microbiol 42: 5644-5649.
26. Enright MC, Spratt BG, (1998) A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144: 3049-3060.
27. Rothberg JM, Leamon JH, (2008) The development and impact of 454 sequencing. Nat Biotechnol 26: 1117-1124.
28. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 347-380.
29. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18: 1638-1642.
30. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, et al. (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158: 1005-1015.
31. Bougnoux ME, Morand S, d'Enfert C, (2002) Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans. J Clin Microbiol 40: 1290-1297.