Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Chen, Linxiang ^a,b   Cai, Ying ^b   Zhou, Guangbiao ^b   Shi, Xiaojun ^a   Su, Jianhui ^b   Chen, Guanwu ^b   Lin, Kun ^a  

^a SHANTOU UNIVERSITY MEDICAL COLLEGE   (China)

^b Shantou Entry Exit Inspection and Quarantine Bureau   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RIBOSOME RNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; ESCHERICHIA COLI; INTERMETHOD COMPARISON; NONHUMAN; PSEUDOMONAS AERUGINOSA; RAPID SANGER SEQUENCING; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SHIGELLA DYSENTERIAE; SHIGELLA SONNEI; STAPHYLOCOCCUS AUREUS; STRAIN IDENTIFICATION; VALIDATION PROCESS;

BACTERIA; BASE SEQUENCE; ELECTROPHORESIS, AGAR GEL; ESCHERICHIA COLI; ETHIDIUM; GENES, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID DENATURATION; POLYMERASE CHAIN REACTION; PSEUDOMONAS AERUGINOSA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; STAPHYLOCOCCUS AUREUS;

EID: 84895861623     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0088886     Document Type: Article

References (27)

1. Gustavsson I, Lindell M, Wilander E, Strand A, Gyllensten U (2009) Use of FTA card for dry collection, transportation and storage of cervical cell specimen to detect high-risk HPV. Journal of Clinical Virology 46: 112-116.
2. Mullen M, Howard D, Powell R, Hanrahan J (2009) A note on the use of FTA™ technology for storage of blood samples for DNA analysis and removal of PCR inhibitors. Irish Journal of Agricultural and Food Research: 109-113.
3. Schuurman T, De Boer RF, Kooistra-Smid A, van Zwet AA (2004) Prospective study of use of PCR amplification and sequencing of 16S ribosomal DNA from cerebrospinal fluid for diagnosis of bacterial meningitis in a clinical setting. J Clin Microbiol 42: 734-740. (Pubitemid 38222655)
4. Smith L, Burgoyne LA (2004) Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper. BMC ecology 4: 4.
5. Aye KS, Matsuoka M, Kai M, Kyaw K, Win AA, et al. (2011) FTA card utility for PCR detection of Mycobacterium leprae. Jpn J Infect Dis 64: 246-248.
6. Fukushima H, Tsunomori Y, Seki R (2003) Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. J Clin Microbiol 41: 5134-5146. (Pubitemid 37429927)
7. Menassa N, Bosshard PP, Kaufmann C, Grimm C, Auffarth GU, et al. (2010) Rapid detection of fungal keratitis with DNA-stabilizing FTA filter paper. Invest Ophthalmol Vis Sci 51: 1905-1910.
8. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Kaczmarski EB, et al. (2000) Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol 38: 1747-1752. (Pubitemid 30253908)
9. Hall L, Doerr KA, Wohlfiel SL, Roberts GD (2003) Evaluation of the MicroSeq system for identification of mycobacteria by 16S ribosomal DNA sequencing and its integration into a routine clinical mycobacteriology laboratory. J Clin Microbiol 41: 1447-1453. (Pubitemid 36428087)
10. Peattie DA (1979) Direct chemical method for sequencing RNA. Proc Natl Acad Sci U S A 76: 1760-1764.
11. Han XY, Pham AS, Tarrand JJ, Sood PK, Luthra R (2002) Rapid and accurate identification of mycobacteria by sequencing hypervariable regions of the 16S ribosomal RNA gene. Am J Clin Pathol 118: 796-801. (Pubitemid 37046326)
12. Tewari D, Cieply S, Livengood J (2011) Identification of bacteria recovered from animals using the 16S ribosomal RNA gene with pyrosequencing and Sanger sequencing. Journal of Veterinary Diagnostic Investigation 23: 1104-1108.
13. Fukushima M, Kakinuma K, Kawaguchi R (2002) Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 40: 2779-2785. (Pubitemid 35284941)
14. Killgore G, Thompson A, Johnson S, Brazier J, Kuijper E, et al. (2008) Comparison of seven techniques for typing international epidemic strains of Clostridium difficile: restriction endonuclease analysis, pulsed-field gel electrophoresis, PCR-ribotyping, multilocus sequence typing, multilocus variable-number tandem-repeat analysis, amplified fragment length polymorphism, and surface layer protein A gene sequence typing. J Clin Microbiol 46: 431-437. (Pubitemid 351231282)
15. Willi B, Meli ML, Luthy R, Honegger H, Wengi N, et al. (2009) Development and application of a universal Hemoplasma screening assay based on the SYBR green PCR principle. J Clin Microbiol 47: 4049-4054.
16. Vliegen I, Jacobs JA, Beuken E, Bruggeman CA, Vink C (2006) Rapid identification of bacteria by real-time amplification and sequencing of the 16S rRNA gene. J Microbiol Methods 66: 156-164. (Pubitemid 43767525)
17. Becker K, Harmsen D, Mellmann A, Meier C, Schumann P, et al. (2004) Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J Clin Microbiol 42: 4988-4995. (Pubitemid 39506200)
18. Bhattacharya D, Sarma PM, Krishnan S, Mishra S, Lal B (2003) Evaluation of genetic diversity among Pseudomonas citronellolis strains isolated from oily sludge-contaminated sites. Appl Environ Microbiol 69: 1435-1441. (Pubitemid 36314278)
19. Li Y, Liu D, Cao B, Han W, Liu Y, et al. (2006) Development of a serotype-specific DNA microarray for identification of some Shigella and pathogenic Escherichia coli strains. J Clin Microbiol 44: 4376-4383. (Pubitemid 44937067)
20. Lan R, Reeves PR (2001) When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol 9: 419-424. (Pubitemid 32844327)
21. Pupo GM, Lan R, Reeves PR (2000) Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proceedings of the National Academy of Sciences 97: 10567-10572.
22. Janda JM, Abbott SL (2007) 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 45: 2761-2764. (Pubitemid 47417311)
23. Petti CA (2007) Detection and identification of microorganisms by gene amplification and sequencing. Clin Infect Dis 44: 1108-1114.
24. Cloud JL, Conville PS, Croft A, Harmsen D, Witebsky FG, et al. (2004) Evaluation of partial 16S ribosomal DNA sequencing for identification of Nocardia species by using the MicroSeq 500 system with an expanded database. J Clin Microbiol 42: 578-584. (Pubitemid 38222631)
25. Monnet C, Correia K, Sarthou AS, Irlinger F (2006) Quantitative detection of Corynebacterium casei in cheese by real-time PCR. Appl Environ Microbiol 72: 6972-6979. (Pubitemid 44748408)
26. Woo PCY, Ng KHL, Lau SKP, Yip K, Fung AMY, et al. (2003) Usefulness of the MicroSeq 500 16S ribosomal DNA-based bacterial identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. J Clin Microbiol 41: 1996-2001. (Pubitemid 36576526)
27. Woo PCY, Cheung EYL, Leung K, Yuen K (2001) Identification by 16S ribosomal RNA gene sequencing of an Enterobacteriaceae species with ambiguous biochemical profile from a renal transplant recipient. Diagn Microbiol Infect Dis 39: 85-93. (Pubitemid 32206626)