Comparison of 16S rRNA sequencing with biochemical testing for species-level identification of clinical isolates of Neisseria spp.

World Journal of Microbiology and Biotechnology

Volumn 30, Issue 8, 2014, Pages 2181-2188

  Mechergui, Arij ^a   Achour, Wafa ^a   Ben Hassen, Assia ^a  

^a CENTRE NATIONAL DE GREFFE DE MOELLE OSSEUSE   (Tunisia)

Author keywords

16S rRNA; Biochemical tests; Identification; Neisseria spp.

Indexed keywords

GENES; IDENTIFICATION (CONTROL SYSTEMS);

16S RRNA; 16S RRNA GENE SEQUENCING; 16S RRNA SEQUENCES; 16S RRNA SEQUENCING; BIOCHEMICAL TESTING; BIOCHEMICAL TESTS; CLINICAL ISOLATES; NEISSERIA SPP;

RNA;

NEISSERIA;

BACTERIAL RNA; RNA 16S;

BACTERIUM IDENTIFICATION; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; GRAM NEGATIVE INFECTION; ISOLATION AND PURIFICATION; MICROBIOLOGY; NEISSERIA; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS;

BACTERIAL TYPING TECHNIQUES; GRAM-NEGATIVE BACTERIAL INFECTIONS; NEISSERIA; REPRODUCIBILITY OF RESULTS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, RNA;

EID: 84903544389     PISSN: 09593993     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11274-014-1637-9     Document Type: Article

References (41)

1. Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186: 2629-2635.
2. Alber D, Oberkotter M, Suerbaum S, Claus H, Frosch M, Vogel U (2001) Genetic diversity of Neisseria lactamica strains from epidemiologically defined carriers. J Clin Microbiol 39: 1710-1715.
3. Alexander S, Ison C (2005) Evaluation of commercial kits for the identification of Neisseria gonorrhoeae. J Med Microbiol 54: 827-831.
4. Barbé G, Babolat M, Boeufgras JM, Monget D, Freney J (1994) Evaluation of API NH, a new 2-hour system for identification of Neisseria and Haemophilus species and Moraxella catarrhalis in a routine clinical laboratory. J Clin Microbiol 32: 187-189.
5. Barrett SJ, Sneath PH (1994) A numerical phenotypic taxonomic study of the genus Neisseria. Microbiology 140: 2867-2891.
6. Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, Stahl DA, Cherni A (2004) Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. J Clin Microbiol 42: 3711-3730.
7. Blackwood KS, Turenne CY, Harmsen D, Kabani AM (2004) Reassessment of sequence-based targets for identification of Bacillus species. J Clin Microbiol 42: 1626-1630.
8. Bosshard PP, Abels S, Zbinden R, Bottger EC, Altwegg M (2003) Ribosomal DNA sequencing for identification of aerobic gram-positive rods in the clinical laboratory (an 18-month evaluation). J Clin Microbiol 41: 4134-4140.
9. Boudewijns M, Bakkers JM, Sturm PDJ, Melchers WJG (2006) 16S rRNA gene sequencing and the routine clinical microbiology laboratory, a perfect marriage? J Clin Microbiol 44: 3469-3470.
10. Condon C, Liveris D, Squires C, Schwartz I, Squires CL (1995) rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J Bacteriol 177: 4152-4156.
11. Drancourt M, Bollet C, Carlioz A, Martelin R, Gayral JP, Raoult D (2000) 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 38: 3623-3630.
12. Dubnau D, Smith I, Morell P, Marmur J (1965) Gene conservation in Bacillus species. Proc Natl Acad Sci USA 54: 491-498.
13. Euzéby JP (2007) List of prokaryotic names with standing in nomenclature-genus Neisseria, http,//www. bacterio. cict. fr/neisseria.
14. Fox GE, Wisotzkey JD, Jurtshuk P Jr (1992) How close is close, 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42: 166-170.
15. Harris C, Perry K (2006). Neisseria spp. identification kits, a review of evaluation literature. Centre for Infections-Health Protection Agency, Report 06040.
16. Hombrouck-Alet C, Poilane I, Janoir-Jouveshomme C, Fain O, Cruaud P, Thomas M, Collignon A (2003) Utilization of 16S ribosomal DNA sequencing for diagnosis of septicemia due to Neisseria elongata subsp. glycolytica in a neutropenic patient. J Clin Microbiol 41: 3436-3437.
17. Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V et al (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423: 87-91.
18. Janda JM, Abbott SL (2002) Bacterial identification for publication, when is enough enough? J Clin Microbiol 40: 1887-1891.
19. 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.
20. Knapp JS (1988) Historical perspectives and identification of Neisseria and related species. Clin Microbiol Rev 1: 415-431.
21. Lavigne JP, Le Bayon A, Michaux Charachon S, Arich C, Bouziges N, Campello C, Sotto A (2004) Bactériémie à Neisseria subflava subsp. perflava: à propos d'un cas et revue de la littérature. Med Mal Infect 34: 331-332.
22. Mangold KA, Regner MA, Tajuddin M, Tajuddin AM, Jennings L, Du H, Kaul KL (2007) Neisseria species identification assay for the confirmation of Neisseria gonorrhoeae positive results of the COBAS amplicor PCR. J Clin Microbiol 45: 1403-1409.
23. Maynard Smith J, Smith NH, O'Rourke M, Spratt BG (1993) How clonal are bacteria? Proc Natl Acad Sci USA 90: 4384-4388.
24. Mechergui A, Touati A, Baaboura R, Achour W, Ben Hassen A (2011) Phenotypic and molecular characterization of β-lactams resistance in commensal Neisseria strains isolated from neutropenic patients in Tunisia. Ann Microbiol 61: 695-697.
25. Mignard S, Flandrois JP (2006) 16S rRNA sequencing in routine bacterial identification, a 30-month experiment. J Microbiol Methods 67: 574-581.
26. Molina F, Duran MT, Llinares P, Diz-Lois F (2000) Encocarditis due to Neisseria subflava with negative blood cultures. Clin Microbiol Newsl 22: 158-159.
27. Palys T, Cohan LK, Nakamura FM (1997) Discovery and classification of ecological diversity in the bacterial world, the role of DNA sequence data. Int J Syst Bacteriol 47: 1145-1156.
28. Petatán-Sagahón I, Anducho-Reyes MA, Silva-Rojas HV, Arana-Cuenca A, Tellez-Jurado A, Cárdenas-Álvarez IO, Mercado-Flores Y (2011) Isolation of bacteria with antifungal activity against the phytopathogenic fungi Stenocarpella maydis and Stenocarpella macrospora. Int J Mol Sci 12: 5522-5537.
29. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE et al (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423: 81-86.
30. Rennie RP, Brosnikoff C, Shokoples S, Reller LB, Mirrett S, Janda W, Ristow K, Krilcich A (2008) Multicenter evaluation of the new vitek 2 Neisseria-Haemophilus identification card. J Clin Microbiol 46: 2681-2685.
31. Sacchi CT, Whitney AM, Mayer LW, Morey R, Steigerwalt A, Boras A, Weyant RS, Popovic T (2002a) Sequencing of 16S rRNA gene, a rapid tool for identification of Bacillus anthracis. Emerg Infect Dis 8: 1117-1123.
32. Sacchi CT, Whitney AM, Reeves MW, Mayer LW, Popovic T (2002b) Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool. J Clin Microbiol 40: 4520-4527.
33. Shetty AK, Nagaraj SK, Lorentz WB, Bitzan M (2005) Peritonitis due to Neisseria mucosa in an adolescent receiving peritoneal dialysis. Infection 33: 390-392.
34. Smith NH, Holmes EC, Donovan GM, Carpenter GA, Spratt BG (1999) Networks and groups within the genus Neisseria, analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species. Mol Biol Evol 16: 773-783.
35. Stein DC (2006) The Neisseria. In: Dworkin MM, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 602-6647.
36. Tsai CM (2011) Lipooligosaccharides of Neisseria species, similarity between N. polysaccharea and N. meningitidis LOSs. Adv Exp Med Biol 705: 381-394.
37. Wilson SP (1928) An investigation of certain gram-negative cocci met with in the nasopharynx, with special reference to their classification. J Pathol Bacteriol 31: 477-492.
38. Wilson GS, Smith MM (1928) Observations on the gram-negative cocci of the nasopharynx, with a description of Neisseria pharyngis. J Pathol Bacteriol 31: 597-608.
39. Woese CR (1987) Bacterial evolution. Microbiol Mol Biol Rev 51: 221-271.
40. Woese CR, Stackebrandt E, Macke TJ, Fox GE (1985) A phylogentic definition of major eubacterial taxa. Syst Appl Microbiol 6: 143-151.
41. Woo PCY, Ng KHI, Lau SKP, Yip KT, Fung AMY, Leung KW, Tam DMW, Que TL, Yuen KY (2003) Usefulness of the MicroSeq 500 16S ribosomal DNA-based identification system for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. J Clin Microbiol 41: 1996-2001.