Laboratory identification methods of nonpathogenic Neisseria species

Reviews in Medical Microbiology

Volumn 25, Issue 4, 2014, Pages 85-92

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

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

Author keywords

16S rRNA; DNADNA hybridization; identification; matrix assisted laser desorption ionization time of flight; multilocus sequence typing; nonpathogenic Neisseria; RT PCR; whole genome sequencing

Indexed keywords

RNA 16S;

ANALYTIC METHOD; BACTERIAL GENOME; BACTERIAL STRAIN; COMMENSAL; DNA DNA HYBRIDIZATION; GENE SEQUENCE; HOUSEKEEPING GENE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MULTILOCUS SEQUENCE TYPING; NEISSERIA; NEISSERIA GONORRHOEAE; NEISSERIA LACTAMICA; NEISSERIA MENINGITIDIS; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; SPECIES IDENTIFICATION;

EID: 84930043143     PISSN: 0954139X     EISSN: 14735601     Source Type: Journal    
DOI: 10.1097/MRM.0000000000000016     Document Type: Review

References (64)

1. Johnson AP. The pathogenic potential of commensal species of Neisseria. J Clin Pathol 1983; 36:213-223.
2. Maiden MCJ. Population genomics, diversity and virulence in the Neisseria. Curr Opin Microbiol 2008; 11:467-471.
3. Guibourdenche M, Riou JY. Bacteriological identification of Neisseria and Branhamella species, meningococcal serogroup-ing. Evolution of the nomenclature [in French]. Méd Mal Infect 1997; 27:763-773.
4. Smith NH, Holmes EC, Donovan GM, Carpenter GA, Spratt BG. Networks and groups within the genus Neisseria, analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species. Mol Biol Evol 1999; 16:773-783.
5. Bennett JS, Griffiths DT, McCarthy ND, Sleeman KL, Jolley KA, Crook DW, Maiden MC. Genetic diversity and carriage dynamics of Neisseria lactamica in infants. Infect Immun 2005; 73:2424-2432.
6. Marri PR, Paniscus M, Weyand NJ, Rendón MA, Calton CM, Hernandez DR, et al. Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. PLoS One 2010; 5:e11835.
7. Bennett JS, Bentley SD, Vernikos GS, Quail MA, Cherevach I, White B, et al. Independent evolution of the core and accessory gene sets in the genus Neisseria, insights gained from the genome of Neisseria lactamica isolate 020-06. BMC Genomics 2010; 11:652.
8. Treangen TJ, Ambur OH, Tonjum T, Rocha EP. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 2008; 9:R60.
9. Alber D, Oberkotter M, Suerbaum S, Claus H, Frosch M, Vogel U. Genetic diversity of Neisseria lactamica strains from epi-demiologically defined carriers. J Clin Microbiol 2001; 39:1710-1715.
10. Knapp JS. Historical perspectives and identification of Neisser-ia and related species. Clin Microbiol Rev 1988; 1:415-431.
11. Holmes B, Costas M, Vandamme P, Falsen E, Kersters K. Neisseria weaveri sp. nov. (formerly CDC grouP M-5 from dog bite wounds of humans. Int J Syst Bacteriol 1993; 43:687-693.
12. Masliah-Planchon J, Breton G, Jarlier V, Simon A, Benveniste O, Herson S, Drieux L. Endocarditis due to Neisseria bacilliformis in a patient with a bicuspid aortic valve. J Clin Microbiol 2009; 47:1973-1975.
13. Vandamme P, Holmes B, Bercovier H, Coenye T. Classification of Centers for Disease Control Group Eugonic Fermenter (EF)-4a and EF-4b as Neisseria animaloris sp. nov. and Neisseria zoodegmatis sp. nov., respectively. Int J Syst Evol Microbiol 2006; 56:1801-1805.
14. Reyn A. Laboratory diagnosis of gonococcal infections. Bull WHO 1965; 32:449-469.
15. Bergey DH, Holt JG. Bergey's manual of determinative bacteriology. Philadelphia, PA: Lippincott, Williams and Wilkins; 1994:91.
16. Stein DC. The Neisseria. In: Dworkin MM, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E, editors. The prokaryotes New York, NY: Springer; 2006. 5, 602-6647.
17. Tønjum T. Family I. Neisseriaceae Prèvot 1933, 119AL emend. Dewhirst, Paster and Bright 1989, 265. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey's Manual of Systematic Bacteriology 2nd ed. vol. 2 (The proteobacteria), part C (The alpha-, beta-, delta-, and epsilonproteobacteria). New York: Springer; 2005. pp. 775-863.
18. Grant PE, Brenner DJ, Steigerwalt AG, Hollis DG, Weaver RE. Neisseria elongata subsp. nitroreducens subsp. nov., Formerly CDC Group M-6 a Gram-negative bacterium associated with endocarditis. J Clin Microbiol 1990; 28:2591-2596.
19. Knapp JS, Holmes KK. Modified oxidation-fermentation medium for detection of acid production from carbohydrates by Neisseria spp. and Branhamella catarrhalis. J Clin Microbiol 1983; 18:56-62.
20. Henriksen SD, Holten E. Neisseria elongata subsp. glycolytica subsp. nov. Int J Syst Bacteriol 1976; 26:478-481.
21. Vedros NA, Hoke C, Chun P. Neisseria macacae sp. nov., a new Neisseria species isolated from the oropharynges of rhesus monkeys (Macaca mulatta). Int J Syst Bacteriol 1983; 33:515-520.
22. Barrett SJ, Schlater LK, Montali RJ, Sneath PHA. A new species of Neisseria from iguanid lizards, Neisseria iguanae sp. nov. Lett Appl Microbiol 1994; 18:200-202.
23. Sneath PHA, Barrett SJ. A new species of Neisseria from the dental plaque of the domestic cow, Neisseria dentiae sp. nov. Lett Appl Microbiol 1996; 23:355-358.
24. Perilla MJ, Ajello G, Bopp C, Elliott J, Facklam R, Knapp JS, et al. Manual for the laboratory identification and antimicrobial, susceptibility testing of bacterial pathogens of public health importance in the developing world. Geneva: World Health Organization; 2003.
25. Barbé G, Babolat M, Boeufgras JM, Monget D, Freney J. 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 1994; 32:187-189.
26. Steel KJ. The oxidase reaction as a taxonomic tool. J Gen Microbiol 1961; 25:297-306.
27. Pontes DS, Lima-Bittencourt CI, Chartone-Souza E, Amaral Nascimento AM. Molecular approaches, advantages and artifacts in assessing bacterial diversity. Ind Microbiol Biotechnol 2007; 34:463-473.
28. Rennie RP, Brosnikoff C, Shokoples S, Reller LB, Mirrett S, Janda W, et al. Multicenter evaluation of the new Vitek 2 Neisser-iahaemophilus identification card. J Clin Microbiol 2008; 46:2681-2685.
29. Mechergui A, Achour W, Ben Hassen A, et al. Comparison of 16S rRNA sequencing with biochemical testing for species-level identification of clinical isolates of Neisseria spp. World J Microbiol Biotechnol 2014; 30:2181-2188.
30. Woo PCY, Lau SKP, Teng JLL, Tse H, Yuen KY. Then and now, use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 2008; 14:908-934.
31. Harmsen D, Singer C, Rothganger J, Tønjum T, de Hoog GS, Shah H, et al. Diagnostics of Neisseriaceae and Moraxellaceae by ribosomal DNA sequencing, ribosomal differentiation of medical microorganisms. J Clin Microbiol 2001; 39:936-942.
32. Maiden M, Bygraves J, Feil E, Morelli G, Russell J, Urwin R, et al. Multilocus sequence typing, a portable approach to the identification of clones within populations of pathogenic micro-rganisms. Proc Natl Acad Sci USA 1998; 95:3140-3145.
33. Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinform 2010; 11:595.
34. Godoy D, Randle G, Simpson AJ, Aanensen DM, Pitt TL, Kinoshita R, Spratt BG. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and B mallei. J Clin Microbiol 2003; 41:2068-2079.
35. Baldwin A, Mahenthiralingam E, Thickett KM, Honeybourne D, Maiden MCJ, Govan JR, et al. Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex. J Clin Microbiol 2005; 43:4665-4673.
36. Hanage WP, Fraser C, Spratt BG. Fuzzy species in recombino-genic bacteria. BMC Biol 2005; 3:6.
37. Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG. Using multilocus sequence data to define the pneu-mococcus. J Bacteriol 2005; 187:6223-6230.
38. Thompson FL, Gevers D, Thompson CC, Dawyndt P, Naser S, Hoste B, et al. Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol 2005; 71:5107-5115.
39. Danial J. Studies on the genetic diversity of the potato brown rot pathogen Ralstonia solanacearum race 3/biovar 2A [Doctoral dissertation]. Edinburgh: Heriot-Watt University; 2010.
40. Fox AJ, Taha MK, Vogel U. Standardized nonculture techniques recommended for European reference laboratories. FEMS Microbiol Rev 2007; 31:84-88.
41. Forquin MP, Duvergey H, Proux C, Loux V, Mounier J, Landaud S, et al. Identification of Brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses. Appl Environ Microbiol 2009; 75:6406-6409.
42. Wattiau P, Van Hessche M, Neubauer H, Zachariah R, Wernery U, Imberechts H. Identification of Burkholderia pseudomallei and related bacteria by multiple-locus sequence typing-derived PCR and real-time PCR. J Clin Microbiol 2007; 45:1045-1048.
43. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, et al. Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 2005; 3:733-739.
44. Bennett JS, Jolley KA, Sparling PF, Saunders NJ, Hart CA, Feavers IM, Maiden MC. Species status of Neisseria gonorrhoeae: evolutionary and epidemiological inferences from multilocus sequence typing. BMC Biol 2007; 5:35.
45. Jolley KA, Kalmusova J, Feil EJ, Gupta S, Musilek M, Kriz P, Maiden MC. Carried meningococci in the Czech Republic: a diverse recombining population. J Clin Microbiol 2000; 38:4492-4498.
46. Dossett JH, Appelbaum PC, Knapp JS, Totten PA. Proctitis associated with Neisseria cinerea misidentified as Neisseria gonorrhoeae in a child. J Clin Microbiol 1985; 21:575-577.
47. Ahmed A, Grobusch MP, Klatser P, Hartskeerl RA. Molecular approaches in the detection and characterization of leptospira. J Bacteriol Parasitol 2012; 3:133.
48. Bleve G, Rizzotti L, Dellaglio F, Torriani S. Development of reverse transcription (RT)-PCR and real-time RT-PCR assays for rapid detection and quantification of viable yeasts and molds contaminating yogurts and pasteurized food products. Appl Environ Microbiol 2003; 69:4116-4122.
49. Mangold KA, Regner MA, TajuddinM, Tajuddin AM, Jennings L, Du H, Kaul KL. Neisseria species identification assay for the confirmation of Neisseria gonorrhoeae positive results of the COBAS amplicor PCR. J Clin Microbiol 2007; 45:1403-1409.
50. Peter-Getzlaff S, Luethy J, Springer B. Diagnostic value of molecular confirmation assays for Neisseria gonorrhoeae. J Clin Microbiol 2007; 45:3856-3858.
51. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043-1047.
52. Oren A. Prokaryote diversity and taxonomy, current status and future challenges. Philol Trans R Soc Lond 2004; 359:623-638.
53. Palys T, Nakamura LK, Cohan FM. Discovery and classification of ecological diversity in the bacterial world, the role of DNA sequence data. Int J Syst Bacteriol 1997; 47:1145-1156.
54. Siqueira JF Jr, Rôças IN, Souto R, Uzeda MD, Colombo AP. Checkerboard DNA-DNA hybridization analysis of endodon-tic infections. Oral Surg Oral Med Oral Pathol Oral Radiol Endodontol 2000; 89:744-748.
55. Bennett JS, Jolley KA, Earle SG, Corton C, Bentley SD, Parkhill J, Maiden MCA. Genomic approach to bacterial taxonomy, an examination and proposed reclassification of species within the genus Neisseria. Microbiology 2012; 158:1570-1580.
56. Bennett JS, Jolley KA, Maiden MC. Genome sequence analyses show that Neisseria oralis is the same species as 'Neisseria mucosa var. heidelbergensis'. Int J Syst Evol Microbiol 2013; 63 (Pt 10):3920-3926.
57. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony CM, Colles FM, et al. Ribosomal multilocus sequence typing, universal characterisation of bacteria from domain to strain. Microbiology 2012; 4:1005-1015.
58. Ferroni A, Suarez S, Beretti JL, Dauphin B, Bille E, Meyer J, et al. Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser deso-rption ionization-time of flight mass spectrometry. J Clin Microbiol 2010; 48:1542-1548.
59. Ilina EN, Borovskaya AD, Malakhova MM, Vereshchagin VA, Kubanova AA, Kruglov AN, et al. Direct bacterial profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for identification of pathogenic Neisseria. J Mol Diagn 2009; 11:75-86.
60. Bizzini A, Greub G. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical micro-bial identification. Clin Microbiol Infect 2010; 16:1614-1619.
61. Burak S, Engels-Schwarzlose S, Erhard M, Gehrt A. Evaluation of MALDI-TOF MS based identification of clinically important bacteria in a routine laboratory. Medizinische laboratorien 2010:DV20.
62. Carbonnelle E, Grohs P, Jacquier H, Day N, Tenza S, Dewailly A, et al. Robustness of two MALDI-TOF mass spectrometry systems for bacterial identification. J Microbiol Meth 2012; 89:133-136.
63. Ilina EN, Vereshchagin VA, Malakhova MV, Priputnevich TV, Al-khafaji NC, Kubanova AA, Govorun VM. Molecular characterization of clinical Neisseria Gonorrhoeae (NG) strains in Russia [Poster # ICAAC06-A-2308-ASM]. 46th ICAAC; USA. San Francisco, CA; 2006
64. Szájli E, Fehér T, Medzihradszky KF. Investigating the quantitative nature of MALDI-TOF MS. Mol Cell Proteomics 2008; 7:2410-2418.