Genotypic and phenotypic applications for the differentiation and species-level identification of Achromobacter for clinical diagnoses

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Gomila, Margarita ^a   Prince Manzano, Claudia ^a   Svensson Stadler, Liselott ^b   Busquets, Antonio ^a   Erhard, Marcel ^c   Martínez, Deny L ^a   Lalucat, Jorge ^a,d   Moore, Edward R B ^b  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

^c Ripac Labor GmbH   (Germany)

^d INSTITUTO MEDITERRÁNEO DE ESTUDIOS AVANZADOS   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACHROMOBACTER; ACHROMOBACTER ANIMICUS; ACHROMOBACTER DENITRIFICANS; ACHROMOBACTER INSOLITUS; ACHROMOBACTER MARPLATENSIS; ACHROMOBACTER MUCICOLENS; ACHROMOBACTER PIECHAUDII; ACHROMOBACTER PULMONIS; ACHROMOBACTER RUHLANDII; ACHROMOBACTER SPANIUS; ACHROMOBACTER XYLOSOXIDANS; ARTICLE; ATPD GENE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; DNA SEQUENCE; GENE SEQUENCE; GYRB GENE; HOUSEKEEPING GENE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; RECA GENE; RPOB GENE; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; UNINDEXED SEQUENCE; BACTERIAL GENE; DIFFERENTIAL DIAGNOSIS; ESSENTIAL GENE; GENETICS; GENOTYPE; GRAM-NEGATIVE BACTERIAL INFECTIONS; HUMAN; MICROBIOLOGY; MOLECULAR DIAGNOSIS; PHENOTYPE; PHYLOGENY;

ACHROMOBACTER;

ACHROMOBACTER; DIAGNOSIS, DIFFERENTIAL; GENES, BACTERIAL; GENES, ESSENTIAL; GENOTYPE; GRAM-NEGATIVE BACTERIAL INFECTIONS; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MULTILOCUS SEQUENCE TYPING; PHENOTYPE; PHYLOGENY;

EID: 84915756275     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0114356     Document Type: Article

References (45)

1. Li Puma JJ (2010) The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 23:299-323.
2. Peleg AY, Hooper DC (2010) Hospital-acquired infections due to Gram-negative bacteria. N Engl J Med 362:1804-1813.
3. Amoureux L, Bador J, Fardeheb S, Mabille C, Couchot C, et al. (2013) Detection of Achromobacter xylosoxidans in hospital, domestic, and outdoor environmental samples and comparison with human clinical isolates. Appl Environ Microbiol 79:7142-7149.
4. De Baets F, Schelstraete P, Van Daele S, Haerynck F, Vaneechoutte M (2007) Achromobacter xylosoxidans in cystic fibrosis: prevalence and clinical relevance. J Cyst Fibros 6:75-78.
5. Barrado L, Brañas P, Orellana MA, Martínez MT, García G, et al. (2013) Molecular characterization of Achromobacter isolates from cystic fibrosis and non-cystic fibrosis patients in Madrid, Spain. J Clin Microbiol 51:1927-1930.
6. Spilker T, Vandamme P, Li Puma JJ (2013) Identification and distribution of Achromobacter species in cystic fibrosis. J Cyst Fibros 12:298-301.
7. De Baets F, Schelstraete P, Haerynck F, Van Bierviet S, De Bruyne R, et al. (2013) Achromobacter xylosoxidans induced bronchiolitis obliterans in cystic fibrosis. Pediatr Pulmonol; doi:10.1002/ppul.22864.
8. Hansen CR, Pressler T, Ridderberg W, Johansen HK, Skov M (2013) Achromobacter spcies in cystic fibrosis: cross-infection caused by indirect patient-to-patient contact. J Cyst Fibros 6:609-615.
9. De Ley J, Segers P, Kersters K, Mannheim W, Lievens A (1986) Intra- and intergeneric similarities of the Bordetella ribosomal ribonucleic acid cistrons: proposal for a new family, Alcaligenaceae. Int J Syst Bacteriol 36:405-414.
10. Yabuuchi E, Kawamura Y, Kosako Y, Ezaki T (1998) Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii (Kiredjian, et al.) comb. nov., and Achromobacter xylosoxidans subsp. denitrificans (Rüger and Tan) comb. nov. Microbiol Immunol 42:429-438.
11. Blümel S, Mark B, Busse HJ, Kämpfer P, Stolz A (2001) Pigmentiphaga kullae gen. nov., sp. nov., a novel member of the family Alcaligenaceae with the ability to decolorize azo dyes aerobically. Int J Syst Evol Microbiol 51:1867-1871.
12. Busse HJ, Auling G (2005) Genus II. Achromobacter Yabuuchi and Yano 1981, 477VP emend. Yabuuchi, Kawamura, Kosako and Ezaki 1998a, 1083. In: Brenner DJ, Krieg NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology, vol. 2: The Proteobacteria, second edition. Springer. pp. 658-662.
13. Coenye T, Vancanneyt M, Cnockaert MC, Falsen E, Swings J, et al. (2003a) Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Rüger and Tan 1983 as Achromobacter denitrificans comb. nov. Int J Syst Evol Microbiol 53:1825-1831.
14. Coenye T, Vancanneyt M, Falsen E, Swings J, Vandamme P (2003b). Achromobacter insolitus sp. nov. and Achromobacter spanius sp. nov., from human clinical samples. Int J Syst Evol Microbiol 53:1819-1824.
15. Gomila M, TvrzováL, Teshim A, Sedlácek I, González-Escalona N, et al. (2011) Achromobacter marplatensis sp. nov., isolated from a pentachlorophenol-contaminated soil. Int J Syst Evol Microbiol 61:2231-2237.
16. Vandamme P, Moore ERB, Cnockaert M, De Brandt E, Svensson-Stadler L, et al. (2013a) Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples. Syst Appl Microbiol 36:1-10.
17. Vandamme P, Moore ERB, Cnockaert M, Peeters C, Svensson-Stadler L, et al. (2013b) Classification of Achromobacter genogroups 2, 5, 7 and 14 as Achromobacter insuavis sp. nov., Achromobacter aegrifaciens sp. nov., Achromobacter anxifer sp. nov. and Achromobacter dolens, sp. nov., respectively. Syst App Microbiol 36:474-482.
18. D'Amato RF, Salemi M, Mathews A, Cleri DJ, Reddy G (1988) Achromobacter xylosoxidans (Alcaligenes xylosoxidans subsp. xylosoxidans) meningitis associated with a gunshot wound. J Clin Microbiol 26:2425-2426.
19. Duggan JM, Goldstein SJ, Chenoweth CE, Kauffman CA, Bradley SF (1996) Achromobacter xylosoxidans bacteremia: report of four cases and review of the literature. Clin Infect Dis 23:569-576.
20. Liu L, Coenye T, Burns JL, Whitby PW, Stull TL, et al. (2002). Ribosomal DNA-Directed PCR for identification of Achromobacter (Alcaligenes) xylosoxidans recovered from sputum samples from cystic fibrosis patients. J Clin Microb 40:1210-1213.
21. Spear JB, Fuhrer J, Kirby BD (1988) Achromobacter xylosoxidans (Alcaligenes xylosoxidans subsp. xylosoxidans) bacteremia associated with a well-water source; case report and review of the literature. J Clin Microbiol 26:598-599.
22. Vu-Thien H, Darbord JC, Moissenet D, Dulot C, Dufourcq JB, et al. (1998) Investigation of an outbreak of wound infections due to Alcaligenes xylosoxidans transmitted by chlorhexidine in a burn unit. Eur J Clin Microbiol Infect Dis 17:724-726.
23. Kersters K, De Ley J (1984) Genus Alcaligenes Castellani and Chalmers 1919, 936AL. In: Krieg NR, Holt JG, editors. Bergey's Manual of Systematic Bacteriology, vol. 1. Baltimore: Williams & Wilkins. pp. 361-373.
24. Kiredjian M, Holmes B, Kersters K, Guilvout I, De Ley J (1986) Alcaligenes piechaudii, a new species from human clinical specimens and the environment. Int J Syst Bacteriol 36:282-287.
25. Spilker T, Vandamme P, Lipuma JJ (2012) A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species. J Clin Microbiol 50:3010-3015.
26. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, et al. (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464.
27. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, et al. (2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043-1047.
28. Hanage WP, Fraser C, Spratt BG (2006) Sequences, sequence clusters and bacterial species. Philos Trans R Soc Lond B Biol Sci 361:1917-1927.
29. Ridderberg W, Wang M, Nørskov-Lauritsen N (2012) Multilocus sequence analysis of isolates of Achromobacter from patients with cystic fibrosis reveals infecting species other than Achromobacter xylosoxidans. J Clin Microbiol 50:2688-2694.
30. Kallow W, Erhard M, Shah HN, Raptakis E, Welker M (2010) MALDI TOF MS for microbial identification: years of experimental development to an established protocol. In: Shah HN, Gharbia SE, Encheva V, editors. Mass Spectrometry for Microbial Proteomics, John Wiley & Sons, London. pp. 255-276.
31. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, et al. (2009) Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49:543-551.
32. Gomila M, Ramirez A, Lalucat J (2007) Diversity of environmental Mycobacterium isolates from hemodialysis water as shown by a multigene sequencing approach. Appl Environ Microbiol 73:3787-3797.
33. Lane DJ (1991) Nucleic acid techniques in bacterial systematics. In: Stackebrand E, Goodfellow M, editors. 16S/23S rDNA sequencing. Wiley, Chichester, United Kingdom. pp. 115-175.
34. Tayeb LA, Lefevre M, Passet V, Diancourt L, Brisse S, et al. (2008) Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences. Res Microbiol 159:169-177.
35. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A, et al. (2000) Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146:2385-2394.
36. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410.
37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876-4882.
38. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN, editors. Mammalian protein metabolism. Academic Press, Inc., New York, NY. pp. 21-132.
39. Felsenstein J (1989) PHYLIP - phylogeny inference package (version3.2). Cladistics 5:164-166.
40. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358.
41. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony methods. Mol Biol Evol 28:2371-2379.
42. Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
43. Ziemke F, Hofle MG, Lalucat J, Rossello-Mora R (1998) Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48:179-186.
44. Fernández-Olmos A, García-Castillo M, Morosini MI, Lamas A, Máiz L, et al. (2012) MALDI-TOF MS improves routine identification of non-fermenting Gram negative isolates from cystic fibrosis patients. J Cyst Fibros 11:59-62.
45. Jacquier H, Carbonnelle E, Corvec S, Illiaquer M, Le Monnier A, et al. (2011) Revisited distribution of nonfermenting Gram-negative bacilli clinical isolates. Eur J Clin Microbiol Infect Dis 30:1579-1586.