Intrapatient diversity of Achromobacter spp. involved in chronic colonization of Cystic Fibrosis airways

Infection, Genetics and Evolution

Volumn 32, Issue , 2015, Pages 214-223

  Dupont, Chloé ^a   Michon, Anne Laure ^a,b   Jumas Bilak, Estelle ^a,c   Nørskov Lauritsen, Niels ^d   Chiron, Raphaël ^b   Marchandin, Hélène ^a,b  

^a UNIV MONTPELLIER   (France)

^b MONTPELLIER UNIVERSITY HOSPITAL   (France)

^c HÔPITAL SAINT ELOI   (France)

^d AARHUS UNIVERSITY HOSPITAL   (Denmark)

Author keywords

Achromobacter; Adaptation; Colonization; Cystic Fibrosis; Diversity; Genome

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL DNA; RNA 16S;

ACHROMOBACTER; ACHROMOBACTER DOLENS; ACHROMOBACTER INSUAVIS; ACHROMOBACTER XYLOSOXIDANS; ADOLESCENT; ADULT; ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; CYSTIC FIBROSIS; GEL ELECTROPHORESIS; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GRAM NEGATIVE INFECTION; HUMAN; LONGITUDINAL STUDY; MICROBIAL DIVERSITY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; NRDA GENE; NUCLEOTIDE SEQUENCE; PRESCHOOL CHILD; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RESPIRATORY TRACT DISEASE; RRS GENE; SCHOOL CHILD; TEMPORAL TEMPERATURE GEL ELECTROPHORESIS; UNINDEXED SEQUENCE; CLASSIFICATION; GENE REARRANGEMENT; GENETIC VARIATION; GENETICS; ISOLATION AND PURIFICATION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; RESPIRATORY SYSTEM; SPECIES DIFFERENCE;

ACHROMOBACTER; ACHROMOBACTER XYLOSOXIDANS;

ACHROMOBACTER; ANTI-BACTERIAL AGENTS; CYSTIC FIBROSIS; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENE REARRANGEMENT; GENETIC VARIATION; GENOME, BACTERIAL; HUMANS; MICROBIAL SENSITIVITY TESTS; RESPIRATORY SYSTEM; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY;

EID: 84925634098     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2015.03.012     Document Type: Article

References (44)

1. Amoureux L., Bador J., Siebor E., Taillefumier N., Fanton A., Neuwirth C. Epidemiology and resistance of Achromobacter xylosoxidans from cystic fibrosis patients in Dijon, Burgundy: First French data. J. Cyst. Fibros. 2013, 12:170-176.
2. Amoureux L., Bador J., Fardeheb S., Mabille C., Couchot C., Massip C., Salignon A.L., Berlie G., Varin V., Neuwirth C. Detection of Achromobacter xylosoxidans in hospital, domestic, and outdoor environmental samples and comparison with human clinical isolates. Appl. Environ. Microbiol. 2013, 79:7142-7149.
3. Aujoulat F., Roger F., Bourdier A., Lotthé A., Lamy B., Marchandin H., Jumas-Bilak E. From environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens. Genes (Basel). 2012, 3:191-232. 10.3390/genes3020191.
4. Barrado L., Brañas P., Orellana M.Á., Martínez M.T., García G., Otero J.R., Chaves F. Molecular characterization of Achromobacter isolates from cystic fibrosis and non-cystic fibrosis patients in Madrid. Spain J. Clin. Microbiol. 2013, 51:1927-1930.
5. Carriço J.A., Silva-Costa C., Melo-Cristino J., Pinto F.R., de Lencastre H., Almeida J.S., Ramirez M. Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes. J. Clin. Microbiol. 2006, 44:2524-2532.
6. De Baets F., Schelstraete P., Van Daele S., Haerynck F., Vaneechoutte M. Achromobacter xylosoxidans in cystic fibrosis: prevalence and clinical relevance. J. Cyst. Fibros. 2007, 6:75-78.
7. Gouby A., Neuwirth C., Bourg G., Bouziges N., Carles-Nurit M.-J., Despaux E., Ramuz M. Epidemiological study by pulsed-field gel electrophoresis of an outbreak of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae in a geriatric hospital. J. Clin. Microbiol. 1994, 32:301-305.
8. Greenwood, D., Barer, M., Slack, R., Irving, W., 2012. Typing of bacteria. Medical Microbiology, C. Linvingstone, Elsevier.
9. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
10. Hauser A.R., Jain M., Bar-Meir M., McColley S.A. Clinical significance of microbial infection and adaptation in cystic fibrosis. Clin. Microbiol. Rev. 2011, 24:29-70.
11. Hansen C.R., Pressler T., Nielsen K.G., Jensen P.Ø., Bjarnsholt T., Høiby N. Inflammation in Achromobacter xylosoxidans infected cystic fibrosis patients. J. Cyst. Fibros. 2010, 9:51-58.
12. Hunter P.R., Gaston M.A. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 1988, 26:2465-2466.
13. Jakobsen T.H., Hansen M.A., Jensen P.Ø., Hansen L., Riber L., Cockburn A., Kolpen M., Rønne Hansen C., Ridderberg W., Eickhardt S., Hansen M., Kerpedjiev P., Alhede M., Qvortrup K., Burmølle M., Moser C., Kühl M., Ciofu O., Givskov M., Sørensen S.J., Høiby N., Bjarnsholt T. Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes. PLoS One 2013, 8:e68484.
14. Jensen S., Frost P., Torsvik V.L. The nonrandom microheterogeneity of 16S rRNA genes in Vibrio splendidus may reflect adaptation to versatile lifestyles. FEMS Microbiol. Lett. 2009, 294:207-215.
15. Kanellopoulou M., Pournaras S., Iglezos H., Skarmoutsou N., Papafrangas E., Maniatis A.N. Persistent colonization of nine cystic fibrosis patients with an Achromobacter (Alcaligenes) xylosoxidans clone. Eur. J. Clin. Microbiol. Infect. Dis. 2004, 23:336-339.
16. Kaur M., Ray P., Bhatty M., Sharma M. Epidemiological typing of clinical isolates of Achromobacter xylosoxidans: comparison of phenotypic and genotypic methods. Eur. J. Clin. Microbiol. Infect. Dis. 2009, 28:1023-1032.
17. Lambiase A., Catania M.R., Del Pezzo M., Rossano F., Terlizzi V., Sepe A., Raia V. Achromobacter xylosoxidans respiratory tract infection in cystic fibrosis patients. Eur. J. Clin. Microbiol. Infect. Dis. 2011, 30:973-980.
18. Li X., Hu Y., Gong J., Zhang L., Wang G. Comparative genome characterization of Achromobacter members reveals potential genetic determinants facilitating the adaptation to a pathogenic lifestyle. Appl. Microbiol. Biotechnol. 2013, 97:6413-6425.
19. López-López A., Benlloch S., Bonfá M., Rodríguez-Valera F., Mira A. Intragenomic 16S rDNA divergence in Haloarcula marismortui is an adaptation to different temperatures. J. Mol. Evol. 2007, 65:687-696.
20. Magni A., Trancassini M., Varesi P., Iebba V., Curci A., Pecoraro C., Cimino G., Schippa S., Quattrucci S. Achromobacter xylosoxidans genomic characterization and correlation of randomly amplified polymorphic DNA profiles with relevant clinical features of cystic fibrosis patients. J. Clin. Microbiol. 2010, 48:1035-1039.
21. Mercier E., Jumas-Bilak E., Allardet-Servent A., O'Callaghan D., Ramuz M. Polymorphism in Brucella strains detected by studying distribution of two short repetitive DNA elements. J. Clin. Microbiol. 1996, 34:1299-1302.
22. Michon A.-L., Aujoulat F., Roudière L., Soulier O., Zorgniotti I., Jumas-Bilak E., Marchandin H. Intragenomic and intraspecific heterogeneity in rrs may surpass interspecific variability in a natural population of Veillonella. Microbiology 2010, 156:2080-2091.
23. Michon A.-L., Jumas-Bilak E., Imbert A., Aleyrangues L., Counil F., Chiron R., Marchandin H. Intragenomic and intraspecific heterogeneity of the 16S rRNA gene in seven bacterial species from the respiratory tract of cystic fibrosis patients assessed by PCR-Temporal Temperature Gel Electrophoresis. Pathol. Biol. (Paris) 2012, 60:e30-35.
24. Ogier J.C., Son O., Gruss A., Tailliez P., Delacroix-Buchet A. Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 2002, 68:3691-3701.
25. Pereira R.H., Carvalho-Assef A.P., Albano R.M., Folescu T.W., Jones M.C., Leão R.S., Marques E.A. Achromobacter xylosoxidans: characterization of strains in Brazilian cystic fibrosis patients. J. Clin. Microbiol. 2011, 49:3649-3651.
26. Raso T., Bianco O., Grosso B., Zucca M., Savoia D. Achromobacter xylosoxidans respiratory tract infections in cystic fibrosis patients. APMIS 2008, 116:837-841.
27. Ridderberg W., Bendstrup K.E., Olesen H.V., Jensen-Fangel S., Nørskov-Lauritsen N. Marked increase in incidence of Achromobacter xylosoxidans infections caused by sporadic acquisition from the environment. J. Cyst. Fibros. 2011, 10:466-469.
28. Ridderberg W., Wang M., Nørskov-Lauritsen N. Multilocus sequence analysis of isolates of Achromobacter from patients with cystic fibrosis reveals infecting species other than Achromobacter xylosoxidans. J. Clin. Microbiol. 2012, 50:2688-2694.
29. Santoyo G., Romero D. Gene conversion and concerted evolution in bacterial genomes. FEMS Microbiol. Rev. 2005, 29:169-183.
30. Severiano A., Pinto F.R., Ramirez M., Carriço J.A. Adjusted Wallace coefficient as a measure of congruence between typing methods. J. Clin. Microbiol. 2011, 49:3997-4000.
31. Spilker T., Vandamme P., Lipuma J.J. A multilocus sequence typing scheme implies population structure and reveals several putative novel Achromobacter species. J. Clin. Microbiol. 2012, 50:3010-3015.
32. Spilker T., Vandamme P., Lipuma J.J. Identification and distribution of Achromobacter species in cystic fibrosis. J. Cyst. Fibros. 2013, 12:298-301.
33. Strnad H., Ridl J., Paces J., Kolar M., Vlcek C., Paces V. Complete genome sequence of the haloaromatic acid-degrading bacterium Achromobacter xylosoxidans A8. J. Bacteriol. 2011, 193:791-792.
34. Tan K., Conway S.P., Brownlee K.G., Etherington C., Peckham D.G. Alcaligenes infection in cystic fibrosis. Pediatr. Pulmonol. 2002, 34:101-104.
35. Tenover F.C., Arbeit R.D., Goering R.V., Mickelsen P.A., Murray B.E., Persing D.H., Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 1995, 33:2233-2239.
36. Teyssier C., Marchandin H., Siméon de Buochberg M., Ramuz M., Jumas-Bilak E. Atypical 16S rRNA gene copies in Ochrobactrum intermedium strains reveal a large genomic rearrangement by recombination between rrn copies. J. Bacteriol. 2003, 185:2901-2909.
37. Traglia G.M., Almuzara M., Merkier A.K., Adams C., Galanternik L., Vay C., Centrón D., Ramírez M.S. Achromobacter xylosoxidans: an emerging pathogen carrying different elements involved in horizontal genetic transfer. Curr. Microbiol. 2012, 65:673-678.
38. Turton J.F., Mustafa N., Shah J., Hampton C.V., Pike R., Kenna D.T. Identification of Achromobacter xylosoxidans by detection of the bla(OXA-114-like) gene intrinsic in this species. Diagn. Microbiol. Infect. Dis. 2011, 70:408-411.
39. Vandamme P., Moore E.R., Cnockaert M., De Brandt E., Svensson-Stadler L., Houf K., Spilker T., Lipuma J.J. Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples. Syst. Appl. Microbiol. 2013, 36:1-10.
40. Vandamme P., Moore E.R., Cnockaert M., Peeters C., Svensson-Stadler L., Houf K., Spilker T., LiPuma J.J. 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. Appl. Microbiol. 2013, 36:474-482.
41. Versalovic J., Kapur V., Koeuth T., Mazurek G.H., Whittam T.S., Musser J.M., Lupski J.R. DNA fingerprinting of pathogenic bacteria by fluorophore-enhanced repetitive sequence-based polymerase chain reaction. Arch. Pathol. Lab. Med. 1995, 119:23-29.
42. Versalovic J., Koeuth T., Lupski J.R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991, 19:6823-6831.
43. Wang M., Ridderberg W., Hansen C.R., Høiby N., Jensen-Fangel S., Olesen H.V., Skov M., Lemming L.E., Pressler T., Johansen H.K., Nørskov-Lauritsen N. Early treatment with inhaled antibiotics postpones next occurrence of Achromobacter in cystic fibrosis. J. Cyst. Fibros. 2013, 12:638-643.
44. Yang L., Jelsbak L., Molin S. Microbial ecology and adaptation in cystic fibrosis airways. Environ. Microbiol. 2011, 13:1682-1689.