Whole genome sequencing for deciphering the resistome of Chryseobacterium indologenes, an emerging multidrug-resistant bacterium isolated from a cystic fibrosis patient in Marseille, France

New Microbes and New Infections

Volumn 12, Issue , 2016, Pages 35-42

  Cimmino, T ^a   Rolain, J M ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Carotenoid; Chryseobacterium indologenes; Microbial genomics; Nonribosomal polyketide synthase; Polyketide synthase; Resistome; Urease

Indexed keywords

AMIKACIN; AMINOGLYCOSIDE; AMOXICILLIN; AMOXICILLIN PLUS CLAVULANIC ACID; BETA LACTAM; CEFTAZIDIME; CEFTRIAXONE; CHLORAMPHENICOL; CIPROFLOXACIN; COLISTIN; COTRIMOXAZOLE; ERTAPENEM; ERYTHROMYCIN; GENTAMICIN; IMIPENEM; POLYKETIDE SYNTHASE; RIFAMPICIN; TIMENTIN; UREASE;

ADOLESCENT; ANTIBIOTIC RESISTANCE; ARTICLE; CHRYSEOBACTERIUM INDOLOGENES; CYSTIC FIBROSIS; DISK DIFFUSION; FEMALE; GENETIC ANALYSIS; HUMAN; MOLECULAR GENETICS; NONHUMAN; OPERON; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; WHOLE GENOME SEQUENCING;

EID: 84965013522     PISSN: 20522975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.nmni.2016.03.006     Document Type: Article

References (41)

1. Vandamme P., Bernardet J.F., Segers P., Kersters K., Holmes B. New perspectives in the classification of the flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 1994, 44:827-831.
2. Deng L., Li M.F., Li Y.H., Yang J.L., Zhou X. Chryseobacterium indologenes in four patients with leukemia. Transpl Infect Dis 2015, 17:583-587.
3. Chen X.Y., Zhao R., Chen Z.L., Liu L., Li X.D., Li Y.H. Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium. Antonie Van Leeuwenhoek 2015, 107:403-410.
4. Chen F.L., Wang G.C., Teng S.O., Ou T.Y., Yu F.L., Lee W.S. Clinical and epidemiological features of Chryseobacterium indologenes infections: analysis of 215 cases. J Microbiol Immunol Infect 2013, 46:425-432.
5. Nemli S.A., Demirdal T., Ural S. A case of healthcare associated pneumonia caused by Chryseobacterium indologenes in an immunocompetent patient. Case Rep Infect Dis 2015, 2015:483923.
6. Kirby J.T., Sader H.S., Walsh T.R., Jones R.N. Antimicrobial susceptibility and epidemiology of a worldwide collection of Chryseobacterium spp.: report from the SENTRY Antimicrobial Surveillance Program (1997-2001). J Clin Microbiol 2004, 42:445-448.
7. Omar A., Camara M., Fall S., Ngom-Cisse S., Fall B., Ba-Diallo A., et al. A. Chryseobacterium indologenes in a woman with acute leukemia in Senegal: a case report. J Med Case Rep 2014, 8:138.
8. Lu P.C., Chan J.C. Flavobacterium indologenes keratitis. Ophthalmologica 1997, 211:98-100.
9. Lin J.T., Wang W.S., Yen C.C., Liu J.H., Chiou T.J., Yang M.H., et al. Chryseobacterium indologenes bacteremia in a bone marrow transplant recipient with chronic graft-versus-host disease. Scand J Infect Dis 2003, 35:882-883.
10. Hsueh P.R., Teng L.J., Yang P.C., Ho S.W., Hsieh W.C., Luh K.T. Increasing incidence of nosocomial Chryseobacterium indologenes infections in Taiwan. Eur J Clin Microbiol Infect Dis 1997, 16:568-574.
11. Christakis G.B., Perlorentzou S.P., Chalkiopoulou I., Athanasiou A., Legakis N.J. Chryseobacterium indologenes non-catheter-related bacteremia in a patient with a solid tumor. J Clin Microbiol 2005, 43:2021-2023.
12. Kienzle N., Muller M., Pegg S. Chryseobacterium in burn wounds. Burns 2001, 27:179-182.
13. Doiz O., Llorente M.T., Mateo A., Seral C., García C., Rubio M.C. Corneal abscess by Flavobacterium indologenes. A case report. Enfermedades Infecc Y Microbiol Clínica 1999, 17:149-150.
14. Nulens E., Bussels B., Bols A., Gordts B., Van Landuyt H.W. Recurrent bacteremia by Chryseobacterium indologenes in an oncology patient with a totally implanted intravascular device. Clin Microbiol Infect 2001, 7:391-393.
15. Marcos Sánchez F., Plaza Díaz R., Juárez Ucelay F., Durán Pérez-Navarro A. Pneumonia from Flavobacterium indologenes (group II B) in an immunodepressed patient. An Med Interna 1993, 10:312.
16. Green B.T., Nolan P.E. Cellulitis and bacteraemia due to Chryseobacterium indologenes. J Infect 2001, 42:219-220.
17. Ferreira M., Fonseca A.G., Cunha V., Diogo J. Community acquired Chryseobacterium indologenes in an immunocompetent patient. JMM Case Reports 2014, 1.
18. Beringer P. The clinical use of colistin in patients with cystic fibrosis. Curr Opin Pulm Med 2001, 7:434-440.
19. Seng P., Drancourt M., Gouriet F., La Scola B., Fournier P.E., Rolain J.M., et al. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009, 49:543-551.
20. Leclercq R., Cantón R., Brown D.F.J., Giske C.G., Heisig P., MacGowan A.P., et al. EUCAST expert rules in antimicrobial susceptibility testing. Clin Microbiol Infect 2013, 19:141-160.
21. Bakour S., Garcia V., Loucif L., Brunel J.M., Gharout-Sait A., Touati A., et al. Rapid identification of carbapenemase-producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii using a modified Carba NP test. New Microbes New Infect 2015, 7:89-93.
22. Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75.
23. Carattoli A., Zankari E., García-Fernández A., Voldby Larsen M., Lund O., Villa L., et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014, 58:3895-3903.
24. Gupta S.K., Padmanabhan B.R., Diene S.M., Lopez-Rojas R., Kempf M., Landraud L., et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014, 58:212-220.
25. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007, 57:81-91.
26. Lagesen K., Hallin P., Rødland E.A., Staerfeldt H.H., Rognes T., Ussery D.W. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35:3100-3108.
27. Zhou Y., Liang Y., Lynch K.H., Dennis J.J., Wishart D.S. PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39:W347-W352.
28. Drissi F., Buffet S., Raoult D., Merhej V. Common occurrence of antibacterial agents in human intestinal microbiota. Front Microbiol 2015, 6:441.
29. Weber T., Blin K., Duddela S., Krug D., Kim H.U., Bruccoleri R., et al. AntiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 2015, 43:W237-W243.
30. Bellais S., Poirel L., Leotard S., Naas T., Nordmann P. Genetic diversity of carbapenem-hydrolyzing metallo-beta-lactamases from Chryseobacterium (Flavobacterium) indologenes. Antimicrob Agents Chemother 2000, 44:3028-3034.
31. Matsumoto T., Nagata M., Ishimine N., Kawasaki K., Yamauchi K., Hidaka E., et al. Characterization of CIA-1, an Ambler class A extended-spectrum β-lactamase from Chryseobacterium indologenes. Antimicrob Agents Chemother 2012, 56:588-590.
32. Aminov R.I. Evolution in action: dissemination of tet(X) into pathogenic microbiota. Front Microbiol 2013, 4:192.
33. Bittar F., Leydier A., Bosdure E., Toro A., Reynaud-Gaubert M., Boniface S., et al. Inquilinus limosus and cystic fibrosis. Emerg Infect Dis 2008, 14:993-995.
34. Klassen J.L. Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics. PLoS One 2010, 5:e11257.
35. Liu G.Y., Nizet V. Color me bad: microbial pigments as virulence factors. Trends Microbiol 2009, 17:406-413.
36. Johnson E.A., Schroeder W.A. Microbial carotenoids. Adv Biochem Eng Biotechnol 1996, 53:119-178.
37. Mobley H.L., Hausinger R.P. Microbial ureases: significance, regulation, and molecular characterization. Microbiol Rev 1989, 53:85-108.
38. James C.E., Davies E.V., Fothergill J.L., Walshaw M.J., Beale C.M., Brockhurst M.A., et al. Lytic activity by temperate phages of Pseudomonas aeruginosa in long-term cystic fibrosis chronic lung infections. ISME J 2015, 9:1391-1398.
39. Nützmann H.W., Reyes-Dominguez Y., Scherlach K., Schroeckh V., Horn F., Gacek A., et al. Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc Natl Acad Sci U S A 2011, 108:14282-14287.
40. Brakhage A.A. Regulation of fungal secondary metabolism. Nat Rev Microbiol 2013, 11:21-32.
41. Huang E., Guo Y., Yousef A.E. Biosynthesis of the new broad-spectrum lipopeptide antibiotic paenibacterin in Paenibacillus thiaminolyticus OSY-SE. Res Microbiol 2014, 165:243-251.