Whole-genome sequence of Chryseobacterium oranimense, a colistin-resistant bacterium isolated from a cystic fibrosis patient in France

• Published in: Antimicrobial agents and chemotherapy 2015-03, Vol.59 (3), p.1696-1706
• Main Authors: Sharma, Poonam, Gupta, Sushim Kumar, Diene, Seydina M, Rolain, Jean-Marc
• Format: Article
• Language: English
• Subjects: Anti-Bacterial Agents - therapeutic use; Bacteria; Bacterial Proteins - genetics; Bacterial Typing Techniques - methods; Base Composition - genetics; beta-Lactamases - genetics; Chryseobacterium; Chryseobacterium - drug effects; Chryseobacterium - genetics; Colistin; Colistin - therapeutic use; Cystic Fibrosis; Cystic Fibrosis - microbiology; DNA, Bacterial - genetics; Drug Resistance, Multiple, Bacterial; Drug Resistance, Multiple, Bacterial - genetics; Flavobacteriaceae Infections - drug therapy; Flavobacteriaceae Infections - microbiology; France; Humans; Imipenem - therapeutic use; Mechanisms of Resistance; Mutation - genetics; Phylogeny; Sequence Analysis, DNA - methods
• ISSN: 0066-4804; 1098-6596
• DOI: 10.1128/AAC.02417-14

For the first time, we report the whole-genome sequence analysis of Chryseobacterium oranimense G311, a multidrug-resistant bacterium, from a cystic fibrosis patient in France, including resistance to colistin. Whole-genome sequencing of C. oranimense G311 was performed using Ion Torrent PGM, and RAST, the EMBL-EBI server, and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT) database were used for annotation of all genes, including antibiotic resistance (AR) genes. General features of the C. oranimense G311 draft genome were compared to the other available genomes of Chryseobacterium gleum and Chryseobacterium sp. strain CF314. C. oranimense G311 was found to be resistant to all β-lactams, including imipenem, and to colistin. The genome size of C. oranimense G311 is 4,457,049 bp in length, with 37.70% GC content. We found 27 AR genes in the genome, including β-lactamase genes which showed little similarity to the known β-lactamase genes and could likely be novel. We found the type I polyketide synthase operon followed by a zeaxanthin glycosyltransferase gene in the genome, which could impart the yellow pigmentation of the isolate. We located the O-antigen biosynthesis cluster, and we also discovered a novel capsular polysaccharide biosynthesis cluster. We also found known mutations in the orthologs of the pmrA (E8D), pmrB (L208F and P360Q), and lpxA (G68D) genes. We speculate that the presence of the capsular cluster and mutations in these genes could explain the resistance of this bacterium to colistin. We demonstrate that whole-genome sequencing was successfully applied to decipher the resistome of a multidrug resistance bacterium associated with cystic fibrosis patients.