title: Genome of the carbapenemase-producing clinical isolate Elizabethkingia miricola EM_CHUV and comparative genomics with Elizabethkingia meningoseptica and Elizabethkingia anophelis: evidence for intrinsic multidrug resistance trait of emerging pathogens.
abstract: Elizabethkingia miricola is a Gram-negative non-fermenting rod emerging as a life-threatening human pathogen. The multidrug-resistant (MDR) carbapenemase-producing clinical isolate E. miricola EM_CHUV was recovered in the setting of severe nosocomial pneumonia. In this study, the genome of E. miricola EM_CHUV was sequenced and a functional analysis was performed, including a comparative genomic study with Elizabethkingia meningoseptica and Elizabethkingia anophelis. The resistome of EM_CHUV revealed the presence of a high number of resistance genes, including the presence of the blaGOB-13and blaB-9carbapenemase-encoding genes. Twelve mobility genes, with only two of them located in the proximity of resistance genes, and four potential genomic islands were identified in the genome of EM_CHUV, but no prophages or CRISPR sequences. Ten restriction-modification system (RMS) genes were also identified. In addition, we report the presence of a putative conjugative plasmid (pEM_CHUV) that does not encode any antibiotic resistance genes. Altogether, these findings point towards a limited number of DNA exchanges with other bacteria and suggest that multidrug resistance is an intrinsic trait of E. miricola owing to the presence of a high number of resistance genes within the bacterial core genome.
authors.affiliation: Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland.
authors.forename: Onya
authors.initials: O
authors.lastname: Opota
authors.affiliation: Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
authors.forename: Seydina M
authors.initials: SM
authors.lastname: Diene
authors.affiliation: Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Claire
authors.initials: C
authors.lastname: Bertelli
authors.affiliation: Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland.
authors.forename: Guy
authors.initials: G
authors.lastname: Prod'hom
authors.affiliation: Service of Adult Intensive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.
authors.forename: Philippe
authors.initials: P
authors.lastname: Eckert
authors.affiliation: Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland; Infectious Diseases Service, University Hospital of Lausanne, Lausanne, Switzerland. Electronic address: gilbert.greub@chuv.ch.
authors.forename: Gilbert
authors.initials: G
authors.lastname: Greub
mesh_terms: D000328:Adult; D000369:Aged, 80 and over; D002675:Child, Preschool; D003428:Cross Infection / Q000382:microbiology; D024901:Drug Resistance, Multiple, Bacterial; D005260:Female; D041965:Flavobacteriaceae / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification; D045826:Flavobacteriaceae Infections / Q000382:microbiology; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D008297:Male; D008875:Middle Aged; D018410:Pneumonia, Bacterial / Q000382:microbiology; D017422:Sequence Analysis, DNA
keywords: Carbapenemase; Comparative genomics; Elizabethkingia miricola; Multidrug resistance; Nosocomial infection; Pneumonia