O OPOTA¹, S-M DIENE², G PROD'HOM¹, P ECKERT³, G GREUB<sup>1

1</sup>Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland, ²Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland, ³Service of Adult Intensive Care Medicine, University Hospital of Lausanne, Lausanne, Switzerland.

Background: Whole genome analysis has emerged as an opportunity for clinical microbiologists to collect, early after description, informations on bacteria traits for newly characterized species of potential medical interest. Elizabethkingia miricola, a recently described ubiquitous non-fermenting Gram negative rod of the Flavobacteriaceae family, is an emerging pathogen causing severe infections in humans including pulmonary abscess and sepsis. We recovered the strain E. miricola CHUV, a multidrug resistant carbapenemase-producing isolate, from the respiratory secretions of a patient who died from a septic choc with a pulmonary origin soon after admission in the intensive care unit of our hospital. We report the complete genome of this bacterium and the functional/comparative analysis to increase our understanding of its pathogenic potential.

Material/methods: The genomic DNA of E. miricola CHUV was extracted and subjected to whole-genome shotgun sequencing by using the MiSeq technology (Illumina, San Diego CA) from a single library of paired-end sequencing reads of 2x150 bp. Genome assembly was performed using the SPAdes v3.5.0 program.

Results: The genome of E. miricola CHUV consists of a 4'286'503 bp chromosome and a plasmid of 176’107 bp, which corresponds to 4006 predicted coding sequences. The strain E. miricola CHUV was resistant to several major classes of antibiotics including carbapenem through the production of a metallo-β-lactamase with carbapenemase activity. The resistome analyses revealed the presence of a high number of resistance genes. Interestingly, we 1) identified only a limited number of mobile elements with only two of them located in the proximity of resistance genes, 2) failed to detect prophage-related sequences and 3) identified 10 restriction-modification system genes in this genome suggesting a very limited rate of DNA exchange with other bacteria.

Conclusions: These findings suggest that multi-drug resistance, a keystone of the pathogenic potential of E. miricola, is an intrinsic trait due to the presence of a high number of resistance genes within the bacterial core genome and is not due to DNA exchanges with other bacteria.