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, Division of High Consequence Pathogens and Pathology, vol.3010
, USA. 9 CIP-Collection de l'Institut Pasteur, Institut Pasteur, vol.53718
, F-75724 Paris, France. 11 Division of Scientific Resources, Pasteur International Bioresources network (PIBnet), Plateforme de Microbiologie Mutualisée (P2M), vol.30329
, * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to, Division of Healthcare Quality Promotion, vol.30329
, Pulsed-field gel electrophoresis subtyping using an in-house developed protocol, modified after consultation with CDC, was used to determine genetic relatedness among all suspect outbreak isolates. All isolates determined to be Elizabethkingia species were submitted to CDC for further characterization. Upon arrival, bacteria were cultivated on heart infusion agar supplemented with 5% rabbit blood agar at 35 °C. The outbreak strain isolates were correctly identified as E. anophelis using an expanded MALDI-TOF spectral library, genome sequencing and optical mapping. Conventional biochemical testing was restricted to oxidase, catalase and Gram stain after the MALDI-TOF spectral library provided by the CDC Special Bacteriology Reference Laboratory proved to be a reliable method of identification, /ncomms15483 | www.nature.com/naturecommunications identified as E. meningoseptica using conventional biochemical assays and the Bruker MALDI-TOF spectral library, vol.8
, For comparative purposes, we included seven isolates stored in the Pasteur Institute's collection (Collection de l'Institut Pasteur or CIP; the Nextera XT DNA Library Preparation kit, p.500
, E. meningoseptica strains, and 10 strains that belonged to the E. miricola cluster (see Results and Supplementary Fig. 1)
, CLC Genomics Workbench v8 (CLC bio, Waltham, MA), and manually aligned using BioEdit 43 . Indels in the circularized genomes were located using BioEdit's Positional Nucleotide Numerical Summary function. Assemblies of the seven genomes from the CIP and from publicly available data sets for which only sequence reads were available (see Supplementary Data 1), were generated using SPAdes v.3.6.2 (ref. 44) on pre-processed reads, Genome assembly and annotation. For each outbreak isolate, an initial assembly was generated using the Celera De Bruijn graph assembler (Celera Genomics Workbench v8
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