Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

Abstract

The taxonomy of Enterobacter species is rapidly changing. Herein we report a bloodstream infection isolate originally identified as Enterobacter cloacae by Vitek2 methodology that we found to be Kosakonia radicincitans using genetic means. Comparative whole genome sequencing of our isolate and other published Kosakonia genomes revealed these organisms lack the AmpC β-lactamase present on the chromosome of Enterobacter sp. A fimbriae operon primarily found in Escherichia coli O157:H7 isolates was present in our organism and other available K. radicincitans genomes. This is the first report of a Kosakonia species, which are typically associated with plants, causing a human infection.

Keywords: AmpC; Enterobacter; Kosakonia radicincitans; bloodstream infection; fimbriae.

FIGURE 1

Whole genome characterization of MB019 and other Kosakonia strains. (A) Whole genome phylogenetic analysis was performed in PhyML as described in the manuscript. The following strains with NCBI accession numbers in parentheses are included: E. cloacae ATCC 13047 (NC_014121.1); E. asburiae LF7a (NC_015968.1); E. cancerogenus ATCC 35316 (GCA_000155995.1); E. hormaechei ATCC 49162 (GCA_000213995.1); E. ludwigii EN-119 (GCA_000818595.1); L. amnigena CHS 78 (GCA_000694955.1); P. gergoviae FB2 (NZ_CP009450.1). C. sakazakii ATCC BAA-894 (NC_009778.1); C. dubliniensis LMB 23823 (NZ_CP01266.1); K. radicincitans DSM 16656 (GCA_000280495.1); K. cowanii JCM_10956 (GCA_001312885.1); K. sacharii (NZ_CP007215.1); K. oryzae (GCA_000958895.1). (B) Phylogenetic analysis of AmpC homologs present in Enterobacter and Enterobacter-like organisms. AmpC homologs were identified using BLASTp, aligned via MUSCLE, and a phylogenetic tree was generated using MEGA v. 6 using nearest neighbor setting. Bootstrapping was performed using 1000 iterations with numbers reflecting confidence of branching. Inset shows genetic distance. (C) Analysis of genetic region of AmpC encoding genes in Enterobacter and Enterobacter-like organisms. Genes are color coded with genetic arrangements grouped by indicated organisms. (D) Identification of fimbriae operon present in K. radicincitans and E. coli O157:H7 strains. Putative functions of encoded genes are shown. Numbers indicate percent identity and similarity, respectively, at the amino acid level for each protein between MB019 and E. coli 0157:H7 EDL933 (NC_02655).