Genomic Analysis of Enterobacter Species Isolated from Patients in United States Hospitals

We analyzed the whole genome sequences (WGS) and antibiograms of 35 <i>Enterobacter</i> isolates, including <i>E. hormaechei</i> and <i>E. asburiae</i>, and the recently described <i>E. bugandensis</i>, <i>E. kobei</i>, <i>E. ludwigii</i>, and <i>E. roggenkampii</i> species. Isolates were obtained from human blood and urinary tract infections in patients in the United States. Our goal was to understand the genetic diversity of antimicrobial resistance genes and virulence factors among the various species. Thirty-four of 35 isolates contained an AmpC class <i>bla_ACT</i> allele; however, the <i>E. roggenkampii</i> isolate contained <i>bla_MIR-5</i>. Of the six <i>Enterobacter</i> isolates resistant to ertapenem, imipenem, and meropenem, four harbored a carbapenemase gene, including <i>bla_KPC</i> or <i>bla_NDM</i>. All four isolates were mCIM-positive. The remaining two isolates had alterations in <i>ompC</i> genes that may have contributed to the resistance phenotype. Interpretations of cefepime test results were variable when disk diffusion and automated broth microdilution results were compared due to the Clinical Laboratory and Standards Institute use of the "susceptible dose-dependent" classification. The diversity of the <i>bla_ACT</i> alleles paralleled species identifications, as did the presence of various virulence genes. The classification of recently described <i>Enterobacter</i> species is consistent with their resistance gene and virulence gene profiles.