Comprehensive Genome Analysis of Carbapenemase-Producing
Enterobacter
spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms
Authors: Chavda Kalyan D. , Chen Liang , Fouts Derrick E. , Sutton Granger , Brinkac Lauren , Jenkins Stephen G. , Bonomo Robert A. , Adams Mark D. , Kreiswirth Barry N. 
Published: December 2016

Knowledge regarding the genomic structure of
Enterobacter
spp., the second most prevalent carbapenemase-producing
Enterobacteriaceae
, remains limited. Here we sequenced 97 clinical
Enterobacter
species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed
bla
KPC-2
, 40 had
bla
KPC-3
, 2 had
bla
KPC-4
, and 2 had
bla
NDM-1
. Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional
Enterobacter
genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups—18 groups (A to R) in the
Enterobacter cloacae
complex and
Enterobacter aerogenes
. Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant
Enterobacter
spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of
bla
KPC
-harboring plasmids between different phylogenomic groups, and repeated transposition of the
bla
KPC
gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique
bla
KPC
-harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant
Enterobacter
spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this genus.

IMPORTANCE
Enterobacter
spp., especially carbapenemase-producing
Enterobacter
spp., have emerged as a clinically significant cause of nosocomial infections. However, only limited information is available on the distribution of carbapenem resistance across this genus. Augmenting this problem is an erroneous identification of
Enterobacter
strains because of ambiguous typing methods and imprecise taxonomy. In this study, we used a whole-genome-based comparative phylogenetic approach to (i) revisit and redefine the genus
Enterobacter
and (ii) unravel the emergence and evolution of the
Klebsiella pneumoniae
carbapenemase-harboring
Enterobacter
spp. Using genomic analysis of 447 sequenced strains, we developed an improved understanding of the species designations within this complex genus and identified the diverse mechanisms driving the molecular evolution of carbapenem resistance. The findings in this study provide a solid genomic framework that will serve as an important resource in the future development of molecular diagnostics and in supporting drug discovery programs.