Genomic and Geographic Context for the Evolution of High-Risk Carbapenem-Resistant Enterobacter cloacae Complex Clones ST171 and ST78

MBio
Angela Gomez-SimmondsAnne-Catrin Uhlemann

Abstract

Recent reports have established the escalating threat of carbapenem-resistant Enterobacter cloacae complex (CREC). Here, we demonstrate that CREC has evolved as a highly antibiotic-resistant rather than highly virulent nosocomial pathogen. Applying genomics and Bayesian phylogenetic analyses to a 7-year collection of CREC isolates from a northern Manhattan hospital system and to a large set of publicly available, geographically diverse genomes, we demonstrate clonal spread of a single clone, ST171. We estimate that two major clades of epidemic ST171 diverged prior to 1962, subsequently spreading in parallel from the Northeastern to the Mid-Atlantic and Midwestern United States and demonstrating links to international sites. Acquisition of carbapenem and fluoroquinolone resistance determinants by both clades preceded widespread use of these drugs in the mid-1980s, suggesting that antibiotic pressure contributed substantially to its spread. Despite a unique mobile repertoire, ST171 isolates showed decreased virulence in vitro While a second clone, ST78, substantially contributed to the emergence of CREC, it encompasses diverse carbapenemase-harboring plasmids, including a potentially hypertransmissible IncN plasmid, also present ...Continue Reading

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Citations

Feb 1, 2019·Clinical Microbiology Reviews·Wenjing WuZhiyong Zong
Sep 13, 2019·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Nenad MacesicAnne-Catrin Uhlemann
Mar 12, 2020·Frontiers in Microbiology·Miklos FuziAkos Toth
Feb 16, 2019·Frontiers in Microbiology·Medini K AnnavajhalaAnne-Catrin Uhlemann
Jun 18, 2020·Infection and Drug Resistance·Chunmei JinChangshan An
May 15, 2020·Clinical Microbiology Reviews·David M P De OliveiraMark J Walker
Jan 13, 2021·Trends in Microbiology·Zhiyong ZongAlan McNally
Feb 6, 2021·Pathogens·Gustavo Henrique Rodrigues Vale de MacedoLuís Cláudio Nascimento da Silva
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Datasets Mentioned

BETA
CP012165
SRP099597
SRP126514
PRJNA374677
PRJNA421733

Methods Mentioned

BETA
genotyping
electrophoresis
PCR

Software Mentioned

BEAUti MultiTypeTree
IslandViewer
Gubbins
LogCombiner
Prokka
SAMtools
PHAST
progressiveMauve
bowtie2
Geneious

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