Genetic Characterization of Enterobacter hormaechei Co-Harboring blaNDM-1 and mcr-9 Causing Upper Respiratory Tract Infection

Abstract

Purpose With the spread of multiple drug-resistant bacteria, bla NDM-1 and mcr-9 have been detected in various bacteria worldwide. However, the simultaneous detection of bla NDM-1 and mcr-9 in Enterobacter hormaechei has been rarely reported. This study identified an E. hormaechei strain carrying both bla NDM-1 and mcr-9 . We investigated the genetic characteristics of these two resistance genes in detail, elucidating various potential mechanisms by which they may be transmitted. Methods Bacterial genomic features and possible origins were assessed by whole-genome sequencing (WGS) with Illumina and PacBio platforms and phylogenetic analysis. Subsequent investigations were performed, including antimicrobial susceptibility testing and multilocus sequence typing (MLST). Results We isolated an E. hormaechei strain DY1901 carrying both bla NDM-1 and mcr-9 from the sputum sample. Susceptibility testing showed that the isolate was multidrug-resistant. Multiple antibiotic resistance genes and virulence genes are widely distributed in DY1901. S1-PFGE, Southern blotting, and plasmid replicon typing showed that DY1901 carried four plasmids. The plasmid carrying mcr-9 was 259Kb in size and belonged to IncHI2, while the plasmid carrying bla NDM-1 was 45Kb in length and belonged to IncX3. Conclusion The E. hormaechei strain isolated in this study has a broad antibiotic resistance spectrum, posing a challenge to clinical treatment. Plasmids carrying mcr-9 are fusion plasmids, and those taking NDM are widely disseminated in China, suggesting that we should conduct routine genomic surveillance on such plasmids to curb the spread of drug-resistant bacteria in the region.

Whole-Genome Analysis of Extensively Drug-Resistant Enterobacter hormaechei Isolated from a Patient with Non-Hodgkin’s Lymphoma

“…The Enterobacter cloacae complex (ECC) is a common hospital pathogen responsible for different infections in humans [ 4 ]. ECC shows genomic heterogeneity and currently comprises seven species: E. cloacae, E. hormaechei, E. asburiae, E. kobei, E. nimipressuralis, E. mori , and E. carcinogenus, of which E. cloacae and E. hormaechei are the most [ 5 , 6 , 7 ] important emerging human pathogens [ 8 ]. The ECC is considered an important member of the Enterobacteriaceae family and is widely distributed in the environment and in the intestinal microbiota of humans and animals [ 6 , 7 , 9 ].…”

“…ECC shows genomic heterogeneity and currently comprises seven species: E. cloacae, E. hormaechei, E. asburiae, E. kobei, E. nimipressuralis, E. mori , and E. carcinogenus, of which E. cloacae and E. hormaechei are the most [ 5 , 6 , 7 ] important emerging human pathogens [ 8 ]. The ECC is considered an important member of the Enterobacteriaceae family and is widely distributed in the environment and in the intestinal microbiota of humans and animals [ 6 , 7 , 9 ]. As an opportunistic pathogen, it can cause different types of infections such as pneumonia, bacteremia, urinary tract infections, skin infections, meningitis, brain abscess, and endocarditis [ 6 , 10 ].…”

“…The ECC is considered an important member of the Enterobacteriaceae family and is widely distributed in the environment and in the intestinal microbiota of humans and animals [ 6 , 7 , 9 ]. As an opportunistic pathogen, it can cause different types of infections such as pneumonia, bacteremia, urinary tract infections, skin infections, meningitis, brain abscess, and endocarditis [ 6 , 10 ].…”

“…These infections can be especially dangerous and even fatal when they occur in immunocompromised individuals or patients such as neonates and those diagnosed with hematological diseases such as leukemia, diabetes mellitus, burns, or multiple traumas, especially those admitted to an intensive care unit (ICU) [ 6 , 7 , 11 , 12 ]. The World Health Organization (WHO) classifies the ECC carbapenemase enzyme producers, and/or extended spectrum β-lactamase (ESβL) as PRIORITY 1: CRITICAL [ 13 ], and some strains of this complex, belonging to sequence type (ST) ST171 and ST78, are considered high-risk disseminators clones of important resistance genes [ 5 ].…”

“…The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) has been increasing since the year 2000, and the mechanism involved in this resistance is due to the constitutive overexpression of AmpC β-lactamases, permeability of membrane (decrease in or loss of the outer membrane proteins OmpF and OmpC), and efflux pumps or plasmid, which encode carbapenem genes. The main mechanism of carbapenem resistance in the ECC is through plasmid transfer [ 6 , 9 , 14 ]. The genes that encode these enzymes are either of chromosomal origin or released by other transferable genetic elements, such as plasmids, transposons, and integrons [ 15 ].…”