Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China

Abstract

Three NDM-5-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Citrobacter braakii, one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis. Methods: In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of bla NDM-5harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the bla NDM-5harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome. Results: Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, bla NDM-5 was carried by an IncX3 plasmid in K. pneumoniae and C. braakii, and on an IncR/IncX1 plasmid in E. coli. Conjugation experiments showed that these bla NDM-5 -haboring plasmids were successfully transferred to E. coli J53. Phylogenetic analysis revealed that E. coli SCLZR49 was present in a cluster with isolates of different origin, K. pneumoniae SCLZR50 was mainly clustered with clinical isolates, and C. braakii SCLZR53 had closely genetic relationship with environmental isolates. Conclusion:This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene bla NDM-5 , raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the "One-Health" perspective.

Persistence and Dissemination Capacities of a blaNDM-5-Harboring IncX-3 Plasmid in Escherichia coli Isolated from an Urban River in Montpellier, France

“…Focusing on hydric environments, this variant has been found in various environments such as urban waters [ 29 , 36 ]; rivers and lakes [ 8 , 37 ]; sediments and soil [ 38 ]; and seawater [ 8 ]. Various plasmid incompatibility groups carrying bla NDM-5 have been reported, with IncX-3 and IncF being among the most prevalent [ 8 , 27 , 34 , 37 , 38 , 39 , 40 ].…”

Genome Assessment of Carbapenem- and Colistin-Resistant Escherichia coli from Patients in a Sentinel Hospital in China

“…It is also higher than the prevalence of CREC (2.38%, 92/3895) in healthy people in healthcare centers located in 19 provinces across China [ 16 ]. The bla NDM gene was also detected from the specimens of various environments, vegetables (0.28%), companion animals (2.3%), and livestock and poultry (0.88%), the amounts of which were significantly lower than that in patients [ 33 , 34 , 35 ]. However, it has a similar prevalence in India (6.22%) [ 15 ].…”

Whole-genome-sequence-based characterization of an NDM-5-producing uropathogenic Escherichia coli EC1390

“…Currently, international circulation of NDM-5-producing E. coli was reported but only a few UPEC isolates harboring bla NDM-5 were identified [ 30 – 32 ]. To our knowledge, there are only 2 studies that reported the E. coli carrying bla NDM-5 in Taiwan [ 33 , 34 ].…”