Abstract
To date, blaNDM and blaKPC genes have been found predominantly in clinical settings around the world. In contrast, bacteria harbouring these two genes from natural environments are relatively less well studied compared to those found in clinical settings. In this study, a carbapenem-resistant Raoultella ornithinolytica strain, WLK218, was isolated from urban river sediment in Zhengzhou City, Henan Province, China. This isolate was subjected to PCR and antimicrobial susceptibility testing. PCR results showed that this isolate was positive for both the blaNDM-1 and blaKPC-2 genes. The antimicrobial susceptibility testing results showed that this isolate exhibited resistance or intermediate resistance to all the antibiotics tested except for streptomycin (susceptible) and cefepime (susceptible-dose dependent). The complete genome sequence of the WLK218 isolate was then determined by using a combination of the PacBio and Illumina sequencing technologies. The de novo assembly of the genome generated one chromosome and six plasmids. Among the six plasmids, the blaNDM-1 gene was carried on the IncX3 plasmid pWLK-NDM, while the blaKPC-2 gene was located on the untypeable plasmid pWLK-KPC. This is the first report of an environmental Raoultella ornithinolytica isolate co-harbouring the blaNDM-1 and blaKPC-2 genes.
Highlights
The increasing prevalence of multidrug-resistant Enterobacteriaceae pathogens has rendered life-saving antibiotics less effective, which has required clinicians to increasingly use last-resort antibiotics, such as carbapenems and polymyxins
The antimicrobial susceptibility testing results showed that the Raoultella ornithinolytica strain WLK218 exhibited resistance or intermediate resistance to meropenem (R, ≥ 16 mg/L), imipenem (R, ≥ 16 mg/L), amikacin (R, ≥ 64 mg/L), ampicillin (R, ≥ 32 mg/L), ampicillin/sulbactam (R, ≥ 32/16 mg/L), aztreonam (R, ≥ 64 mg/L), cefazolin (R, ≥ 64 mg/L), cefotetan (R, ≥ 64 mg/L), ceftazidime (R, ≥ 64 mg/L), ceftriaxone (R, ≥ 64 mg/L), cefuroxime (R, ≥ 64 mg/L), ciprofloxacin (R, 2 mg/L), gentamicin (R, ≥ 16 mg/L), piperacillin (R, ≥ 128 mg/L), piperacillin/tazobactam (R, ≥ 128/4 mg/L), tobramycin (R, ≥ 16 mg/L), trimethoprim/sulfamethoxazole (R, ≥ 320(16/304) mg/L), levofloxacin (I, 1 mg/L) and nitrofurantoin (I, 64 mg/L) but was susceptible-dose dependent to cefepime (SDD, 8 mg/L)
The carbapenem resistance genes blaNDM-1 and blaKPC-2 were found to be present on two different plasmids, with blaNDM-1 located on the pWLK-NDM plasmid and blaKPC-2 located on the pWLK-Klebsiella pneumoniae carbapenemases (KPCs) plasmid
Summary
The increasing prevalence of multidrug-resistant Enterobacteriaceae pathogens has rendered life-saving antibiotics less effective, which has required clinicians to increasingly use last-resort antibiotics, such as carbapenems and polymyxins. The blaNDM-1 gene was first discovered in Klebsiella pneumoniae and Escherichia coli clinical isolates in India in 20088. Klebsiella pneumoniae carbapenemases (KPCs) are another type of carbapenemases which have gained worldwide attention. In China, environmentally isolated blaNDM-carrying and blaKPC carrying strains have been found in different environmental samples, such as poultry production environments, hospital sewage systems and wastewater, and river sedimens[13,14,15,16,17]. In the present www.nature.com/scientificreports study, we report the isolation of a Raoultella ornithinolytica strain co-harbouring the blaNDM-1 and blaKPC-2 genes from urban river sediment. To the best of our knowledge, this is the first report of an environmental Raoultella ornithinolytica isolate co-harbouring the blaNDM-1 and blaKPC-2 genes. Comprehensive sequence analysis was conducted to gain insight into the genetic structures and organizations of the plasmids that harboured the blaNDM-1 and blaKPC-2 genes
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