Dissemination of the blaNDM-5 Gene via IncX3-Type Plasmid among Enterobacteriaceae in Children

Abstract

The continuous emergence of novel New Delhi metallo-β-lactamase-5 (NDM-5)-producing Enterobacteriaceae isolates is receiving more and more public attention. Twenty-two NDM-5-producing strains were identified from 146 carbapenemase-producing Enterobacteriaceae (CRE) strains isolated from pediatric patients between January and March 2017, indicating that the bla_NDM-5 gene has spread to children. All 22 isolates, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, showed significantly high resistance to β-lactam antibiotics (except aztreonam) but remained susceptible to tigecycline and colistin. K. pneumoniae and K. aerogenes strains were respectively defined as homologous clonal isolates by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) results confirmed the genetic relatedness with all K. pneumoniae strains belonging to sequence type (ST) 48. Two E. coli isolates (ST617 and ST1236) were considered genetically unrelated. Twenty-two bla_NDM-5 plasmids were positive for the IncX3 amplicon and showed almost identical profiles after digestion with HindIII and EcoRI. Four representative strains (K. pneumoniae K725, K. aerogenes CR33, E. coli Z214, and E. coli Z244) were selected for further study. Plasmids harboring bla_NDM-5 showed strong stability in both clinical isolates and transconjugants, without apparent plasmid loss after 100 serial generations. S1-PFGE followed by Southern blot analysis demonstrated that the bla_NDM-5 gene was located on an ∼46-kb plasmid. Plasmid sequences of pNDM-K725, pNDM-CR33, and pNDM-Z214 were almost identical but were slightly different from that of pNDM-Z244. Compared with pNDM-Z244, ΔISAba125 and partial copies of IS3000 were missing. The genetic backgrounds of the bla_NDM-5 gene in four strains were slightly different from that of the typical pNDM_MGR194. This study comprehensively characterized the horizontal gene transfer of the bla_NDM-5 gene among different Enterobacteriaceae isolates in pediatric patients, and the IncX3-type plasmid was responsible for the spread.IMPORTANCE The emergence of CRE strains resistant to multiple antibiotics is considered a substantial threat to human health. Therefore, all the efforts to provide a detailed molecular transmission mechanism of specific drug resistance can contribute positively to prevent the further spread of multidrug-resistant bacteria. Although the new superbug harboring bla_NDM-5 has been reported in many countries, it was mostly identified among E. coli strains, and the gene transfer mechanism has not been fully recognized and studied. In this work, we identified 22 bla_NDM-5-positive strains in different species of Enterobacteriaceae, including 16 Klebsiella pneumoniae strains, four Klebsiella aerogenes strains, and two Escherichia coli strains, which indicated the horizontal gene transfer of bla_NDM-5 among Enterobacteriaceae strains in pediatric patients. Moreover, bla_NDM-5 was located on a 46-kb IncX3 plasmid, which is possibly responsible for this widespread horizontal gene transfer. The different genetic contexts of the bla_NDM-5 gene indicated some minor evolutions of the plasmid, based on the complete sequences of the bla_NDM-5 plasmids. These findings are of great significance to understand the transmission mechanism of drug resistance genes, develop anti-infection treatment, and take effective infection control measures.

Keywords: Enterobacterales; Enterobacteriaceae; IncX3-type plasmid; NDM-5; ST48; carbapenemase; children.

FIG 1

PFGE profiles and MLST results for NDM-5-producing Enterobacteriaceae isolates.

FIG 2

RFLP analysis of bla_NDM-5-positive plasmids. (A) bla_NDM-5-positive plasmids digested with EcoRI. (B) bla_NDM-5-positive plasmids digested with HindIII. Lane M, 1 kb plus DNA ladder marker.

FIG 3

S1-digested plasmid DNA and Southern blot hybridization. Bands indicated with arrows showed positive signals in Southern blot hybridization with the bla_NDM-5 probe. Lane M, Salmonella serotype Braenderup strain H9812 molecular marker.

FIG 4

Sequence analysis of bla_NDM-5-positive plasmids. (A) Comparative analysis of pNDM-K725, pNDM-CR33, pNDM-Z214, and pNDM-Z244. The circular map was created by BRIG tools. Concentric rings represent the similarity between the reference sequence (pNDM-Z244) in the outer ring and other sequences in the inner rings. Color levels indicate the results of BLAST with a matched degree in the shared regions. Genes shown in purple, blue, green, and orange are involved in replication, stability, propagation, and application, respectively. Genes encoding unknown functions or those not directly related to the above-mentioned roles are indicated in gray and are shown unlabeled. (B) Comparative analysis of the genetic contexts of bla_NDM-5 in pNDM-5-IT (GenBank accession no. MG649062), pNDM-MGR194 (GenBank accession no. KF220657), pNDM-Z244, pNDM-K725, pNDM-KZ214, and pNDM-CR33. The putative open reading frames are shown as arrowheads according to the direction of transcription. Regions with similar sequences are indicated in gray between the different plasmids.