Detection of an Escherichia coli Sequence Type 167 Strain with Two Tandem Copies of bla _NDM-1 in the Chromosome

Abstract

New Delhi metallo-␤-lactamase-1 (NDM-1)-producing Enterobacteriaceae has disseminated rapidly throughout the world and poses an urgent threat to public health. Previous studies confirmed that the bla NDM-1 gene is typically carried in plasmids but rarely in chromosome. We discovered a multidrug-resistant Escherichia coli strain Y5, originating from a urine sample and containing the bla NDM-1 gene, which did not transfer by either conjugation or electrotransformation. We confirmed the possibility of its chromosome location by S1-pulsed-field gel electrophoresis (PFGE) and XbaI-PFGE, followed by Southern blotting. To determine the genomic background of bla NDM-1 , the genome of Y5 was completely sequenced and compared to other reference genomes. The results of our study revealed that this isolate consists of a 4.8-Mbp chromosome and three plasmids, it is an epidemic clone of sequence type (ST) 167, and it shows 99% identity with Escherichia coli 6409 (GenBank accession no. CP010371), which lacks the same bla NDM-1 gene-surrounding structure as Y5. The bla NDM-1 gene is embedded in the chromosome along with two tandem copies of an insertion sequence common region 1 (ISCR1) element (sul1-ARR-3-catbla NDM-1 -bleo-ISCR1), which appears intact in the plasmid from Proteus mirabilis (GenBank accession no. KP662515). The genomic context indicates that the ISCR1 element mediated the bla NDM-1 transposition from a single source plasmid to the chromosome. Our study is the first report of an Enterobacteriaceae strain harboring a chromosomally integrated bla NDM-1 , which directly reveals the vertical spreading pattern of the gene. Close surveillance is urgently needed to monitor the emergence and potential spread of ST167 strains that harbor bla NDM-1 .KEYWORDS New Delhi metallo-␤-lactamase-1, chromosome, ISCR1, Enterobacteriaceae T he bacteria containing the New Delhi metallo-␤-lactamase gene (bla NDM-1 ) have swiftly spread worldwide and are considered a serious public health concern (1, 2). Studies confirmed that mobile-resistance elements, such as plasmids, transposons (Tn) and insertion sequences (IS), are responsible for the distribution of this superresistant gene, and they are regarded as major mechanisms driving the dramatically increased prevalence of carbapenem-resistant Enterobacteriaceae isolates (3-5).Plasmids constitute the main vehicles carrying the bla NDM-1 gene and are the primary media for its horizontal dissemination. Additional bla NDM-1 plasmids ranging

First Indian report on genome-wide comparison of multidrug-resistant Escherichia coli from blood stream infections

“…Though ST131 clones were predominantly reported worldwide, the STs observed in our study were striking for clustering in distinct phylogenetic lineages. ST167 was previously reported for its ability to carry bla NDM genes in China [38][39][40]. ST405 has been known as another global clonal group similar to ST131 [41] and has been reported to carry bla NDM genes in hospital settings [42], in addition to blaKPC-2 [43].…”

Structure, Genetics and Worldwide Spread of New Delhi Metallo-β-lactamase (NDM): a threat to public health

“…For example, a RB151 strain was reported to harbour 108 kb plasmid carrying NDM-1 gene on 4.8 Mbp chromosome [55]. E. coli Y5 isolate was found to have bla NDM-1 on chromosome as well [56]. The bla NDM-1 was also carried by more than one plasmid in some isolates.…”

Genomic Characterization of Carbapenemase-Producing Klebsiella pneumoniae with Chromosomally Carried bla NDM-1

“…However, only a limited number of CRE have been found to carry carbapenemase genes on their chromosomes (3)(4)(5)(6). Notably, only two strains of Escherichia coli have been reported to carry chromosomally integrated bla NDM-1 in China and India (7,8). However, no such organisms have been found among Klebsiella pneumoniae strains.…”

“…There have been several reports of Enterobacteriaceae carrying bla NDM-1 on their chromosomes, although only two cases have been reported for E. coli, in China (7) and India (8), but none have been reported for K. pneumoniae. A WGS analysis of Chinese E. coli strain Y5 showed that bla NDM-1 was embedded in its chromosome, and an ISCR1 element probably mediated the transposition of bla NDM-1 from a plasmid possibly derived from Proteus mirabilis PM58.…”