A Novel SXT/R391 Integrative and Conjugative Element Carries Two Copies of the bla _NDM-1 Gene in Proteus mirabilis

ABSTRACT

The rapid spread of the bla _NDM-1 gene is a major public health concern. Here, we describe the multidrug-resistant Proteus mirabilis strain XH1653, which contains a novel SXT/R391 integrative and conjugative element (ICE), harboring two tandem copies of bla _NDM-1 and 21 other resistance genes. XH1653 was resistant to all antibiotics tested, apart from aztreonam. Whole-genome data revealed that two copies of bla _NDM-1 embedded in the IS CR1 element are located in HS4 of the novel ICE, which we named ICE PmiChnXH1653. A circular intermediate of ICE PmiChnXH1653 was detected by PCR, and conjugation experiments showed that the ICE can be transferred to the Escherichia coli strain EC600 with frequencies of 1.5 × 10 ⁻⁷. In the recipient strain, the ICE exhibited a higher excision frequency and extrachromosomal copy number than the ICE in the donor strain. We also observed that the presence of ICE PmiChnXH1653 has a negative impact on bacterial fitness and leads to changes in the transcriptome of the host. In vitro evolution experiments under nonselective conditions showed that the two tandem copies of the IS CR1 element and the IS Vsa3 element can be lost during repeated laboratory passage. This is the first report of a novel SXT/R391 ICE carrying two tandem copies of bla _NDM-1, which also illustrates the role that ICEs may play as platforms for the accumulation and transmission of antibiotic resistance genes.

IMPORTANCE The occurrence of carbapenemase-producing Proteus mirabilis, especially those strains producing NDM-1 and its variants, is a major public health concern worldwide. The integrative conjugative element (ICE) plays an important role in horizontal acquisition of resistance genes. In this study, we characterized a novel SXT/R391 ICE from a clinical P. mirabilis isolate that we named ICE PmiChnXH1653, which contains two tandem copies of the carbapenemase gene bla _NDM-1. We performed an integrative approach to gain insights into different aspects of ICE PmiChnXH1653 evolution and biology and observed that ICE PmiChnXH1653 obtained the carbapenemase gene bla _NDM-1 by IS CR1-mediated homologous recombination. Our study reveals that the transmission of bla _NDM-1 by IS CR1 elements or ICEs may be an important contributor to the carbapenem resistance development across species, which could improve our understanding of horizontal gene transfer in clinical environments.