Novel IncFII plasmid harbouring blaNDM-4 in a carbapenem-resistant Escherichia coli of pig origin, Italy

Abstract

Objectives: To the best of our knowledge, we describe the first evidence in Europe of an MDR, blaNDM-4-positive Escherichia coli isolated from a food-producing animal, harboured by a novel IncFII plasmid of which we report the complete sequence.

Methods: One blaNDM-4-positive E. coli isolated in 2019 from the caecal contents of a fattening pig in Italy was in-depth characterized by combined bioinformatic analysis of Oxford Nanopore long reads and Illumina short reads, for in silico typing, determination of the blaNDM-4 genetic context and full reconstruction of the blaNDM-4-carrying plasmid.

Results: The isolate belonged to ST641 and to the genoserotype O108:H23 and tested positive for different virulence genes and plasmid replicons. The MDR phenotype of resistance to all β-lactams, carbapenems, sulfamethoxazole and trimethoprim was mediated by blaTEM-1B, blaNDM-4, sul1/sul3 and dfrA12, respectively. The blaNDM-4 gene was harboured by a novel 53 043 bp IncFII plasmid (pMOL412_FII) composed of four main genetic regions, including an MDR region (MRR-NDM-4) of 16 kb carrying blaNDM-4 and several antimicrobial resistance genes located in a class 1 integron. pMOL412_FII was closely related to another ∼90.3 kb plasmid (pM109_FII) harbouring blaNDM-4 in an E. coli isolated from a human patient in Myanmar.

Conclusions: To the best of our knowledge, we have identified for the first time in Europe an NDM-producing Enterobacterales in livestock and resolved the complete sequence of the novel pMOL412_FII plasmid harbouring blaNDM-4 in an MRR. A global One Health approach, comparing genomic data from different sources and geographical areas, may help to trace back and control possible plasmid-borne carbapenemase gene transmission between animals and humans and along the food chain at international level.

Figure 1.

(a) Circular representation (ring diagram) of plasmid pMOL412_FII. Circles indicate, from the innermost to the outermost: plot of the G + C content, specific plasmid regions having important functions, plus and minus strands (third and fourth circles, respectively) with all the annotated regions located on the plasmid and the fifth circle represents the scale. (b) Linear representation of MRR-NDM-4. All the genetic elements of MRR-NDM-4 are represented proportionally with their length and orientation. The full names of the genetic elements are listed below the diagram. Coding sequences and resistance genes are indicated by blue arrows, while IS elements are indicated by pink arrows. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.

Figure 2.

Comparative analysis of closely related plasmids pMOL412_FII and pM109_FII harbouring bla_NDM-4. From the outside inwards, the outer circle shows a plot of the G + C content, the second circle shows the homologous regions of pMOL412_FII and pM109_FII, the third and fourth circles show the two contigs (MRR_N74 and N41) obtained with Illumina short-read assembly that partially reconstruct the pMOL412_FII sequence and the fifth circle shows the size (kb) of the resolved pM109_FII. Two framed areas indicate the replication region (RepA_incFII) and the MRR (MRR-NDM-4). This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.