Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece

The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of bla(NDM1)-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of bla(NDM-1), the isolates carried a combination of various to beta-lactams encoding resistance genes: bla(TEM-1B), bla(CTX-15), bla(OXA-1), bla(VIM-1), bla(SHV-5), bla(OXA-16), bla(OXA-10) and bla(VEB-1). Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of bla(NDM-1) genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). tau his latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer.

Automated summary

The present study genetically characterized ten NDM-1 producing Escherichia coli isolates from a hospital in Central Greece between 2017 and 2021. Whole genome sequencing was used to determine the multi-locus sequencing typing (MLST), bla(NDM1)-environment, resistome, and plasmid content. The isolates showed a diverse range of sequence types and carried multiple resistance genes to beta-lactams and other classes of antibiotics. The analysis also revealed the presence of various plasmids, indicating continuous horizontal gene transfer among the isolates.