Analysis of blaSHV-12-carrying Escherichia coli clones and plasmids from human, animal and food sources

Objectives: This study aimed at characterizing 23 Escherichia coli isolates from various sources and their respective bla(SHV-12)-carrying plasmids and sequencing one of these plasmids completely. Methods: Isolates were typed by XbaI-PFGE, MLST and PCR-based phylotyping. Transformed bla(SHV-12)-carrying plasmids were examined by replicon typing, S1-nuclease, conjugation, EcoRI-HindIII-BamHI digests and plasmid MLST, Co-located resistance genes and integrons as well as the blasHv 12 genetic environment were analysed by PCR and sequencing. One IncI1 plasmid was sequenced completely using HiSeq 2500 and gap closure by PCRs and Sanger sequencing. Results: Among the 23 SHV-12-positive E. coil, some isolates from different sources showed the same characteristics: ST23/phylogroup A (human, dog, livestock), ST57/D (wild bird, chicken meat) and ST117/D (chicken meat, chicken). All bla(SHV-12) genes were horizontally transferable via 30-120 kb plasmids of incompatibility groups Inch (n 17), IncK (n 3), IncE (n 1), IncX3 (n 1) and a non-typeable plasmid. IncK plasmids, indistinguishable in size and restriction patterns, were found in isolates from different sources (ST57/D, meat; ST131/B2, meat; ST57/B1, dog). The IncI1-bla(SHV-12)-carrying plasmids were mostly assigned to plasmid ST (pST) 26 and pST3. Three plasmids showed novel pSTs (pST214, pST215). The majority of the IncI1 transformants exhibited resistance to 13-lactams, chloramphenicol and streptomycin (in relation with a class 1 integron containing an estX-psp-aadA2-cmIA1-aadA1-qacI gene cassette array), and to tetracycline. A novel bla(SHV-12) environment was detected and whole plasmid sequencing revealed a Tn21-derived-bla(SHV-12)-Delta Tn1721 resistance complex. Conclusions: Results from this study suggest that the dissemination of bla(SHV-12) genes occurs by vertical (clonal) and horizontal transfer, the latter mainly mediated through IncI1 multidrug-resistance plasmids.