Exploring the Global Spread of Klebsiella grimontii Isolates Possessing blaVIM-1 and mcr-9.

Abstract

The spread of plasmid-mediated carbapenemases within Klebsiella oxytoca is well-documented. In contrast, data concerning the closely related species Klebsiella grimontii are scarce. In fact, despite the recent report of the first blaKPC-2-producing K. grimontii, nothing is known about its clonality and antibiotic resistance patterns. In a retrospective search in our collection, we identified 2 blaVIM-positive K. oxytoca strains. Whole-genome sequencing with both Illumina and Nanopore indicated that our strains actually belonged to K. grimontii and were of sequence type 172 (ST172) and ST189. Moreover, the two strains were associated with 297-kb IncHI2/HI2A-pST1 and 90.6-kb IncFII(Yp) plasmids carrying blaVIM-1 together with mcr-9 and blaVIM-1, respectively. In the IncHI2/HI2A plasmid, blaVIM-1 was located in a class 1 integron (In110), while mcr-9 was associated with the qseC-qseB-like regulatory elements. Overall, this plasmid was shown to be very similar to those carried by other Enterobacterales isolated from food and animal sources (e.g., Salmonella and Enterobacter spp. detected in Germany and Egypt). The IncFII(Yp) plasmid was unique, and its blaVIM-1 region was associated with a rare integron (In1373). Mapping of In1373 indicated a possible origin in Austria from an Enterobacter hormaechei carrying a highly similar plasmid. Core-genome phylogenies indicated that the ST172 K. grimontii belonged to a clone of identical Swedish and Swiss strains (≤15 single nucleotide variants [SNVs] to each other), whereas the ST189 strain was sporadic. Surveillance of carbapenemase-producing K. oxytoca strains should be reinforced to detect and prevent the dissemination of new species belonging to the Klebsiella genus.