Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance (mcr)-9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy
Elena Lavinia Diaconu, Patricia Alba, Fabiola Feltrin, Paola Di Matteo, Manuela Iurescia, Eleonora Chelli, Valentina Donati, Ilaria Marani, Angelo Giacomi, Alessia Franco, Virginia Carfora
Abstract
A collection of 177 genomes of Salmonella Typhimurium and its monophasic variant isolated in 2014–2019 from Italian poultry/livestock ( n = 165) and foodstuff ( n = 12), previously screened for antimicrobial susceptibility and assigned to ST34 and single-locus variants, were studied in-depth to check the presence of the novel mcr-9 gene and to investigate their genetic relatedness by whole genome sequencing (WGS). The study of accessory resistance genes revealed the presence of mcr -9.1 in 11 ST34 isolates, displaying elevated colistin minimum inhibitory concentration values up to 2 mg/L and also a multidrug-resistant (MDR) profile toward up to seven antimicrobial classes. Five of them were also extended-spectrum beta-lactamases producers ( bla SHV – 12 type), mediated by the corresponding antimicrobial resistance (AMR) accessory genes. All mcr -9-positive isolates harbored IncHI2-ST1 plasmids. From the results of the Mash analysis performed on all 177 genomes, the 11 mcr-9 -positive isolates fell together in the same subcluster and were all closely related. This subcluster included also two mcr -9-negative isolates, and other eight mcr -9-negative ST34 isolates were present within the same parental branch. All the 21 isolates within this branch presented an IncHI2/2A plasmid and a similar MDR gene pattern. In three representative mcr -9-positive isolates, mcr-9 was demonstrated to be located on different IncHI2/IncHI2A large-size (∼277–297 kb) plasmids, using a combined Illumina–Oxford Nanopore WGS approach. These plasmids were also compared by BLAST analysis with publicly available IncHI2 plasmid sequences harboring mcr -9. In our plasmids, mcr -9 was located in a ∼30-kb region lacking different genetic elements of the typical core structure of mcr -9 cassettes. In this region were also identified different genes involved in heavy metal metabolism. Our results underline how genomics and WGS-based surveillance are increasingly indispensable to achieve better insights into the genetic environment and features of plasmid-mediated AMR, as in the case of such IncHI2 plasmids harboring other MDR genes beside mcr -9, that can be transferred horizontally also to other major Salmonella serovars spreading along the food chain.