AUTHOR=Diaconu Elena Lavinia , Alba Patricia , Feltrin Fabiola , Di Matteo Paola , Iurescia Manuela , Chelli Eleonora , Donati Valentina , Marani Ilaria , Giacomi Angelo , Franco Alessia , Carfora Virginia 

TITLE=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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.705230

DOI=10.3389/fmicb.2021.705230

ISSN=1664-302X

ABSTRACT=<p>A collection of 177 genomes of <italic>Salmonella</italic> Typhimurium and its monophasic variant isolated in 2014–2019 from Italian poultry/livestock (<italic>n</italic> = 165) and foodstuff (<italic>n</italic> = 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 <italic>mcr-9</italic> gene and to investigate their genetic relatedness by whole genome sequencing (WGS). The study of accessory resistance genes revealed the presence of <italic>mcr</italic>-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 (<italic>bla</italic><sub><italic>SHV</italic></sub><sub>–</sub><sub>12</sub> type), mediated by the corresponding antimicrobial resistance (AMR) accessory genes. All <italic>mcr</italic>-9-positive isolates harbored IncHI2-ST1 plasmids. From the results of the Mash analysis performed on all 177 genomes, the 11 <italic>mcr-9</italic>-positive isolates fell together in the same subcluster and were all closely related. This subcluster included also two <italic>mcr</italic>-9-negative isolates, and other eight <italic>mcr</italic>-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 <italic>mcr</italic>-9-positive isolates, <italic>mcr-9</italic> 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 <italic>mcr</italic>-9. In our plasmids, <italic>mcr</italic>-9 was located in a ∼30-kb region lacking different genetic elements of the typical core structure of <italic>mcr</italic>-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 <italic>mcr</italic>-9, that can be transferred horizontally also to other major <italic>Salmonella</italic> serovars spreading along the food chain.</p>