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

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 (blaSHV–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.

House Flies (Musca domestica) from Swine and Poultry Farms Carrying Antimicrobial Resistant Enterobacteriaceae and Salmonella

“…These antimicrobials are widely employed in livestock, and this could be the cause of these findings. No ESBL and carbapenemase producers salmonellae were detected in our investigation, accordingly with EU data [ 54 ] and recent studies [ 55 , 56 ].…”

Emergence of Mobile Colistin Resistance Genes within Los Angeles County Wastewater

“…The mcr -9.1 gene within all five alignments share an IS110, IS6, and IS481 family transposase downstream of the detected mcr -9.1 gene, which suggests the mcr -9.1 cassette in this study is mobile between plasmids and chromosomes. Mob-suite was used to assess and type plasmid sequences in the H. alvei draft genome assembly. , Interestingly, scaffold_26 encoding mcr -9 was not typed as a plasmid sequence, while scaffold_9 (202 kbp), scaffold_42 (1.2 kbp), and scaffold_43 (1 kbp) were identified as plasmid Inc.HI2a, which have been previously reported as mcr -9 carriers such as pEL-ars2 and several mcr -9.1-positive Inc.HI/Inc.HI2a plasmids identified in Salmonella typhimurium . Given the gaps in our draft genome assembly, we cannot confirm if the mcr -9.1 identified in this study is encoded in the H. alvei chromosome or a part of an unassembled plasmid.…”

“…37,38 Interestingly, scaffold_26 encoding mcr-9 was not typed as a plasmid sequence, while scaffold_9 (202 kbp), scaffold_42 (1.2 kbp), and scaffold_43 (1 kbp) were identified as plasmid Inc.HI2a, which have been previously reported as mcr-9 carriers such as pEL-ars2 and several mcr-9.1-positive Inc.HI/Inc.HI2a plasmids identified in Salmonella typhimurium. 39 Given the gaps in our draft genome assembly, we cannot confirm if the mcr-9.1 identified in this study is encoded in the H. alvei chromosome or a part of an unassembled plasmid. Despite reports of increased H. alvei infections in immunocompromised patients during the COVID-19 pandemic, 40−42 there were no corresponding sequenced data in the NCBI database.…”

Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium

“…The Inc (C, F, H, I1) conjugative plasmids found in the analyzed genomes are frequently reported in different S. enterica serotypes, including Typhimurium, which together carry genes for all kind of antibiotics, some of which can be within an integron [ 37 , 38 ]. The simultaneous presence of IncHI2/IncHI2A and IncFIB(S)/IncFII(S) plasmids in the same ST213 genomes has previously been observed in S. enterica strains from Asia [ 86 ], Europe [ 87 ], and South America [ 88 ] for the first pair and in Africa for the second [ 89 ]. In addition, the IncHI2/IncHI2A pair was only found in the genomes of North American strains, while the presence of the IncFIB(S)/IncFII(S) pair was predominant in European strains.…”