Background: the co-production of carbapenemases and mcr-genes represents a worrisome event in the treatment of Enterobacteriaceae infections. The aim of the study was to characterize the genomic features of two clinical Enterobacter cloacae complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. Methods: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the blaVIM- and mcr- type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). Results: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The mcr-9.2 gene was harbored on a conjugative IncHI2 plasmid, while the blaVIM-1 determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: mcr-9 gene and its two component regulatory genes for increased expression on the chromosome, mcr-4.3 on non-conjugative (yet co-transferable) ColE plasmid, and blaVIM-1 on a non-conjugative IncA plasmid. Conclusions: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.

Salmonella enterica variants exhibit diverse host adaptation, outcome of infection, and associated risk to food safety. Analysis of the distribution of Salmonella enterica serovar Derby (S. Derby) subtypes in human and swine identified isolates with a distinct PFGE profile that were significantly under-represented in human infections, consistent with further host adaptation to swine. Here we show that isolates with this PFGE profile form a distinct phylogenetic sub-clade within S. Derby and exhibit a profound reduction in invasion of human epithelial cells, and a relatively small reduction in swine epithelial cells. A single missense mutation in hilD, that encodes the master-regulator of the Salmonella Pathogenicity Island 1 (SPI-1), was present in the adapted lineage. The missense mutation resulted in a loss of function of HilD that accounted for reduced invasion in human epithelial cells. The relatively small impact of the mutation on interaction with swine cells was consistent with an alternative mechanism of invasion in this pathogen-host combination.

This study aims to describe trends of mcr-positive Enterobacterales in humans based on laboratory surveillance with a defined catchment population. The data source is the Micro-RER surveillance system, established in Emilia-Romagna region (Italy), to monitor the trend of mcr resistance. Enterobacterales isolates from human clinical samples with minimum inhibitory concentration (MIC) ≥ 2 mg/L for colistin were sent to the study reference laboratory for the detection of mcr genes. Isolates prospectively collected in the period 2018-2020 were considered for the assessment of population rates and trends; further analyses were carried out for the evaluation of clonality and horizontal mcr gene transfer. Previous isolates from local laboratory collection were also described. In the period 2018-2020, 1164 isolates were sent to the reference laboratory, and 51 (4.4%) were confirmed as mcr-positive: 50 mcr-1 (42 Escherichia coli, 6 Klebsiella pneumoniae, 2 Salmonella enterica) and 1 mcr-4 (Enterobacter cloacae). The number of mcr-positive isolates dropped from 24 in the first half of 2018 to 3 in the whole of 2020 (trend p value < 0.001). Genomic analyses showed the predominant role of the horizontal transfer of mcr genes through plasmids or dissemination of transposable elements compared to clonal dissemination of mcr-positive microorganisms. The study results demonstrate a substantial decrease in the circulation of mcr-1 plasmid genes in Emilia-Romagna Region.

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Background Listeria monocytogenes is a foodborne pathogen with low incidence but severe manifestations in at risk categories (up to 30% fatality rate in YOPI). L. monocytogenes can form biofilm and persist in food processing environments for decades. In the Lombardy Region up to 50% of listeriosis cases have been attributed to dairy products. This study aimed at investigating a L. monocytogenes clone widely present in one of the most important Italian cheese production chain. Methods Through a retrospective analysis of the Lombardy Region PFGE database a cluster comprising isolates from eight PDO Gorgonzola and Taleggio dairies (2013-2019) was identified. A representative subset of 33 isolates was typed with MLVA and MLST. All isolates were further typed with WGS and compared to all Lombardy clinical isolates (n = 9) that shared the same Sequence Type (ST). Genomic relationship among isolates were investigated with cgMLST and SNP analysis. Results All isolates had the same MVLA/MLST profile (ST325). cgMLST and SNP analysis divided the isolates in two clusters that however shared a very high similarity (99.4%). Interestingly, isolates collected from same production plants clustered separately. Conversely, isolates collected in different years and plants clustered together. By querying the L. monocytogenes MLVA database it was possible to identify isolates of the same production chain with identical profile back to the year 2005. ST325 clinical isolates represented 2% of all typed clinical isolates and have an incidence of 0.007 cases/100000 inhabitants. Due to the high genomic similarity, it was not possible to link any clinical isolate to a putative source. Conclusions Our data suggest a persistent contamination by a L. monocytogenes ST325 clone traced back to the year 2005 present in the dairy production chain of Lombardy. Given the high similarity among the isolates further analyses with a larger dataset and are needed to elucidate the epidemiology of this clone. Key messages A highly clonal contamination by L. monocytogenes is widespread in the Lombardy Region dairy production chain. The low incidence of ST325 among the population suggests a low pathogenicity of the strain, however the occurrence of an ongoing long-term outbreak cannot be excluded.