The global food chain may significantly promote the dissemination of bacteria resistant to antibiotics around the world. This study was aimed at determining the prevalence and genetic characteristics of Enterobacteriaceae with mcr-mediated colistin (CT) resistance in retail meat of different origins. Bacteria of the Enterobacteriaceae family carrying the mcr-1 gene were detected in 21% (18/86) of the examined samples, especially in turkey meat and liver originating from EU and non-EU countries (19%) and in rabbit meat imported from China (2%). The examined samples of the meat and liver of chicken and other poultry and of pork and beef were negative for the presence of bacteria carrying the mcr-1 to mcr-5 genes. A huge number of isolates belonging to Escherchia coli (n = 54), Klebsiella pneumoniae (n = 6), and Citrobacter braakii (n = 1) carrying the mcr-1 gene were obtained. Despite the high heterogeneity of the tested isolates, the mcr-1 gene was localized on only three types of plasmids (IncX4, IncHI2, and IncI2). The most frequent type of plasmid was IncX4, which carried the mcr-1 gene in 77% of E. coli and K. pneumoniae isolates from turkey meat and liver samples from the Czechia, Germany, Poland, and Brazil. Our findings indicate highly probable interspecies transfer of IncX4 and IncI2 plasmids within one meat sample. The co-resistance of plasmid-mediated CT resistance encoded by the mcr-1 and ESBL genes was detected in 18% of the isolates. Another noteworthy finding was the fosA3 gene coding for fosfomycin resistance in a multidrug-resistant isolate of E. coli from rabbit meat imported from China. The observed high level of Enterobacteriaceae with plasmids carrying the mcr-1 gene in retail meat reflects the need for Europe-wide monitoring of mcr-mediated CT resistance throughout the whole food chain.

Since 2012–2016 an increased number of listeriosis cases, especially from one region of the Czech Republic, were observed. Most of them were caused by strains of serotype 1/2a, clonal complex 8, indistinguishable by pulsed-field gel electrophoresis. Twenty-six human cases were reported, including two neonatal cases in twins. Three cases were fatal. The typing of Listeria monocytogenes isolates from food enabled to confirm a turkey meat delicatessen as the vehicle of infection for this local outbreak in the Moravian-Silesian Region. The food strains belonging to identical pulsotype were isolated from ready-to-eat turkey meat products packaged by the same producer between 2012 and 2016. This fact confirms that the described L. monocytogenes outbreak strain probably persisted in the environment of the aforementioned food-processing plant over several years. Whole-genome sequencing confirmed a very close relationship (zero to seven different alleles) between isolates from humans, foods and swabs from the environment of the food-processing plant under investigation.

Aquaculture systems are widely recognised as hotspots for horizontal gene transfer, and the need for screening for bacteria carrying antimicrobial resistance genes in aquaculture systems is becoming more important. In this study, we characterised seventeen bacterial strains (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and A. nosocomialis) resistant to colistin originating from retailed aquaculture products imported from Vietnam to the Czech Republic. The mcr-1.1 gene was found located on plasmid types IncHI2, IncI2, and IncX4, as well as on the rarely described plasmid types IncFIB-FIC and IncFIB(K), phage-like plasmid p0111, and on the chromosome of E. coli. One E. coli strain carried the mcr-3.5 gene on IncFII(pCoo) plasmid in addition to the mcr-1.1 gene located on IncHI2 plasmid. K. pneumoniae was found to carry the mcr-1.1 and mcr-8.2 genes on IncFIA(HI1) plasmid. The mcr-4.3 gene was found on similar untypeable plasmids of A. baumannii and A. nosocomialis strains, pointing to the possible interspecies transfer of plasmids carrying the mcr-4 gene. Our results highlight that some aquaculture products of Asian origin can represent an important source of variable plasmids carrying mcr genes. The results showed an involvement of phages in the incorporation of the mcr-1 gene into plasmids or the chromosome in E. coli strains from aquaculture. The detection of E. coli with the mcr-1 gene in the chromosome points to the risks associated with the stabilisation of the mcr genes in the bacterial chromosome.

EFSA and ECDC were requested by the European Commission to jointly evaluate the possible solutions for the collection and analysis of whole genome sequencing (WGS) data for at least Listeria monocytogenes, Salmonella and Escherichia coli by: (1) analysing the outcome of the surveys on the status of the use of WGS of food‐borne pathogens in EU/EEA countries in both the food and public health sectors; (2) conducting a consultation of relevant actors to assess state‐of‐the‐art pipelines for collecting and analysing WGS data in Europe; (3) involving relevant stakeholders to assess the needs and requirements for the analysis of WGS data and their comparability; and (4) preparing a technical report on the identification and comparison of potential solutions for the set‐up and running of a joint EFSA‐ECDC pipeline to collect and analyse WGS data. Logical components of the overall system were identified and technical requirements were prioritised and grouped according to functionality. Eleven platforms (solutions) that integrate the relevant functionalities for collecting, analysing and visualising WGS data were thoroughly described. The degree to which the requirements are met by the different solutions (as of 31 December 2018) was evaluated. The assessment made clear that no single solution meets all the critical requirements and each solution has significant gaps regarding the unmet critical requirements. Therefore, scenarios consisting of a combination of several solutions were considered. As there may be many suitable scenarios, and the choice among them will depend on strategic or financial elements that are not within the scope of this report, it contains the scientific and technical elements necessary to generate scenarios, rather proposing individual scenarios. A scenario builder is presented which includes the significant gaps for each solution/functionality and the limitations and risks to be considered when setting up a joint ECDC‐EFSA database for the collection and analysis of WGS data.