The ENGAGE project (http://www.engage-europe.eu/) was a collaboration between eight institutions across Europe. The aim was to boost the scientific cooperation to use whole genome sequencing (WGS) analysis in food safety and public health protection. ENGAGE focused on Escherichia coli (commensal E. coli) and different Salmonella spp. serotypes. A total of 3,360 genomes, 778 and 2,582 of E. coli and Salmonella, respectively, were produced. These genomes were stored and shared among partners in a temporary repository to be submitted to the European Nucleotide Archive by the end of the project. Generated genomes were used for benchmarking exercises to assess the possibility of replacing conventional typing with WGS for outbreak investigation. For the analysed strains, the benchmarking exercises showed that SPAdes assembly performed better than Velvet and that, by using different bioinformatics tools, WGS Salmonella serotyping and antimicrobial resistance genes detection, were largely in concordance with phenotypic data. Discrepancies were related to sequence quality and phenotype misclassification rather than to limitations of the bioinformatics tools.All partners were able to infer the expected phylogeny for the Salmonella and Campylobacter isolates in benchmarking exercises. Two WGS proficiency tests (assessing different genomic quality markers) were conducted among partners with satisfactory results. Guidelines including available bioinformatics tools and standard operating procedures (wet and dry lab) were prepared and posted online. Workshops, training courses and twinning programmes were conducted. The training focused on ENGAGE www.efsa.europa.eu/publications 2 EFSA Supporting publication 2018:EN-1431The present document has been produced and adopted by the bodies identified above as author(s). In accordance with Article 36 of Regulation (EC) No 178/2002, this task has been carried out exclusively by the author(s) in the context of a grant agreement between the European Food Safety Authority and the author(s). The present document is published complying with the transparency principle to which the Authority is subject. It cannot be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the author(s).online, Galaxy-based, and command line bioinformatics tools. To reach out beyond ENGAGE, an elearning course (17 videos) was developed and made available online. Several proof of concept projects were run and some outcomes published, e.g. the discovery of colistin resistance gene, mcr-5.Overall, the project showed that laboratories without previous WGS experience need a period of time to implement and perform WGS for foodborne pathogens routine analysis. All developed material will remain available on the ENGAGE website. The present document has been produced and adopted by the bodies identified above as author(s). In ...

The purpose of this study was to evaluate the potential of chitosan units released during natural degradation of the polymer to activate the immune system against T. spiralis infection. High molecular weight chitosan was injected intraperitoneally into C57BL/6 mice. Flow cytometry and cytokine concentration, measured by ELISA, were used to characterize peritoneal cell populations during T. spiralis infection. The strong chemo-attractive properties of chitosan caused considerable infiltration into the peritoneal cavity of CD11b+ cells, with reduced expression of MHC class II, CD80, CD86, Dectin-1 or CD23 receptors in comparison to T. spiralis-infected mice. After prolonged chitosan biodegradation, cell populations expressing IL-4R, MR and Dectin-1 receptors were found to coexist with elevated IL-6, IL-10, TGF-β and IgA production. IgA cross-reacted with T. spiralis antigen and chitosan. It was found that chitosan treatment attracted immune cells with low activity, which resulted in the number of nematodes increasing. The glucosamine and N-acetyl-D-glucosamine residues were recognized by wheat germ agglutinin (WGA) lectin and therefore any biodegradable chitosan units may actively downregulate the immune response to the parasite. The findings are relevant for both people and animals treated with chitosan preparations.

Background. Plasmid-mediated extended-spectrum β-lactamases (ESBLs), 16S rRNA methylases and quinolone resistance mechanisms (PMQRs) are well-known agents conferring resistance to more than 1 antimicrobial in its group. The accumulation of these agents poses, therefore, a serious risk to public health. Objectives. The objective of this study was to investigate the presence of common ß-lactamases and 16S rRNA methylases in Qnr-producing Enterobacteriaceae and their genetic relatedness. Material and methods. We examined 18 Qnr-producing isolates (Klebsiella pneumoniae n = 8, Enterobacter cloacae n = 6 and Escherichia coli n = 4) selected from a collection of 215 ciprofloxacin-resistant strains obtained from patients in a 1030-bed tertiary hospital from 1 March to 31 August 2010. The antibiotics minimum inhibitory concentration (MIC) was determined using E-test. The detection of common ß-lactamases, 16S rRNA methyltransferases and PMQR genes was performed using polymerase chain reaction (PCR) and sequencing. Genetic relatedness was assessed with pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Results. All the isolates tested were susceptible to carbapenems and colistin, while 16 were multidrug-resistant. Thirteen, 2 and 2 isolates carried qnrB1, qnrA1 and qnrS1, respectively. Ten of 13 qnrB1-positive Enterobacteriaceae also carried genes encoding for aac(6')-Ib-cr and at least 1 ESBL. The blaCTX-M-15 gene was the most common ESBL. The most prevalent combination of genes was qnrB1+aac(6')-Ib-cr+bla TEM-1 +bla CTX-M-15. Two isolates of K. pneumoniae and E. cloacae were found to bear multiple extended range resistance traits: ArmA, CTX-M-15, QnrB1, and AAC (6')-Ib-cr. The PFGE showed that most of the isolates exhibited individual DNA patterns, whilst MLST assigned K. pneumoniae (n = 8) to 5 sequence types (STs) (ST15, ST323, ST336, ST147, and ST525), E. coli (n = 4) to 2 (ST131 and ST1431) and E. cloacae (n = 5) to 4 (ST90, ST89, ST133, and the novel ST407). Conclusions. Our findings reveal the accumulation of resistance traits and their important role in spreading of multiresistant bacteria among hospitalized patients.

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Koronawirus SARS-CoV-2 odpowiedzialny jest za wystąpienie światowej pandemii choroby COVID-19, w czasie której powstała konieczność przeprowadzania bardzo dużej liczby badań na obecność tego wirusa przez laboratoria diagnostyczne. Podstawową, rekomendowaną przez WHO metodą pozwalającą na laboratoryjne potwierdzenia zakażenia wirusem SARS-CoV-2 są metody biologii molekularnej, w tym technika real-time PCR z etapem odwrotnej transkrypcji. Pozwalają one na wykrycie RNA wirusa w próbkach od osób spełniających kryteria definicji podejrzenia przypadku lub z kontaktu. Wiąże się to z ogromnym zapotrzebowaniem na odpowiednie, komercyjne testy diagnostyczne. Odpowiedzią na to zapotrzebowanie było pojawienie się na światowym rynku szeregu testów molekularnych. Testy te różnią się m.in. liczbą i rodzajem wykrywanych genów, zastosowanymi barwnikami. W pracy przedstawiono wyniki sprawdzenia różnych komercyjnych testów diagnostycznych przeprowadzonego w Laboratorium Zakładu Wirusologii NIZP-PZH w ramach dobrej praktyki laboratoryjnej.