Background and aimPlasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.3, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing.

National Salmonella surveillance systems from France, England and Wales, Denmark, and the United States identified the recent emergence of multidrug-resistant isolates of Salmonella enterica serotype Kentucky displaying high-level resistance to ciprofloxacin. A total of 489 human cases were identified during the period from 2002 (3 cases) to 2008 (174 cases). These isolates belonged to a single clone defined by the multilocus sequence type ST198, the XbaI-pulsed-field gel electrophoresis cluster X1, and the presence of the Salmonella genomic island 1 variant SGI1-K. This clone was probably selected in 3 steps in Egypt during the 1990s and the early 2000s and has now spread to several countries in Africa and, more recently, in the Middle East. Poultry has been identified as a potential major vehicle for infection by this clone. Continued surveillance and appropriate control measures should be implemented by national and international authorities to limit the spread of this strain.

While the spread of Salmonella enterica serotype Kentucky resistant to ciprofloxacin across Africa and the Middle-East has been described recently, the presence of this strain in humans, food, various animal species (livestock, pets, and wildlife) and in environment is suspected in other countries of different continents. Here, we report results of an in-depth molecular epidemiological study on a global human and non-human collection of S. Kentucky (n = 70). We performed XbaI-pulsed field gel electrophoresis and multilocus sequence typing, assessed mutations in the quinolone resistance-determining regions, detected β-lactam resistance mechanisms, and screened the presence of the Salmonella genomic island 1 (SGI1). In this study, we highlight the rapid and extensive worldwide dissemination of the ciprofloxacin-resistant S. Kentucky ST198-X1-SGI1 strain since the mid-2000s in an increasingly large number of contaminated sources, including the environment. This strain has accumulated an increasing number of chromosomal and plasmid resistance determinants and has been identified in the Indian subcontinent, Southeast Asia and Europe since 2010. The second substitution at position 87 in GyrA (replacing the amino acid Asp) appeared helpful for epidemiological studies to track the origin of contamination. This global study provides evidence leading to the conclusion that high-level resistance to ciprofloxacin in S. Kentucky is a simple microbiological trait that facilitates the identification of the epidemic clone of interest, ST198-X1-SGI1. Taking this into account is essential in order to detect and monitor it easily and to take rapid measures in livestock to ensure control of this infection.

All supporting data, code and protocols have been provided within the article or through supplementary data files. Ten supplementary figures and six supplementary tables are available with the online version of this article.

Since 1988, France has been committed to drafting laws regulating clinical research. These laws must both reflect general legal standards relating to personal data protection and patient information and comply with EU regulations, which are supra-national norms. The 2012 legislation known as "Jardé law" came into force in 2016 and distinguishes between 3 different types of research involving human subjects: Category 1: Interventional research implying an intervention on the patient which is not justified by their usual treatment. Category 2: Interventional research which does not focus on medicinal products and only entails minimal risks and constraints. Category 3: Non-interventional research implying one or multiple acts or proceedings devoid of listed risks. These studies require preliminary favourable opinions from the French Ethical Research Committees (CPP), who are appointed by the State, and must ensure the protection of personal data. For the other types of studies (retrospective data, practice surveys), French legislation only requires that the protection of personal data is ensured. However, it is highly recommended to submit these studies to an Institutional Review Board (IRB) in order to confirm that human subjects are not involved and to obtain an ethical opinion in the event of a scientific journal submission. These laws are constantly evolving in order to comply with the various international recommendations and European regulations, which are binding in France.

Bacillus cereus is the 2nd most frequent bacterial agent responsible for food-borne outbreaks in France and the 3rd in Europe. In addition, local and systemic infections have been reported, mainly describing individual cases or single hospital setting. The real incidence of such infection is unknown and information on genetic and phenotypic characteristics of the incriminated strains is generally scarce. We performed an extensive study of B. cereus strains isolated from patients and hospital environments from nine hospitals during a 5-year study, giving an overview of the consequences, sources and pathogenic patterns of B. cereus clinical infections. We demonstrated the occurrence of several hospital-cross-contaminations. Identical B. cereus strains were recovered from different patients and hospital environments for up to 2 years. We also clearly revealed the occurrence of inter hospital contaminations by the same strain. These cases represent the first documented events of nosocomial epidemy by B. cereus responsible for intra and inter hospitals contaminations. Indeed, contamination of different patients with the same strain of B. cereus was so far never shown. In addition, we propose a scheme for the characterization of B. cereus based on biochemical properties and genetic identification and highlight that main genetic signatures may carry a high pathogenic potential. Moreover, the characterization of antibiotic resistance shows an acquired resistance phenotype for rifampicin. This may provide indication to adjust the antibiotic treatment and care of patients.

Please cite this article as: Cavaco, L.M., Hasman, H., Aarestrup, F.M., on behalf of the MRSA collaborating group (MRSA-CG), Zinc resistance of Staphylococcus aureus of animal origin is strongly associated with methicillin resistance, Veterinary Microbiology (2010Microbiology ( ), doi:10.1016Microbiology ( /j.vetmic.2011 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. The test population consisted of 476 porcine MRSA isolates from ten European 30 countries, 18 porcine MRSA isolates from Canada and seven MRSA from China, 92 31 MRSA and 60 methicillin-susceptible S. aureus (MSSA) isolates from veal calves in the 32Netherlands and 88 porcine MSSA isolates from four European countries. Most porcine 33 MRSA (n=454) and all bovine MRSA belonged to clonal complex (CC) 398 whereas 37 34 of the pig MRSA from Europe and the seven Chinese isolates belonged to other CCs 35 and 3 isolates were not classified into a CC. 36All isolates were tested for susceptibility to zinc chloride and copper sulphate using 37 agar dilution and tested by PCR for the czrC gene encoding zinc resistance. 38Phenotypic zinc resistance (MIC>2mM) was observed in 74% (n=324) and 42% (n=39) 39 of European MRSA CC398 from pigs and veal calves respectively, and in 44% of the 40 Canadian isolates (n=8), but not among the Chinese isolates. Almost all (99%) zinc-41 resistant MRSA carried czrC. Of the 37 European non-CC398 MRSA, 62% were 42 resistant to zinc, but only 46% of them carried czrC,. The MICs of the MSSA isolates to 43 zinc chloride ranged from 1 to 4 mM and none carried czrC. The MICs of copper 44 sulphate were neither associated with methicillin resistance nor with the detection of 45 czrC. 46This study showed that zinc resistance and the czrC gene is widespread among 47 CC398 MRSA isolates. This suggests that the use of zinc in feed might have 48 contributed to the emergence of MRSA. 49 50

In France, Salmonella Derby is one of the most prevalent serotypes in pork and poultry meat. Since 2006, it has ranked among the 10 most frequent Salmonella serotypes isolated in humans. In previous publications, Salmonella Derby isolates have been characterized by pulsed field gel electrophoresis (PFGE) and antimicrobial resistance (AMR) profiles revealing the existence of different pulsotypes and AMR phenotypic groups. However, these results suffer from the low discriminatory power of these typing methods. In the present study, we built a collection of 140 strains of S. Derby collected in France from 2014 to 2015 representative of the pork and poultry food sectors. The whole collection was characterized using whole genome sequencing (WGS), providing a significant contribution to the knowledge of this underrepresented serotype, with few genomes available in public databases. The genetic diversity of the S. Derby strains was analyzed by single-nucleotide polymorphism (SNP). We also investigated AMR by both genome and phenotype, the main Salmonella pathogenicity island (SPI) and the fimH gene sequences. Our results show that this S. Derby collection is spread across four different lineages genetically distant by an average of 15k SNPs. These lineages correspond to four multilocus sequence typing (MLST) types (ST39, ST40, ST71, and ST682), which were found to be associated with specific animal hosts: pork and poultry. While the ST71 and ST682 strains are pansusceptible, ST40 isolates are characterized by the multidrug resistant profile STR-SSS-TET. Considering virulence determinants, only ST39 and ST40 present the SPI-23, which has previously been associated with pork enterocyte invasion. Furthermore, the pork ST682 isolates were found to carry mutations in the fimH sequence that could participate in the host tropism of this group. Our phylogenetic analysis demonstrates the polyphyletic nature of the Salmonella serotype Derby and provides an opportunity to identify genetic factors associated with host adaptation and markers for the monitoring of these different lineages within the corresponding animal sectors. The recognition of these four lineages is of primary importance for epidemiological surveillance throughout the food production chains and constitutes the first step toward refining monitoring and preventing dispersal of this pathogen.