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In recent years in France, England, Wales, Denmark and the USA about 500 human infections occurred, which were caused by multidrug-resistant Salmonella enterica Serovar (S.) Kentucky isolates displaying high-level resistance to fluoroquinolones (ciprofloxacin, MIC > or = 4 mg/l). The responsible clone was referred to as ST198-X1.To determine whether this clone is also present in German S. Kentucky isolates, the National Reference Laboratory for Salmonella (NRL-Salm) at the BfR analyzed the trend of S. Kentucky isolates received over the past years. Since 2010 the first entries of highly ciprofloxacin resistant S. Kentucky isolates, especially from turkey meat products, were recorded. 15 isolates originating from animal or food as well as one human isolate displayed MIC values of > or = 8 mg/l to ciprofloxacin. Molecular biological typing methods showed the in Germany isolated S. Kentucky isolates to be identical to the clone described by Le Hello et al. (2011) and to carry a multidrug resistance conferring region (SGI1). Since fluoroquinolones are considered by the WHO in human and veterinary medicine as drugs of critical importance, this trend demands attention. The implementation of mitigation strategies for this highly resistant clone seems to be required.

The sul3 gene recently described in Escherichia coli was found in 22 of 512 (4.3%) German Salmonella isolates from different regions and sources and of different serotypes, antimicrobial resistance phenotypes, and genomic groups. This is the first report on the prevalence of sul3 among Salmonella strains, and the findings support the strong potential of this determinant to spread within bacterial populations.

The European Food Safety Authority (EFSA) is an agency funded by the European Union that acts as a source of scientific advice and communication on risks associated with the food chain. EFSA is actively involved in many activities in the area of antimicrobial resistance (AMR). It provides scientific advice used to support the European legislator and Member States in making effective and timely risk management decisions in the fight against AMR for example, in reducing the need to use antimicrobials in food-producing animals or in managing emerging threats such as resistance of microorganisms to beta-lactams, carbapenems and colistin. EFSA provides advice on how to monitor AMR in food-producing animals and food, and gathers and analyzes data collected at the national level in Europe. Finally, it actively communicates the risks linked to antimicrobial resistance. This paper provides an overview of the activities of EFSA in the area of AMR. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium incapable of expressing the second-phase flagellar antigen (fljAB operon), and it is recognized to be one of the most prevalent serovars causing human infections. A clonal lineage characterized by phage type DT193, PulseNet PFGE profile STYMXB.0131 and multidrug resistance to ampicillin, streptomycin, sulphonamides and tetracycline (R-type ASSuT) is commonly circulating in Europe. In this study we determined the deletions affecting the fljAB operon and the resistance region responsible for the R-type ASSuT in a strain of Salmonella enterica serovar 4,5,12:i:- DT193/STYMXB.0131, through an approach based on PCRs and Southern blot hybridization of genomic DNA. Using a set of nine specific PCRs, the prevalence of the resistance region was assessed in a collection of 144 S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains isolated from Germany, Switzerland and Italy. A 28 kb-region is embedded between the loci STM2759 and iroB, replacing the DNA located in between, including the fljAB operon. It encompasses the genes blaTEMâ?'1, strA-strB, sul2 and tet(B) responsible for the R-type ASSuT together with genes involved in plasmid replication and orfs of unknown function characteristically located on IncH1 plasmids. Its location and internal structure is fairly conserved in S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 strains regardless of the isolation source or country. Hence, in the S. enterica serovar 4,[5],12:i:-/ASSuT/STYMXB.0131 clonal lineage widespread in Germany, Switzerland and Italy, a resistance region derived from IncH1 plasmids has replaced the chromosomal region encoding the second flagellar phase and is an example of the stabilization of new plasmid-derived genetic material due to integration into the bacterial chromosome. [ABSTRACT FROM AUTHOR]

During antimicrobial drug resistance testing for Vibrio spp. from coastal waters of Germany, we identified 4 nontoxigenic, carbapenem-resistant V. cholerae isolates. We used whole-genome sequencing to identify the carbapenemase gene blaVCC-1. In addition, a molecular survey showed that more blaVCC-1-harboring isolates are present in coastal waters of Germany. [ABSTRACT FROM AUTHOR]

Escherichia (E.) coli producing extended-spectrum beta-lactamases (ESBLs) are an increasing problem for public health. The success of ESBLs may be due to spread of ESBL-producing bacterial clones, transfer of ESBL gene-carrying plasmids or exchange of ESBL encoding genes on mobile elements. This makes it difficult to identify transmission routes and sources for ESBL-producing bacteria. The objectives of this study were to compare the distribution of genotypic and phenotypic properties of E. coli isolates from different animal and human sources collected in studies in the scope of the national research project RESET. ESBL-producing E. coli from two longitudinal and four cross-sectional studies in broiler, swine and cattle farms, a cross-sectional and a case–control study in humans and diagnostic isolates from humans and animals were used. In the RESET consortium, all laboratories followed harmonized methodologies for antimicrobial susceptibility testing, confirmation of the ESBL phenotype, specific PCR assays for the detection of bla TEM , bla CTX , and bla SHV genes and sequence analysis of the complete ESBL gene as well as a multiplex PCR for the detection of the four major phylogenetic groups of E . coli . Most ESBL genes were found in both, human and non-human populations but quantitative differences for distinct ESBL-types were detectable. The enzymes CTX-M-1 (63.3% of all animal isolates, 29.3% of all human isolates), CTX-M-15 (17.7% vs. 48.0%) and CTX-M-14 (5.3% vs. 8.7%) were the most common ones. More than 70% of the animal isolates and more than 50% of the human isolates contained the broadly distributed ESBL genes bla CTX-M-1 , bla CTX-M-15 , or the combinations bla SHV-12 + bla TEM or bla CTX-M-1 + bla TEM . While the majority of animal isolates carried bla CTX-M-1 (37.5%) or the combination bla CTX-M-1 + bla TEM (25.8%), this was the case for only 16.7% and 12.6%, respectively, of the human isolates. In contrast, 28.2% of the human isolates carried bla CTX-M-15 compared to 10.8% of the animal isolates. When grouping data by ESBL types and phylogroups bla CTX-M-1 genes, mostly combined with phylogroup A or B1, were detected frequently in all settings. In contrast, bla CTX-M-15 genes common in human and animal populations were mainly combined with phylogroup A, but not with the more virulent phylogroup B2 with the exception of companion animals, where a few isolates were detectable. When E . coli subtype definition included ESBL types, phylogenetic grouping and antimicrobial susceptibility data, the proportion of isolates allocated to common clusters was markedly reduced. Nevertheless, relevant proportions of same subtypes were detected in isolates from the human and livestock and companion animal populations included in this study, suggesting exchange of bacteria or bacterial genes between these populations or a common reservoir. In addition, these results clearly showed that there is some similarity between ESBL genes, and bacterial properties in isolates from the different populations. Finally, our current approach provides good insight into common and population-specific clusters, which can be used as a basis for the selection of ESBL-producing isolates from interesting clusters for further detailed characterizations, e.g. by whole genome sequencing. [ABSTRACT FROM AUTHOR]

Objectives Between 20 000 and 35 000 cases of salmonellosis are detected annually in Germany, but only a few Salmonella are resistant to third-generation cephalosporins. The German National Reference Centre for Salmonella and other Enterics obtained 150 Salmonella enterica isolates from human infections between 2005 and 2011. In the present study we identified the β-lactamase genes causing resistance to third-generation cephalosporins in these isolates. Methods For all isolates serotyping and antimicrobial susceptibility testing were performed. The presence of β-lactamase genes was detected by PCR amplification and sequencing. Isolates with identical serovar and β-lactamase genes were typed by XbaI macrorestriction followed by PFGE. Broth mate conjugation assays and plasmid analysis using S1 nuclease restriction of genomic DNA and subsequent PFGE as well as PCR-based replicon typing were performed for selected isolates. Results The 150 isolates were assigned to 30 different serovars, with S. enterica serovar Typhimurium (n = 73; 48.7%) as the most prevalent. Two different AmpC β-lactamase genes (blaCMY-2, n = 8; blaACC-1, n = 6) and various extended-spectrum β-lactamase (ESBL) genes were identified. The majority harboured the blaCTX-M-1 gene (n = 91; 60.7%) followed by blaCTX-M-14 (n = 12; 8.0%) and blaSHV-12 (n = 11; 7.3%). Typing of strains and subsequent comparison with selected Salmonella isolates from livestock revealed the presence of several clones in both humans and livestock. Conclusions The wide spread of ESBL and AmpC genes in Salmonella of various serovars is most probably due to transfer of conjugative plasmids. Furthermore, our data indicate the clonal spread of distinct cephalosporin-resistant Salmonella strains from livestock to humans. [ABSTRACT FROM PUBLISHER]

Objectives To broaden knowledge of the molecular bases and genetics of multidrug resistance in clinical isolates of Salmonella enterica serotype 4,5,12:i:− belonging to the Spanish clone. Methods The relatedness of the isolates was determined by phage typing and XbaI-PFGE. Resistance genes, integrons and transposable elements were identified by PCR amplification and sequencing. Plasmids were characterized by alkaline lysis, S1-PFGE, conjugation, replicon typing and Southern blot hybridization. Results The isolates were closely related and resistant to five to seven antimicrobials (ampicillin, chloramphenicol, gentamicin, streptomycin/spectinomycin, sulphonamides, trimethoprim and tetracycline, arranged in different combinations). Most of the responsible genes were provided by a conventional class 1 integron with the dfrA12-orfF-aadA2 variable region, an atypical class 1 integron containing sul3 next to the estX-psp-aadA2-cmlA1-aadA1 variable region and a truncated Tn1721 transposon carrying tet(A). A defective Tn21 with the mer operon and ISVsa3 associated with sul2 were also detected. All resistance genes and mobile genetic elements were located on large, non-conjugative and highly variable plasmids carrying one (A/C) or two (A/C and N) replicons, as well as virulence genes of pSLT. Conclusions IncA/C plasmids are responsible for multidrug resistance in an increasing number of relevant human and animal bacterial pathogens, and hence are regarded as an important threat to public health. Those found in the Spanish clone of Salmonella 4,5,12:i:− constitute a relevant example of short-term evolution, and could have been involved in the successful adaptation of this pathogen. [ABSTRACT FROM PUBLISHER]

This manual provides guidance for reporting antimicrobial resistance under the framework of Directive 2003/99/EC and Commission Implementing Decision 2013/652/EU in food‐producing animals and foodstuffs derived thereof. The objective is to harmonise and streamline the reporting made by the Member States to ensure that the antimicrobial resistance data collected are relevant and easy to analyse at the European Union level. Detailed guidelines are provided for the reporting of data and text forms. This guidance typically applies to Salmonella spp., Campylobacter coli and Campylobacter jejuni, and the animal populations and food categories to be reported on. Guidance is also provided on indicator commensal Escherichia coli, indicator Enterococcus and meticillin‐resistant Staphylococcus aureus. The manual notably includes specific guidance for reporting mandatory data on Salmonella spp. and commensal indicator E. coli producers of ESBLs/AmpCs/carbapenemases obtained from the harmonised routine monitoring, and ESBL‐/AmpC‐/Carbapenemase‐producing E. coli derived from specific monitoring, as well as voluntary data on specific monitoring of carbapenemase‐producers. This manual is specifically aimed at guiding the reporting of information deriving from the year 2018. [ABSTRACT FROM AUTHOR]

The putative virulence and antimicrobial resistance gene contents of extended spectrum β-lactamase (ESBL)-positive E. coli (n=629) isolated between 2005 and 2009 from humans, animals and animal food products in Germany, The Netherlands and the UK were compared using a microarray approach to test the suitability of this approach with regard to determining their similarities. A selection of isolates (n=313) were also analysed by multilocus sequence typing (MLST). Isolates harbouring blaCTX-M-group-1 dominated (66%, n=418) and originated from both animals and cases of human infections in all three countries; 23% (n=144) of all isolates contained both blaCTX-M-group-1 and blaOXA-1-like genes, predominantly from humans (n=127) and UK cattle (n=15). The antimicrobial resistance and virulence gene profiles of this collection of isolates were highly diverse. A substantial number of human isolates (32%, n=87) did not share more than 40% similarity (based on the Jaccard coefficient) with animal isolates. A further 43% of human isolates from the three countries (n=117) were at least 40% similar to each other and to five isolates from UK cattle and one each from Dutch chicken meat and a German dog; the members of this group usually harboured genes such as mph(A), mrx, aac(6’)-Ib, catB3, blaOXA-1-like and blaCTX-M-group-1. forty-four per cent of the MLST-typed isolates in this group belonged to ST131 (n=18) and 22% to ST405 (n=9), all from humans. Among animal isolates subjected to MLST (n=258), only 1.2% (n=3) were more than 70% similar to human isolates in gene profiles and shared the same MLST clonal complex with the corresponding human isolates. The results suggest that minimising human-to-human transmission is essential to control the spread of ESBL-positive E. coli in humans. [ABSTRACT FROM AUTHOR]

Highlights • A total of 469 isolates originating from 150 livestock farms in Germany were investigated. • In pig and cattle isolates, blaCTX-M family genes were most frequent (94.0%). • Phylogroups A (44.6%) and B1 (35.0%) were the most frequent. • Isolates from broilers differed substantially from those of other isolates. • Associations of farm-related factors with isolate characteristics are demonstrated. Abstract Resistance to β-lactam antibiotics, including third-generation cephalosporins, is of major concern for animal and human health. In this study, extended-spectrum β-lactamase (ESBL) / plasmid-mediated AmpC (pAmpC) β-lactamase -producing Escherichia coli isolates from German livestock farms were characterised and associations of these isolate characteristics with farm-related factors were investigated across different types of livestock. A total of 469 isolates originating from 150 farms (34 broiler farms, 38 fattening pig farms, 43 dairy cattle farms, 35 beef cattle farms) was included in the analyses. ESBL-gene family, phylogroup and phenotypic antimicrobial susceptibility for several antimicrobial agents were determined. This data was used to define different profiles characterising the isolates. Multivariate analyses using a distance-based non-parametric approach were performed to investigate associations between the profiles of the isolates and farm-related factors (e.g. management, husbandry, and environment of the farms). Co-occurrence of ESBL-gene families were not found in any of the isolates analysed. Sixty-eight percent of the isolates carried bla CTX-M variant genes. The frequency of phylogroups was as follows: A (55%), B1 (35%), D (17%) and B2 (3%). The most frequent phenotypic non-wildtype profile was non-wildtype status of solely cefepime (27%). Profiles of isolates from broilers differed substantially from those of other isolates. Associations between farm-related factors and characteristics profiles differed, depending on the isolate characteristics included in the analyses. Some factors describing the farm environment, like waterfowl in the surrounding of the farm, were associated with all tested profiles. The epidemiological method applied defines distances between isolates on basis of isolate characteristics data and is capable of analysing associations between isolate characteristics and epidemiological factors. As additional data, such as plasmid characteristics, gene type, or sequence information could be included in future studies, the method is suitable to identify points of action to reduce the occurrence of antimicrobial resistant bacteria. [ABSTRACT FROM AUTHOR]

Livestock associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has emerged in animal production worldwide. Most LA-MRSA in Europe belong to the clonal complex (CC) 398. The reason for the LA-MRSA emergence is not fully understood. Besides antimicrobial agents used for therapy, other substances with antimicrobial activity applied in animal feed, including metal-containing compounds might contribute to their selection. Some of these genes have been found in various novel SCC mec cassettes. The aim of this study was to assess the occurrence of metal-resistance genes among a LA- S. aureus collection [n = 554, including 542 MRSA and 12 methicillin-susceptible S. aureus (MSSA)] isolated from livestock and food thereof. Most LA-MRSA isolates (76%) carried at least one metal-resistance gene. Among the LA-MRSA CC398 isolates (n = 456), 4.8%, 0.2%, 24.3% and 71.5% were positive for arsA (arsenic compounds), cadD (cadmium), copB (copper) and czrC (zinc/cadmium) resistance genes, respectively. In contrast, among the LA-MRSA non-CC398 isolates (n = 86), 1.2%, 18.6% and 16.3% were positive for the cadD , copB and czrC genes, respectively, and none were positive for arsA. Of the LA-MRSA CC398 isolates, 72% carried one metal-resistance gene, and the remaining harboured two or more in different combinations. Differences between LA-MRSA CC398 and non-CC398 were statistically significant for arsA and czrC . The czrC gene was almost exclusively found (98%) in the presence of SCC mec V in both CC398 and non-CC398 LA-MRSA isolates from different sources. Regarding the LA-MSSA isolates (n = 12), some (n = 4) were also positive for metal-resistance genes. This study shows that genes potentially conferring metal-resistance are frequently present in LA-MRSA. [ABSTRACT FROM AUTHOR]

Abstract: Plasmids implicated in the mobilisation of β-lactamase genes in extended-spectrum β-lactamase (ESBL)- and AmpC-producing Salmonella enterica isolates recovered from three Spanish hospitals were characterised. The temporal stability of these plasmids and of the resistance phenotype without antimicrobial pressure was also assessed in the laboratory setting. The resistance determinants and their genetic environments were characterised by PCR sequencing, and their genomic location was analysed by S1 nuclease pulsed-field gel electrophoresis (PFGE) and I-CeuI PFGE, followed by Southern blot hybridisation. The 11 S. enterica studied strains carried bla CTX-M-9 (serovar Virchow, 2 isolates), bla CTX-M-10 (Virchow, 2), bla CTX-M-14 (Enteritidis, 1), bla CTX-M-15 (Gnesta and S. enterica group C, 2), bla SHV-2 (Livingstone, 1), bla SHV-12 (Enteritidis, 1) and bla CMY-2 (Bredeney, 2). The ISEcp1–bla CTX-M-14–IS903 and ISEcp1–bla CTX-M-15–orf477 genetic structures were detected. IncI1 and IncA/C plasmids carried bla CTX-M-14, bla CTX-M-15, bla SHV-2, bla SHV-12 and bla CMY-2 genes. bla CTX-M-9 included in an In60 complex integron and bla CTX-M-10 linked to a phage-related element were found in non-typeable plasmids. Conjugation and temporal stability experiments were performed in vitro through daily passages (100 days) in the absence of antimicrobial pressure. In the stability experiments, 5 of the 11 tested isolates lost the ESBL or AmpC plasmidic genes and this was associated with concomitant loss of the whole or partial plasmid. In conclusion, successful plasmids belonging to different Inc groups mobilise ESBL- and AmpC-encoding genes in S. enterica. Loss of ESBL/AmpC genes in the absence of antimicrobial pressure might explain the low prevalence of these β-lactamases among Salmonella isolates. [Copyright &y& Elsevier]