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The European Commission requested scientific and technical assistance in the preparation of a EU‐wide baseline survey of antimicrobial resistance (AMR) in bacteria from aquaculture animals. It is recommended that the survey would aim at estimating the occurrence of AMR in Aeromonas spp. isolated from Atlantic Salmon (Salmo salar), European seabass (Dicentrarchus labrax) and trout (Salmo trutta, Salvelinus fontinalis, Oncorhynchus mykiss) intended to consumption, at harvesting (at farm/slaughter), at the EU level and in addition, at estimating the occurrence and diversity of AMR of Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Vibrio parahaemolyticus and Vibrio alginolyticus in blue mussel (Mytilus edulis) and Mediterranean mussel (Mytilus galloprovincialis) from production areas and at dispatch centres at the EU level. These technical specifications define the target populations, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic analysis of some of the bacteria targeted) and the data reporting requirements. The data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA reporting system. This publication is linked to the following EFSA Journal article: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2024.8896/full [ABSTRACT FROM AUTHOR]

The European Commission requested scientific and technical assistance in the preparation of a EU‐wide baseline survey protocol for a European Union (EU) coordinated monitoring programme on the prevalence of methicillin‐resistant Staphylococcus Aureus (MRSA) in pigs. The objective of the survey is to estimate the MRSA prevalence in batches of fattening pigs at slaughter at both European and national levels, with a 95% level of confidence and a level of precision of 10% considering an expected prevalence of 50%. The survey protocol defines the target population, the sample size for the survey, sample collection requirements, the analytical methods (for isolation, identification, phenotypic susceptibility testing and further genotypic testing of MRSA isolates), the data reporting requirements and the plan of analysis. The samples are to be analysed according to the laboratory protocols available on the European Union Reference Laboratory (EURL‐AR) website. Generalised linear models will be used to estimate proportion (with 95% confidence intervals) of batches of slaughter pigs tested positive to MRSA. The necessary data to be reported by the EU Member States to support this baseline survey are presented in three data models. The results of the survey should be reported using the EFSA data collection framework. [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]

Objectives The characterization of CTX-M-15 β-lactamase-producing Escherichia coli and Salmonella isolates originating mainly from German livestock and food. Methods E. coli (526, mainly commensals) and Salmonella (151) non-human isolates resistant to third-generation cephalosporins, originating from routine and monitoring submissions (2003–12) to the Federal Institute for Risk Assessment and different national targeted studies (2011–12), were examined for the presence of blaCTX-M-15 genes by PCR amplification/sequencing. Additional resistance and virulence genes were screened by DNA microarray and PCR amplification. E. coli isolates with blaCTX-M-15 were characterized by phylogenetic grouping, PFGE and multilocus sequence typing (MLST). The blaCTX-M-15 plasmids were analysed by replicon typing, plasmid MLST, S1 nuclease PFGE and Southern blot hybridization experiments. Results Twenty-one E. coli (livestock, food and a toy; 4.0%) and two Salmonella (horse and swine; 1.3%) isolates were CTX-M-15 producers. E. coli isolates were mainly ascribed to three clonal lineages of sequence types ST678 (German outbreak with enteroaggregative Shiga-toxin-producing E. coli O104:H4; salmon, cucumber and a toy), ST410 (poultry, swine and cattle farms) and ST167/617 (swine farms and turkey meat). The blaCTX-M-15 genes were located on IncI1 and multireplicon IncF plasmids or on the chromosome of E. coli ST410 isolates. Conclusions The prevalence of CTX-M-15-producing isolates from non-human sources in Germany is still low. The blaCTX-M-15 gene is, however, present in multidrug-resistant E. coli clones with pathogenic potential in livestock and food. The maintenance of the blaCTX-M-15 gene due to chromosomal carriage is noteworthy. The possibility of an exchange of CTX-M-15-producing isolates or plasmids between livestock and humans (in both directions) deserves continuous surveillance. [ABSTRACT FROM PUBLISHER]

Abstract: Worldwide, the emergence and global spread of microorganisms with acquired carbapenemases is of great concern. The reservoirs for such organisms are increasing, not only in hospitals, but also in the community and environment. A new and important development is the presence of such organisms in livestock, companion animals and wildlife. During the last three years, carbapenemase-producing Escherichia coli, Salmonella spp. (VIM-1 producers) and Acinetobacter spp. (producing OXA-23 and NDM-1) in livestock animals (poultry, cattle and swine) and their environment have been reported. In addition, the isolation of NDM-1-producing E. coli, OXA-48 in E. coli and Klebsiella pneumoniae or OXA-23 in Acinetobacter spp. from companion animals (cats, dogs or horses) has also been observed. Other reports have described the presence of NDM-1-producing Salmonella isolated from wild birds, as well as OXA-23-like-producing Acinetobacter baumannii in ectoparasites. However, until now carbapenemase producers from foods have not been detected. For humans in contrast carbapenem-producing Salmonella isolates are increasingly reported. The real prevalence of carbapenemase-encoding genes in zoonotic bacteria or commensals from animals is unknown. Consequently, there is a need for intensified surveillance on the occurrence of carbapenemase-producing bacteria in the food chain and other animal sources in order to assist in the formulation of measures to prevent their potential spread. [Copyright &y& Elsevier]

Objectives To discern the relevance of ST648 extended-spectrum β-lactamase (ESBL)-producing Escherichia coli as a putative new group of multiresistant and extraintestinal pathogenic strains in animals, its frequency, ESBL types, antimicrobial resistance patterns and virulence gene (VG) profiles should be determined and compared with ST131 strains from the same collection of strains. Methods ESBL-producing E. coli isolates (n = 1152), consecutively sampled from predominantly dogs, cats and horses between 2008 and 2011, were assigned to a phylogenetic group by PCR. Partial multilocus sequence typing was performed for group D and B2 strains and strains presumed to be D-ST648 and B2-ST131 were fully typed. ESBL genes and extraintestinal pathogenic E. coli (ExPEC)-like VGs were characterized by PCR and sequence analysis and antimicrobial resistance was determined by broth dilution. Clonal analysis was done by PFGE. Results Forty (3.5%) ESBL-producing E. coli were determined as D-ST648, whereas B2-ST131 isolates occurred less frequently (2.8%). Although the predominant ESBL type in both groups was CTX-M-15 (72.5% versus 46.9%), ST648 strains from companion animals and horses displayed a lower variety of ESBL types (CTX-M-1, -3, -14, -15 and -61 versus CTX-M-1,-2,-14,-15,-27 and -55 and SHV-12). In contrast to ST131 strains, a higher proportion of ST648 strains showed resistance to most non-β-lactam antibiotics. Overall, VGs were less abundant in ST648 strains, although some strains had VG profiles comparable to those of ST131 strains. ExPEC-associated serotype O1:H6 was predominant (46.8%) among the ST648 strains. Some PFGE clusters comprised ST648 isolates from pets, horses and wild birds and humans included from previous studies. Conclusions Our findings demonstrate that certain subgroups of E. coli D-ST648-CTX-M may represent a novel genotype that combines multiresistance, extraintestinal virulence and zoonotic potential. [ABSTRACT FROM PUBLISHER]

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]

The article offers information on a study which examined extended-spectrum β-lactamases in German Salmonella enterica isolate subsp. enterica serovar Typhimurium 4,[5],12:i:-European clone. Nine strains of German Salmonella enterica were examined for the presence of β-lactams. Study authors found that the strains share the resistance phenotype ampicillin/cefalotin/cefuroxime/ticarcillin/piperacillin/ceftiofur/ceftriaxone/cefotaxime/aztreonam/cefopodoxime.

Objectives: In view of the intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15 extended-spectrum b-lactamase (ESBL) in human clinical settings it would be of great interest to explore its existence in animals to unravel a possible reservoir function and the origin and transmission of this group of multiresistant strains. Methods: A total of 177 clinical phenotypically ESBL-producing E. coli isolates, mainly obtained from companion animals with urinary tract infections, wound infections and diarrhoea, were collected in a veterinary diagnostic laboratory covering a European-wide service area. They were screened for molecular subtype O25b and multilocus sequence type 131. O25b-ST131 isolates were subsequently tested for ESBL types, and phenotypic and genotypic resistance determinants. Further characterization of the strains was performed by PFGE and virulence gene typing. Results: Ten (5.6%) of 177 phenotypically ESBL-producing E. coli isolates, nine strains from dogs and one strain from a horse, were allocated to the B2-O25b-ST131 lineage. Nine of these isolates harboured a CTX-M-15-type b-lactamase enzyme while one strain possessed an SHV-12-type ESBL. Macrorestriction analysis revealed a cluster formation of six of the animal CTX-M-15-type ESBL-producing strains from five different European countries together with a human control strain constituting a group of clonally related strains at a similarity value of 87.0%. Conclusions: Our findings demonstrate that the group of clonally related human B2-O25:H4-ST131 CTX-M-15-type ESBL-producing E. coli strains is present in companion animals from various European countries. This highlights the possibility of inter-species transmission of these multiresistant strains from human to animal and vice versa. [ABSTRACT FROM AUTHOR]

A letter to the editor about extended-spectrum β-lactamases (ESBL) of the CTX-M-8-positive isolates of species Escherichia coli, Salmonella enterica and Enterobacter aerogenes in Garmany is presented.

A letter to the editor is presented discussing research on the New Delhi metallo-beta-lactamase-1 (NDM-1)-producing Salmonella enterica subsp. enterica serovar Corvallis isolated from a wild bird in Germany.

A letter to the editor is presented about the presence of a carbapenemase-encoding gene in Salmonella enterica isolated from poultry and pig farms.

The article examines the presence of a carbapenemase-encoding gene in Escherichia coli isolated from a livestock farm. It states that the occurrence of extended spectrum Β-lactamase (ESBL) in Enterobacteriaceae isolated from food-producing animals and the increase in their prevalence is a worldwide problem, however, the presence of carbapenemases is restricted to humans. It cites that the presence of this gene and the possibility of their transmission is a major concern for public health.

The article discusses a research study on the prevalence of plasmid-mediated quinolone resistance (PMQR) determinants in Salmonella and Escherichia isolates from reptiles in Germany. Isolates with nalixidic acid MIC and ciprofloxacin MIC were tested for the presence of PMQR-encoding genes. Plasmid profile analysis by DNA extraction showed the presence of qnrB19 gene in seven strains belonging to different Salmonella subspecies and serotypes. The study also confirmed the plasmid location of the qnr genes.

The article focuses on a study which determined the prevalence of Escherichia coli harbouring genes of the CTX-M-ESBL type on wildlife animal species with close contact with human settlements, the brown rat. Faecal samples from urban brown rats were collected in Berlin, Germany. The isolates which were identified using CHORM agar orientation and were further processed by agar disk diffusion testing as a preliminary screen for antimicrobial resistance. Antibiotics wherein phenotypic antimicrobial resistance were detected include cefatoxime and cefalotin.

The article describes the complete nucleotide sequence of the 2699 bp ColE-like quinolone resistance (qnrB19) plasmid pSGI15. It examines several mutiresistant Salmonella strains isolated from animals, food and humans between 2001 and 2006. It reveals that of the isolates studied, 53 percent were found to beSGI1 positive.

The occurrence of carbapenemase-producing Enterobacteriaceae in livestock is considered as a threat for public health. In Germany, VIM-1-producing Escherichia ( E .) coli sequence type (ST) 88 and Salmonella Infantis isolates harbouring bla VIM-1 Inc HI2 plasmids have been isolated from swine and poultry farms. A retrospective study was performed to determine if there was a broader distribution of VIM-1-positive isolates in any of the carbapenemase-positive swine farms. Selective incubation (carbapenem-containing broth) of 249 conserved cultures collected in three farms (2011–2012), allowed the detection of 40 bla VIM-1 -positive isolates. Apart from the already known non-motile Salmonella Infantis isolate R25 (farm S1) and R27 (S2), a third isolate was recovered from farm S3. For E. coli , additional to isolates R29 and R178 (S2), 35 new isolates were identified in the same farm during all the sampling periods (three dates, 2011) and in samples from different animals, farm environment, manure and flies. The newly identified E. coli and Salmonella isolates showed similar genetic and phenotypic characteristics (XbaI-PFGE profiles, antimicrobial resistance patterns, plasmid content, phylogroups, antigenic formula) to those in the previously described strains, suggesting microevolution within the clonal lines within one fattening period. The study shows that persistence of carbapenemase-producing clonal lines in livestock farms is possible, and underlines the need for harmonised monitoring and surveillance studies to follow up the occurrence of such bacteria in European livestock. [ABSTRACT FROM AUTHOR]

Multidrug-resistant Escherichia coli encoding CTX-M-type extended-spectrum β-lactamases (ESBLs) are isolated in increasing numbers from humans, companion animals and livestock, raising concern regarding the exchange and spread of isolates in these populations. In this study, whole-genome sequencing of CTX-M-15-producing E. coli isolates recently sampled from humans, companion animals, livestock and farm environments was performed. In total, 26 different sequence types (STs) were detected, of which ST410 was the most frequent and was the only ST present in all populations studied. Five clades (designated A–E) were detected within the ST410 isolates. In particular, isolates of clade B were present in all four populations and had core genomes that differed by less than 70 single nucleotide polymorphisms (SNPs). Isolates of clades B and C were also clonally marked, exhibiting identical chromosomal insertions of bla CTX-M-15 at distinct loci. These data provide strong evidence for the clonal dissemination of specific clades of CTX-M-15-producing E. coli ST410 in human and animal populations. [ABSTRACT FROM AUTHOR]