Occurrence and characterization of rmtB-harbouring Salmonella and Escherichia coli isolates from a pig farm in the UK.

Objectives: To characterize and elucidate the spread of amikacin-resistant Enterobacteriaceae isolates from environmental samples on a pig farm in the UK, following the previous identification of index Salmonella isolates harbouring the rmtB gene, a 16S rRNA methylase.

Methods: Environmental samples were collected during two visits to a pig farm in the UK. Isolates were recovered using selective media (amikacin 128 mg/L) followed by real-time PCR and WGS to analyse rmtB-carrying Salmonella and Escherichia coli isolates.

Multicentre evaluation of a selective isolation protocol for detection of mcr-positive E. coli and Salmonella spp. in food-producing animals and meat.

This study was conducted to evaluate the performance of a screening protocol to detect and isolate mcr-positive Escherichia coli and Salmonella spp. from animal caecal content and meat samples. We used a multicentre approach involving 12 laboratories from nine European countries.

Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage.

Food animals may be reservoirs of antimicrobial resistance (AMR) passing through the food chain, but little is known about AMR prevalence in bacteria when selective pressure from antimicrobials is low or absent. We monitored antimicrobial-resistant over 1 year in a UK outdoor pig farm with low antimicrobial usage (AMU) compared to conventional pig farms in the United Kingdom. Short and selected long-read whole-genome sequencing (WGS) was performed to identify AMR genes, phylogeny and mobile elements in 385 isolates purified mainly from pig and some seagull faeces.

A European multicenter evaluation study to investigate the performance on commercially available selective agar plates for the detection of carbapenemase producing Enterobacteriaceae.

The European Food Safety Authority (EFSA) advised to prioritize monitoring carbapenemase producing Enterobacteriaceae (CPE) in food producing animals. Therefore, this study evaluated the performance of different commercially available selective agars for the detection of CPE using spiked pig caecal and turkey meat samples and the proposed EFSA cultivation protocol. Eleven laboratories from nine countries received eight samples (four caecal and four meat samples).

sp. nov., isolated from sheep.

Five strains of an unidentified Gram-positive, catalase-negative, chain-forming coccus-shaped organism recovered from sheep in Scotland were characterized using phenotypic and molecular taxonomic methods. Based on morphological and biochemical criteria, the strains were tentatively identified as streptococci but they did not appear to correspond to any recognised species of the genus. Comparative 16S rRNA gene sequencing showed the strains were highly related to each other and confirmed their placement in the genus , with a maximum nucleotide identity of around 97 % to extant species.

Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study.

Background: Extended-spectrum β-lactamase-producing Escherichia coli isolates (ESBL-E coli) cause more than 5000 cases of bacteraemias annually in the UK. The contribution of the food chain to these infections is debated. We aimed to identify the most important reservoirs of ESBL-E coli that colonise and infect humans to identify strategic intervention points.

Molecular epidemiology of isolates with multiple mcr plasmids from a pig farm in Great Britain: the effects of colistin withdrawal in the short and long term.

Background: The environment, including farms, might act as a reservoir for mobile colistin resistance (mcr) genes, which has led to calls for reduction of usage in livestock of colistin, an antibiotic of last resort for humans.

Objectives: To establish the molecular epidemiology of mcr Enterobacteriaceae from faeces of two cohorts of pigs, where one group had initially been treated with colistin and the other not, over a 5 month period following stoppage of colistin usage on a farm in Great Britain; faecal samples were also taken at ∼20 months.

Methods: mcr-1 Enterobacteriaceae were isolated from positive faeces and was WGS performed; conjugation was performed on selected Escherichia coli and colistin MICs were determined.

mcr-1 and mcr-2 variant genes identified in Moraxella species isolated from pigs in Great Britain from 2014 to 2015.

Objectives: To determine the occurrence of mcr-1 and mcr-2 genes in Gram-negative bacteria isolated from healthy pigs in Great Britain.

Methods: Gram-negative bacteria (n = 657) isolated from pigs between 2014 and 2015 were examined by WGS.

Results: Variants of mcr-1 and mcr-2 were identified in Moraxella spp.

Risk for the development of Antimicrobial Resistance (AMR) due to feeding of calves with milk containing residues of antibiotics.

EFSA was requested to: 1) assess the risk for the development of antimicrobial resistance (AMR) due to feeding on farm of calves with colostrum potentially containing residues of antibiotics; 2) assess the risk for the development of AMR due to feeding on farm of calves with milk of cows treated during lactation with an antibiotic and milked during the withdrawal period, and 3) propose possible options to mitigate the risk for the development of AMR derived from such practices. Treatment of dairy cows during the dry period and during lactation is common in the EU Member States. Penicillins, alone or in combination with aminoglycosides, and cephalosporins are most commonly used.

In vitro investigations into the use of antimicrobials in combination to maintain efficacy of fluoroquinolones in poultry.

The aim of this study was to determine if apramycin, colistin or lincomycin-spectinomycin, in combination with enrofloxacin, was able prevent the emergence of mutants with reduced susceptibility to fluoroquinolone antibiotics in vitro. MICs were determined for enrofloxacin alone and in combination for panels of Campylobacter (n=37), Escherichia coli (n=52) and Salmonella (n=52) isolates. MIC results suggested that apramycin, colistin and lincomycin-spectinomycin worked in an additive/indifferent way when each was combined with enrofloxacin.

Colistin resistance in Salmonella and Escherichia coli isolates from a pig farm in Great Britain.

Objectives: The objective of this study was to characterize colistin-resistant bacteria isolated from pigs on a farm in Great Britain following identification of a plasmid-borne colistin resistance mechanism in Escherichia coli from China.

Methods: Phenotypic antimicrobial susceptibility testing was undertaken by broth dilution and WGS was performed to detect the presence of genes encoding resistance and virulence. Transferable colistin resistance was investigated by conjugation.

Evaluation of MALDI-ToF as a method for the identification of bacteria in the veterinary diagnostic laboratory.

Matrix-Assisted Laser Desorption Ionisation-Time of Flight (MALDI-ToF) Mass Spectrometry with Bruker MALDI Biotyper software was evaluated as a method for identifying veterinary bacteria. For 620 isolates (~100 bacterial species), identification by MALDI-ToF and non-16S rDNA methods (mainly phenotypic/biochemical) agreed to species-level (95.3%) and to species/genus-level (100%), but in the absence of 16S rDNA as a gold standard.

Detection of antibiotic residues and association of cefquinome residues with the occurrence of Extended-Spectrum β-Lactamase (ESBL)-producing bacteria in waste milk samples from dairy farms in England and Wales in 2011.

Waste milk samples from 103 farms in England and Wales were examined for the presence of β-lactam antibiotics and ESBL-producing Enterobacteriaceae. Approximately 10 months after the initial sampling, further waste milk, environmental and faecal samples from farms shown to be positive for CTX-M Escherichia coli were investigated further. Isolates with an ESBL phenotype were tested by PCR for the presence of blaCTX-M, blaOXA, blaSHV and blaTEM genes.

Quantification and characterization of mucosa-associated and intracellular Escherichia coli in inflammatory bowel disease.

Background: Mucosa-associated Escherichia coli are abundant in inflammatory bowel disease (IBD), but whether these bacteria gain intracellular access within the mucosa is uncertain. If E. coli does gain intracellular access, the contribution of bacterial pathogenicity to this requires further elucidation.

Molecular and phenotypic characterisation of extended spectrum β-lactamase CTX-M Escherichia coli from farm animals in Great Britain.

The aim of this study was to characterise CTX-M Escherichia coli isolates from cattle, chickens and turkeys in Great Britain with respect to CTX-M sequence type, replicon type, ability to transfer plasmids, and for the presence of antibiotic resistance, fitness and virulence genes as determined by micro-arrays. The main CTX-M enzymes identified in E. coli from cattle, chicken and turkeys were 14 and 15, 1 and 15, and 1 and 14 respectively.

Virulence genes in bla(CTX-M) Escherichia coli isolates from chickens and humans.

The aim of this study was to determine the presence of virulence genes in isolates of CTX-M Escherichia coli from diseased chickens, from healthy chickens and from urinary tract infections in people. Three CTX-M E. coli strains from three different instances of disease in poultry (two of which were E.

Persistence of a wild type Escherichia coli and its multiple antibiotic-resistant (MAR) derivatives in the abattoir and on chilled pig carcasses.

The aim of this study was to evaluate the ability of an Escherichia coli with the multiple antibiotic resistance (MAR) phenotype to withstand the stresses of slaughter compared to an isogenic progenitor strain. A wild type E. coli isolate (345-2RifC) of porcine origin was used to derive 3 isogenic MAR mutants.

Development and evaluation of internal amplification controls for use in a real-time duplex PCR assay for detection of Campylobacter coli and Campylobacter jejuni.

A common problem of both conventional and real-time PCR assays is failure of DNA amplification due to the presence of inhibitory substances in samples. In view of this, our aim was to develop and evaluate internal amplification controls (IACs) for use with an existing duplex real-time PCR assay for Campylobacter coli and Campylobacter jejuni. Both competitive and non-competitive IACs were developed and evaluated.

Triclosan resistance in Salmonella enterica serovar Typhimurium.

Objectives: The aim of this study was to characterize the mechanisms of resistance to triclosan in Salmonella enterica serovar Typhimurium.

Methods: Mutants resistant to triclosan were selected from nine S. enterica serovar Typhimurium strains.

Phenotypic and proteomic characterization of multiply antibiotic-resistant variants of Salmonella enterica serovar Typhimurium selected following exposure to disinfectants.

In previous work, Salmonella enterica serovar Typhimurium strain SL1344 was exposed to sublethal concentrations of three widely used farm disinfectants in daily serial passages for 7 days in an attempt to investigate possible links between the use of disinfectants and antimicrobial resistance. Stable variants OXCR1, QACFGR2, and TOPR2 were obtained following treatment with an oxidizing compound blend, a quaternary ammonium disinfectant containing formaldehyde and glutaraldehyde, and a tar acid-based disinfectant, respectively. All variants exhibited ca.