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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., Results: E. coli of diverse ST harbouring mcr-1 and multiple resistance genes were isolated over 5 months from both cohorts. Two STs, from treated cohorts, contained both mcr-1 and mcr-3 plasmids, with some isolates also harbouring multiple copies of mcr-1 on different plasmids. The mcr-1 plasmids grouped into four Inc types (X4, pO111, I2 and HI2), with mcr-3 found in IncP. Multiple copies of mcr plasmids did not have a noticeable effect on colistin MIC, but they could be transferred simultaneously to a Salmonella host in vitro. Neither mcr-1 nor mcr-3 was detected in samples collected ∼20 months after colistin cessation., Conclusions: We report for the first known time on the presence in Great Britain of mcr-3 from MDR Enterobacteriaceae, which might concurrently harbour multiple copies of mcr-1 on different plasmids. However, control measures, including stoppage of colistin, can successfully mitigate long-term on-farm persistence.

In the study, we examined the molecular characteristics of cattle-associated Escherichia coli carrying CTX-M genes and their plasmids. Between July 2006 and July 2007, 18 E. coli were collected from cattle that were found to possess a bla(CTX-M) belonging to group 1. bla(CTX-M-15/28) was the predominant type, and it was associated with plasmids of several different inc/rep types. In addition, bla(CTX-M-1) and bla(CTX-M-3) were also detected. Plasmids encoding the bla(CTX-M) genes belonged to incompatibility groups I1, F, and A/C. Analysis of the non-beta-lactam resistance genes associated with each CTX-M-bearing plasmid demonstrated that F plasmids frequently carried a larger number of resistance genes than IncI1 plasmids, which rarely carried additional resistance genes. All bla(CTX-M) carrying plasmids were positive by polymerase chain reaction for an ISEcp1-like element.

Fluoroquinolones resistance in bacteria can be due to chromosomal and plasmid-mediated mechanisms. Of growing concern is the acquisition of genes encoding quinolone resistance in combination with other resistance mechanisms such as extended-spectrum beta-lactamases. In this study we describe the identification of an isolate of Escherichia coli from cattle which carried qnrS1 in combination with a blaCTX-M gene, although they were not co-localised on the same plasmid. In addition, using a DNA array it was possible to identify several other antimicrobial resistance genes in this isolate. This is the first report of a qnr gene in E. coli from cattle in the UK and highlights the need for surveillance of these emerging resistance mechanisms., (Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.)

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. Results Salmonella and E. coli isolates harbouring the rmtB gene were detected at both farm visits. All Salmonella isolates were found to be monophasic S. enterica serovar Typhimurium variant Copenhagen of ST34. rmtB -harbouring E. coli isolates were found to be one of three STs: ST4089, ST1684 and ST34. Long-read sequencing identified the rmtB gene to be chromosomally located in Salmonella isolates and on IncFII-type plasmids in E. coli isolates. The results showed the rmtB gene to be flanked by IS 26 elements and several resistance genes. Conclusions We report on the occurrence of rmtB -harbouring Enterobacteriaceae on a pig farm in the UK. rmtB confers resistance to multiple aminoglycosides and this work highlights the need for surveillance to assess dissemination and risk. [ABSTRACT FROM AUTHOR]

To tackle the problem of antimicrobial resistance (AMR) surveillance programmes are in place within Europe applying phenotypic methods, but there are plans for implementing whole genome sequencing (WGS). We tested the benefits of WGS using Escherichia coli collected from pig surveillance performed between 2013 to 2017. WGS was performed on 498 E. coli producing ESBL and AmpC enzymes, recovered from pig caeca on MacConkey + cefotaxime (McC + CTX) agar, as recommended by the European Commission, or ESBL agar, used additionally by United Kingdom. Our results indicated WGS was extremely useful for monitoring trends for specific ESBL genes, as well as a plethora of AMR genotypes, helping to establish their prevalence and co-linkage to certain plasmids. Recovery of isolates with multi-drug resistance (MDR) genotypes was lower from McC + CTX than ESBL agar. The most widespread ESBL genes belonged to the blaCTX-M family. blaCTX-M-1 dominated all years, and was common in two highly stable IncI1 MDR plasmids harbouring (blaCTX-M-1,sul2, tetA) or (blaCTX-M-1, aadA5, sul2, dfrA17), in isolates which were phylogenetically dissimilar, suggesting plasmid transmission. Therefore, WGS provided a wealth of data on prevalence of AMR genotypes and plasmid persistence absent from phenotypic data and, also, demonstrated the importance of culture media for detecting ESBL E. coli. [ABSTRACT FROM AUTHOR]