IBRAHIM, DELVEEN
(2017)
Phenotypic and genotypic study of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from a dairy farm.
PhD thesis, University of Nottingham.
Abstract
Approximately 400 tonnes of antibiotics (including synthetic antibiotics) are used every year in treating infections in farm animals, and as prophylactics against infection. Antimicrobial resistance is a crucial problem that is now of great concern in public health, with food and food producing animals as a potential route for spread of these resistances, especially resistance to cephalosporins, which is increasing. The main aim of this study was to determine the prevalence and range of multidrug resistance (MDR) and extended spectrum β-lactamase (ESBL) or ampicillin C (AmpC) β-lactamase producing Escherichia coli within a commercial dairy farm, to understand the diversity of resistance to β-lactam antibiotics, and to determine if co-carriage of other antimicrobial resistance (AMR) was associated with ESBL/AmpC producers. This would allow a better understanding of the contributions that farms and farm slurry may make to the presence of AMR in the environment, and the reservoir of resistance in agriculture. In this study, E. coli strains were isolated from a single dairy farm (East Midlands, England, United Kingdom) on two visits, a preliminary isolation using TBX agar in 2012 and more targeted isolation using antibiotic supplemented TBX media in 2014. Confirmed E. coli (126 out of 155 selected strains) were genotyped using ERIC-PCR and analysis of the ERIC profiles showed that, in comparison to the 2014 isolates, the 2012 isolates were a quite distinct genetic population. Antimicrobial sensitivity tests were performed using a disk diffusion test for all the strains against 17 antimicrobials representing seven different antimicrobial groups: β-lactams, aminoglycosides, tetracyclines, sulphonamides, chloramphenicols, nitrofuran derivatives and quinolones. Antimicrobial resistance profiling showed 92% of isolates showed resistance to at least 1 antimicrobial, of which 27.8% of the isolates were isolated without antibiotic selection, and 57.9% of the isolates were multidrug resistant to between 3 and 15 antimicrobials, of which 43.6% of the isolates were isolated using antibiotic supplemented media. Two strains showed resistance to imipenem which appeared to be an unstable phenotype and was subsequently lost. The finding was unexpected and of concern as imipenem is not used in veterinary medicine. blaCTX-M, blaTEM and blaOXA genes were detected by PCR among the cephalosporin resistant strains. No plasmid ampC genes were detected. Four strains were fully sequenced and the genetic/genomic environment surrounding β-lactamase genes and analysis of some other AMR genes showed these genes are associated with transposable elements, such as ISEcp1, ISCR2, IS26-IS26, Tn2, Tn10 or within a class I integron carried by a Tn-21 like transposon. The association of AMR genes with these transposable elements might make the dissemination rate of these genes greater. Some of the insertion sequence-AMR gene combinations are thought to be novel, such as the unique insertion of ISEcp1- blaCTX_M14 unit into the fdeC chromosomal gene.
This is the first study of this type performed on this dairy farm; the data showed a diverse range of resistance genes present in the E. coli population in the farm, including resistance to historically used antimicrobials as well as cephalosporins in contemporary use, and a high level of multidrug resistance. The spread of such highly resistant strains to the environment and possibly to humans could present a real threat to human health especially if they are pathogenic.
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