O'Neill, Colette (2010) Antibiotic-resistant staphylococci in the agricultural environment : reservoirs of resistance and infection. PhD thesis, University of Warwick.

Abstract

Antibiotic resistance is a serious problem in human and animal infections. Heavy use of antibiotics in the agricultural environment selects for antibiotic resistance among the microflora of food animals, providing a reservoir of antibiotic-resistant bacteria. These may enter the human population through the food chain or by direct contact, as demonstrated by the recent emergence of livestock-associated MRSA strains. Antibiotic resistance determinants selected in this environment may also be available for transfer to human commensals and pathogenic bacteria. Milk from conventional and organic farms was screened for methicillin-resistant staphylococci to explore the hypothesis that organic farming methods result in reduced selection for antibiotic resistance. A significantly greater number isolates from conventionally farmed milk were resistant to clindamycin, erythromycin, fusidic acid, tetracycline and tobramycin than isolates from organic milk. Isolates from organic milk mostly belonged to S. fleurettii, which does not cause any known pathogenesis or contribute to the mobile methicillin resistance reservoir. Conventional milk harboured a greater number of pathogens, including S. epidermidis and S. sciuri, both of which carried SCCmec. SCCmec elements were diverse, some similar to those found in human-associated staphylococci, and some distinct. The virulence-associated biofilm cluster icaADBC was identified in some S. epidermidis isolates, indicating increased human pathogenesis. A putative new species, S. lactis sp. nov. was isolated from a conventionally farmed herd, reflecting the high diversity of staphylococci in this environment. In pig nasal swabs originating from Thailand, LA-MRSA was identified for the first time. These isolates belonged to the ST9/t337 lineage which has been identified previously in Europe, suggesting importation of colonised pigs as the most likely route of dissemination. These contained apossible new SCCmecvariant, and harboured toxin genes associated with human disease. Isolates were resistant to medically important antibiotics including ciprofloxacin and chloramphenicol. These data support the hypothesis that use of antibiotics in agricultural practice may select for increased resistance in the microbiome of farm animals, and that some of these may be able to cause infections in humans. Early detection of MRSA is the key to effective treatment and control of dissemination; in food production this would allow early identification of contaminated meat or dairy products and prevent these from entering the food chain. The novel application of an isothermal amplification assay, LAMP, was investigated for the sensitive and specific detection of MRSA. Unfortunately, false negative reactions were common due to high variability among SCCmec subtypes, and the possession of non-mec SCC elements by methicillin-sensitive strains precluded this from offering a reliable alternative to existing methods.

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