Elucidation of Novel and Established Campylobacter Species With Clinical and Agricultural Significance Through Phenotypic, Genotypic, and Taxonomic Investigation
Date of Award
Doctor of Philosophy
Prof. Aidan Coffey
Dr Brigid Lucey
Campylobacter spp. are well-established human, veterinary and economic pathogens, with a broad host range spanning from terrestrial and marine mammalian, avian and reptilian hosts. The scope of the study includes novel and notorious species within the genus, with reference to zoonotic agents Campylobacter jejuni and Campylobacter coli - the leading cause of human bacterial gastroenteritis in the EU and Ireland, Campylobacter fetus that represents the most common campylobacter causing bacteraemia and two novel species isolated from pigs not described in the literature previously. C. jejuni and C. coli isolates (n = 350) recovered from broiler caecal and neck skin samples, collected from the three main poultry processing plants in Ireland between September 2017 and September 2018, were tested for the susceptibility to six clinically relevant antimicrobials. Overall, 45.1% of Campylobacter spp. isolates tested were resistant to at least one antimicrobial. Resistance rates were broadly in line with figures reported nationally over the past 20 years, indicating that resistance is stable and persistent, and an increasing incidence of tetracycline resistance in C. jejuni was noted. Known or related antimicrobial resistance genes were identified in all isolates with phenotypic resistance, and we highlight the importance of clonal expansion of resistant strains and potential for horizontal gene transfer in Campylobacter. A C. fetus subsp. fetus (Cff) isolate (CITCf01) recovered from a case of prosthetic valve endocarditis (2017) was tested for its ability to form a biofilm. Biofilms were stronger than that of a known Campylobacter jejuni biofilm forming strain and this was the first report of biofilm formation within the species, using a modified crystal violet staining method developed in this study. A second Cff (CITCf02) was isolated from the recurrent case of prosthetic valve endocarditis in late 2018. Genomic and phenotypic comparisons of the isolates were performed, and their taxonomic position among previously described Cff isolates from humans (n = 83) was determined. Cff isolates CITCf01 and CITCf02 were confirmed to be the same strain and the polymorphic sap island (known to contribute to immune evasion) defined their temporal separation. These Cff isolates were marked for their unusual ability to grow aerobically, despite a high degree of genetic relatedness to ix other members of the subspecies that are not capable of growth in air. Mutations in genes putatively involved in stress response were identified in CITCf01 and CITCf02. Campylobacter isolated from the porcine gastrointestinal tract in the 1980s were formally classified as novel species in this study, using a polyphasic approach encompassing biochemical, phenotypic, genomic and taxonomic analyses. The pathogenic potential of the genus was explored, and factors contributing to their persistence.
Lynch, Caoimhe, "Elucidation of Novel and Established Campylobacter Species With Clinical and Agricultural Significance Through Phenotypic, Genotypic, and Taxonomic Investigation" (2022). Theses [online].
Available at: https://sword.cit.ie/allthe/14
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