The comparative staphylococcal microbiome of the skin and oral mucosa of captive and free-ranging fruit bats (Pteropus livingstonii), and the skin of red squirrels (Sciurus vulgaris).
: (Alternative Format Thesis)

  • Kay Fountain

Student thesis: Doctoral ThesisPhD


Bacteria in the genus Staphylococcus, in particular Staphylococcus aureus, are pathogens of serious concern in human and veterinary medicine, but despite decades of research effort much remains to be learnt about their epidemiology and mechanisms of virulence. The increasing availability of whole genome sequencing (WGS) has allowed the development of new tools to analyse the genomic basis of infection, transmission and virulence. In addition, new methods of sequencing are able to produce long reads, sometimes of tens of kilobases, which permit the resolution of repetitive regions which short-read sequencing alone cannot resolve. These methods are particularly valuable in the study of horizontal gene transfer (HGT) which is an important driver of the evolution of staphylococci.
Previous work has rarely examined carriage of staphylococci by wildlife, even though it is acknowledged that the ‘one health’ approach is vital if we are to fully understand the epidemiology of pathogens. Livingstone’s fruit bats (Pteropus livingstonii) are critically endangered and as part of a species survival plan a captive breeding colony was established at Jersey Zoo in 1993-95. S. aureus has caused serious disease in this colony, and to understand if this disease was the result of the acquisition of ‘foreign’ strains of S. aureus during captivity we used WGS to compare strains carried by the captive bats and their free-ranging counterparts. Unexpectedly, the captive bats had retained the strains brought with them from the wild 25 years earlier, and we found evidence of variants in genes for immune evasion and carbohydrate metabolism which suggested bat adaptation.
Red squirrels (Sciurus vulgaris) in the UK are endangered, and remnant populations on islands are vital to ensure the survival of the species in Britain. Red squirrels on Jersey (Channel Islands) and the Isle of Wight are affected by a fatal form of dermatitis which is associated with a particular clone of S. aureus (ST49). Little is known about the normal carriage dynamics of S. aureus in red squirrels, so we sampled over 200 healthy squirrels on Jersey, Isle of Arran and Brownsea island, and 16 diseased squirrels on Jersey and Isle of Wight. Using WGS our findings reinforced the strong association of the ST49 lineage with disease and suggested it is not a normal carriage strain in red squirrels. Instead we found a pattern of ‘spillover’ of strains from other hosts in the same environment, however some ruminant-associated strains may have undergone some long-term adaptation to red squirrels. We speculate that infection with ST49 results from contact with a reservoir host which is most likely the bank vole (Myodes glareolus).
The virulence of ST49 strains may be partly associated with a prophage carrying leucotoxin genes. In the genomes of our collection of strains from bats and squirrels we found several intact prophages which carried these and other genes encoding for virulence factors. Our investigation suggested a link between these prophages and a second phage integration site in the S. aureus beta genomic island which provides new insight into the evolution of virulence in this island.
During this genomic investigation we found the genomes of several presumptive staphylococci which did not fit into any known species designation. We examined these genomes using digital DNA-DNA hybridisation techniques to assign new species designations to two coagulase negative staphylococci closely related to S. kloosii, and one coagulase-positive isolate in the S. aureus complex, closely related to S. argenteus.
In conclusion, using WGS as a tool to investigate epidemiology, species designation and virulence in strains of staphylococci associated with wildlife, we have provided valuable new insights into this important genus.
Date of Award8 Sept 2021
Original languageEnglish
Awarding Institution
  • University of Bath
SupervisorEdward Feil (Supervisor), Anette Loeffler (Supervisor) & Samuel Sheppard (Supervisor)


  • Staphylococcus aureus,
  • fruit bats,
  • red squirrels,
  • endangered
  • prophages
  • virulence
  • novel species
  • closed genomes

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