Genomics of Staphylococcus aureus and Enterococcus faecalis isolated from the ocular surface of dry eye disease sufferers
Peer reviewed, Journal article
Published version
Date
2024Metadata
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Original version
https://doi.org/10.1016/j.exer.2024.110071Abstract
Ocular surface inflammatory disorders, such as dry eye, are becoming increasingly prevalent. Developing new
treatment strategies targeting harmful bacteria could provide significant therapeutic benefits. The purpose of this
study was to characterize the common ocular pathogen Staphylococcus aureus and the rarer endophthalmitis-
associated species Enterococcus faecalis isolated from the ocular surface of dry eye disease patients in Norway.
Together the 7 isolates (5 S. aureus and 2 E. faecalis) comprise the complete set of members of each species
isolated in our previous study of the ocular microbiome of 61 dry eye sufferers. We aimed to investigate the
pathogenic potential of these isolates in relation to ocular surface health. To this end, we used whole genome
sequencing, multiplex PCR directed at virulence genes and antibiotic susceptibility tests encompassing clinically
relevant agents. The E. faecalis isolates showed resistance to only gentamicin. S. aureus isolates displayed susceptibility
to most of the tested antibiotics, except for two isolates which showed resistance to trimethoprim/
sulfamethoxazole and three isolates which were resistant to ampicillin. Susceptibilities included sensitivity to
several first-line antibiotics for treatment of ocular infections by these species. Thus, treatment options would be
available if required. However, spontaneous resistance development to gentamicin and rifampicin occurred in
some S. aureus which could be a cause for concern. Whole genome sequencing of the isolates showed genome
sizes ranging from 2.74 to 2.83 Mbp for S. aureus and 2.86 Mbp for E. faecalis, which is typical for these species.
Multilocus sequence typing and phylogenetic comparisons with previously published genomes, did not suggest
the presence of eye-specific clusters for either species. Genomic analysis indicated a high probability of pathogenicity
among all isolates included in the study. Resistome analysis revealed the presence of the beta-lactamase
blaZ gene in all S. aureus isolates and the dfrG gene in two of them; while E. faecalis isolates carried the lsa(A)
gene which confers intrinsic resistance to lincosamides and streptogramin A in this species. Screening for
virulence factors revealed the presence of various pathogenicity associated genes in both S. aureus and E. faecalis
isolates. These included genes coding for toxin production and factors associated with evading the host immune
system. Some of the identified genes (tst, hylA & hylB) are suggested to be linked to the pathophysiology of dry
eye disease. Lastly, the presence of specific S. aureus virulence genes was confirmed through multiplex PCR
analysis.