Genomic Epidemiology and Antimicrobial Resistance of MRSA Isolates Causing Keratitis
Camille André and Paulo J.M. Bispo
Massachusetts Eye and Ear, Harvard Medical School, Department of Ophthalmology, Boston, Massachusetts
Purpose: Staphylococcus aureus is a major cause of keratitis. Methicillin-resistant S. aureus (MRSA) is commonly associated with multidrug-resistant (MDR) infections, resulting in treatment failure and poor visual outcome. To assess the emergence of high-risk MDR clones of MRSA causing keratitis and the repertoire of antimicrobial resistance (AMR) genes circulating among this population, we have sequenced the genomes of all MRSA isolates recovered from patients presenting with keratitis between January 2014 and December 2021 at the Massachusetts Eye and Ear.
Methods: Whole Genome Sequencing was performed on 40 MRSA isolates causing keratitis using Illumina HiSeq. Molecular typing was performed by multilocus sequence typing. CARD algorithm was used to identify genes and mutations that confer AMR. Minimum inhibitory concentrations (MICs) were determined by broth microdilution.
Results: The population structure of MRSA isolates causing keratitis was dominated by lineages grouped within the clonal complex 5 (CC5) (68.2%). 86.7% of MRSA CC5 isolates were MDR (resistance to ≥3 antimicrobial classes) and only one isolate was susceptible to fluoroquinolones. In line with these observations, we found that the resistome of these CC5 strains was comprised of multiple acquired AMR genes that confer resistance to various clinically important antibiotics including aminoglycosides, macrolides, lincosamides, streptograminB, and fosfomycin. Transference of some of these genes between strains is facilitated by horizontal gene transfer as they are found in mobile genetic elements such as transposons. In our CC5 population the mecA gene is integrated into a SCCmec cassette which also carries a full transposon (Tn554) containing the ermA and ant(9)-Ia genes, both present in 86.7% of our isolates. We found between 2 and 4 mutations in the quinolone resistance-determining regions (QRDR) of gyrA and parC genes for MRSA isolates that were associated with high levels of resistance to fluoroquinolones.
Conclusions: MRSA keratitis is caused by strains mainly clustered within the CC5, which is also a common cause of hospital-acquired MDR infections. CC5 strains carried a constellation of AMR genes and mutations that result in high levels of phenotypic resistance to first-line topical therapies.
Support: Fondation pour la Recherche Médicale (FDM202006011203)