Comparison of antimicrobial resistance genes on the ocular surface of patients with corneal infections in California and Malawi
Data files
May 22, 2025 version files 12.88 KB
Abstract
Background: Antimicrobial resistance (AMR) determinants on the ocular surface may contribute to poor treatment responses.
Results: Mutations conferring macrolide resistance were present on the ocular surface in 58% (95% CI 44 to 71%) of the participants in Malawi and 32% (95% CI 20 to 46%) of the participants in San Francisco. Amino-glycosides resistance genes were also common on the ocular surface with 58% (95% CI 44 to 71%) prevalence in Malawi and 21% (95% CI 12 to 35%) in San Francisco. AMR was associated with poorer visual outcomes in a subset of patients.
Conclusions: As determined by RNA-seq, ocular surface AMR gene mutations are common in patients with infectious keratitis. Surveillance may be important for infectious keratitis treatment selection as well as providing guidance for antibiotic stewardship.
Dataset DOI: 10.5061/dryad.6t1g1jx9s
Description of the data and file structure
Patients presenting with infectious keratitis at UCSF and the Queen Elizabeth Central Hospital, Department of Ophthalmology of Kamuzu College of Health Sciences, and who gave consent, were examined and underwent sample collection. Swabs obtained from their affected cornea were prepared for RNA-seq.
Files and variables
File: CAPRICORN_Malawi_UCSF_counts_cpm_per_patient_AMR_classes.csv
Description: Counts per million (rpm) of various AMR determinants. (MEGARES 3.0.0 alignment, SNP-confirmed, deduplicated.)
Variables
- study_id: unique identifier for study participant
- Aminocoumarins: rpm of hits for this AMR class
- Aminoglycosides: rpm of hits for this AMR class
- betalactams: rpm of hits for this AMR class
- Cationic_antimicrobial_peptides: rpm of hits for this AMR class
- Fluoroquinolones: rpm of hits for this AMR class
- Fosfomycin: rpm of hits for this AMR class
- MLS: rpm of hits for this AMR class (macrolides)
- Oxazolidinone: rpm of hits for this AMR class
- Rifampin: rpm of hits for this AMR class
- Sulfonamides: rpm of hits for this AMR class
- Tetracyclines: rpm of hits for this AMR class
File: CAPRICORN_Malawi_UCSF_manuscript_data_share.csv
Description: Ocular exam summary data
Variables
- study_id: unique identifier for study participant
- study_site: study site (Malawi or UCSF)
- pathogen_type: pathogen(s) identified in patient
- num_amr_determinants: number of antimicrobial resistance determinants identified in patient
- baseline_va: visual acuity at baseline visit (see * below)
- week4_va: visual acuity at 4 weeks follow-up visit (see * below)
- baseline_logmar: logMAR visual acuity at baseline visit (empty denotes missing)
- week4_logmar: logMAR visual acuity at 4 weeks follow-up visit (empty denotes missing)
*Note on the visual acuity columns (baseline_va and week4_va) :
A leading quote character was added to prevent Excel displaying the data as dates. In addition to Snellen fractions, the following acuity types are represented in the data:
- LP: Light Perception
- NLP: No Light Perception
- HM: Hand Motion
- CF: Counting Fingers
- nan / NA: missing data
Code/software
no special software needed
Human subjects data
Ethical approvals from the institutional review board of the University of California, San Francisco (approval #21–34439), and the ethical committee of Kamuzu College of Health Sciences (approval #P.06/22/3669), were obtained, and allow for publication of de-identified data in the public domain. Each sample is de-identified by using an integer "study id" not linked to any identifiable metadata.
An exploratory comparative analysis of ocular surface AMR determinants, as determined by RNA-sequencing (RNA-seq), on patients presenting with keratitis infections at the Proctor Medical Clinic at the University of California San Francisco in San Francisco, CA, USA, and the Queen Elizabeth Central Hospital at the Department of Ophthalmology of Kamuzu College of Health Sciences in Blantyre, Malawi, was conducted. All patients underwent swabbing of three sites on the ocular surface: cornea and bilateral conjunctiva.