DOI: 10.5061/dryad.6t1g1jx9s
title: Comparison of antimicrobial resistance genes on the ocular surface of patients with corneal infections in California and Malawi

description: 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.
description: 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.
description: # Comparison of antimicrobial resistance genes on the ocular surface of
 patients with corneal infections in California and Malawi Dataset DOI:
 [10.5061/dryad.6t1g1jx9s](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.