Epidemiology and Species Distribution of Candidemia at a Healthcare Institution in Puerto Rico, 2024–2025

This record provides the de-identified analysis dataset and the complete R/Quarto analysis code accompanying the study "Post–COVID-19 Epidemiology of Nosocomial Candidiasis in Puerto Rico: Predominance of Non-albicans Candida in a Caribbean Cohort." We conducted a single-center, retrospective observational cohort study of 257 hospitalized patients with at least one clinical Candida isolate at a secondary-care medical center in northern Puerto Rico between February 2024 and June 2025. The dataset supports reproduction of all reported analyses: species distribution, colonization versus candidemia, healthcare-associated risk factors, length of stay, and in-hospital mortality (including a severity-adjusted mortality analysis). Key findings include a predominance of non-albicans Candida (78.5% of isolates), Candida parapsilosis as the leading bloodstream species, and substantially higher mortality among patients with candidemia than among those with colonization only. The dataset (candidiasis_analysis_deidentified.csv; 257 patients × 50 variables) contains demographic, clinical, microbiologic, and outcome variables in analysis-ready form, documented in data/data_dictionary.md. The code/ directory contains the numbered data-cleaning, Cox regression, species, mortality, and length-of-stay scripts, with README_code.md mapping each script to its manuscript tables and figures. The data were de-identified in accordance with the HIPAA Safe Harbor standard: all dates of service were removed (retaining only length of stay in days), ages over 89 were top-coded to 90, free-text clinical narrative was replaced by coded variables, and medical-record identifiers were removed. The study was approved by the Institutional Review Board (EMSJBIRB-10-2025); informed consent was waived given the anonymized nature of the data. Please cite this record (DOI) together with the accompanying article once published. Version 2 accompanies the manuscript submitted to Revista Iberoamericana de Micología. It adds 06_final_manuscript_analysis.R, which reproduces every number, table and Figure 1 of the manuscript from candidiasis_clean.rds, the cleaned dataset produced by 01_data_cleaning.R (July 2026). The cleaned data are unchanged from version 1. Figure 1 labels were updated ("Candida spp. (not speciated)" and "Other non-albicans Candida"), and the figure is provided as a 300 dpi TIFF. Files: candidiasis_clean.rds and candidiasis_clean.csv (de-identified patient-level dataset, N = 257); 01_data_cleaning.R (data cleaning); 06_final_manuscript_analysis.R (all manuscript analyses); manuscript_numbers.txt (output of 06, every number cited in the manuscript); Figure1_final.tiff (Figure 1). To reproduce: place the files in one folder, set it as the working directory in R, and run source("06_final_manuscript_analysis.R"). Required packages: tidyverse, patchwork, scales and logistf.