Predictors of Hospital Onset Infection: A Matched Retrospective Cohort Dataset

This repository contains a de-identified and curated patient-level dataset for
modeling the impact of fine-grained environmental and patient-level factors on
nosocomial acquisition of a wide range of drug-susceptible and drug-resistant
pathogens. The data are derived from the clinical data warehouses of the Mass
General Brigham health system and span all adult inpatients admitted between
May 2015 and July 2024.

We use a matched case/control design and provide two datasets reflecting
distinctive but complementary strategies to model our outcome. The first,
which we call the **environmental analysis** , investigates the impact of the
hospital unit microbiome, using colonization pressure as a proxy, and matches
on prior antibiotic exposure to equalize its selective impact across cases and
controls. The second strategy, which we call the **patient analysis** ,
investigates the impact of prior fine-grained antibiotic exposures and matches
controls spatiotemporally to cases based on their time of entry into the same
ward, to equalize the impact of the hospital microbiome.

Each observation in the dataset corresponds to a hospitalization. We look at
nosocomial acquisition of 11 common drug-susceptible and drug-resistant
pathogens, with cases having a culture positive for the target pathogen
between day 3 and day 30 after admission into their room.