Predicting probability of perirectal colonization with carbapenem-resistant Enterobacteriaceae (CRE) and other carbapenem-resistant organisms (CROs) at hospital unit admission

Katherine E. Goodman, Patricia Simner, Eili Klein, Abida Q. Kazmi, Avinash Gadala, Matthew F. Toerper, Scott Levin, Pranita Tamma, Clare Rock, Sara Cosgrove, Lisa Maragakis, Aaron Milstone

Research output: Contribution to journalArticle

Abstract

Background:Targeted screening for carbapenem-resistant organisms (CROs), including carbapenem-resistant Enterobacteriaceae (CRE) and carbapenemase-producing organisms (CPOs), remains limited; recent data suggest that existing policies miss many carriers.Objective:Our objective was to measure the prevalence of CRO and CPO perirectal colonization at hospital unit admission and to use machine learning methods to predict probability of CRO and/or CPO carriage.Methods:We performed an observational cohort study of all patients admitted to the medical intensive care unit (MICU) or solid organ transplant (SOT) unit at The Johns Hopkins Hospital between July 1, 2016 and July 1, 2017. Admission perirectal swabs were screened for CROs and CPOs. More than 125 variables capturing preadmission clinical and demographic characteristics were collected from the electronic medical record (EMR) system. We developed models to predict colonization probabilities using decision tree learning.Results:Evaluating 2,878 admission swabs from 2,165 patients, we found that 7.5% and 1.3% of swabs were CRO and CPO positive, respectively. Organism and carbapenemase diversity among CPO isolates was high. Despite including many characteristics commonly associated with CRO/CPO carriage or infection, overall, decision tree models poorly predicted CRO and CPO colonization (C statistics, 0.57 and 0.58, respectively). In subgroup analyses, however, models did accurately identify patients with recent CRO-positive cultures who use proton-pump inhibitors as having a high likelihood of CRO colonization.Conclusions:In this inpatient population, CRO carriage was infrequent but was higher than previously published estimates. Despite including many variables associated with CRO/CPO carriage, models poorly predicted colonization status, likely due to significant host and organism heterogeneity.

Original languageEnglish (US)
JournalInfection control and hospital epidemiology
DOIs
StatePublished - Jan 1 2019

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Hospital Units
Carbapenems
Enterobacteriaceae
Decision Trees
carbapenemase
Electronic Health Records
Proton Pump Inhibitors
Observational Studies
Intensive Care Units
Inpatients
Cohort Studies

ASJC Scopus subject areas

  • Epidemiology
  • Microbiology (medical)
  • Infectious Diseases

Cite this

@article{a993cdb1e5414ca2aaad0aadc088a7c5,
title = "Predicting probability of perirectal colonization with carbapenem-resistant Enterobacteriaceae (CRE) and other carbapenem-resistant organisms (CROs) at hospital unit admission",
abstract = "Background:Targeted screening for carbapenem-resistant organisms (CROs), including carbapenem-resistant Enterobacteriaceae (CRE) and carbapenemase-producing organisms (CPOs), remains limited; recent data suggest that existing policies miss many carriers.Objective:Our objective was to measure the prevalence of CRO and CPO perirectal colonization at hospital unit admission and to use machine learning methods to predict probability of CRO and/or CPO carriage.Methods:We performed an observational cohort study of all patients admitted to the medical intensive care unit (MICU) or solid organ transplant (SOT) unit at The Johns Hopkins Hospital between July 1, 2016 and July 1, 2017. Admission perirectal swabs were screened for CROs and CPOs. More than 125 variables capturing preadmission clinical and demographic characteristics were collected from the electronic medical record (EMR) system. We developed models to predict colonization probabilities using decision tree learning.Results:Evaluating 2,878 admission swabs from 2,165 patients, we found that 7.5{\%} and 1.3{\%} of swabs were CRO and CPO positive, respectively. Organism and carbapenemase diversity among CPO isolates was high. Despite including many characteristics commonly associated with CRO/CPO carriage or infection, overall, decision tree models poorly predicted CRO and CPO colonization (C statistics, 0.57 and 0.58, respectively). In subgroup analyses, however, models did accurately identify patients with recent CRO-positive cultures who use proton-pump inhibitors as having a high likelihood of CRO colonization.Conclusions:In this inpatient population, CRO carriage was infrequent but was higher than previously published estimates. Despite including many variables associated with CRO/CPO carriage, models poorly predicted colonization status, likely due to significant host and organism heterogeneity.",
author = "Goodman, {Katherine E.} and Patricia Simner and Eili Klein and Kazmi, {Abida Q.} and Avinash Gadala and Toerper, {Matthew F.} and Scott Levin and Pranita Tamma and Clare Rock and Sara Cosgrove and Lisa Maragakis and Aaron Milstone",
year = "2019",
month = "1",
day = "1",
doi = "10.1017/ice.2019.42",
language = "English (US)",
journal = "Infection Control and Hospital Epidemiology",
issn = "0899-823X",
publisher = "University of Chicago Press",

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TY - JOUR

T1 - Predicting probability of perirectal colonization with carbapenem-resistant Enterobacteriaceae (CRE) and other carbapenem-resistant organisms (CROs) at hospital unit admission

AU - Goodman, Katherine E.

AU - Simner, Patricia

AU - Klein, Eili

AU - Kazmi, Abida Q.

AU - Gadala, Avinash

AU - Toerper, Matthew F.

AU - Levin, Scott

AU - Tamma, Pranita

AU - Rock, Clare

AU - Cosgrove, Sara

AU - Maragakis, Lisa

AU - Milstone, Aaron

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Background:Targeted screening for carbapenem-resistant organisms (CROs), including carbapenem-resistant Enterobacteriaceae (CRE) and carbapenemase-producing organisms (CPOs), remains limited; recent data suggest that existing policies miss many carriers.Objective:Our objective was to measure the prevalence of CRO and CPO perirectal colonization at hospital unit admission and to use machine learning methods to predict probability of CRO and/or CPO carriage.Methods:We performed an observational cohort study of all patients admitted to the medical intensive care unit (MICU) or solid organ transplant (SOT) unit at The Johns Hopkins Hospital between July 1, 2016 and July 1, 2017. Admission perirectal swabs were screened for CROs and CPOs. More than 125 variables capturing preadmission clinical and demographic characteristics were collected from the electronic medical record (EMR) system. We developed models to predict colonization probabilities using decision tree learning.Results:Evaluating 2,878 admission swabs from 2,165 patients, we found that 7.5% and 1.3% of swabs were CRO and CPO positive, respectively. Organism and carbapenemase diversity among CPO isolates was high. Despite including many characteristics commonly associated with CRO/CPO carriage or infection, overall, decision tree models poorly predicted CRO and CPO colonization (C statistics, 0.57 and 0.58, respectively). In subgroup analyses, however, models did accurately identify patients with recent CRO-positive cultures who use proton-pump inhibitors as having a high likelihood of CRO colonization.Conclusions:In this inpatient population, CRO carriage was infrequent but was higher than previously published estimates. Despite including many variables associated with CRO/CPO carriage, models poorly predicted colonization status, likely due to significant host and organism heterogeneity.

AB - Background:Targeted screening for carbapenem-resistant organisms (CROs), including carbapenem-resistant Enterobacteriaceae (CRE) and carbapenemase-producing organisms (CPOs), remains limited; recent data suggest that existing policies miss many carriers.Objective:Our objective was to measure the prevalence of CRO and CPO perirectal colonization at hospital unit admission and to use machine learning methods to predict probability of CRO and/or CPO carriage.Methods:We performed an observational cohort study of all patients admitted to the medical intensive care unit (MICU) or solid organ transplant (SOT) unit at The Johns Hopkins Hospital between July 1, 2016 and July 1, 2017. Admission perirectal swabs were screened for CROs and CPOs. More than 125 variables capturing preadmission clinical and demographic characteristics were collected from the electronic medical record (EMR) system. We developed models to predict colonization probabilities using decision tree learning.Results:Evaluating 2,878 admission swabs from 2,165 patients, we found that 7.5% and 1.3% of swabs were CRO and CPO positive, respectively. Organism and carbapenemase diversity among CPO isolates was high. Despite including many characteristics commonly associated with CRO/CPO carriage or infection, overall, decision tree models poorly predicted CRO and CPO colonization (C statistics, 0.57 and 0.58, respectively). In subgroup analyses, however, models did accurately identify patients with recent CRO-positive cultures who use proton-pump inhibitors as having a high likelihood of CRO colonization.Conclusions:In this inpatient population, CRO carriage was infrequent but was higher than previously published estimates. Despite including many variables associated with CRO/CPO carriage, models poorly predicted colonization status, likely due to significant host and organism heterogeneity.

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U2 - 10.1017/ice.2019.42

DO - 10.1017/ice.2019.42

M3 - Article

C2 - 30915928

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JO - Infection Control and Hospital Epidemiology

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SN - 0899-823X

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