Host gene expression classifiers diagnose acute respiratory illness etiology

Abstract

Acute respiratory infections caused by bacterial or viral pathogens are among the most common reasons for seeking medical care. Despite improvements in pathogen-based diagnostics, most patients receive inappropriate antibiotics. Host response biomarkers offer an alternative diagnostic approach to direct antimicrobial use. This observational cohort study determined whether host gene expression patterns discriminate noninfectious from infectious illness and bacterial from viral causes of acute respiratory infection in the acute care setting. Peripheral whole blood gene expression from 273 subjects with community-onset acute respiratory infection (ARI) or noninfectious illness, as well as 44 healthy controls, was measured using microarrays. Sparse logistic regression was used to develop classifiers for bacterial ARI (71 probes), viral ARI (33 probes), or a noninfectious cause of illness (26 probes). Overall accuracy was 87% (238 of 273 concordant with clinical adjudication), which was more accurate than procalcitonin (78%, P < 0.03) and three published classifiers of bacterial versus viral infection (78 to 83%). The classifiers developed here externally validated in five publicly available data sets (AUC, 0.90 to 0.99). A sixth publicly available data set included 25 patients with co-identification of bacterial and viral pathogens. Applying the ARI classifiers defined four distinct groups: a host response to bacterial ARI, viral ARI, coinfection, and neither a bacterial nor a viral response. These findings create an opportunity to develop and use host gene expression classifiers as diagnostic platforms to combat inappropriate antibiotic use and emerging antibiotic resistance.

Fig. 1. Experimental flow

A cohort of patients encompassing bacterial ARI, viral ARI, or non-infectious illness was used to develop classifiers of each condition. This combined ARI classifier was validated using leave-one-out cross-validation and compared to three published classifiers of bacterial vs. viral infection. The combined ARI classifier was also externally validated in six publically available datasets. In one experiment, healthy volunteers were included in the training set to determine their suitability as “no-infection” controls. All subsequent experiments were performed without the use of this healthy subject cohort.

Fig. 2. Evaluation of healthy adults as a no-infection control

Classifiers of bacterial ARI, viral ARI, and no infection as represented by healthy controls were generated and applied using leave-one-out cross-validation. Each patient, represented along the horizontal axis, is assigned three distinct probabilities: bacterial ARI (black triangle), viral ARI (blue circle), and no infection (green square). The group on the right represents subjects with non-infectious illness.

Fig. 3. Leave-one-out cross-validation

Classifiers of bacterial ARI, viral ARI, and no infection as represented by non-infectious illness were generated and applied using leave-one-out cross-validation. Each patient, represented along the horizontal axis, is assigned probabilities of having bacterial ARI (black triangle), viral ARI (blue circle), and non-infectious illness (red square). Patients clinically adjudicated as having bacterial ARI, viral ARI, or non-infectious illness are presented in the top, center, and bottom panels, respectively.

Fig. 4. Classifier performance in patients with co-infection defined by the identification of bacterial and viral pathogens

Bacterial and Viral ARI classifiers were trained on subjects with bacterial (N=22) or viral (N=71) infection (GSE60244). This same dataset also included 25 subjects with bacterial/viral co-infection. Bacterial and viral classifier predictions were normalized to the same scale. Each subject receives two probabilities: that of a bacterial ARI host response and a viral ARI host response. A probability score of 0.5 or greater was considered positive. Subjects 1-6 have a bacterial host response. Subjects 7-9 have both bacterial and viral host responses. Subjects 10-23 have a viral host response. Subjects 24-25 do not have bacterial or viral host responses.