Gene expression-based classifiers identify Staphylococcus aureus infection in mice and humans

Abstract

Staphylococcus aureus causes a spectrum of human infection. Diagnostic delays and uncertainty lead to treatment delays and inappropriate antibiotic use. A growing literature suggests the host's inflammatory response to the pathogen represents a potential tool to improve upon current diagnostics. The hypothesis of this study is that the host responds differently to S. aureus than to E. coli infection in a quantifiable way, providing a new diagnostic avenue. This study uses Bayesian sparse factor modeling and penalized binary regression to define peripheral blood gene-expression classifiers of murine and human S. aureus infection. The murine-derived classifier distinguished S. aureus infection from healthy controls and Escherichia coli-infected mice across a range of conditions (mouse and bacterial strain, time post infection) and was validated in outbred mice (AUC>0.97). A S. aureus classifier derived from a cohort of 94 human subjects distinguished S. aureus blood stream infection (BSI) from healthy subjects (AUC 0.99) and E. coli BSI (AUC 0.84). Murine and human responses to S. aureus infection share common biological pathways, allowing the murine model to classify S. aureus BSI in humans (AUC 0.84). Both murine and human S. aureus classifiers were validated in an independent human cohort (AUC 0.95 and 0.92, respectively). The approach described here lends insight into the conserved and disparate pathways utilized by mice and humans in response to these infections. Furthermore, this study advances our understanding of S. aureus infection; the host response to it; and identifies new diagnostic and therapeutic avenues.

Figure 1. Schematic of derivation and validation cohorts.

The Murine Derivation Cohort includes S. aureus infection (n = 83), healthy control mice (n = 54), and E. coli infection (n = 50). It served as a validation cohort to assess Mouse Strain Effect, S. aureus Genetic Background Effect, Time Course, and to compare S. aureus vs. E. coli and E. coli vs. Healthy. The murine S. aureus classifier was externally validated in Outbred Mice (n = 30) and the CAPSOD Human Cohort. The CAPSOD Human Cohort includes S. aureus BSI (n = 32), healthy volunteers (n = 43), and E. coli BSI (n = 19). It served as a validation cohort to compare S. aureus vs. Healthy, S. aureus vs. E. coli, and E. coli vs. Healthy. Model derivation and validation using the entire cohort of animals or humans is depicted by the blue outline and arrows. An independent classifier was generated using only subjects with S. aureus or E. coli BSI (green outline). This classifier was validated using leave one out cross validation (green arrow). The Human Pediatric Cohort (n = 46 S. aureus, 10 Healthy) used for external validation does not include patients with E. coli infection. Therefore, S. aureus classifiers were generated from the murine and CAPSOD cohorts that excluded E. coli data (red outline and thick red arrow). The Human Pediatric Cohort was used to derive a Human S. aureus vs. Healthy classifier which was validated in the S. aureus-infected and Healthy populations within the murine and CAPSOD human cohorts (thin red arrow).

Figure 2. Murine S. aureus classifier accurately identifies S. aureus infection under a variety of conditions.

Conditions represented include different murine hosts (A), bacterial genetic backgrounds (B), and time from inoculation (C). Animals with S. aureus infection are depicted by a red “x”. Uninfected control mice are depicted by black circles.

Figure 3. The murine S. aureus classifier differentiates S. aureus from E. coli infection.

(A) Inbred mice were tested under three conditions: uninfected controls (black circles), S. aureus infected (red “x”), and E. coli infected (blue triangles). The y-axis represents the predicted probability that a given animal was infected with S. aureus. (B) The murine S. aureus classifier is validated in outbred CD-1 mice where it differentiates S. aureus infection from E. coli infection and uninfected controls.

Figure 4. Performance of the human S. aureus classifier.

(A) The human S. aureus classifier differentiates S. aureus BSI from both uninfected controls and E. coli BSI. (B) A separate classifier was generated using only S. aureus and E. coli-infected human subjects and tested using leave-one-out cross-validation.

Figure 5. Projecting the mouse S. aureus classifier onto human subjects.

The murine S. aureus classifier identifies humans with S. aureus BSI, but does not differentiate S. aureus from E. coli BSI.

Figure 6. Validation in an independent human cohort .

(A) The murine S. aureus classifier differentiates between S. aureus infection and healthy. (B) The human S. aureus classifier differentiates between S. aureus infection and healthy.