The host response to infection: advancing a novel diagnostic paradigm

Current and Future Opportunities for Rapid Diagnostics in Antimicrobial Stewardship

Rapid diagnostic testing has improved clinical care of patients with infectious syndromes when combined with antimicrobial stewardship. The authors review the current data on antimicrobial stewardship and rapid diagnostic testing in bloodstream, respiratory tract, and gastrointestinal tract infections. Evidence for the potential benefit of rapid tests in bloodstream infections seems strong, respiratory tract infections mixed, and gastrointestinal tract infections still evolving. The authors also review future directions in rapid diagnostic testing and suggest areas of focus for antimicrobial stewardship efforts.

The potential role of exhaled breath analysis in the diagnostic process of pneumonia-a systematic review

Diagnostic strategies currently used for pneumonia are time-consuming, lack accuracy and suffer from large inter-observer variability. Exhaled breath contains thousands of volatile organic compounds (VOCs), which include products of host and pathogen metabolism. In this systematic review we investigated the use of so-called 'breathomics' for diagnosing pneumonia. A Medline search yielded 18 manuscripts reporting on animal and human studies using organic and inorganic molecules in exhaled breath, that all could be used to answer whether analysis of VOC profiles could potentially improve the diagnostic process of pneumonia. Papers were categorised based on their specific aims; the exclusion of pneumonia; the detection of specific respiratory pathogens; and whether targeted or untargeted VOC analysis was used. Ten studies reported on the association between VOCs and presence of pneumonia. Eight studies demonstrated a difference in exhaled VOCs between pneumonia and controls; in the individual studies this discrimination was based on unique sets of VOCs. Eight studies reported on the accuracy of a breath test for a specific respiratory pathogen: five of these concerned pre-clinical studies in animals. All studies were valued as having a high risk of bias, except for one study that used an external validation cohort. The findings in the identified studies are promising. However, as yet no breath test has been shown to have sufficient diagnostic accuracy for pneumonia. We are in need of studies that further translate the knowledge from discovery studies to clinical practice.

Anomaly Detection in Host Signaling Pathways for the Early Prognosis of Acute Infection

Clinical diagnosis of acute infectious diseases during the early stages of infection is critical to administering the appropriate treatment to improve the disease outcome. We present a data driven analysis of the human cellular response to respiratory viruses including influenza, respiratory syncytia virus, and human rhinovirus, and compared this with the response to the bacterial endotoxin, Lipopolysaccharides (LPS). Using an anomaly detection framework we identified pathways that clearly distinguish between asymptomatic and symptomatic patients infected with the four different respiratory viruses and that accurately diagnosed patients exposed to a bacterial infection. Connectivity pathway analysis comparing the viral and bacterial diagnostic signatures identified host cellular pathways that were unique to patients exposed to LPS endotoxin indicating this type of analysis could be used to identify host biomarkers that can differentiate clinical etiologies of acute infection. We applied the Multivariate State Estimation Technique (MSET) on two human influenza (H1N1 and H3N2) gene expression data sets to define host networks perturbed in the asymptomatic phase of infection. Our analysis identified pathways in the respiratory virus diagnostic signature as prognostic biomarkers that triggered prior to clinical presentation of acute symptoms. These early warning pathways correctly predicted that almost half of the subjects would become symptomatic in less than forty hours post-infection and that three of the 18 subjects would become symptomatic after only 8 hours. These results provide a proof-of-concept for utility of anomaly detection algorithms to classify host pathway signatures that can identify presymptomatic signatures of acute diseases and differentiate between etiologies of infection. On a global scale, acute respiratory infections cause a significant proportion of human co-morbidities and account for 4.25 million deaths annually. The development of clinical diagnostic tools to distinguish between acute viral and bacterial respiratory infections is critical to improve patient care and limit the overuse of antibiotics in the medical community. The identification of prognostic respiratory virus biomarkers provides an early warning system that is capable of predicting which subjects will become symptomatic to expand our medical diagnostic capabilities and treatment options for acute infectious diseases. The host response to acute infection may be viewed as a deterministic signaling network responsible for maintaining the health of the host organism. We identify pathway signatures that reflect the very earliest perturbations in the host response to acute infection. These pathways provide a monitor the health state of the host using anomaly detection to quantify and predict health outcomes to pathogens.

Lessons from the Ebola Outbreak: Action Items for Emerging Infectious Disease Preparedness and Response

As the Ebola outbreak in West Africa wanes, it is time for the international scientific community to reflect on how to improve the detection of and coordinated response to future epidemics. Our interdisciplinary team identified key lessons learned from the Ebola outbreak that can be clustered into three areas: environmental conditions related to early warning systems, host characteristics related to public health, and agent issues that can be addressed through the laboratory sciences. In particular, we need to increase zoonotic surveillance activities, implement more effective ecological health interventions, expand prediction modeling, support medical and public health systems in order to improve local and international responses to epidemics, improve risk communication, better understand the role of social media in outbreak awareness and response, produce better diagnostic tools, create better therapeutic medications, and design better vaccines. This list highlights research priorities and policy actions the global community can take now to be better prepared for future emerging infectious disease outbreaks that threaten global public health and security.