Abstract
Etiologic diagnosis of bacterial pneumonia relies on identification of causative pathogens by cultures, which require extended incubation periods and have limited sensitivity. Next-generation sequencing of microbial DNA directly from patient samples may improve diagnostic accuracy for guiding antibiotic prescriptions. In this study, we hypothesized that enhanced pathogen detection using sequencing can improve upon culture-based diagnosis and that certain sequencing profiles correlate with host response. We prospectively collected endotracheal aspirates and plasma within 72 h of intubation from patients with acute respiratory failure. We performed 16S rRNA gene sequencing to determine pathogen abundance in lung samples and measured plasma biomarkers to assess host responses to detected pathogens. Among 56 patients, 12 patients (21%) had positive respiratory cultures. Sequencing revealed lung communities with low diversity (p < 0.02) dominated by taxa (>50% relative abundance) corresponding to clinically isolated pathogens (concordance p = 0.009). Importantly, sequencing detected dominant pathogens in 20% of the culture-negative patients exposed to broad-spectrum empiric antibiotics. Regardless of culture results, pathogen dominance correlated with increased plasma markers of host injury (receptor of advanced glycation end-products-RAGE) and inflammation (interleukin-6, tumor necrosis factor receptor 1-TNFR1) (p < 0.05), compared to subjects without dominant pathogens in their lung communities. Machine-learning algorithms identified pathogen abundance by sequencing as the most informative predictor of culture positivity. Thus, enhanced detection of pathogenic bacteria by sequencing improves etiologic diagnosis of pneumonia, correlates with host responses, and offers substantial opportunity for individualized therapeutic targeting and antimicrobial stewardship. Clinical translation will require validation with rapid whole meta-genome sequencing approaches to guide real-time antibiotic prescriptions.
Highlights
Severe pneumonia is a leading cause of hospitalization and death among adults in the US, often requiring admission to an intensive care unit (ICU) (Chalmers et al, 2011; Barrett et al, 2014; Jain et al, 2015; Valley et al, 2015)
We considered microbiologic cultures of respiratory specimens [sputum, endotracheal aspirates (ETAs), or bronchoalveolar lavage – (BAL)] as positive when pathogenic bacterial species had been isolated by the clinical laboratory and treating physicians covered these bacteria with antibiotics
Our prospective study in mechanically ventilated patients provides the largest examination to date of the clinical validity of Next-generation sequencing (NGS) for etiologic diagnosis of index severe pneumonia
Summary
Severe pneumonia is a leading cause of hospitalization and death among adults in the US, often requiring admission to an intensive care unit (ICU) (Chalmers et al, 2011; Barrett et al, 2014; Jain et al, 2015; Valley et al, 2015). Antibiotic prescriptions for severe pneumonia are empiric and typically include two or three broad-spectrum agents prescribed for seven or more days (Mandell et al, 2007; Kalil et al, 2016). This “onesize-fits-all” practice is hazardous for individual patients, who may receive insufficient or disproportionately intense antibiotics, and further contributes to antibiotic resistance, a global health threat (Laxminarayan et al, 2013; Modi et al, 2014; Kitsios et al, 2017). Despite the theoretical advantages of NGS, the technology has not yet been validated as a diagnostic tool to guide antimicrobial prescriptions in the ICU
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