Improved Detection of Culprit Pathogens by Bacterial DNA Sequencing Affects Antibiotic Management Decisions in Severe Pneumonia

Abstract

Patient: Male, 21Final Diagnosis: Bacterial pneumoniaSymptoms: Cough • feverMedication: —Clinical Procedure: —Specialty: Critical Care MedicineObjective:Unusual clinical courseBackground:Severe pneumonia requiring admission to an intensive care unit carries high morbidity and mortality. Evidence-based management includes early administration of empiric antibiotics against plausible bacterial pathogens while awaiting results of microbiologic cultures. However, in over 60% of pneumonia cases, no causative pathogen is identified with conventional diagnostic techniques. In this case report, we demonstrate how direct-from-sample sequencing of bacterial DNA could have identified the multiple culprit pathogens early in the disease course to guide appropriate antibiotic management.Case Report:A previously healthy, 21-year-old man presented with neck pain and fever and rapidly developed acute respiratory distress syndrome (ARDS) requiring mechanical ventilation. He was started on broad-spectrum antibiotics and was found to have septic thrombophlebitis of the left internal jugular vein (Lemierre syndrome), with blood cultures growing Fusobacterium necrophorum. While his antibiotics were narrowed to piperacillin-tazobactam monotherapy, his clinical condition worsened, but repeated efforts to define an additional/alternative respiratory pathogen resulted in negative cultures. He eventually developed bilateral empyemas growing Mycoplasma hominis. Once azithromycin was added to the patient’s regimen, he improved dramatically. Retrospective sequencing of consecutive endotracheal aspirates showed Fusobacterium as the dominant pathogen early in the course, but with significant and increasing Mycoplasma abundance several days prior to clinical detection.Conclusions:Had sequencing information been available to the treating clinicians, the causative pathogens could have been detected earlier, guiding appropriate antibiotic therapy and perhaps preventing his clinical complications. Real-time bacterial DNA sequencing has the potential to shift the diagnostic paradigm in severe pneumonia.

Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study

“…Nanopore sequencing had good concordance with cultures by detecting high abundance of the causative pathogenic bacteria in culture-positive cases, but also revealed profiles with low abundance of typical respiratory pathogens in selected culture-negative cases with clinical suspicion of bacterial pneumonia. Nanopore metagenomic sequencing holds promise as a potential diagnostic tool due to its comprehensive scope, in-depth resolution with long read sequencing and real-time data generation [6]. However, contaminating human DNA has been a rate-limiting step for clinical implementation.…”

“…Recently developed rapid polymerase-chain reaction (PCR) tests represent a significant advancement in the field [4], but these tests can only detect the presence/absence of selected panels of pathogens, and thus are not comprehensive enough in breadth or resolution. Cultureindependent methods using next-generation sequencing of microbial communities may help overcome the limitations of current diagnostic testing [5][6][7].…”

Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever

“…Identification of organisms, especially from non-sterile sites such as sputum, may simply represent commensal colonization rather than infection. As demonstrated here and by others, unbiased metagenomic sequencing can be used to characterize complex disease landscapes, especially for diagnostically challenging pulmonary diseases in which multiple organisms contribute to a pathogenic microbiome [23, 24]. In addition to being unbiased, direct sequencing from blood is less invasive than routine bronchoscopy, mitigating associated procedural risks.…”

Metagenomic identification of severe pneumonia pathogens with rapid Nanopore sequencing in mechanically-ventilated patients

“…Recently developed rapid polymerase-chain reaction (PCR) tests represent a significant advancement in the field (4), but these tests can only detect the presence/absence of selected panels of pathogens, and thus are not comprehensive enough in breadth or resolution. Culture-independent methods using next-generation sequencing of microbial communities may help overcome the limitations of current diagnostic testing (5)(6)(7).…”