Table 3.
Patient diagnoses and results of clinical microbiology testing for bacterial and viral pathogens
| No. | PNA Group | Diagnosis | Single vs. Polymicrobial | Microbe(s) Detected by Culture | Rank, TA | Rank, mBAL |
|---|---|---|---|---|---|---|
| 209 | PNA-pos | Community-acquired pneumonia | Polymicrobial | Haemophilus | 1 | 1 |
| Streptococcus | 2 | 2 | ||||
| 212 | PNA-pos | Hospital-acquired pneumonia | Polymicrobial | Staphylococcus | 2 | 1 |
| 213 | PNA-pos | Ventilator-associated pneumonia | Polymicrobial | Escherichia | 1 | 1 |
| Klebsiella | 4 | 5 | ||||
| 225 | PNA-pos | Community-acquired pneumonia | Single microbe | Staphylococcus | 1 | 1 |
| 232 | PNA-pos | Community-acquired pneumonia | Single microbe | Klebsiella | 1 | 1 |
| 251 | PNA-pos | Community-acquired pneumonia | Single microbe | Klebsiella | 1 | 1 |
| 252 | PNA-pos | Community-acquired pneumonia | Polymicrobial | Streptococcus | 1 | 1 |
| Enterobacter | 4 | 3 | ||||
| Staphylococcus | 7 | * | ||||
| 257 | PNA-pos | Hospital-acquired pneumonia | Single microbe | Enterobacter | 1 | 1 |
| 268 | PNA-pos | Community-acquired pneumonia | Polymicrobial | Pseudomonas | 1 | 1 |
| Stenotrophomonas | 2 | 2 | ||||
| 278 | PNA-pos | Hospital-acquired pneumonia | Single microbe | Moraxella | 1 | 1 |
| 288 | PNA-pos | Community-acquired pneumonia | Single microbe | Staphylococcus | 1 | 2 |
| 289 | PNA-pos | Community-acquired pneumonia | Single microbe | Staphylococcus | 2 | 2 |
| 290 | PNA-pos | Community-acquired pneumonia | Single microbe | Moraxella | 1 | 1 |
| 297 | PNA-pos | Hospital-acquired pneumonia | Polymicrobial | Enterobacter | 1 | 1 |
| Morganella | 2 | 2 | ||||
| Klebsiella | 3 | 3 | ||||
| Pseudomonas | 5 | 5 | ||||
| 298 | PNA-pos | Community-acquired pneumonia | Single microbe | Enterobacter | 1 | 1 |
| No. | PNA Group | Diagnosis | Microbe(s) Detected by Culture or PCR | |||
| 208 | PNA-neg | Septic shock due to Enterococcus bacteremia | ||||
| 211 | PNA-neg | Acute myocardial infarction | ||||
| 215 | PNA-neg | Craniotomy for resection of arteriovenous malformation | ||||
| 218 | PNA-neg | Small bowel obstruction, pancreatitis, and hypoxic respiratory failure | ||||
| 220 | PNA-neg | Elective craniotomy for aneurysm bypass surgery | ||||
| 221 | PNA-neg | Seizure | ||||
| 227 | PNA-neg | Hemorrhagic shock and PEA cardiac arrest | ||||
| 256 | PNA-neg | Status after heart transplant with suspected drug-related fever | ||||
| 261 | PNA-neg | Volume overload secondary to constrictive pericarditis | ||||
| 273 | PNA-neg | Hemorrhagic stroke | ||||
| 319 | PNA-neg | Status after balloon angioplasty of hepatic artery | ||||
| 331 | PNA-neg | Acute liver failure secondary to portal vein thrombosis | ||||
| 202 | PNA-ind | MSSA bacteremia, septic shock, and suspected pneumonia | ||||
| 204 | PNA-ind | Osteomyelitis and hypercarbic respiratory failure | ||||
| 205 | PNA-ind | Community-acquired pneumonia | Rhinovirus | |||
| 214 | PNA-ind | Intracranial hemorrhage | ||||
| 216 | PNA-ind | COPD exacerbation with hypercarbic respiratory failure and suspected pneumonia | ||||
| 217 | PNA-ind | Hypoxic respiratory failure and suspected pneumonia | ||||
| 226 | PNA-ind | Hypoxic respiratory failure and suspected pneumonia | ||||
| 228 | PNA-ind | Community-acquired pneumonia | RSV | |||
| 229 | PNA-ind | Altered mental status, septic shock, and suspected pneumonia | ||||
| 234 | PNA-ind | Severe sepsis and hypoxia with urinary tract infection | ||||
| 235 | PNA-ind | Acute renal failure, shock, hypoxic respiratory failure, and suspected pneumonia | ||||
| 236 | PNA-ind | Aspiration secondary to altered mental status | ||||
| 237 | PNA-ind | Seizure, hypernatremia, and suspected pneumonia | ||||
| 238 | PNA-ind | Hypoxemic and hypercarbic respiratory failure following PEA arrest | ||||
| 245 | PNA-ind | Seizure, altered mental status, and suspected aspiration | ||||
| 246 | PNA-ind | Hypoxic respiratory failure and suspected pneumonia | ||||
| 254 | PNA-ind | Respiratory failure, shock, and suspected pneumonia | ||||
| 255 | PNA-ind | Status after aortic valve repair | ||||
| 258 | PNA-ind | Subarachnoid hemorrhage | ||||
| 263 | PNA-ind | Altered mental status and hypoxic respiratory failure | ||||
| 272 | PNA-ind | Sepsis with possible aspiration pneumonia | ||||
| 274 | PNA-ind | Altered mental status following perioperative intubation | ||||
| 295 | PNA-ind | Community-acquired pneumonia | RSV | |||
| 301 | PNA-ind | Acute respiratory distress syndrome | ||||
| 325 | PNA-ind | Hypoxic respiratory failure |
For patients with positive clinical microbiology results, the rank of each bacterial genus based on abundance (reads per million reads mapped, rpM) of sequencing reads in matched mini-bronchial alveolar lavage or tracheal aspirate specimens is listed. Samples for which clinical diagnostics returned polymicrobial cultures contain multiple lines and are noted as polymicrobial. COPD, chronic obstructive pulmonary disease; MSSA, methicillin-sensitive Staphylococcus aureus; PEA, pulseless electrical activity; PNA-ind, acute respiratory illnesses of indeterminate etiology including patients with negative bacterial cultures but suspected bacterial pneumonia based on clinical criteria alone; PNA-neg, subjects with a clear alternative noninfectious etiology of acute respiratory failure; PNA-pos, clinically identified pneumonia with a positive bacterial culture; RSV, respiratory syncytial virus.
Present at <1% relative abundance.