Table 3.
Categorizing Impact of Respiratory Metagenomic Results on Antibiotic Prescribing
| Treatment Category | Organisms Identified by RMg* | Antibiotic Changes (n) |
|---|---|---|
| Start or escalate to active antimicrobials (n = 24, 22%) | AmpC Enterobacterales (9), anaerobes (3), Candida spp. (2), P. aeruginosa (3), VRE (1), ESBL K. pneumoniae (1), H. influenza and K. variicola (1),† H. influenza and M. morganii (1), E. faecium (2), and C. striatum (1) | Started: meropenem (10), linezolid (3), linezolid and anidulafungin (1), ciprofloxacin (1), piperacillin–tazobactam (2), ciprofloxacin (1), and other (6) |
| De-escalate or stop (n = 29, 26%) | No significant organisms (29), comprising no organisms (13), Candida spp. (3), URTF (3), anaerobes (3), MSSA (2), K. variicola and H. influenzae (3), E. faecalis (1), and E. coli (1) | Stopped: meropenem (6), piperacillin–tazobactam (4), piperacillin–tazobactam and gentamicin (2), linezolid (1), meropenem and linezolid (4), meropenem and other (5), co-amoxiclav (1), ciprofloxacin (1), levofloxacin (2), and other (3) |
| Prevent escalation, reassure, or inform other therapy (n = 35, 32%) | No significant organisms, comprising no organisms (10), Candida spp. only (3), URTF (2), anaerobes (6), K. pneumoniae (3), other Enterobacterales (4), MSSA (4), Candida spp. (with MSSA) (1), C. striatum (1), and E. faecium (1) | Reassure correct antimicrobial chosen (17), exclude organisms to bring forward immunomodulation (7), exclude untreated organisms in complex or immunosuppressed patients (8), and persistent inflammation on current antibiotics (3) |
| No treatment impact (n = 22, 20%) | No significant organisms: No organisms (11); C. albicans (2); K. pneumoniae (3); other Enterobacterales (3); and 1 each of P. aeruginosa, E. faecalis, and MSSA (3) | Clinical concern prevented deescalation in response to RMg result (6); potential or proven infection at other site (8); delay returning result (4); missed information (resistance) (2); quantity of organism (1); and organism missed (1) |
Definition of abbreviations: ESBL = extended spectrum β-lactamases; MSSA = methicillin-sensitive S. aureus; RMg = respiratory metagenomics; URTF = upper respiratory tract flora; VRE = vancomycin-resistant E. faecium.
Impact categories were as follows: 1) earlier appropriate antimicrobials where the result prompted changes to existing therapy to target the identified organism(s); 2) deescalating antimicrobials where the result contributed to stopping or narrowing antimicrobial spectrum; 3) prevent antimicrobial escalation, reassuring that current therapy was appropriate, or informing nonantimicrobial treatment therapy; and 4) no identified benefit for range of reasons.
Organisms identified by RMg in monomicrobial and polymicrobial LRT samples.
K. variicola and H. influenza were grown, but susceptibilities were not available. H. influenza was resistant to coamoxiclav, but the patient showed improvement and was extubated so the patient completed the 5-day course. Coamoxiclav was started 2 days later.