BACKGROUND: Metagenomic next-generation sequencing (mNGS) is an effective method for detecting pathogenic pathogens of bloodstream infection (BSI). However, there is no consensus on whether the use of antibiotics affects the diagnostic performance of mNGS. We conducted a prospective clinical study aiming to evaluate the effect of antimicrobial treatment on mNGS. METHODS: Blood samples were collected for mNGS testing within 24 h of culture-confirmed with BSI, with re-examination conducted every 2-3 days. RESULTS: A total of 38 patients with BSI were enrolled. The mNGS positive (mNGS-pos) rate declined sharply after the use of antibiotics, with only 17 (44.78%) patients remaining mNGS-pos while the rest were mNGS negative (mNGS-neg). The median duration of pathogen identification was significantly longer for mNGS compared to blood culture (BC) (4 days vs 1 days
P <
0.0001). A positivity duration of ≥ 3 days was an independent risk factor of septic shock (OR, 20.671
95% CI, 1.958-218.190
P = 0.012). Patients with mNGS-pos and mNGS-neg differed by the median duration of fever (6 days vs 3 days
P = 0.038), rates of drug resistance (35.3% vs 4.8%
P = 0.017), rates of septic shock (47.1% vs 14.3%
P = 0.029), and 28-day mortality (29.4% vs 4.8%
P = 0.041). CONCLUSIONS: The antimicrobial treatment will greatly reduce the positive rate of mNGS. The duration of mNGS is significantly longer than that of BC. The prolonged duration of mNGS suggests an increased risk of septic shock and could be identified as a high-risk factor of adverse infection outcome, requiring more aggressive anti-infective treatment measures.