Comprehensive analysis of microorganisms in severe septic patients in the intensive care unit by mNGS and microbial culture

BACKGROUND: Severe sepsis is a life-threatening condition involving dysregulated systemic inflammatory responses and acute organ dysfunctions. Timely and accurate pathogen identification is critical for the effective treatment of severe septic patients in the intensive care unit (ICU). Although metagenomic next-generation sequencing (mNGS) enables the sensitive and unbiased detection of pathogens, its clinical implications in identification of causative pathogens, the association with the outcomes and the development of treatment regimens in such patients remain underexplored. METHODS: 184 clinical samples were collected from 81 severe septic patients and subjected to mNGS analysis. Blood and bronchoalveolar lavage fluid (BAL) samples were collected from the majority of patients, while sputum, cerebrospinal fluid (CSF), pleural effusion (PE), ascites, urine, hydropericardium (HPC) and blister effusion (BE) samples were also collected from select patients. Microorganisms were detected by DNA and RNA mNGS and the top 5 microorganisms detected by mNGS in each sample were used for analysis. Microbes were isolated from most patients and the isolates were tested for drug susceptibility. RESULTS: mNGS identified 183 top 5 microorganisms, with bacteria (92.3%), viruses (3.3%) and fungi (2.7%) as the major detected microbes. Among them, 40, 98 and 45 were pathogenic (21.9%), opportunistic (53.6%) and non-pathogenic (24.6%), respectively. Significantly more pathogenic microbes were detected in the sputum (83.3%) and the bronchoalveolar lavage fluid (BAL; 75.0%) than the blood (36.1%) by RNA mNGS (87.4%) than DNA mNGS (58.2%). Patients having the top-1 pathogenic microorganism detected by DNA mNGS or 4-5 pathogenic microorganisms detected by RNA mNGS had a poor association with clinical outcomes. Moreover, detection of R. pickettii, C. difficile and S. enterica were significantly associated with high mortality. The majority of patients (89.5%) were positive for microbial cultures. Each of these patients had at least one drug-resistant organism and nearly half (45.1%) were infected with two or more drug-resistant strains. CONCLUSIONS: Detection of predominant pathogenic microorganisms or particular bacteria in the sputum or BAL samples by mNGS are associated with poor clinical outcomes among severe septic patients in ICU in this cohort. The high prevalence of multidrug-resistant bacteria among these patients underscores the importance of integration of mNGS with antimicrobial susceptibility assessment in the clinical practice to develop the most effective treatment regimens.