ICU care through NGS - Based identification of infectious agents: A comparative study

Area of Science:

• Clinical microbiology and infectious diseases.
• Genomic technologies for pathogen identification.
• Intensive care unit (ICU) diagnostics and patient management.

Background:

• Sepsis is a leading cause of mortality, accounting for 20% of global deaths and a significant proportion of ICU admissions.
• Accurate and rapid diagnosis of causative pathogens in sepsis is challenging due to polymicrobial infections, commensals, and contaminants.
• Traditional methods like culture and PCR have limitations in overcoming these diagnostic complexities.

Purpose of the Study:

• To evaluate the efficacy of Bactfast® and Fungifast® assays as advanced diagnostic tools for non-resolving ICU sepsis.
• To assess the ability of next-generation sequencing (NGS)-based assays to differentiate true pathogens from commensals and contaminants.
• To determine the diagnostic performance of Bactfast® and Fungifast® in a real-world ICU setting.

Main Methods:

• A retrospective study was conducted across four ICUs in Chennai, India.
• Samples were processed using Bactfast® and Fungifast® assays at a central NGS facility.
• Results were correlated with conventional microbiological testing and clinical data by a multidisciplinary team.

Main Results:

• The Bactfast® assay achieved a sensitivity of 94.1% and a specificity of 86.6%, outperforming previous data.
• Bactfast® showed positive correlation with clinical confirmation, indicating reliable pathogen identification.
• Fungifast® demonstrated high specificity (99.4%), but further research is needed due to a low number of positive fungal cultures.

Conclusions:

• Bactfast® offers unbiased pathogen identification, with potential to reduce mortality and morbidity in life-threatening ICU sepsis.
• The NGS-based approach effectively distinguishes pathogens from contaminants and commensals.
• Further investigation of Fungifast® using diverse methodologies and larger sample sizes is warranted to fully evaluate its diagnostic sensitivity.