Journal Article

Comparing NGS-Based identification of bloodstream infections to traditional culture methods for enhanced ICU care: a comprehensive study

Chauhan, Varun, Li, Chenxi, Chen, Huaisheng, Luo, Yutian, Sharma, Sonu, Wang, Wei

2024

Overview

Accurate identification of infectious diseases using molecular techniques, such as PCR and NGS, is well-established. This study aims to assess the utility of Bactfast and Fungifast in diagnosing bloodstream infections in ICU settings, comparing them against traditional culture methods. The objectives include evaluating sensitivity and specificity and identifying a wide range of pathogens, including non-culturable species. We collected 500 non-duplicate blood samples from ICU patients between January 2023 and December 2023. Specimens underwent traditional culture, MALDI-TOF, VITEK 2 compact system, and NGS-based Bactfast and Fungifast analyses. Out of the 500 samples, 26.8% (n=134) showed bacterial growth via traditional culture methods, while 4.8% (n=24) were positive for fungal growth. MALDI-TOF and VITEK 2 compact system yielded comparable results, identifying 26.4% (n=132) of specimens with bacterial growth. NGS-based Bactfast detected bacterial presence in 38.2% (n=191) of samples, including non-culturable bacteria missed by traditional methods. However, NGS-based Fungifast showed concordant fungal detection rates with culture methods. Among identified pathogens by culture method included 20.89% (n=28), 18.65% (n=25), 15.67% (n=21), 12.68% (n=17), 10.44% (n=14), various species 7.46% (n=10), 6.71% (n=9), 4.47% (n=6), and 2.98% (n=4). Non-culture-based NGS identified additional (n=33) pathogens, including 27.27% (n=9), 21.21% (n=7), 15.15% (n=5), 12.12% (n=4), 9% (n=3), 9% (n=3), and 6% (n=2). was reported in 5% (n=24) of samples by both methods. NGS-based Bactfast and Fungifast demonstrate high sensitivity in identifying a wide array of bacterial and fungal pathogens in ICU patients, outperforming traditional culture methods in detecting non-culturable organisms. These molecular assays offer rapid and comprehensive diagnostic capabilities, potentially improving clinical outcomes through timely and accurate pathogen identification.

• Publisher: Frontiers Media SA,Frontiers Media S.A
• Subject: Accuracy / Adult / Aged / Antibiotics / Bacteremia - diagnosis / Bacteremia - microbiology / Bacteria / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Bactfast and Fungifast / Blood Culture - methods / bloodstream infections (BSIs) / Cellular and Infection Microbiology / Chronic illnesses / Clinical outcomes / Critical Care - methods / Female / Fungi - classification / Fungi - genetics / Fungi - isolation & purification / Hematological diseases / High-Throughput Nucleotide Sequencing - methods / Humans / ICU pathogen identification / Identification / Infectious diseases / Intensive Care Units / Klebsiella pneumoniae / Laboratories / Male / Middle Aged / Molecular Diagnostic Techniques - methods / molecular diagnostics / NGS-based identification in bloodstream infection next-generation sequencing (NGS) / Nosocomial infections / Pathogens / Patients / Sensitivity analysis / Sensitivity and Specificity / Sepsis - diagnosis / Sepsis - microbiology / Software / Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods