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ORIGINAL RESEARCH article

Front. Cell. Infect. Microbiol.
Sec. Clinical Infectious Diseases
Volume 14 - 2024 | doi: 10.3389/fcimb.2024.1454549
This article is part of the Research Topic Targeted Next-Generation Sequencing for Pathogen and Antimicrobial Resistance (AMR) Identification and Profiling View all articles

Comparing NGS-Based Identification of Bloodstream Infections to Traditional Culture Methods for Enhanced ICU Care: A Comprehensive Study

Provisionally accepted
Wei Wang Wei Wang 1Varun Chauhan Varun Chauhan 2Yutian Luo Yutian Luo 1Sonu Sharma Sonu Sharma 3Chenxi Li Chenxi Li 1Huai-Sheng Chen Huai-Sheng Chen 1*
  • 1 Shenzhen People's Hospital, Jinan University, Shenzhen, China
  • 2 Department of Medical Parasitology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, Haryana, India
  • 3 School of Phrmaceutical and Populations Health Informatics, DIT University, Dehradun, India

The final, formatted version of the article will be published soon.

    Background: 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.Results: 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 Klebsiella pneumoniae 20.89% (n=28), Enterococcus faecalis 18.65% (n=25), Escherichia coli 15.67% (n=21), Pseudomonas aeruginosa 12.68% (n=17), Acinetobacter baumannii 10.44% (n=14), various Streptococcus species 7.46% (n=10), Mycobacterium tuberculosis 6.71% (n=9), Mycobacterium abscessus 4.47% (n=6), and Salmonella spp 2.98% (n=4). Non-culturebased NGS identified additional (n=33) pathogens, including Klebsiella pneumoniae 27.27% (n=9), Bacteroides fragilis 21.21% (n=7), Aerococcus viridans 15.15% (n=5), Elizabethkingia anopheles 12.12% (n=4), Aeromonas salmonicida 9% (n=3), Clostridium 9% (n=3), and Bacteroides vulgatus 6% (n=2). Candida albicans was reported in 5% (n=24) of samples by both methods. Conclusion: 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.

    Keywords: NGS-Based Identification in bloodstream infection Next-Generation Sequencing (NGS), Bloodstream infections (BSIs), Molecular diagnostics, ICU Pathogen Identification, Bactfast and Fungifast

    Received: 25 Jun 2024; Accepted: 26 Aug 2024.

    Copyright: © 2024 Wang, Chauhan, Luo, Sharma, Li and Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Huai-Sheng Chen, Shenzhen People's Hospital, Jinan University, Shenzhen, China

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