Molecular Rapid Diagnostic Testing for Bloodstream Infections: Nanopore Targeted Sequencing with Pathogen-Specific Primers

Author:

Han Dongsheng1,Yu Fei1,Zhang Dan1,Hu Juan1,Zhang Xuan1,Xiang Dairong1,Wang Jingchao1,Zheng Jieyuan1,Lou Bin1,Zheng Shufa1,Chen Yu1

Affiliation:

1. the First Affiliated Hospital, Zhejiang University school of Medicine

Abstract

Abstract Background Nanopore sequencing, known for real-time analysis, shows promise for rapid clinical infection diagnosis but lacks effective assays for bloodstream infections (BSIs). Methods We prospectively assessed a novel nanopore targeted sequencing (NTS) assay's performance in identifying pathogens and predicting antibiotic resistance in BSIs, analyzing 387 blood samples from December 2021 to April 2023. Results The positivity rate for NTS (69.5%, 269/387) nearly matches that of metagenomic next-generation sequencing (mNGS) (74.7%, 289/387; p = 0.128) and surpasses the positivity rate of conventional blood culture (BC) (33.9%, 131/387; p < 0.01). Frequent pathogens detected by NTS included Klebsiella pneumoniae (n = 54), Pseudomonas aeruginosa (n = 36), Escherichia coli (n = 36), Enterococcus faecium (n = 30), Acinetobacter baumannii(n = 26), Staphylococcus aureus(n = 23), and Human cytomegalovirus (n = 37). Against a composite BSI diagnostic standard, NTS demonstrated a sensitivity and specificity of 84.0% (95% CI 79.5%-87.7%) and 90.1% (95% CI 81.7%-88.5%), respectively. The concordance between NTS and mNGS results (the percentage of total cases where both either detected BSI-related pathogens or were both negative) was 90.2% (359/387), whereas the consistency between NTS and BC was only 60.2% (233/387). In 80.6% (50/62) of the samples with identical pathogens identified by both NTS tests and BCs, the genotypic resistance identified by NTS correlated with culture-confirmed phenotypic resistance. Using NTS, 95% of samples can be tested and analyzed in approximately 7 hours, allowing for early patient diagnosis. Conclusions NTS is rapid, sensitive, and efficient for detecting BSIs and drug-resistant genes, making it a potential preferred diagnostic tool for early infection identification in critically ill patients.

Publisher

Research Square Platform LLC

Reference37 articles.

1. Burden of bacterial bloodstream infections and recent advances for diagnosis;Costa SP

2. The Healthy Human Blood Microbiome: Fact or Fiction? FRONT CELL INFECT MI 2019 2019-1-1;9;Castillo DJ

3. Improving the recovery and detection of bloodstream pathogens from blood culture. J MED MICROBIOL 2020 2020-6-1;Falconer K

4. Lamy B, Sundqvist M, Idelevich EA. Bloodstream infections – Standard and progress in pathogen diagnostics. CLIN MICROBIOL INFEC 2020 2020-1-1;26(2):142 – 50.

5. Diagnosis of Bloodstream Infections: An Evolution of Technologies towards Accurate and Rapid Identification and Antibiotic Susceptibility Testing. Antibiotics (Basel) 2022 2022-4-12;11(4);Tjandra KC

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