生物
病菌
DNA提取
微生物学
抗药性
抗生素耐药性
聚合酶链反应
金标准(测试)
临床微生物学
基因组DNA
核酸
血培养
计算生物学
DNA
基因
抗生素
遗传学
医学
内科学
作者
Qian Li,Wenhua Huang,Shengwei Zhang,Yinan Zheng,Qingyu Lv,Decong Kong,Lei Zhang,Yan Zhang,Zhihu Zhao,Miaoyu Wang,Hua Jiang,Peng Liu,Yongqiang Jiang
标识
DOI:10.1016/j.mimet.2021.106391
摘要
Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accurate identification of bacteria, fungi, and antimicrobial resistance determinants directly from blood samples. In this study, we included removal of human genomic DNA during nucleic acid extraction, optimized the target sequence set and drug resistance genes, performed antimicrobial resistance profiling of clinical isolates, and evaluated mock specimens and clinical samples by ADS. ADS successfully identified pathogens at the species-level in 36 h, from nucleic acid extraction to results. Besides pathogen identification, ADS can also present drug resistance profiles. ADS enabled detection of all bacteria and accurate identification of 47 pathogens. In 20 spiked samples and 8 clinical specimens, ADS detected at least 92.81% of reads mapped to pathogens. ADS also showed consistency with the three culture-negative samples, and correctly identified pathogens in four of five culture-positive clinical blood specimens. This Ampliseq-based technology promises broad coverage and accurate pathogen identification, helping clinicians to accurately diagnose and treat bloodstream infections.
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