Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study.
Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study.
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使用鸟枪法宏基因组测序和常规培养鉴定传染病病原体：比较研究
作者：
Chen H;Li J;Yan S;Sun H;Tan C;Liu M;Liu K;Zhang H;Zou M;Xiao X
早期和准确的微生物诊断对于优化抗菌治疗非常重要。鸟枪式宏基因组测序技术是一种无偏见的、全面的病原体鉴定方法，在传染病的诊断中可能有助于甚至取代传统的微生物学方法。然而，该平台的临床应用证据相对有限。为评价鸟枪法宏基因组测序技术在临床应用中的可行性，对20例疑似感染患者的PCR阳性体液标本进行鸟枪法宏基因组测序和常规培养。然后利用生物信息学管道对测序数据进行分析，用于微生物的分类鉴定和抗生素抗性基因预测。鸟枪宏基因组测序结果显示，在细菌检测中与培养结果的一致性为17/20，在真菌检测中与培养结果的一致性为20/20。此外，抗生素耐药基因注释的耐药类型与药敏试验鉴定的抗生素类别具有很大的相似性，超过一半的标本在鸟枪法宏基因组测序和培养结果之间具有一致的药物类型。鸟枪法宏基因组测序鉴定病原体和预测耐药基因对感染性疾病中微生物的诊断具有潜在意义，特别是对多种微生物合并感染和标准培养方法无法鉴定微生物的情况有帮助。
Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.
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影响因子：
3.7
作者：
Abayasekara LM;Perera J;Chandrasekharan V;Gnanam VS;Udunuwara NA;Liyanage DS;Bulathsinhala NE;Adikary S;Aluthmuhandiram JVS;Thanaseelan CS;Tharmakulasingam DP;Karunakaran T;Ilango J
通讯作者：
Ilango J
影响因子：
12.3
作者：
Grumaz S;Stevens P;Grumaz C;Decker SO;Weigand MA;Hofer S;Brenner T;von Haeseler A;Sohn K
通讯作者：
Sohn K
通过宏基因组下一代测序检测术前少量抽吸滑液中细菌的存在
影响因子：
8.4
作者：
Fang, Xinyu;Cai, Yuanqing;Guan, Zhenpeng
通讯作者：
Guan, Zhenpeng
影响因子：
4.6
作者：
Couto N;Schuele L;Raangs EC;Machado MP;Mendes CI;Jesus TF;Chlebowicz M;Rosema S;Ramirez M;Carriço JA;Autenrieth IB;Friedrich AW;Peter S;Rossen JW
通讯作者：
Rossen JW
影响因子：
7
作者：
Naccache SN;Federman S;Veeraraghavan N;Zaharia M;Lee D;Samayoa E;Bouquet J;Greninger AL;Luk KC;Enge B;Wadford DA;Messenger SL;Genrich GL;Pellegrino K;Grard G;Leroy E;Schneider BS;Fair JN;Martínez MA;Isa P;Crump JA;DeRisi JL;Sittler T;Hackett J Jr;Miller S;Chiu CY
通讯作者：
Chiu CY