Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study.
Detection of bacterial pathogens from clinical specimens using conventional microbial culture and 16S metagenomics: a comparative study.
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利用传统微生物培养法与16S宏基因组学方法从临床标本中检测细菌病原体的对比研究。
DOI：
10.1186/s12879-017-2727-8
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发表时间：
2017-09-19
影响因子：
3.7
通讯作者：
Ilango J
中科院分区：
文献类型：
--
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
传染病是世界范围内死亡的主要原因，多微生物和真菌感染的诊断在临床环境中越来越具有挑战性。传统上，分子检测仍然是临床样品中物种鉴定的最佳方法。然而，Sanger测序的局限性使得多微生物感染的诊断成为治疗的最大障碍之一。大规模平行测序或下一代测序（NGS）的发展彻底改变了宏基因组学领域，广泛应用于环境源、人体肠道等微生物群落的鉴定。然而，到目前为止，这项技术还没有在传染病诊断方面的商业应用。Credence Genomics快速感染检测™测试是一种基于分子的诊断测试，使用下一代细菌16S rRNA基因和真菌ITS1基因区域测序，在临床样本中提供准确的物种鉴定。在这里，我们提出了一项比较16S和ITS1宏基因组鉴定与常规培养临床样品的研究。以培养结果为金标准，采用临床微生物实验室的患者标本进行比较。基于宏基因组学的结果显示，培养阳性标本的符合率为91.8%，培养阴性标本的符合率为52.8%。10.3%的标本也检出未通过培养调查的真菌种类。宏基因组分析的特异性和敏感性分别为91.8%和52.7%。基于16S的临床标本中细菌种类的宏基因组鉴定与传统的基于培养的技术相当，当与临床信息相结合时，可以导致传染病诊断的准确诊断工具。本文的在线版本（10.1186/s12879-017-2727-8）包含补充内容，仅供授权用户使用。
Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others. However, to date there has been no commercial application of this technology in infectious disease diagnostic settings. Credence Genomics Rapid Infection Detection™ test, is a molecular based diagnostic test that uses next generation sequencing of bacterial 16S rRNA gene and fungal ITS1 gene region to provide accurate identification of species within a clinical sample. Here we present a study comparing 16S and ITS1 metagenomic identification against conventional culture for clinical samples. Using culture results as gold standard, a comparison was conducted using patient specimens from a clinical microbiology lab. Metagenomics based results show a 91.8% concordance rate for culture positive specimens and 52.8% concordance rate with culture negative samples. 10.3% of specimens were also positive for fungal species which was not investigated by culture. Specificity and sensitivity for metagenomics analysis is 91.8 and 52.7% respectively. 16S based metagenomic identification of bacterial species within a clinical specimen is on par with conventional culture based techniques and when coupled with clinical information can lead to an accurate diagnostic tool for infectious disease diagnosis. The online version of this article (10.1186/s12879-017-2727-8) contains supplementary material, which is available to authorized users.
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DOI：
10.1186/2042-5783-2-3
发表时间：
2012-02-09
期刊：
Microbial informatics and experimentation
影响因子：
--
作者：
Thomas T;Gilbert J;Meyer F
通讯作者：
Meyer F
DOI：
10.1155/2013/168742
发表时间：
2013
期刊：
International journal of bacteriology
影响因子：
--
作者：
Cunningham SA;Mandrekar JN;Rosenblatt JE;Patel R
通讯作者：
Patel R
DOI：
10.1073/pnas.82.20.6955
发表时间：
1985-01-01
影响因子：
11.1
作者：
LANE, DJ;PACE, B;PACE, NR
通讯作者：
PACE, NR
影响因子：
3.8
作者：
Decuypere S;Meehan CJ;Van Puyvelde S;De Block T;Maltha J;Palpouguini L;Tahita M;Tinto H;Jacobs J;Deborggraeve S
通讯作者：
Deborggraeve S
影响因子：
3.7
作者：
Salipante SJ;Sengupta DJ;Rosenthal C;Costa G;Spangler J;Sims EH;Jacobs MA;Miller SI;Hoogestraat DR;Cookson BT;McCoy C;Matsen FA;Shendure J;Lee CC;Harkins TT;Hoffman NG
通讯作者：
Hoffman NG