...
  • 主题
高级搜索  >
历史搜索 清空历史
首页> 外文期刊>Journal of Clinical Microbiology >Species Identification and Antibiotic Resistance Prediction by Analysis of Whole-Genome Sequence Data by Use of ARESdb: an Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial
【24h】

Species Identification and Antibiotic Resistance Prediction by Analysis of Whole-Genome Sequence Data by Use of ARESdb: an Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial

机译：通过使用ARESDB分析全基因组序列数据的物种鉴定和抗生素抗性预测：非复呼吸道感染试验的分离物分析

获取原文
           
页面导航
  • 摘要
  • 著录项
  • 相似文献
  • 相关主题

摘要

Whole-genome sequencing (WGS) is now routinely performed in clinical microbiology laboratories to assess isolate relatedness. With appropriately developed analytics, the same data can be used for prediction of antimicrobial susceptibility. We assessed WGS data for identification using open-source tools and antibiotic susceptibility testing (AST) prediction using ARESdb compared to matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification and broth microdilution phenotypic susceptibility testing on clinical isolates from a multicenter clinical trial of the FDA-cleared Unyvero lower respiratory tract infection (LRTI) application (Curetis). ABSTRACT Whole-genome sequencing (WGS) is now routinely performed in clinical microbiology laboratories to assess isolate relatedness. With appropriately developed analytics, the same data can be used for prediction of antimicrobial susceptibility. We assessed WGS data for identification using open-source tools and antibiotic susceptibility testing (AST) prediction using ARESdb compared to matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification and broth microdilution phenotypic susceptibility testing on clinical isolates from a multicenter clinical trial of the FDA-cleared Unyvero lower respiratory tract infection (LRTI) application (Curetis). For the trial, more than 2,000 patient samples were collected from intensive care units across nine hospitals and tested for LRTI. The isolate subset used in this study included 620 clinical isolates originating from 455 LRTI culture-positive patient samples. Isolates were sequenced using the Illumina Nextera XT protocol and FASTQ files with raw reads uploaded to the ARESdb cloud platform (ares-genetics.cloud; released for research use in 2020). The platform combines Ares Genetics’ proprietary database ARESdb with state-of-the-art bioinformatics tools and curated public data. For identification, WGS showed 99 and 93% concordance with MALDI-TOF MS at the genus and species levels, respectively. WGS-predicted susceptibility showed 89% categorical agreement with phenotypic susceptibility across a total of 129 species-compound pairs analyzed, with categorical agreement exceeding 90% in 78 species-compound pairs and reaching 100% in 32. Results of this study add to the growing body of literature showing that, with improvement of analytics, WGS data could be used to predict antimicrobial susceptibility.
机译：现在常规在临床微生物实验室进行全基因组测序（WGS）以评估孤立相关性的孤立相关性。通过适当开发的分析，相同的数据可用于预测抗微生物易感性。我们使用aresdb评估了使用aresdb的抗生素易感性测试（AST）预测的WGS数据，与临床上的飞行质谱（MALDI-TOF MS）鉴定和肉汤微量渗透表型易感性测试相比，使用aresdb预测来自FDA清除的非复呼吸道感染（LRTI）应用（LRTI）的多中心临床试验中的分离物。摘要现在在临床微生物学实验室常规进行全基因组测序（WGS），以评估孤立相关性。通过适当开发的分析，相同的数据可用于预测抗微生物易感性。我们使用aresdb评估了使用aresdb的抗生素易感性测试（AST）预测的WGS数据，与临床上的飞行质谱（MALDI-TOF MS）鉴定和肉汤微量渗透表型易感性测试相比，使用aresdb预测来自FDA清除的非复呼吸道感染（LRTI）应用（LRTI）的多中心临床试验中的分离物。对于审判，从九个医院的重症监护室中收集超过2,000名患者样品并对LRTI进行测试。本研究中使用的分离亚群包括源自455LRTI培养阳性患者样品的620个临床分离物。使用Illumina Nextera XT协议和FASTQ文件进行测序，使用原始读取的FASTQ文件上传到ARESDB云平台（ares-genetics.cloud;在2020年发布研究使用）。该平台将Ares Genetics的专有数据库ARESDB与最先进的生物信息学工具和策划公共数据相结合。对于鉴定，WG分别显示出99％和93％，分别在属和物种水平的MALDI-TOF MS的一致性。 WGS预测的易感性显示出89％的分类协议，在分析了129种 - 复合对对中的表型易感性，分类在78种 - 化合物对中超过90％，在32年达到100％。本研究的结果增加了不断增长的结果文学的身体表明，随着分析的改善，WGS数据可用于预测抗微生物易感性。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱：kefu@zhangqiaokeyan.com

京公网安备：11010802029741号 ICP备案号：京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有

  • 客服微信

  • 服务号