A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance.
A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance.
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DOI：
10.1371/journal.pone.0157718
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Lund O
中科院分区：
文献类型：
--
作者：
Thomsen MC;Ahrenfeldt J;Cisneros JL;Jurtz V;Larsen MV;Hasman H;Aarestrup FM;Lund O
全基因组测序的最新进展使该技术可用于微生物实验室的常规使用。然而，使用这项技术的一个主要障碍是简单和自动的生物信息学工具的可用性。基于以前发表的和已经可用的基于网络的工具，我们开发了一个单一的管道，用于批量上传来自多个细菌分离株的全基因组测序数据。该管道将自动识别细菌物种，并在适用的情况下组装基因组，识别多位点序列类型、质粒、毒力基因和抗菌素耐药基因。将提供每份样品的简短可打印报告，并可下载包含所有元数据的Excel电子表格和所有提交样品的结果摘要。管道使用以前用于测试单个服务的数据集进行基准测试。报告的结果可以快速概述主要结果，并将其与先前发现的结果进行比较，表明该平台是可靠的，能够正确预测物种并自动找到大多数预期的基因。总之，开发了一个组合生物信息学平台并公开提供，提供了易于使用的细菌全基因组测序数据的自动分析。该平台可以作为使用全基因组测序进行临床诊断和监测的研究人员的指南。该平台可在https://cge.cbs.dtu.dk/services/CGEpipeline-1.1上免费获得，并打算在新功能可用时继续扩展。
Recent advances in whole genome sequencing have made the technology available for routine use in microbiological laboratories. However, a major obstacle for using this technology is the availability of simple and automatic bioinformatics tools. Based on previously published and already available web-based tools we developed a single pipeline for batch uploading of whole genome sequencing data from multiple bacterial isolates. The pipeline will automatically identify the bacterial species and, if applicable, assemble the genome, identify the multilocus sequence type, plasmids, virulence genes and antimicrobial resistance genes. A short printable report for each sample will be provided and an Excel spreadsheet containing all the metadata and a summary of the results for all submitted samples can be downloaded. The pipeline was benchmarked using datasets previously used to test the individual services. The reported results enable a rapid overview of the major results, and comparing that to the previously found results showed that the platform is reliable and able to correctly predict the species and find most of the expected genes automatically. In conclusion, a combined bioinformatics platform was developed and made publicly available, providing easy-to-use automated analysis of bacterial whole genome sequencing data. The platform may be of immediate relevance as a guide for investigators using whole genome sequencing for clinical diagnostics and surveillance. The platform is freely available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 and it is the intention that it will continue to be expanded with new features as these become available.