PDF(Pubmed)
Abstract：
Bacterial pathogens are one of the major threats to biosafety and environmental health, and advanced assessment is a prerequisite to combating bacterial pathogens. Currently, 16S rRNA gene sequencing is efficient in the open-view detection of bacterial pathogens. However, the taxonomic resolution and applicability of this method are limited by the domain-specific pathogen database, taxonomic profiling method, and sequencing target of 16S variable regions. Here, we present a pipeline of multiple bacterial pathogen detection (MBPD) to identify the animal, plant, and zoonotic pathogens. MBPD is based on a large, curated database of the full-length 16S genes of 1986 reported bacterial pathogen species covering 72,685 sequences. In silico comparison allowed MBPD to provide the appropriate similarity threshold for both full-length and variable-region sequencing platforms, while the subregion of V3-V4 (mean: 88.37%, accuracy rate compared to V1-V9) outperformed other variable regions in pathogen identification compared to full-length sequencing. Benchmarking on real data sets suggested the superiority of MBPD in a broader range of pathogen detections compared with other methods, including 16SPIP and MIP. Beyond detecting the known causal agent of animal, human, and plant diseases, MBPD is capable of identifying cocontaminating pathogens from biological and environmental samples. Overall, we provide a MBPD pipeline for agricultural, veterinary, medical, and environmental monitoring to achieve One Health.
摘要：
细菌病原体是生物安全和环境健康的主要威胁之一,高级评估是对抗细菌病原体的先决条件。目前,16SrRNA基因测序在细菌病原体的开放式检测中是有效的。然而,该方法的分类分辨率和适用性受到特定领域病原体数据库的限制，分类学分析方法，和16S可变区的测序靶。这里,我们提出了一种管道的多细菌病原体检测（MBPD）来鉴定动物，植物,和人畜共患病原体。MBPD是基于一个大的，1986年全长16S基因的数据库报告了涵盖72,685个序列的细菌病原体物种。计算机比较允许MBPD为全长和可变区测序平台提供适当的相似性阈值。而V3-V4的子区域(平均值：88.37%，与全长测序相比，与V1-V9相比，准确率）在病原体鉴定方面优于其他可变区。与其他方法相比，对真实数据集进行基准测试表明，MBPD在更广泛的病原体检测中具有优势。包括16SPIP和MIP。除了检测已知的动物病原体，人类,和植物病害,MBPD能够从生物和环境样品中鉴定共污染病原体。总的来说,我们为农业提供MBPD管道，兽医,medical,和环境监测，以实现一个健康。
