Rapid phylogenetic analysis using open reading frame content patterns acquired by Oxford nanopore sequencing
Rapid phylogenetic analysis using open reading frame content patterns acquired by Oxford nanopore sequencing
复制标题
使用牛津纳米孔测序获得的开放阅读框内容模式进行快速系统发育分析
DOI：
10.1111/jam.15807
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发表时间：
2022
影响因子：
4
通讯作者：
Suzuki Masahiro
中科院分区：
文献类型：
--
作者：
Hayashi Kengo;Doi Yohei;Suzuki Masahiro
基于核心基因组单核苷酸多态性（cgSNPs）的全基因组测序（WGS）系统发育分析越来越多地用于细菌的流行病学调查。然而，这种方法既耗费资源又耗时。Oxford Nanopore Technologies（ONT）测序能够进行真实的实时数据分析，但高错误率阻碍了其在基于cgSNP的系统发育分析中的应用。在这里，我们开发了一个cgSNP-独立的系统发育分析方法使用ONT读组件通过专注于开放阅读框架（ORF）内容patterns.Methods和ResultsWGS数据的66肠杆菌hormaecheistries获得的ONT和Illumina测序和162菌株从NCBI数据库中获得的转换为基于的存在或不存在的ORF使用BLASTn的二进制序列。将从二元序列计算的系统发育树（ORF树）与来自Illumina序列的cgSNP树进行比较。cgSNP树中密切相关菌株的簇在用二元序列构建的ORF树中形成可比较的簇，它们之间的树形拓扑结构基于Fowlkes相似结论使用ONT测序的基于ORF的系统发育分析在流行病学调查中可能是有用的，并提供优于基于cgSNP的方法的优势。ORF的存在或不存在避免了ONT测序的读取错误问题。由于ONT测序能够真实的生成数据，并且不需要大量投资，因此这种基于ORF的系统发育分析方法具有在护理点进行系统发育和流行病学分析的潜力。
AimsPhylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) using whole‐genome sequencing (WGS) is increasingly used in epidemiological investigations of bacteria. The approach, however, is both resource intensive and time‐consuming. Oxford Nanopore Technologies (ONT) sequencing is capable of real‐time data analysis but the high error rate hampers its application in cgSNP‐based phylogenetic analysis. Here, we developed a cgSNP‐independent phylogenetic analysis method using ONT read assemblies by focusing on open reading frame (ORF) content patterns.Methods and ResultsWGS data of 66Enterobacter hormaecheistrains acquired by both ONT and Illumina sequencing and 162 strains obtained from NCBI database were converted to binary sequences based on the presence or absence of ORFs using BLASTn. Phylogenetic trees calculated from binary sequences (ORF trees) were compared with cgSNP trees derived from Illumina sequences. Clusters of closely related strains in the cgSNP trees formed comparable clusters in the ORF trees built with binary sequences, and the tree topologies between them were similar based on Fowlkes–Mallows index.ConclusionsThe ORF‐based phylogenetic analysis using ONT sequencing may be useful in epidemiological investigations and offer advantages over the cgSNP‐based approach.Significance and Impact of the studyConversion of assembled WGS data to binary sequences based on the presence or absence of ORFs circumvents read error concerns with ONT sequencing. Since ONT sequencing generates data in real time and does not require major investment, this ORF‐based phylogenetic analysis method has the potential to enable phylogenetic and epidemiological analysis at the point of care.
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