Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data
Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data
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DOI：
10.1128/jcm.00323-15
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发表时间：
2015-05-01
影响因子：
9.4
通讯作者：
Deng, Xiangyu
中科院分区：
文献类型：
--
作者：
Zhang, Shaokang;Yin, Yanlong;Deng, Xiangyu
血清分型是沙门氏菌国家和国际监测网络的基础，沙门氏菌是世界上最普遍的食源性病原体之一（1-3）。公共卫生微生物学目前正在被全基因组测序（WGS）所改变，这为利用WGS数据确定血清型打开了大门。SeqSero （www.denglab.info/SeqSero）是一种新型的基于网络的工具，用于使用高通量基因组测序数据确定沙门氏菌血清型。SeqSero基于沙门氏菌血清型决定因子（rfb基因簇、fliC和fljB等位基因）数据库，预计可通过原始测序读取和基因组组装，快速准确地确定几乎所有沙门氏菌血清型（超过2300种血清型）的血清型。SeqSero的性能通过以下测试进行评估：(1)308株已知血清型沙门氏菌的原始基因组读数；（ii）由美国食品和药物管理局（fda）运营的美国国家监测网络GenomeTrakr对3306株沙门氏菌分离物进行测序并公开的原始基因组读数；（iii） 354个其他可公开获得的沙门氏菌基因组草案或完整基因组。我们还演示了从口腔感染沙门氏菌的小鼠粪便宏基因组的原始测序读数确定沙门氏菌血清型。当SeqSero整合到基于wgs的病原体亚型和表征平台时，可以帮助维持沙门氏菌血清分型的完善效用。
Serotyping forms the basis of national and international surveillance networks for Salmonella, one of the most prevalent food-borne pathogens worldwide (1-3). Public health microbiology is currently being transformed by whole-genome sequencing (WGS), which opens the door to serotype determination using WGS data. SeqSero (www.denglab.info/SeqSero) is a novel Web-based tool for determining Salmonella serotypes using high-throughput genome sequencing data. SeqSero is based on curated databases of Salmonella serotype determinants (rfb gene cluster, fliC and fljB alleles) and is predicted to determine serotype rapidly and accurately for nearly the full spectrum of Salmonella serotypes (more than 2,300 serotypes), from both raw sequencing reads and genome assemblies. The performance of SeqSero was evaluated by testing (i) raw reads from genomes of 308 Salmonella isolates of known serotype; (ii) raw reads from genomes of 3,306 Salmonella isolates sequenced and made publicly available by GenomeTrakr, a U.S. national monitoring network operated by the Food and Drug Administration; and (iii) 354 other publicly available draft or complete Salmonella genomes. We also demonstrated Salmonella serotype determination from raw sequencing reads of fecal metagenomes from mice orally infected with this pathogen. SeqSero can help to maintain the well-established utility of Salmonella serotyping when integrated into a platform of WGS-based pathogen subtyping and characterization.