Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria.
Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria.
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DOI：
10.1099/mgen.0.000717
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发表时间：
2022-03
影响因子：
3.9
通讯作者：
Goodman LB
中科院分区：
文献类型：
--
作者：
Mitchell PK;Wang L;Stanhope BJ;Cronk BD;Anderson R;Mohan S;Zhou L;Sanchez S;Bartlett P;Maddox C;DeShambo V;Mani R;Hengesbach LM;Gresch S;Wright K;Mor S;Zhang S;Shen Z;Yan L;Mackey R;Franklin-Guild R;Zhang Y;Prarat M;Shiplett K;Ramachandran A;Narayanan S;Sanders J;Hunkapiller AA;Lahmers K;Carbonello AA;Aulik N;Lim A;Cooper J;Jones A;Guag J;Nemser SM;Tyson GH;Timme R;Strain E;Reimschuessel R;Ceric O;Goodman LB
公共卫生和兽医实验室越来越需要进行全基因组测序（WGS），以监测抗菌素耐药性（AMR）并保护人和动物的安全。随着更小和更实惠的测序平台的可用性，加上明确的生物信息学协议，将这种技术用于实时监测和基因组流行病学的技术能力大大扩展。然而，有必要确保数据的高质量。本研究的目的是使用多实验室验证方法评估小型台式测序平台的实用性。向13个实验室提供了相同的设备、试剂、方案和细菌参考菌株。比较Illumina DNA Prep和Nextera XT文库制备试剂盒，并使用2×150 bp iSeq i100化学进行测序。使用开源程序进行分析，将本研究产生的序列与所提供菌株的封闭基因组进行比较。详细的分步方案可通过protocols.io（https：//www.protocols.io/view/iseq-bacterial-wgs-protocol-bij8kcrw）公开获得。该方法的通量为每次测序运行约4-6个细菌分离株（20-26 Mb总负载）。Illumina DNA Prep文库制备试剂盒产生了高质量的组装体和几乎完整的AMR基因注释。与XT相比，Prep方法产生了更一致的覆盖率，并且当覆盖率基准得到满足时，几乎所有AMR、毒力和亚型基因靶标都得到了正确鉴定。由于减少了生成WGS数据的技术和财务障碍，iSeq平台是对微生物病原体基因组监测感兴趣的小型实验室的可行选择。
There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. With the availability of smaller and more affordable sequencing platforms coupled with well-defined bioinformatic protocols, the technological capability to incorporate this technique for real-time surveillance and genomic epidemiology has greatly expanded. There is a need, however, to ensure that data are of high quality. The goal of this study was to assess the utility of a small benchtop sequencing platform using a multi-laboratory verification approach. Thirteen laboratories were provided the same equipment, reagents, protocols and bacterial reference strains. The Illumina DNA Prep and Nextera XT library preparation kits were compared, and 2×150 bp iSeq i100 chemistry was used for sequencing. Analyses comparing the sequences produced from this study with closed genomes from the provided strains were performed using open-source programs. A detailed, step-by-step protocol is publicly available via protocols.io (https://www.protocols.io/view/iseq-bacterial-wgs-protocol-bij8kcrw). The throughput for this method is approximately 4–6 bacterial isolates per sequencing run (20–26 Mb total load). The Illumina DNA Prep library preparation kit produced high-quality assemblies and nearly complete AMR gene annotations. The Prep method produced more consistent coverage compared to XT, and when coverage benchmarks were met, nearly all AMR, virulence and subtyping gene targets were correctly identified. Because it reduces the technical and financial barriers to generating WGS data, the iSeq platform is a viable option for small laboratories interested in genomic surveillance of microbial pathogens.
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影响因子：
5
作者：
Orsi RH;Wiedmann M
通讯作者：
Wiedmann M
影响因子：
5.2
作者：
Chen, Yanyun;Liu, Zhihai;Xia, Zhaofei
通讯作者：
Xia, Zhaofei
影响因子：
0.8
作者：
Tyson, Gregory H.;Li, Cong;Rankin, Shelley C.
通讯作者：
Rankin, Shelley C.
影响因子：
2.8
作者：
Nemser, Sarah M.;Doran, Tara;Reimschuessel, Renate
通讯作者：
Reimschuessel, Renate
影响因子：
2.6
作者：
Hong, Jun Sung;Song, Wonkeun;Jeong, Seok Hoon
通讯作者：
Jeong, Seok Hoon