Optimized conditions for Listeria, Salmonella and Escherichia whole genome sequencing using the Illumina iSeq100 platform with point-and-click bioinformatic analysis.
Optimized conditions for Listeria, Salmonella and Escherichia whole genome sequencing using the Illumina iSeq100 platform with point-and-click bioinformatic analysis.
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DOI：
10.1371/journal.pone.0277659
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发表时间：
2022
期刊：
影响因子：
3.7
通讯作者：
Sanchez, Susan
中科院分区：
文献类型：
--
作者：
Alvarez Narvaez, Sonsiray;Shen, Zhenyu;Yan, Lifang;Stenger, Brianna L. S.;Goodman, Laura B. B.;Lim, Ailam;Nissly, Ruth H. H.;Nair, Meera Surendran;Zhang, Shuping;Sanchez, Susan
全基因组测序(WGS)数据已经成为公共卫生调查和临床诊断中不可或缺的组成部分。尽管如此，许多兽医诊断实验室仍然负担不起实施下一代测序(NGS)的费用，因为它的成本很高，而且缺乏人员的生物信息学知识来分析NGS数据。为了克服这些问题，并使每个诊断实验室都能访问NGS，美国13个兽医诊断实验室启动了Illumina iSeq100测序平台的评估，用于重要的人畜共患食源性致病菌大肠杆菌、单核细胞增生性李斯特菌和肠沙门氏菌的全基因组测序。这份手稿中提出的工作是这种多个实验室努力的延续。在这里，七个AAVLD认证的诊断实验室探索了进一步降低测序成本和使用用户友好的基因组数据分析平台的方法。我们的调查表明，使用推荐试剂体积的四分之一即可获得相同的基因组文库质量，因此只需实际价格的一小部分，并确认Illumina iSeq100是对WGS需求较低的实验室最负担得起的测序技术。此外，我们在三个流行的用户友好软件(BaseSpace、Geneious和GalaxyTrakr)中准备了用于基因组数据分析的逐步协议，并从基因组组装质量、物种和抗菌素耐药基因(AMR)鉴定的角度对结果进行了比较。三种分析方法在装配质量上无显著差异，可鉴定出目标菌种。然而，只有使用BaseSpace和GalaxyTrakr才能识别抗菌素耐药基因；而GalaxyTrakr是完成这项任务的最佳工具。
Whole-genome sequencing (WGS) data have become an integral component of public health investigations and clinical diagnostics. Still, many veterinary diagnostic laboratories cannot afford to implement next generation sequencing (NGS) due to its high cost and the lack of bioinformatic knowledge of the personnel to analyze NGS data. Trying to overcome these problems, and make NGS accessible to every diagnostic laboratory, thirteen veterinary diagnostic laboratories across the United States (US) initiated the assessment of Illumina iSeq100 sequencing platform for whole genome sequencing of important zoonotic foodborne pathogens Escherichia coli, Listeria monocytogenes, and Salmonella enterica. The work presented in this manuscript is a continuation of this multi-laboratory effort. Here, seven AAVLD accredited diagnostic laboratories explored a further reduction in sequencing costs and the usage of user-friendly platforms for genomic data analysis. Our investigation showed that the same genomic library quality could be achieved by using a quarter of the recommended reagent volume and, therefore a fraction of the actual price, and confirmed that Illumina iSeq100 is the most affordable sequencing technology for laboratories with low WGS demand. Furthermore, we prepared step-by-step protocols for genomic data analysis in three popular user-friendly software (BaseSpace, Geneious, and GalaxyTrakr), and we compared the outcomes in terms of genome assembly quality, and species and antimicrobial resistance gene (AMR) identification. No significant differences were found in assembly quality, and the three analysis methods could identify the target bacteria species. However, antimicrobial resistance genes were only identified using BaseSpace and GalaxyTrakr; and GalaxyTrakr was the best tool for this task.
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影响因子：
2.8
作者：
Stirling C;Andrews S;Croft T;Vickers J;Turner P;Robinson A
通讯作者：
Robinson A
影响因子：
3.7
作者：
Bushnell B;Rood J;Singer E
通讯作者：
Singer E
影响因子：
2.6
作者：
Ceric, Olgica;Tyson, Gregory H.;Reimschuessel, Renate
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Reimschuessel, Renate
DOI：
10.1016/j.cmi.2017.10.013
发表时间：
2018-04
期刊：
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
影响因子：
--
作者：
Besser J;Carleton HA;Gerner-Smidt P;Lindsey RL;Trees E
通讯作者：
Trees E
DOI：
10.1093/jac/dkaa345
发表时间：
2020-12-01
期刊：
The Journal of antimicrobial chemotherapy
影响因子：
--
作者：
Bortolaia V;Kaas RS;Ruppe E;Roberts MC;Schwarz S;Cattoir V;Philippon A;Allesoe RL;Rebelo AR;Florensa AF;Fagelhauer L;Chakraborty T;Neumann B;Werner G;Bender JK;Stingl K;Nguyen M;Coppens J;Xavier BB;Malhotra-Kumar S;Westh H;Pinholt M;Anjum MF;Duggett NA;Kempf I;Nykäsenoja S;Olkkola S;Wieczorek K;Amaro A;Clemente L;Mossong J;Losch S;Ragimbeau C;Lund O;Aarestrup FM
通讯作者：
Aarestrup FM