Staphylococcus aureus whole genome sequence-based susceptibility and resistance prediction using a clinically amenable workflow.
Staphylococcus aureus whole genome sequence-based susceptibility and resistance prediction using a clinically amenable workflow.
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DOI：
10.1016/j.diagmicrobio.2020.115060
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发表时间：
2020-07
影响因子：
2.9
通讯作者：
Patel R
中科院分区：
文献类型：
--
作者：
Cunningham SA;Jeraldo PR;Schuetz AN;Heitman AA;Patel R
我们使用来自Next Gen Diagnostics（山景，加州）和1928 Diagnostics（哥德堡，瑞典）的基于图形用户界面（GUI）的自动分析工具，分析来自102株独特的金黄色葡萄球菌血培养分离株的全基因组序列（WGS）数据，以预测抗菌药物的耐药性，并将结果与表型敏感性测试的结果进行比较。在使用Next Gen Diagnostics工具分析的916个分离株/抗生素组合中，WGS预测与表型敏感性/耐药性之间存在9个差异，包括克林霉素的8个差异和米诺环素的1个差异。在使用1928年诊断工具分析的612个分离株/抗生素组合中，WGS预测与表型敏感性/耐药性之间存在13个差异，包括克林霉素9个，甲氧苄啶-磺胺甲恶唑3个和利福平1个。Next Gen Diagnostics未评估甲氧苄啶-磺胺甲恶唑，1928 Diagnostics未评估米诺环素。使用苯唑西林、万古霉素和莫匹罗星的两种分析平台以及左氧氟沙星的Next Gen Diagnostics分析工具（1928年诊断工具未评估左氧氟沙星），表型敏感性/耐药性与敏感性/耐药性的基因型预测之间完全一致。这些结果表明，从性能的角度来看，有一些警告，自动生物信息学工具可能是可以接受的，以预测敏感性和耐药性的一组抗生素的链球菌。金黄色的
We used graphical user interface (GUI)-based automated analytical tools from Next Gen Diagnostics (Mountain View, California) and 1928 Diagnostics (Gothenburg, Sweden) to analyze whole genome sequence (WGS) data from 102 unique blood culture isolates of Staphylococcus aureus to predict antimicrobial susceptibly, with results compared to those of phenotypic susceptibility testing. Of 916 isolate/antibiotic combinations analyzed using the Next Gen Diagnostics tool, there were 9 discrepancies between WGS-predictions and phenotypic susceptibility/resistance, including 8 for clindamycin and 1 for minocycline. Of 612 isolate/antibiotic combinations analyzed using the 1928 Diagnostics tool, there were 13 discrepancies between WGS-predictions and phenotypic susceptibility/resistance, including 9 for clindamycin, 3 for trimethoprim-sulfamethoxazole and 1 for rifampin. Trimethoprim-sulfamethoxazole was not assessed by Next Gen Diagnostics, and minocycline was not assessed by 1928 Diagnostics. There was complete concordance between phenotypic susceptibility/resistance and genotypic prediction of susceptibility/resistance using both analytical platforms for oxacillin, vancomycin and mupirocin, as well as by the Next Gen Diagnostics analytical tool for levofloxacin (the 1928 Diagnostics tool did not assess levofloxacin). These results suggest that from a performance standpoint, with some caveats, automatic bioinformatics tools may be acceptable to predict susceptibility and resistance to a panel of antibiotics for S. aureus.
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影响因子：
9.4
作者：
Gordon NC;Price JR;Cole K;Everitt R;Morgan M;Finney J;Kearns AM;Pichon B;Young B;Wilson DJ;Llewelyn MJ;Paul J;Peto TE;Crook DW;Walker AS;Golubchik T
通讯作者：
Golubchik T
影响因子：
9.4
作者：
Mason, Amy;Foster, Dona;Peto, Tim
通讯作者：
Peto, Tim
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作者：
Enstrom, Josefine;Froding, Inga;Fang, Hong
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Fang, Hong
影响因子：
9.4
作者：
Brown, Nicholas M.;Blane, Beth;Peacock, Sharon J.
通讯作者：
Peacock, Sharon J.
影响因子：
3.7
作者：
Park KH;Greenwood-Quaintance KE;Uhl JR;Cunningham SA;Chia N;Jeraldo PR;Sampathkumar P;Nelson H;Patel R
通讯作者：
Patel R