Comparative Analysis of Short- and Long-Read Sequencing of Vancomycin-Resistant Enterococci for Application to Molecular Epidemiology.
Comparative Analysis of Short- and Long-Read Sequencing of Vancomycin-Resistant Enterococci for Application to Molecular Epidemiology.
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DOI：
10.3389/fcimb.2022.857801
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发表时间：
2022
影响因子：
5.7
通讯作者：
中科院分区：
文献类型：
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作者：
万古霉素耐药肠球菌（VRE）是一种具有遗传可塑性和广泛耐药性（AMR）的医院内致病菌。为了防止VRE在医院环境中的传播，已经实施了分子流行病学方法，如脉冲场凝胶电泳和多位点序列分型用于病原体爆发监测。然而，由于这些方法的鉴别能力不足，使得能够对整个基因组序列进行高分辨率分析的全基因组测序（WGS）正被越来越多地使用。在此，我们使用短读下一代测序（SR-NGS）和长读下一代测序（LR-NGS）进行了VRE的WGS。由于缺乏基于WGS的细菌流行病学的标准化工作流程和管道，我们为SR和LR-NGS建立了三步管道，作为菌株分型和AMR分析的标准化WGS方法。对于菌株分型，我们分析了VRE分离株的单核苷酸多态性（SNP），并构建了基于SNP的最大似然遗传学。使用短读段和长读段构建的系统发育树显示出良好的对应性。尽管如此，SR-NGS表现出更高的灵敏度，用于检测细菌序列的核苷酸取代。在AMR分析期间，我们检查了AMR基因和耐药突变。我们还评估了基因型和表型抗性之间的一致性，LR-NGS的一致性通常优于SR-NGS。有必要根据爆发病例对我们的管道进行进一步验证，以确保管道的整体性能。
Vancomycin-resistant enterococci (VRE) are nosocomial pathogens with genetic plasticity and widespread antimicrobial resistance (AMR). To prevent the spread of VRE in the hospital setting, molecular epidemiological approaches such as pulsed-field gel electrophoresis and multilocus sequence typing have been implemented for pathogen outbreak surveillance. However, due to the insufficient discriminatory power of these methods, whole-genome sequencing (WGS), which enables high-resolution analysis of entire genomic sequences, is being used increasingly. Herein, we performed WGS of VRE using both short-read next-generation sequencing (SR-NGS) and long-read next-generation sequencing (LR-NGS). Since standardized workflows and pipelines for WGS-based bacterial epidemiology are lacking, we established three-step pipelines for SR- and LR-NGS, as a standardized WGS-based approach for strain typing and AMR profiling. For strain typing, we analyzed single-nucleotide polymorphisms (SNPs) of VRE isolates and constructed SNP-based maximum-likelihood phylogenies. The phylogenetic trees constructed using short and long reads showed good correspondence. Still, SR-NGS exhibited higher sensitivity for detecting nucleotide substitutions of bacterial sequences. During AMR profiling, we examined AMR genes and resistance-conferring mutations. We also assessed the concordance between genotypic and phenotypic resistance, which was generally better for LR-NGS than SR-NGS. Further validation of our pipelines based on outbreak cases is necessary to ensure the overall performance of pipelines.
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影响因子：
5.2
作者：
Carter, Glen P.;Buultjens, Andrew H.;Howden, Benjamin P.
通讯作者：
Howden, Benjamin P.
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
影响因子：
4.6
作者：
Lee JY;Kong M;Oh J;Lim J;Chung SH;Kim JM;Kim JS;Kim KH;Yoo JC;Kwak W
通讯作者：
Kwak W
影响因子：
9.3
作者：
Bayley H
通讯作者：
Bayley H
影响因子：
9.4
作者：
Homan, WL;Tribe, D;Willems, RJL
通讯作者：
Willems, RJL