1Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK.
2Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Microb Genom. 2018 Apr;4(4). doi: 10.1099/mgen.0.000173. Epub 2018 Apr 5.
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.
在临床环境中进行细菌全基因组测序有可能极大地改善感染控制和临床实践。目前，全球大多数常规微生物学实验室都没有测序仪器，但可以选择使用外部测序服务提供商。为了促进对此问题的讨论，我们调查了发送服务是否是可行的选择。根据成本选择了四家提供 MiSeq 测序的服务提供商，并根据所提供的服务和序列数据质量进行了评估。从五株耐甲氧西林金黄色葡萄球菌（MRSA）分离株中制备 DNA，其中四株与英国先前发表的一次暴发有关，另外还包括一株参考 MRSA 分离株（ST22 HO 5096 0412）。每个分离株的测序成本从 155 英镑到 342 英镑不等，从 DNA 邮寄到序列数据到达的周转时间从 12 天到 63 天不等。对商业生成的基因组与原始序列数据进行比较表明，高度一致，对于所有四家服务提供商，在核心基因组图谱上，原始序列和新序列之间的单核苷酸多态性（SNP）差异不超过一个。由于每个分离株的序列数据输出量较低，可能导致组装不完整，因此最便宜的两个测序服务提供商无法根据组装确定多位点序列类型。我们的结果表明，外部提供商返回了高度准确的基因组数据，但需要改进周转时间，使其成为临床实践中可行的选择。
