Abstract
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.
Highlights
The utility of whole-genome sequencing (WGS) for accurately identifying the population structure and genetic relatedness of pathogenic bacteria has been demonstrated for a range of species [1,2,3,4]
Selecting commercial sequencing providers In November 2016, we searched the internet for commercial sequencing providers using ‘DNA sequencing’, ‘bacterial’ and ‘service’ as search terms. This resulted in the identification of eight providers, who were contacted and quotes requested for library preparation and paired-end whole genome sequencing of five methicillin-resistant Staphylococcus aureus (MRSA) isolates multiplexed in a single run on an Illumina MiSeq instrument
The bacterial isolates used for the evaluation were four MRSA isolates sequenced previously as part of an outbreak investigation on a Special Care Baby Unit (SCBU) [8], and the MRSA reference isolate ST22 HO 5096 0412
Summary
The utility of whole-genome sequencing (WGS) for accurately identifying the population structure and genetic relatedness of pathogenic bacteria has been demonstrated for a range of species [1,2,3,4] Associated with this is growing support for its translation into diagnostic and public health microbiology, including for the investigation of suspected outbreaks. This could improve the accuracy of the current infection control paradigm, in which suspected outbreaks are largely based on epidemiological evaluation of two or more patients positive for the same pathogen to determine whether an opportunity for transmission could have occurred. The generation of the entire genome has the potential to detect genes encoding antibiotic resistance and virulence factors
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