A pilot study evaluating nanopore sequencing technology for Salmonella serotype prediction
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The sequencing platforms developed by Oxford Nanopore Technologies (ONT) using long-read, single-molecule nanopore sequencing technology have advantages in portability, affordability, real-time base calling, and simplicity compared with other sequencing technologies. They provide a potential whole genome sequencing (WGS) method to meet the needs of food industry for effective and efficient Salmonella identification. This pilot study sequenced 24 Salmonella enterica strains (17 serovars) to explore whether WGS data generated by the ONT sequencing system could accurately predict Salmonella serotypes. WGS data generated by Illumina Hiseq (200X) of the same isolates were used to predict serotype as the benchmark of accuracy. We found that the quality score and high-quality data percentage of the reads declined over the sequencing time, whilst the data generated within the first two hours were sufficient for serotype prediction. The size of data generated within the first two hours ranged from 201 to 1,072 MB (42-203X), and the mean read lengths ranged from 3,589 to 11,721 bp. Consensus serotype prediction results were obtained after assembly from SeqSero2 and SISTR for all 24 isolates using the ONT sequencing data. All predictions were identical to the corresponding results generated by Illumina Hiseq. This pilot study indicated that the WGS data generated by the ONT sequencing system had the potential to be used to predict Salmonella serotypes within two hours of sequencing time, and the accuracy was comparable with that of the Illumina sequencing system.