High-throughput rapid amplicon sequencing for multilocus sequence typing of from archived clinical DNA samples.

INTRODUCTION

Spillover events of have devastating effects on the wild sheep populations. Multilocus sequence typing (MLST) is used to monitor spillover events and the spread of between the sheep populations. Most studies involving the typing of have used Sanger sequencing. However, this technology is time-consuming, expensive, and is not well suited to efficient batch sample processing.

METHODS

Our study aimed to develop and validate an MLST workflow for typing of using Nanopore Rapid Barcoding sequencing and multiplex polymerase chain reaction (PCR). We compare the workflow with Nanopore Native Barcoding library preparation and Illumina MiSeq amplicon protocols to determine the most accurate and cost-effective method for sequencing multiplex amplicons. A multiplex PCR was optimized for four housekeeping genes of using archived DNA samples ( = 68) from nasal swabs.

RESULTS

Sequences recovered from Nanopore Rapid Barcoding correctly identified all MLST types with the shortest total workflow time and lowest cost per sample when compared with Nanopore Native Barcoding and Illumina MiSeq methods.

DISCUSSION

Our proposed workflow is a convenient and effective method for strain typing of and can be applied to other bacterial MLST schemes. The workflow is suitable for diagnostic settings, where reduced hands-on time, cost, and multiplexing capabilities are important.