Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing.

ABSTRACT: Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic relatedness and to look for microevolutionary events in the core and accessory genomes to assess the within-outbreak variation of four genetically and epidemiologically linked isolates. Analysis of both Illumina and ONT sequencing data detected one SNP between the four sequences of the outbreak isolates. The variant calling procedure highlighted the importance of masking homologous sequences in the reference genome regardless of the sequencing technology used. Variant calling also highlighted the syste

SUBMITTER: Greig DR 

PROVIDER: S-EPMC8190617 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature