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Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli
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Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli
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Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli
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Journal Article
Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli
2019
Overview
Whole genome sequencing can provide essential public health information. However, it is now known that widely used short-read methods have the potential to miss some randomly-distributed segments of genomes. This can prevent phages, plasmids, and virulence factors from being detected or properly identified. Here, we compared assemblies of three complete Shiga toxin-producing Escherichia coli (STEC) O26:H11/H- genomes from two different sequence types (ST21 and 29), each acquired using the Nextera XT MiSeq, MinION nanopore-based sequencing, and Pacific Biosciences (PacBio) sequencing. Each closed genome consisted of a single chromosome, approximately 5.7 Mb for CFSAN027343, 5.6 Mb for CFSAN027346, and 5.4 MB for CFSAN027350. However, short-read whole genome sequencing (WGS) using Nextera XT MiSeq failed to identify some virulence genes in plasmids and on the chromosome, both of which were detected using the long-read platforms. Results from long-read MinION and PacBio allowed us to identify differences in plasmid content: a single 88 kb plasmid in CFSAN027343; a 157kb plasmid in CFSAN027350; and two plasmids in CFSAN027346 (one 95 Kb, one 72 Kb). These data enabled rapid characterization of the virulome, detection of antimicrobial genes, and composition/location of Stx phages. Taken together, positive correlations between the two long-read methods for determining plasmids, virulome, antimicrobial resistance genes, and phage composition support MinION sequencing as one accurate and economical option for closing STEC genomes and identifying specific virulence markers.
Publisher
Public Library of Science,Public Library of Science (PLoS)
Subject
/ Analysis
/ Anti-Bacterial Agents - pharmacology
/ Antiinfectives and antibacterials
/ Bacteria
/ Computer and Information Sciences
/ DNA
/ Drug Resistance, Bacterial - genetics
/ E coli
/ Escherichia coli Infections - drug therapy
/ Escherichia coli Infections - microbiology
/ Genes
/ Genomes
/ Genomics
/ Humans
/ Markers
/ Nanopore Sequencing - methods
/ Phages
/ Plasmids
/ Porosity
/ Research and Analysis Methods
/ Shiga-Toxigenic Escherichia coli - classification
/ Shiga-Toxigenic Escherichia coli - drug effects
/ Shiga-Toxigenic Escherichia coli - genetics
/ Toxins
/ Virulence Factors - analysis
