Sequencing of E. coli strain UTI89 on multiple sequencing platforms

Area of Science:

• Genomics
• Microbiology
• Bioinformatics

Background:

• Matched sequencing data across platforms is crucial for validating and comparing sequencing technologies.
• The commonly used Escherichia coli MG1655 strain is not representative of pathogenic strains.
• Pathogenic E. coli strains possess more complex genomes, including pathogenicity islands and plasmids.

Purpose of the Study:

• To generate and provide comprehensive, matched whole genome sequencing data for the pathogenic E. coli UTI89 strain.
• To establish a more medically relevant dataset for the validation of sequencing platforms and analytical methods.
• To facilitate the development and benchmarking of algorithms for complex bacterial genomes.

Main Methods:

• Whole genome sequencing of the E. coli UTI89 strain using PacBio RSII, Oxford Nanopore MinION R9.4, Ion Torrent, ABI SOLiD, and Illumina NextSeq.
• Generation of six new, matched sequencing datasets.
• Integration with publicly available datasets to create a near-complete suite of data from major sequencing platforms.

Main Results:

• Six new, matched whole genome sequencing datasets for the pathogenic E. coli UTI89 strain are now available.
• The UTI89 strain possesses a larger genome (10% increase), pathogenicity islands, and a large plasmid, characteristic of pathogenic isolates.
• The generated data provides a comprehensive resource for second- and third-generation sequencing technologies.

Conclusions:

• The UTI89 sequencing data serves as a valuable, medically relevant validation set for new sequencing technologies and bioinformatics tools.
• This resource aids in the development of algorithms for analyzing complex and pathogenic bacterial genomes.
• The availability of diverse, matched sequencing data enhances the reliability and comparability of genomic studies.