MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling
| Autor: | Cheryl M.T. Dvorak, Michael P. Murtaugh, Douglas Marthaler, Shaoyuan Tan, April A. Estrada, Connie J. Gebhart |
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| Rok vydání: | 2019 |
| Předmět: |
Microbiology (medical)
Streptococcus suis Swine Sequence assembly Computational biology Microbial Sensitivity Tests Microbiology Genome 03 medical and health sciences Streptococcal Infections Drug Resistance Bacterial Consensus sequence Animals Humans Molecular Biology 030304 developmental biology Whole genome sequencing Swine Diseases 0303 health sciences biology Whole Genome Sequencing 030306 microbiology High-Throughput Nucleotide Sequencing Sequence Analysis DNA biology.organism_classification Anti-Bacterial Agents Minion Multilocus sequence typing Nanopore sequencing Genome Bacterial Multilocus Sequence Typing |
| Zdroj: | Journal of microbiological methods. 169 |
| ISSN: | 1872-8359 |
| Popis: | In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unparalleled potential as a rapid disease diagnostic tool due to its high mobility, accessibility, and short turnaround time. However, there is a lack of rigorous quality assessment and control processes standardizing the testing on the MinION, which is necessary for incorporation into a diagnostic workflow. Thus, our study examined the use of the MinION sequencer for bacterial whole genome generation and characterization. Using Streptococcus suis as a model, we optimized DNA isolation and treatments to be used for MinION sequencing and standardized de novo assembly to quickly generate a full-length consensus sequence achieving a 99.4% average accuracy. The consensus genomes from MinION sequencing were able to accurately predict the multilocus sequence type in 8 out of 10 samples and identified antimicrobial resistance profiles for 100% of the samples, despite the concern of a high error rate. The inability to unequivocally predict sequence types was due to difficulty in differentiating high identity alleles, which was overcome by applying additional error correction methods to increase consensus accuracy. This manuscript provides methods for the use of MinION sequencing for identification of S. suis genome sequence, sequence type, and antibiotic resistance profile that can be used as a framework for identification and classification of other pathogens. |
| Databáze: | OpenAIRE |
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