Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks
| Autor: | Heidi Nelson, Patricio Jeraldo, Angela J. Taylor, Nicholas Chia, Travis M. Drucker, Daniel J. Quest, Jun Chen, Robin Patel, Julie A. Johnson, Scott A. Cunningham, Gregory D. Jenkins, Dave Boxrud |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Microbiology (medical) Methicillin-Resistant Staphylococcus aureus Epidemiology 030106 microbiology Computational biology Biology Staphylococcal infections Genome SmaI Disease Outbreaks 03 medical and health sciences Pulsed-field gel electrophoresis medicine Cluster Analysis Humans Typing Whole genome sequencing Molecular Epidemiology Whole Genome Sequencing Computational Biology Staphylococcal Infections medicine.disease Molecular Typing Multilocus sequence typing Restriction digest |
| Zdroj: | Journal of clinical microbiology. 55(6) |
| ISSN: | 1098-660X |
| Popis: | Whole-genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus . Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied. Near-complete genomes, assembled de novo with paired-end and long-mate-pair (8 kb) libraries were first assembled and analyzed utilizing an in-house assembly and analytical informatics pipeline. In addition, paired-end data were assembled and analyzed using a commercial software package. Single nucleotide variant (SNP) analysis was performed using the in-house pipeline. Two assembly strategies were used to generate core genome multilocus sequence typing (cgMLST) data. First, the near-complete genome data generated with the in-house pipeline were imported into the commercial software and used to perform cgMLST analysis. Second, the commercial software was used to assemble paired-end data, and resolved assemblies were used to perform cgMLST. Similar isolate clustering was observed using SNP calling and cgMLST, regardless of data assembly strategy. All methods provided more discrimination between outbreaks than did PFGE. Overall, all of the evaluated WGS strategies yielded statistically similar results for S. aureus typing. |
| Databáze: | OpenAIRE |
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