Rapid identification, capsular typing and molecular characterization of Streptococcus pneumoniae by using whole genome nanopore sequencing
| Autor: | Desiree Henares, S. Garcia-Garcia, Carmen Muñoz-Almagro, Amaresh Perez-Argüello, N. Timoneda |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
MinION
Epidemiology lcsh:QR1-502 Children -- Health and hygiene Genome lcsh:Microbiology Microorganismes patògens Whole genome sequencing Wg-MLST Streptococcus pneumoniae 0303 health sciences Pneumococs Pneumococcus Molecular Diagnostic Techniques Quellung reaction Niños -- Salud e higiene Research Article DNA Bacterial Microbiology (medical) FASTQ format Computational biology Biology Serogroup Microbiology Pneumococcal Infections 03 medical and health sciences Multiplex polymerase chain reaction Capsular typing Humans Epidemiología Neumococos Typing Epidemiologia Bacterial Capsules Genoma Infants -- Salut i higiene 030304 developmental biology 030306 microbiology Sequence Analysis DNA Nanopore Sequencing Minion Nanopore sequencing Genome Bacterial Multilocus Sequence Typing |
| Zdroj: | BMC Microbiology, Vol 20, Iss 1, Pp 1-6 (2020) BMC MICROBIOLOGY r-FSJD. Repositorio Institucional de Producción Científica de la Fundació Sant Joan de Déu instname BMC Microbiology r-FSJD: Repositorio Institucional de Producción Científica de la Fundació Sant Joan de Déu Fundació Sant Joan de Déu |
| ISSN: | 1471-2180 |
| DOI: | 10.1186/s12866-020-02032-x |
| Popis: | Background Whole genome sequencing has emerged as a useful tool for identification and molecular characterization of pathogens. MinION (Oxford Nanopore) is a real-time third generation sequencer whose portability, affordability and speed in data production make of it an attractive device for whole genome sequencing. The objective of this study is to evaluate MinION sequencer for pathogen identification and molecular characterization of Streptococcus pneumoniae isolated at a children’s Hospital. Whole genome sequencing of 32 Streptococcus pneumoniae invasive isolates, previously characterized by standard methods (Quellung reaction, Multiplex PCR and Sanger-MLST), were performed. DNA was extracted using ZymoBIOMICS DNA Microprep kit. Quantification and purity of DNA was assessed by Qubit and Nanodrop, respectively. Library preparation was performed using the Rapid Barcoding Kit. Real-time workflow EPI2ME platform “What’s it in my pot” was used for species identification. Fast5 sequences were converted into FASTQ by Albacore software. Reads were assembled using CANU software. PathogenWatch, genomic epidemiology and pubmlst online tools were used for capsular typing and/or whole genome-MLST profile. Results Rapid identification of Streptococcus pneumoniae was achieved by “What’s in my pot”. Capsular typing was correctly assigned with PathogenWatch in all 32 isolates at serogroup level and 24 at serotype level. Whole genome-MLST results obtained by genomic epidemiology and pubmlst were consistent with double locus variant clonal complex obtained by Sanger-MLST in 31 isolates. Conclusion MinION sequencer provides a rapid, cost-effective and promising pathway for performing WGS by a pocked-sized device for epidemiological purposes but improving its sequencing accuracy will make it more appealing to be used in clinical microbiology laboratories. |
| Databáze: | OpenAIRE |
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