Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F.
| Title: | Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F. |
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| Authors: | Xianding Deng, Memari, Nader, Teatero, Sarah, Athey, Taryn, Isabel, Marc, Mazzulli, Tony, Fittipaldi, Nahuel, Gubbay, Jonathan B., Yildirim, Suleyman |
| Source: | Frontiers in Microbiology; 12/27/2016, Vol. 7, p1-11, 11p |
| Subject Terms: | STREPTOCOCCUS pneumoniae, DRUG resistance in bacteria, GENOTYPES |
| Abstract: | Background: Molecular typing is essential for inferring genetic relatedness between bacterial pathogens. In this study, we applied whole genome sequencing (WGS) for rapid prediction of sequence type and antibiotic resistance for invasive pneumococcal isolates. Methods: 240 isolates from adults (≥50 years old) in Ontario, Canada during 2009 to 2013 were subjected to WGS. Sequence type, antibiotic susceptibility and resistance were predicted directly from short reads. Emerging non-vaccine serotype 22F was further characterized by WGS. Results: Sequence type was successfully determined for 98.3% of isolates. The overall sensitivity and specificity for antibiotic resistance prediction were 95 and 100% respectively, compared to standard susceptibility testing methods. WGS-based phylogeny divided emerging 22F (ST433) strains into two distinct clades: clade A harboring a 23 kb-prophage and anti-phage PhD/Doc system and clade B with virulence-related proteases. Five isolates in clade A developed macrolide resistance via 5.1 kb mega element recombination (encoding mefE and msrD), while one isolate in clade B displayed quinolone resistance via a gyrA mutation. Conclusions: WGS is valuable for routine surveillance of pneumococcal clinical isolates and facilitates prediction of genotype and antibiotic resistance. The emergence of 22F in Ontario in the post-vaccine era and evidence of evolution and divergence of the 22F population warrants heightened pneumococcal molecular surveillance. [ABSTRACT FROM AUTHOR] |
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| Database: | Complementary Index |
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| Items | – Name: Title Label: Title Group: Ti Data: Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Xianding+Deng%22">Xianding Deng</searchLink><br /><searchLink fieldCode="AR" term="%22Memari%2C+Nader%22">Memari, Nader</searchLink><br /><searchLink fieldCode="AR" term="%22Teatero%2C+Sarah%22">Teatero, Sarah</searchLink><br /><searchLink fieldCode="AR" term="%22Athey%2C+Taryn%22">Athey, Taryn</searchLink><br /><searchLink fieldCode="AR" term="%22Isabel%2C+Marc%22">Isabel, Marc</searchLink><br /><searchLink fieldCode="AR" term="%22Mazzulli%2C+Tony%22">Mazzulli, Tony</searchLink><br /><searchLink fieldCode="AR" term="%22Fittipaldi%2C+Nahuel%22">Fittipaldi, Nahuel</searchLink><br /><searchLink fieldCode="AR" term="%22Gubbay%2C+Jonathan+B%2E%22">Gubbay, Jonathan B.</searchLink><br /><searchLink fieldCode="AR" term="%22Yildirim%2C+Suleyman%22">Yildirim, Suleyman</searchLink> – Name: TitleSource Label: Source Group: Src Data: Frontiers in Microbiology; 12/27/2016, Vol. 7, p1-11, 11p – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22STREPTOCOCCUS+pneumoniae%22">STREPTOCOCCUS pneumoniae</searchLink><br /><searchLink fieldCode="DE" term="%22DRUG+resistance+in+bacteria%22">DRUG resistance in bacteria</searchLink><br /><searchLink fieldCode="DE" term="%22GENOTYPES%22">GENOTYPES</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Background: Molecular typing is essential for inferring genetic relatedness between bacterial pathogens. In this study, we applied whole genome sequencing (WGS) for rapid prediction of sequence type and antibiotic resistance for invasive pneumococcal isolates. Methods: 240 isolates from adults (≥50 years old) in Ontario, Canada during 2009 to 2013 were subjected to WGS. Sequence type, antibiotic susceptibility and resistance were predicted directly from short reads. Emerging non-vaccine serotype 22F was further characterized by WGS. Results: Sequence type was successfully determined for 98.3% of isolates. The overall sensitivity and specificity for antibiotic resistance prediction were 95 and 100% respectively, compared to standard susceptibility testing methods. WGS-based phylogeny divided emerging 22F (ST433) strains into two distinct clades: clade A harboring a 23 kb-prophage and anti-phage PhD/Doc system and clade B with virulence-related proteases. Five isolates in clade A developed macrolide resistance via 5.1 kb mega element recombination (encoding mefE and msrD), while one isolate in clade B displayed quinolone resistance via a gyrA mutation. Conclusions: WGS is valuable for routine surveillance of pneumococcal clinical isolates and facilitates prediction of genotype and antibiotic resistance. The emergence of 22F in Ontario in the post-vaccine era and evidence of evolution and divergence of the 22F population warrants heightened pneumococcal molecular surveillance. [ABSTRACT FROM AUTHOR] – Name: Abstract Label: Group: Ab Data: <i>Copyright of Frontiers in Microbiology is the property of Frontiers Media S.A. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.3389/fmicb.2016.02099 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 1 Subjects: – SubjectFull: STREPTOCOCCUS pneumoniae Type: general – SubjectFull: DRUG resistance in bacteria Type: general – SubjectFull: GENOTYPES Type: general Titles: – TitleFull: Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Xianding Deng – PersonEntity: Name: NameFull: Memari, Nader – PersonEntity: Name: NameFull: Teatero, Sarah – PersonEntity: Name: NameFull: Athey, Taryn – PersonEntity: Name: NameFull: Isabel, Marc – PersonEntity: Name: NameFull: Mazzulli, Tony – PersonEntity: Name: NameFull: Fittipaldi, Nahuel – PersonEntity: Name: NameFull: Gubbay, Jonathan B. – PersonEntity: Name: NameFull: Yildirim, Suleyman IsPartOfRelationships: – BibEntity: Dates: – D: 27 M: 12 Text: 12/27/2016 Type: published Y: 2016 Identifiers: – Type: issn-print Value: 1664302X Numbering: – Type: volume Value: 7 Titles: – TitleFull: Frontiers in Microbiology Type: main |
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