scholarly journals Application of Whole-Genome Sequencing to an Unusual Outbreak of Invasive Group A Streptococcal Disease

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
Jessica Galloway-Peña ◽  
Meredith E. Clement ◽  
Batu K. Sharma Kuinkel ◽  
Felicia Ruffin ◽  
Anthony R. Flores ◽  
...  
Keyword(s):  
Point Source ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Invasive Group ◽  
Streptococcal Disease ◽  
Group A ◽  
Genome Analyses

Abstract Whole-genome analysis was applied to investigate atypical point-source transmission of 2 invasive group A streptococcal (GAS) infections. Isolates were serotype M4, ST39, and genetically indistinguishable. Comparison with MGAS10750 revealed nonsynonymous polymorphisms in ropB and increased speB transcription. This study demonstrates the usefulness of whole-genome analyses for GAS outbreaks.

scholarly journals Severe emm89 Group A Streptococcal Disease Characterized by Toxic Shock and Endocarditis

2019 ◽  
Vol 2019 ◽  
pp. 1-4
Author(s):  
Morouge Alramadhan ◽  
Gloria P. Heresi ◽  
Anthony R. Flores
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rare Case ◽  
Whole Genome ◽  
Toxic Shock ◽  
Invasive Group ◽  
Streptococcal Disease ◽  
Group A ◽  
Common Infections

Invasive group A Streptococcus infections are associated with diverse presentations. We report a severe, rare case of GAS infection with dissemination including endocarditis and STSS. While whole genome sequencing of blood and pharyngeal isolates did not reveal any unique features attributable to the severe presentation, our approach serves as a template for investigation of severe manifestations of common infections.

scholarly journals Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy

2014 ◽  
Vol 53 (1) ◽  
pp. 323-326 ◽  
Author(s):  
Birgit De Smet ◽  
Derek S. Sarovich ◽  
Erin P. Price ◽  
Mark Mayo ◽  
Vanessa Theobald ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Burkholderia Pseudomallei ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Sequence Types

Burkholderia pseudomalleiisolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.

scholarly journals Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

2020 ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment NGS from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.

scholarly journals Surveillance of Influenza A resistance to polymerase complex inhibitors by whole genome analysis, 2016-17, 2017-18 and 2018-19 Seasons, Eastern Spain

2021 ◽  
Author(s):  
Beatriz Mengual-Chuliá ◽  
Andrés Alonso-Cordero ◽  
Laura Cano ◽  
M. del Mar Mosquera ◽  
Patricia de Molina ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Influenza A ◽  
Natural Resistance ◽  
Whole Genome ◽  
Influenza A Viruses ◽  
Whole Genome Analysis ◽  
Molecular Surveillance ◽  
Polymerase Complex

Molecular surveillance by whole genome sequencing was used to monitor the susceptibility of circulating Influenza A viruses to three polymerase complex inhibitors. A total of 12 resistance substitutions were found among 285 genomes analysed, but none associated with high levels of resistance. Natural resistance to these influenza A antivirals is currently uncommon.

scholarly journals Whole-genome sequencing in the investigation of recurrent invasive group A streptococcus outbreaks in a maternity unit

2019 ◽  
Vol 101 (3) ◽  
pp. 320-326 ◽  
Author(s):  
H. Dickinson ◽  
M. Reacher ◽  
B. Nazareth ◽  
H. Eagle ◽  
D. Fowler ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Group A Streptococcus ◽  
Whole Genome ◽  
Maternity Unit ◽  
Invasive Group ◽  
Group A

scholarly journals A Protracted Outbreak of Invasive Group A Streptococcal Infection at a UK Long-Term Facility Investigated Using Whole Genome Sequencing

2016 ◽  
Vol 3 (suppl_1) ◽  
Author(s):  
Savita Gossain ◽  
Vicki Chalker ◽  
Georgia Kapatai ◽  
Juliana Coelho ◽  
Huda Mohamed ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Streptococcal Infection ◽  
Whole Genome ◽  
Invasive Group ◽  
Group A

scholarly journals Increase in Invasive Group A Streptococcal Disease and Emergence of Mucoid Strains in a Pediatric Population: February–June 2017

2019 ◽  
Vol 6 (7) ◽  
Author(s):  
Lorne W Walker ◽  
Lindsay Montoya ◽  
Sopio Chochua ◽  
Bernard Beall ◽  
Michael Green
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Hospital Admissions ◽  
Disease Incidence ◽  
Tertiary Care ◽  
Incidence Rates ◽  
Screening Tests ◽  
Whole Genome ◽  
Invasive Group ◽  
Group A

Abstract Background Infection with group A Streptococcus (GAS) can cause severe systemic and locally invasive disease. Invasive group A streptococcal (iGAS) disease incidence varies both seasonally and year-to-year, and it may exhibit clustered outbreaks. We observed an upswing in iGAS cases at a tertiary care Children’s Hospital, prompting further characterization of local iGAS disease. Methods Cases of iGAS disease were abstracted from the medical record by manual chart review of all positive screening tests and cultures for GAS over a 4-year span. Incidence rates per 1000 hospital admissions and per 100 positive GAS tests were calculated and compared. Selected isolates were further characterized by whole-genome sequencing. Results Significant year-to-year differences in per-admission iGAS incidence rate were observed in February and June, although per-positive test incidence rates were not significantly different. Whole-genome sequencing revealed 2 dominant serotypes—emm3 and emm6—with high rates of mucoid phenotype and systemic bacteremia. Conclusions We document a significant but transient increase in iGAS disease incidence in 2 months of 2017. Genome sequencing revealed 2 dominant serotypes associated with mucoid phenotypes and severe disease, highlighting the dynamic nature of iGAS disease pattern.

scholarly journals Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

2020 ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment NGS from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.

scholarly journals Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

2021 ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment NGS from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.

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