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

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

10.21203/rs.3.rs-48863/v3 ◽

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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Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Gut Pathogens ◽

10.1186/s13099-021-00398-5 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Andreas Papoutsis ◽

Thomas Borody ◽

Siba Dolai ◽

Jordan Daniels ◽

Skylar Steinberg ◽

...

Keyword(s):

Next Generation Sequencing ◽

Nasopharyngeal Swab ◽

Whole Genome ◽

Rt Pcr ◽

Whole Genome Analysis ◽

Fecal Samples ◽

Oral Transmission ◽

Study Participants ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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 next-generation sequencing (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. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1).

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

Journal of Clinical Microbiology ◽

10.1128/jcm.02574-14 ◽

2014 ◽

Vol 53 (1) ◽

pp. 323-326 ◽

Cited By ~ 28

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.

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

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02718-20 ◽

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.

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

Open Forum Infectious Diseases ◽

10.1093/ofid/ofw042 ◽

2016 ◽

Vol 3 (1) ◽

Cited By ~ 8

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.

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Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

Antibiotics ◽

10.3390/antibiotics10101152 ◽

2021 ◽

Vol 10 (10) ◽

pp. 1152

Author(s):

Samuel M. Chekabab ◽

John R. Lawrence ◽

Alvin C. Alvarado ◽

Bernardo Z. Predicala ◽

Darren R. Korber

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Fecal Samples ◽

Time Points ◽

Conventional Farms ◽

Production Practices ◽

On Farm ◽

The Impact

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

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False COVID-19 cases due to contamination by inactivated virus vaccine

Clinical Infectious Diseases ◽

10.1093/cid/ciab684 ◽

2021 ◽

Author(s):

Kelvin Kai-Wang To ◽

Xin Li ◽

David Christopher Lung ◽

Jonathan Daniel Ip ◽

Wan-Mui Chan ◽

...

Keyword(s):

Public Health ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Virus Vaccine ◽

False Positive ◽

Spike Protein ◽

Whole Genome ◽

Rt Pcr ◽

Health Measures ◽

Respiratory Specimens

Abstract A false-positive SARS-CoV-2 RT-PCR result can lead to unnecessary public-health measures. We report two individuals whose respiratory specimens were contaminated by inactivated SARS-CoV-2 vaccine strain(CoronaVac), likely at vaccination premises. Incidentally, whole-genome sequencing of CoronaVac showed adaptive deletions on the spike protein, which do not result in observable changes of antigenicity.

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Setup, Validation, and Quality Control of a Centralized Whole-Genome-Sequencing Laboratory: Lessons Learned

Journal of Clinical Microbiology ◽

10.1128/jcm.00261-18 ◽

2018 ◽

Vol 56 (8) ◽

Cited By ~ 6

Author(s):

Cath Arnold ◽

Kirstin Edwards ◽

Meeta Desai ◽

Steve Platt ◽

Jonathan Green ◽

...

Keyword(s):

Public Health ◽

Quality Control ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Food Poisoning ◽

Drug Susceptibility ◽

Lessons Learned ◽

Microbial Pathogens ◽

Whole Genome ◽

Whole Genome Analysis

ABSTRACT Routine use of whole-genome analysis for infectious diseases can be used to enlighten various scenarios pertaining to public health, including identification of microbial pathogens, relating individual cases to an outbreak of infectious disease, establishing an association between an outbreak of food poisoning and a specific food vehicle, inferring drug susceptibility, source tracing of contaminants, and study of variations in the genome that affect pathogenicity/virulence. We describe the setup, validation, and ongoing verification of a centralized whole-genome-sequencing (WGS) laboratory to carry out sequencing for these public health functions for the National Infection Services, Public Health England, in the United Kingdom. The performance characteristics and quality control metrics measured during validation and verification of the entire end-to-end process (accuracy, precision, reproducibility, and repeatability) are described and include information regarding the automated pass and release of data to service users without intervention.

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Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis

Thorax ◽

10.1136/thoraxjnl-2018-211616 ◽

2019 ◽

Vol 74 (9) ◽

pp. 882-889 ◽

Cited By ~ 8

Author(s):

Keira A Cohen ◽

Abigail L Manson ◽

Thomas Abeel ◽

Christopher A Desjardins ◽

Sinead B Chapman ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Data Sharing ◽

Genome Sequencing ◽

Multidrug Resistant ◽

Whole Genome ◽

Whole Genome Analysis ◽

Global Spread ◽

Mdr Tb ◽

Global Movement ◽

Genomic Studies

BackgroundWhile the international spread of multidrug-resistant (MDR) Mycobacterium tuberculosis strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed.MethodsIn a global dataset of 5310 M. tuberculosis whole-genome sequences isolated from five continents, we performed a phylogenetic analysis to identify and characterise clades of MDR-TB with respect to geographic dispersion.ResultsExtensive international dissemination of MDR-TB was observed, with identification of 32 migrant MDR-TB clades with descendants isolated in 17 unique countries. Relatively recent movement of strains from both Beijing and non-Beijing lineages indicated successful global spread of varied genetic backgrounds. Migrant MDR-TB clade members shared relatively recent common ancestry, with a median estimate of divergence of 13–27 years. Migrant extensively drug-resistant (XDR)-TB clades were not observed, although development of XDR-TB within migratory MDR-TB clades was common.ConclusionsApplication of genomic techniques to investigate global MDR migration patterns revealed extensive global spread of MDR clades between countries of varying TB burden. Further expansion of genomic studies to incorporate isolates from diverse global settings into a single analysis, as well as data sharing platforms that facilitate genomic data sharing across country lines, may allow for future epidemiological analyses to monitor for international transmission of MDR-TB. In addition, efforts to perform routine whole-genome sequencing on all newly identified M. tuberculosis, like in England, will serve to better our understanding of the transmission dynamics of MDR-TB globally.

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