Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses
Objectives: Infectious diseases are common but are not easily or readily diagnosed with current methodologies. This problem is further exacerbated by the constant presence of mutated, emerging, and novel pathogens. One of the most common sites of infection by many pathogens is the human throat. Howe...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-09-01
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| Series: | International Journal of Infectious Diseases |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1201971222003265 |
| _version_ | 1811274948178608128 |
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| author | Ryan Toma Nathan Duval Nan Shen Pedro J. Torres Francine R. Camacho Jiapeng Chen Oyetunji Ogundijo Guruduth Banavar Momchilo Vuyisich |
| author_facet | Ryan Toma Nathan Duval Nan Shen Pedro J. Torres Francine R. Camacho Jiapeng Chen Oyetunji Ogundijo Guruduth Banavar Momchilo Vuyisich |
| author_sort | Ryan Toma |
| collection | DOAJ |
| description | Objectives: Infectious diseases are common but are not easily or readily diagnosed with current methodologies. This problem is further exacerbated by the constant presence of mutated, emerging, and novel pathogens. One of the most common sites of infection by many pathogens is the human throat. However, there is no universal diagnostic test that can distinguish these pathogens. Metatranscriptomic (MT) analysis of the throat represents an important and novel development in infectious disease detection and characterization, because it is able to identify all pathogens using a fully unbiased approach. Methods: To test the utility of an MT approach to pathogen detection, throat samples were collected from participants before, during, and after an acute sickness. Results: Clear sickness-associated shifts in pathogenic microorganisms were detected in the patients. Important insights into microbial functions and antimicrobial resistance genes were obtained. Conclusion: MT analysis of the throat represents an effective method for the unbiased identification and characterization of pathogens. Because MT data include all microorganisms in the sample, this approach should not only allow the identification of pathogens, but provide an understanding of the effects of the resident throat microbiome in the context of human health and disease. |
| first_indexed | 2024-04-12T23:29:31Z |
| format | Article |
| id | doaj.art-54d501c2d5d24b0098081f92ea81d513 |
| institution | Directory Open Access Journal |
| issn | 1201-9712 |
| language | English |
| last_indexed | 2024-04-12T23:29:31Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | International Journal of Infectious Diseases |
| spelling | doaj.art-54d501c2d5d24b0098081f92ea81d5132022-12-22T03:12:20ZengElsevierInternational Journal of Infectious Diseases1201-97122022-09-01122260265Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analysesRyan Toma0Nathan Duval1Nan Shen2Pedro J. Torres3Francine R. Camacho4Jiapeng Chen5Oyetunji Ogundijo6Guruduth Banavar7Momchilo Vuyisich8Corresponding author.; Viome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAViome Life Sciences, Inc., Bellevue, WA and New York, NY, USAObjectives: Infectious diseases are common but are not easily or readily diagnosed with current methodologies. This problem is further exacerbated by the constant presence of mutated, emerging, and novel pathogens. One of the most common sites of infection by many pathogens is the human throat. However, there is no universal diagnostic test that can distinguish these pathogens. Metatranscriptomic (MT) analysis of the throat represents an important and novel development in infectious disease detection and characterization, because it is able to identify all pathogens using a fully unbiased approach. Methods: To test the utility of an MT approach to pathogen detection, throat samples were collected from participants before, during, and after an acute sickness. Results: Clear sickness-associated shifts in pathogenic microorganisms were detected in the patients. Important insights into microbial functions and antimicrobial resistance genes were obtained. Conclusion: MT analysis of the throat represents an effective method for the unbiased identification and characterization of pathogens. Because MT data include all microorganisms in the sample, this approach should not only allow the identification of pathogens, but provide an understanding of the effects of the resident throat microbiome in the context of human health and disease.http://www.sciencedirect.com/science/article/pii/S1201971222003265Antibiotic resistanceInfectious diseaseMetatranscriptomicsPathogen detectionThroat swab |
| spellingShingle | Ryan Toma Nathan Duval Nan Shen Pedro J. Torres Francine R. Camacho Jiapeng Chen Oyetunji Ogundijo Guruduth Banavar Momchilo Vuyisich Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses International Journal of Infectious Diseases Antibiotic resistance Infectious disease Metatranscriptomics Pathogen detection Throat swab |
| title | Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses |
| title_full | Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses |
| title_fullStr | Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses |
| title_full_unstemmed | Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses |
| title_short | Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses |
| title_sort | pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses |
| topic | Antibiotic resistance Infectious disease Metatranscriptomics Pathogen detection Throat swab |
| url | http://www.sciencedirect.com/science/article/pii/S1201971222003265 |
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