Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective
ABSTRACT Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are presc...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2018-04-01
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| Series: | mSystems |
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| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00153-17 |
| _version_ | 1818855633522262016 |
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| author | Georgios D. Kitsios |
| author_facet | Georgios D. Kitsios |
| author_sort | Georgios D. Kitsios |
| collection | DOAJ |
| description | ABSTRACT Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a “one-size-fits-all” manner, which may be inappropriate for their individual needs and promote antibiotic resistance. My research focuses on leveraging next-generation sequencing of microbial DNA directly from patient samples for the development of new, culture-independent definitions of pneumonia. In this perspective article, I discuss the current state of the field and focus on the conceptual and research design challenges for clinical translation. With ongoing technological advancements and application of computational biology methods for assessing clinical validity and utility, I anticipate that sequencing-based diagnostics will soon be able to positively disrupt the way we think about, diagnose, and treat pulmonary infections. |
| first_indexed | 2024-12-19T08:11:42Z |
| format | Article |
| id | doaj.art-2aca53aa734848e1bb258b471c0beb1b |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-19T08:11:42Z |
| publishDate | 2018-04-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-2aca53aa734848e1bb258b471c0beb1b2022-12-21T20:29:36ZengAmerican Society for MicrobiologymSystems2379-50772018-04-013210.1128/mSystems.00153-17Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s PerspectiveGeorgios D. Kitsios0Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USAABSTRACT Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a “one-size-fits-all” manner, which may be inappropriate for their individual needs and promote antibiotic resistance. My research focuses on leveraging next-generation sequencing of microbial DNA directly from patient samples for the development of new, culture-independent definitions of pneumonia. In this perspective article, I discuss the current state of the field and focus on the conceptual and research design challenges for clinical translation. With ongoing technological advancements and application of computational biology methods for assessing clinical validity and utility, I anticipate that sequencing-based diagnostics will soon be able to positively disrupt the way we think about, diagnose, and treat pulmonary infections.https://journals.asm.org/doi/10.1128/mSystems.00153-17intensive care unitlung microbiomemetagenomicsnext-generation sequencingpneumonia |
| spellingShingle | Georgios D. Kitsios Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective mSystems intensive care unit lung microbiome metagenomics next-generation sequencing pneumonia |
| title | Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective |
| title_full | Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective |
| title_fullStr | Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective |
| title_full_unstemmed | Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective |
| title_short | Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective |
| title_sort | translating lung microbiome profiles into the next generation diagnostic gold standard for pneumonia a clinical investigator s perspective |
| topic | intensive care unit lung microbiome metagenomics next-generation sequencing pneumonia |
| url | https://journals.asm.org/doi/10.1128/mSystems.00153-17 |
| work_keys_str_mv | AT georgiosdkitsios translatinglungmicrobiomeprofilesintothenextgenerationdiagnosticgoldstandardforpneumoniaaclinicalinvestigatorsperspective |