Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype
Summary: Antimicrobial resistance poses a serious threat to global public health. The COVID-19 pandemic underscored the need to monitor the dissemination of antimicrobial resistance genes and understand the mechanisms driving this process. In this study, we analyzed changes to the oropharyngeal and...
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Elsevier
2024-12-01
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| author | Elizaveta V. Starikova Yulia S. Galeeva Dmitry E. Fedorov Elena V. Korneenko Anna S. Speranskaya Oksana V. Selezneva Polina Y. Zoruk Ksenia M. Klimina Vladimir A. Veselovsky Maxim D. Morozov Daria I. Boldyreva Evgenii I. Olekhnovich Alexander I. Manolov Alexander V. Pavlenko Ivan E. Kozlov Oleg O. Yanushevich Natella I. Krikheli Oleg V. Levchenko Dmitry N. Andreev Filipp S. Sokolov Aleksey K. Fomenko Mikhail K. Devkota Nikolai G. Andreev Andrey V. Zaborovsky Sergei V. Tsaregorodtsev Vladimir V. Evdokimov Petr A. Bely Igor V. Maev Vadim M. Govorun Elena N. Ilina |
| author_facet | Elizaveta V. Starikova Yulia S. Galeeva Dmitry E. Fedorov Elena V. Korneenko Anna S. Speranskaya Oksana V. Selezneva Polina Y. Zoruk Ksenia M. Klimina Vladimir A. Veselovsky Maxim D. Morozov Daria I. Boldyreva Evgenii I. Olekhnovich Alexander I. Manolov Alexander V. Pavlenko Ivan E. Kozlov Oleg O. Yanushevich Natella I. Krikheli Oleg V. Levchenko Dmitry N. Andreev Filipp S. Sokolov Aleksey K. Fomenko Mikhail K. Devkota Nikolai G. Andreev Andrey V. Zaborovsky Sergei V. Tsaregorodtsev Vladimir V. Evdokimov Petr A. Bely Igor V. Maev Vadim M. Govorun Elena N. Ilina |
| author_sort | Elizaveta V. Starikova |
| collection | DOAJ |
| description | Summary: Antimicrobial resistance poses a serious threat to global public health. The COVID-19 pandemic underscored the need to monitor the dissemination of antimicrobial resistance genes and understand the mechanisms driving this process. In this study, we analyzed changes to the oropharyngeal and fecal resistomes of patients with COVID-19 undergoing therapy in a hospital setting. A targeted sequencing panel of 4,937 resistance genes was used to comprehensively characterize resistomes. Our results demonstrated that the oropharyngeal resistome is homogeneous, showing low variability over time. In contrast, fecal samples clustered into two distinct resistotypes that were only partially related to enterotypes. Approximately half of the patients changed their resistotype within a week of therapy, with the majority transitioning to a less diverse and ermB-dominated resistotype 2. Common macrolide resistance genes were identified in over 80% of both oropharyngeal and fecal samples, likely originating from streptococci. Our findings suggest that the fecal resistome is a dynamic system that can exist in certain “states” and is capable of transitioning from one state to another. To date, this is the first study to comprehensively describe the oropharyngeal resistome and its variability over time, and one of the first studies to demonstrate the temporal dynamics of the fecal resistotypes. |
| format | Article |
| id | doaj-art-934e30453e9049b0b29a060575cd80e7 |
| institution | OA Journals |
| issn | 2589-0042 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
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| spelling | doaj-art-934e30453e9049b0b29a060575cd80e72025-08-20T01:59:47ZengElsevieriScience2589-00422024-12-01271211131910.1016/j.isci.2024.111319Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotypeElizaveta V. Starikova0Yulia S. Galeeva1Dmitry E. Fedorov2Elena V. Korneenko3Anna S. Speranskaya4Oksana V. Selezneva5Polina Y. Zoruk6Ksenia M. Klimina7Vladimir A. Veselovsky8Maxim D. Morozov9Daria I. Boldyreva10Evgenii I. Olekhnovich11Alexander I. Manolov12Alexander V. Pavlenko13Ivan E. Kozlov14Oleg O. Yanushevich15Natella I. Krikheli16Oleg V. Levchenko17Dmitry N. Andreev18Filipp S. Sokolov19Aleksey K. Fomenko20Mikhail K. Devkota21Nikolai G. Andreev22Andrey V. Zaborovsky23Sergei V. Tsaregorodtsev24Vladimir V. Evdokimov25Petr A. Bely26Igor V. Maev27Vadim M. Govorun28Elena N. Ilina29Research Institute for Systems Biology and Medicine, Moscow 117246, Russian Federation; Corresponding authorResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationLopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian FederationLopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian FederationLopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian FederationLopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian FederationLopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian FederationLopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian FederationLopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationMoscow State University of Medicine and Dentistry, Moscow 127473, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationResearch Institute for Systems Biology and Medicine, Moscow 117246, Russian FederationSummary: Antimicrobial resistance poses a serious threat to global public health. The COVID-19 pandemic underscored the need to monitor the dissemination of antimicrobial resistance genes and understand the mechanisms driving this process. In this study, we analyzed changes to the oropharyngeal and fecal resistomes of patients with COVID-19 undergoing therapy in a hospital setting. A targeted sequencing panel of 4,937 resistance genes was used to comprehensively characterize resistomes. Our results demonstrated that the oropharyngeal resistome is homogeneous, showing low variability over time. In contrast, fecal samples clustered into two distinct resistotypes that were only partially related to enterotypes. Approximately half of the patients changed their resistotype within a week of therapy, with the majority transitioning to a less diverse and ermB-dominated resistotype 2. Common macrolide resistance genes were identified in over 80% of both oropharyngeal and fecal samples, likely originating from streptococci. Our findings suggest that the fecal resistome is a dynamic system that can exist in certain “states” and is capable of transitioning from one state to another. To date, this is the first study to comprehensively describe the oropharyngeal resistome and its variability over time, and one of the first studies to demonstrate the temporal dynamics of the fecal resistotypes.http://www.sciencedirect.com/science/article/pii/S2589004224025446Clinical microbiologyEvolutionary mechanismsMicrobial geneticsMicrobiome |
| spellingShingle | Elizaveta V. Starikova Yulia S. Galeeva Dmitry E. Fedorov Elena V. Korneenko Anna S. Speranskaya Oksana V. Selezneva Polina Y. Zoruk Ksenia M. Klimina Vladimir A. Veselovsky Maxim D. Morozov Daria I. Boldyreva Evgenii I. Olekhnovich Alexander I. Manolov Alexander V. Pavlenko Ivan E. Kozlov Oleg O. Yanushevich Natella I. Krikheli Oleg V. Levchenko Dmitry N. Andreev Filipp S. Sokolov Aleksey K. Fomenko Mikhail K. Devkota Nikolai G. Andreev Andrey V. Zaborovsky Sergei V. Tsaregorodtsev Vladimir V. Evdokimov Petr A. Bely Igor V. Maev Vadim M. Govorun Elena N. Ilina Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype iScience Clinical microbiology Evolutionary mechanisms Microbial genetics Microbiome |
| title | Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype |
| title_full | Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype |
| title_fullStr | Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype |
| title_full_unstemmed | Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype |
| title_short | Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype |
| title_sort | oropharyngeal resistome remains stable during covid 19 therapy while fecal resistome shifts toward a less diverse resistotype |
| topic | Clinical microbiology Evolutionary mechanisms Microbial genetics Microbiome |
| url | http://www.sciencedirect.com/science/article/pii/S2589004224025446 |
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