Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics
IntroductionDuring the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sep...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-02-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1346762/full |
| _version_ | 1797294135342792704 |
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| author | Patricia Buendia Krystal Fernandez Castle Raley Ali Rahnavard Keith A. Crandall Keith A. Crandall Jose Guillermo Castro |
| author_facet | Patricia Buendia Krystal Fernandez Castle Raley Ali Rahnavard Keith A. Crandall Keith A. Crandall Jose Guillermo Castro |
| author_sort | Patricia Buendia |
| collection | DOAJ |
| description | IntroductionDuring the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving broad-spectrum antibiotics (BSA).MethodsThe saliva samples were analyzed with shotgun DNA metagenomics and respiratory RNA virome sequencing. Medical records for the period of hospitalization were obtained for all patients. Once hospitalization outcomes were known, patients were classified based on their COVID-19 disease severity and the antibiotics they received.ResultsOur study reveals that BSA regimens differentially impacted the human salivary microbiome and disease progression. 12 patients died and all of them received BSA. Significant associations were found between the composition of the COVID-19 saliva microbiome and BSA use, between SARS-CoV-2 genome coverage and severity of disease. We also found significant associations between the non-bacterial microbiome and severity of disease, with Candida albicans detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests Staphylococcus aureus as a potential risk factor for sepsis.DiscussionOur results indicate that the course of the infection may be explained by both monitoring antibiotic treatment and profiling a patient’s salivary microbiome, establishing a compelling link between microbiome and the specific antibiotic type and timing of treatment. This approach can aid with emergency room triage and inpatient management but also requires a better understanding of and access to narrow-spectrum agents that target pathogenic bacteria. |
| first_indexed | 2024-03-07T21:25:52Z |
| format | Article |
| id | doaj.art-6c3001ebf16549ea80a1e25d4fc8a3b0 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-07T21:25:52Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-6c3001ebf16549ea80a1e25d4fc8a3b02024-02-27T04:47:51ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2024-02-011510.3389/fmicb.2024.13467621346762Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibioticsPatricia Buendia0Krystal Fernandez1Castle Raley2Ali Rahnavard3Keith A. Crandall4Keith A. Crandall5Jose Guillermo Castro6Lifetime Omics, Miami, FL, United StatesLifetime Omics, Miami, FL, United StatesThe George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United StatesDepartment of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United StatesThe George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United StatesDepartment of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United StatesDivision of Infectious Diseases, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United StatesIntroductionDuring the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving broad-spectrum antibiotics (BSA).MethodsThe saliva samples were analyzed with shotgun DNA metagenomics and respiratory RNA virome sequencing. Medical records for the period of hospitalization were obtained for all patients. Once hospitalization outcomes were known, patients were classified based on their COVID-19 disease severity and the antibiotics they received.ResultsOur study reveals that BSA regimens differentially impacted the human salivary microbiome and disease progression. 12 patients died and all of them received BSA. Significant associations were found between the composition of the COVID-19 saliva microbiome and BSA use, between SARS-CoV-2 genome coverage and severity of disease. We also found significant associations between the non-bacterial microbiome and severity of disease, with Candida albicans detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests Staphylococcus aureus as a potential risk factor for sepsis.DiscussionOur results indicate that the course of the infection may be explained by both monitoring antibiotic treatment and profiling a patient’s salivary microbiome, establishing a compelling link between microbiome and the specific antibiotic type and timing of treatment. This approach can aid with emergency room triage and inpatient management but also requires a better understanding of and access to narrow-spectrum agents that target pathogenic bacteria.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1346762/fullbroad-spectrum antibioticsCOVID-19sepsissaliva microbiomeCandida albicans (C. albicans)Staphylococcus aureus (S. aureus) |
| spellingShingle | Patricia Buendia Krystal Fernandez Castle Raley Ali Rahnavard Keith A. Crandall Keith A. Crandall Jose Guillermo Castro Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics Frontiers in Microbiology broad-spectrum antibiotics COVID-19 sepsis saliva microbiome Candida albicans (C. albicans) Staphylococcus aureus (S. aureus) |
| title | Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics |
| title_full | Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics |
| title_fullStr | Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics |
| title_full_unstemmed | Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics |
| title_short | Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics |
| title_sort | hospital antimicrobial stewardship profiling the oral microbiome after exposure to covid 19 and antibiotics |
| topic | broad-spectrum antibiotics COVID-19 sepsis saliva microbiome Candida albicans (C. albicans) Staphylococcus aureus (S. aureus) |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1346762/full |
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