SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adults
IntroductionThe COVID-19 pandemic has impacted global health and altered respiratory pathogens. While SARS-CoV-2 vaccines have mitigated COVID-19 severity, emerging variants remain challenging. Co-infection of Streptococcus pneumoniae with respiratory viruses is associated with increased disease sev...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Cellular and Infection Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1624521/full |
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| author | Sara Calvo-Silveria Sara Calvo-Silveria Lucía Fernández-Delgado Lucía Fernández-Delgado Aida González-Díaz Aida González-Díaz Rocío España-Bonilla Laura Calatayud Laura Calatayud Jordi Niubó Sara Martí Sara Martí Sara Martí Ma Ángeles Domínguez Ma Ángeles Domínguez Ma Ángeles Domínguez Jordi Càmara Jordi Càmara Carmen Ardanuy Carmen Ardanuy Carmen Ardanuy |
| author_facet | Sara Calvo-Silveria Sara Calvo-Silveria Lucía Fernández-Delgado Lucía Fernández-Delgado Aida González-Díaz Aida González-Díaz Rocío España-Bonilla Laura Calatayud Laura Calatayud Jordi Niubó Sara Martí Sara Martí Sara Martí Ma Ángeles Domínguez Ma Ángeles Domínguez Ma Ángeles Domínguez Jordi Càmara Jordi Càmara Carmen Ardanuy Carmen Ardanuy Carmen Ardanuy |
| author_sort | Sara Calvo-Silveria |
| collection | DOAJ |
| description | IntroductionThe COVID-19 pandemic has impacted global health and altered respiratory pathogens. While SARS-CoV-2 vaccines have mitigated COVID-19 severity, emerging variants remain challenging. Co-infection of Streptococcus pneumoniae with respiratory viruses is associated with increased disease severity, but its relationship with SARS-CoV-2 remains unclear. This study aims to analyze their co-occurrence, focusing on disease progression, colonization rates and clinical outcomes.MethodsTo this end, three approaches were used. First, a laboratory-based analysis of invasive pneumococcal disease (IPD) in adults (2019-2023). Second, a retrospective analysis of COVID-19 clinical cases with pneumococcal isolates (March,2020–December,2023), including clinical and microbiological data such as patients’ comorbidities, episode severity, serotypes and resistance genes. Third, a retrospective analysis to assess pneumococcal colonization in SARS-CoV-2 positive nasopharyngeal samples (May-October 2023; dual-target RT-PCR). WGS and bioinformatics were performed on both bacterial (serotyping and resistance analysis) and viral genomes (lineage determination). Statistical comparisons (Chi-square, Fisher’s test), with significance set at p<0.05.ResultsFirst, IPD incidence declined during the COVID-19 pandemic, with cases dropping by 70% in both age groups (18–64 and >64) from 2019 to 2021 and rebounding after 2021, concomitant with the relaxation of non-pharmaceutical measures, especially among older adults. Pneumococcal serotype distribution remained stable with dominance of serotypes 3 and 8. Serotype 12F disappeared during the lockdown and re-emerged in 2023 as a multidrug-resistant sub-lineage through multi-fragment recombination, derived from the former GPSC26. Second, SARS-CoV-2 and pneumococcal co-infection occurred in 66 hospitalized patients, mainly by serotype 3 (15%), with resistance to macrolides (26.3%) and tetracycline (22.8%). Third, pneumococcal colonization in SARS-CoV-2-infected patients was low (2.8%), especially in older adults (>64 years; 1.5%), with slightly higher rates in severe cases (4.7% vs 2.5%; p=0.404; IC95% 0.13-3.05) and young adults (4.8% vs 1.5%; p=0.04; IC95% 0.92-15.21). Compared to colonized patients, those with co-infection had more comorbidities, more severe clinical presentations, higher hospitalization rates and lower vaccination rates.DiscussionThis study highlights how non-pharmaceutical measures disrupt S. pneumoniae dynamics. Although pneumococcal colonization in SARS-CoV-2 patients appears to be infrequent, our data suggest an increase in disease severity. Then, vaccination programs and their monitoring remain critical in the prevention of respiratory infections. |
| format | Article |
| id | doaj-art-7aac2423aa5f45b7b456978bae321395 |
| institution | DOAJ |
| issn | 2235-2988 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj-art-7aac2423aa5f45b7b456978bae3213952025-08-20T03:12:46ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882025-07-011510.3389/fcimb.2025.16245211624521SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adultsSara Calvo-Silveria0Sara Calvo-Silveria1Lucía Fernández-Delgado2Lucía Fernández-Delgado3Aida González-Díaz4Aida González-Díaz5Rocío España-Bonilla6Laura Calatayud7Laura Calatayud8Jordi Niubó9Sara Martí10Sara Martí11Sara Martí12Ma Ángeles Domínguez13Ma Ángeles Domínguez14Ma Ángeles Domínguez15Jordi Càmara16Jordi Càmara17Carmen Ardanuy18Carmen Ardanuy19Carmen Ardanuy20Department of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, SpainDepartment of Medicine, School of Medicine and Health Sciences, University of Barcelona, Barcelona, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Infectious Diseases (CIBERINFC), ISCIII, Madrid, SpainDepartment of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, SpainDepartment of Microbiology, Hospital Universitari de Bellvitge – IDIBELL-UB, Barcelona, SpainResearch Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, SpainDepartment of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, SpainIntroductionThe COVID-19 pandemic has impacted global health and altered respiratory pathogens. While SARS-CoV-2 vaccines have mitigated COVID-19 severity, emerging variants remain challenging. Co-infection of Streptococcus pneumoniae with respiratory viruses is associated with increased disease severity, but its relationship with SARS-CoV-2 remains unclear. This study aims to analyze their co-occurrence, focusing on disease progression, colonization rates and clinical outcomes.MethodsTo this end, three approaches were used. First, a laboratory-based analysis of invasive pneumococcal disease (IPD) in adults (2019-2023). Second, a retrospective analysis of COVID-19 clinical cases with pneumococcal isolates (March,2020–December,2023), including clinical and microbiological data such as patients’ comorbidities, episode severity, serotypes and resistance genes. Third, a retrospective analysis to assess pneumococcal colonization in SARS-CoV-2 positive nasopharyngeal samples (May-October 2023; dual-target RT-PCR). WGS and bioinformatics were performed on both bacterial (serotyping and resistance analysis) and viral genomes (lineage determination). Statistical comparisons (Chi-square, Fisher’s test), with significance set at p<0.05.ResultsFirst, IPD incidence declined during the COVID-19 pandemic, with cases dropping by 70% in both age groups (18–64 and >64) from 2019 to 2021 and rebounding after 2021, concomitant with the relaxation of non-pharmaceutical measures, especially among older adults. Pneumococcal serotype distribution remained stable with dominance of serotypes 3 and 8. Serotype 12F disappeared during the lockdown and re-emerged in 2023 as a multidrug-resistant sub-lineage through multi-fragment recombination, derived from the former GPSC26. Second, SARS-CoV-2 and pneumococcal co-infection occurred in 66 hospitalized patients, mainly by serotype 3 (15%), with resistance to macrolides (26.3%) and tetracycline (22.8%). Third, pneumococcal colonization in SARS-CoV-2-infected patients was low (2.8%), especially in older adults (>64 years; 1.5%), with slightly higher rates in severe cases (4.7% vs 2.5%; p=0.404; IC95% 0.13-3.05) and young adults (4.8% vs 1.5%; p=0.04; IC95% 0.92-15.21). Compared to colonized patients, those with co-infection had more comorbidities, more severe clinical presentations, higher hospitalization rates and lower vaccination rates.DiscussionThis study highlights how non-pharmaceutical measures disrupt S. pneumoniae dynamics. Although pneumococcal colonization in SARS-CoV-2 patients appears to be infrequent, our data suggest an increase in disease severity. Then, vaccination programs and their monitoring remain critical in the prevention of respiratory infections.https://www.frontiersin.org/articles/10.3389/fcimb.2025.1624521/fullStreptococcus pneumoniaeserotypesSARS-CoV-2COVID-19co-infection |
| spellingShingle | Sara Calvo-Silveria Sara Calvo-Silveria Lucía Fernández-Delgado Lucía Fernández-Delgado Aida González-Díaz Aida González-Díaz Rocío España-Bonilla Laura Calatayud Laura Calatayud Jordi Niubó Sara Martí Sara Martí Sara Martí Ma Ángeles Domínguez Ma Ángeles Domínguez Ma Ángeles Domínguez Jordi Càmara Jordi Càmara Carmen Ardanuy Carmen Ardanuy Carmen Ardanuy SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adults Frontiers in Cellular and Infection Microbiology Streptococcus pneumoniae serotypes SARS-CoV-2 COVID-19 co-infection |
| title | SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adults |
| title_full | SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adults |
| title_fullStr | SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adults |
| title_full_unstemmed | SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adults |
| title_short | SARS-CoV-2 and Streptococcus pneumoniae colonization and disease: an observational study in adults |
| title_sort | sars cov 2 and streptococcus pneumoniae colonization and disease an observational study in adults |
| topic | Streptococcus pneumoniae serotypes SARS-CoV-2 COVID-19 co-infection |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2025.1624521/full |
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