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The objective of this study was to characterize the nasopharyngeal microbiota of children and adults and its relation to SARS-CoV-2 infection and COVID-19 severity during the pandemic lockdown in Spain. This cross-sectional study included family households located in metropolitan Barcelona, Spain, with one adult with a previous confirmed COVID-19 episode and one or more exposed co-habiting child contacts. Nasopharyngeal swabs were used to determine SARS-CoV-2 infection status, characterize the nasopharyngeal microbiota and determine common respiratory DNA\/RNA viral co-infections. A total of 173 adult cases and 470 exposed children were included. Overall, a predominance of Corynebacterium and Dolosigranulum and a limited abundance of common pathobionts including Haemophilus and Streptococcus were found both among adults and children. Children with current SARS-CoV-2 infection presented higher bacterial richness and increased Fusobacterium, Streptococcus and Prevotella abundance than non-infected children. Among adults, persistent SARS-CoV-2 RNA was associated with an increased abundance of an unclassified member of the Actinomycetales order. COVID-19 severity was associated with increased Staphylococcus and reduced Dolosigranulum abundance. The stringent COVID-19 lockdown in Spain had a significant impact on the nasopharyngeal microbiota of children, reflected in the limited abundance of common respiratory pathobionts and the predominance of Corynebacterium, regardless of SARS-CoV-2 detection. COVID-19 severity in adults was associated with decreased nasopharynx levels of healthy commensal bacteria.<\/jats:p>","DOI":"10.3390\/v14071521","type":"journal-article","created":{"date-parts":[[2022,7,12]],"date-time":"2022-07-12T23:02:01Z","timestamp":1657666921000},"page":"1521","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Impact of COVID-19 Lockdown on the Nasopharyngeal Microbiota of Children and Adults Self-Confined at Home"],"prefix":"10.3390","volume":"14","author":[{"given":"Muntsa","family":"Rocafort","sequence":"first","affiliation":[{"name":"Institut de Recerca Sant Joan de D\u00e9u (IRSJD), Hospital Sant Joan de Deu, Esplugues de Llobregat, 08950 Barcelona, Spain"},{"name":"CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, 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Engl. J. Med."},{"key":"ref_2","unstructured":"Rosenwald, M.S. (2022, June 14). History\u2019s Deadliest Pandemics: Plague, Smallpox, Flu, Covid-19. Available online: https:\/\/www.washingtonpost.com\/graphics\/2020\/local\/retropolis\/coronavirus-deadliest-pandemics\/."},{"key":"ref_3","unstructured":"(2022, June 14). Government Decrees State of Emergency to Stop Spread of Coronavirus COVID-19 [Government\/Council of Ministers], Available online: https:\/\/www.lamoncloa.gob.es\/lang\/en\/gobierno\/councilministers\/Paginas\/2020\/20200314council-extr.aspx."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Ahmed, F., Zviedrite, N., and Uzicanin, A. (2018). Effectiveness of workplace social distancing measures in reducing influenza transmission: A systematic review. 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Health"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1093\/cid\/ciab568","article-title":"Bacterial and viral respiratory tract microbiota and host characteristics in adults with lower respiratory tract infections: A case-control study","volume":"74","author":"Haak","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1080\/14787210.2017.1349609","article-title":"Respiratory microbiota and lower respiratory tract disease","volume":"15","author":"Lanaspa","year":"2017","journal-title":"Expert Rev. Anti. Infect. Ther."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"20140294","DOI":"10.1098\/rstb.2014.0294","article-title":"The role of the local microbial ecosystem in respiratory health and disease","volume":"370","author":"Sanders","year":"2015","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_10","first-page":"000661","article-title":"Differential nasopharyngeal microbiota composition in children according to respiratory health status","volume":"7","author":"Henares","year":"2021","journal-title":"Microb. Genom."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"929","DOI":"10.3389\/fcimb.2021.744727","article-title":"Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease","volume":"11","author":"Henares","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nrmicro.2017.14","article-title":"The microbiota of the respiratory tract: Gatekeeper to respiratory health","volume":"15","author":"Man","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e970","DOI":"10.1093\/cid\/ciaa1721","article-title":"Susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Children and Adults: A Seroprevalence Study of Family Households in the Barcelona Metropolitan Region, Spain","volume":"72","author":"Brotons","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","article-title":"Ribosomal Database Project: Data and tools for high throughput rRNA analysis","volume":"42","author":"Cole","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"McMurdie, P.J., and Holmes, S. (2013). phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0061217"},{"key":"ref_17","first-page":"254","article-title":"Package \u2018vegan\u2019","volume":"2","author":"Oksanen","year":"2013","journal-title":"R Package Version 2.0\u20138"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3514","DOI":"10.1038\/s41467-020-17041-7","article-title":"Analysis of compositions of microbiomes with bias correction","volume":"11","author":"Lin","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"11","DOI":"10.3389\/fmicb.2019.00011","article-title":"Nasopharyngeal Microbiota in Children With Invasive Pneumococcal Disease: Identification of Bacteria With Potential Disease-Promoting and Protective Effects","volume":"10","author":"Henares","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1582","DOI":"10.1164\/rccm.201703-0554OC","article-title":"Maturation of the Infant Respiratory Microbiota, Environmental Drivers, and Health Consequences. A Prospective Cohort Study","volume":"196","author":"Bosch","year":"2017","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Bogaert, D., Keijser, B., Huse, S., Rossen, J., Veenhoven, R., van Gils, E., Bruin, J., Montijn, R., Bonten, M., and Sanders, E. (2011). Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0017035"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1164\/rccm.201401-0073OC","article-title":"The impact of breastfeeding on nasopharyngeal microbial communities in infants","volume":"190","author":"Biesbroek","year":"2014","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.ebiom.2016.05.031","article-title":"Development of Upper Respiratory Tract Microbiota in Infancy is Affected by Mode of Delivery","volume":"9","author":"Bosch","year":"2016","journal-title":"EBioMedicine"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1038\/s41467-020-16429-9","article-title":"Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection","volume":"11","author":"Kaul","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1080\/14787210.2019.1621168","article-title":"Relationship between nasopharyngeal microbiota and patient\u2019s susceptibility to viral infection","volume":"17","author":"Dubourg","year":"2019","journal-title":"Expert Rev. Anti. Infect. Ther."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/j.chom.2015.03.008","article-title":"The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development","volume":"17","author":"Teo","year":"2015","journal-title":"Cell Host Microbe"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e2126114","DOI":"10.1001\/jamanetworkopen.2021.26114","article-title":"Trends in Outpatient Antibiotic Prescriptions in the United States During the COVID-19 Pandemic in 2020","volume":"4","author":"Buehrle","year":"2021","journal-title":"JAMA Netw. Open"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1016\/j.cmi.2021.01.021","article-title":"Effect of the coronavirus disease 2019 pandemic on antibiotic use in primary care","volume":"27","author":"Benavente","year":"2021","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e01725-15","DOI":"10.1128\/mBio.01725-15","article-title":"Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols","volume":"7","author":"Bomar","year":"2016","journal-title":"MBio"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e00852-20","DOI":"10.1128\/mSphere.00852-20","article-title":"Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota","volume":"5","author":"Brugger","year":"2020","journal-title":"mSphere"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/2049-2618-2-44","article-title":"The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition","volume":"2","author":"Cremers","year":"2014","journal-title":"Microbiome"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.3389\/fmicb.2017.02372","article-title":"Comparing the healthy nose and nasopharynx microbiota reveals continuity as well as niche-specificity","volume":"8","author":"Wittouck","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"652464","DOI":"10.3389\/fmed.2021.652464","article-title":"The Unique Impact of COVID-19 on Human Gut Microbiome Research","volume":"8","author":"Burchill","year":"2021","journal-title":"Front. Med."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1016\/j.jgg.2021.05.004","article-title":"Progressive deterioration of the upper respiratory tract and the gut microbiomes in children during the early infection stages of COVID-19","volume":"48","author":"Xu","year":"2021","journal-title":"J. Genet. Genom."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"18","DOI":"10.3389\/fcimb.2021.625581","article-title":"Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to Fusobacterium periodonticum?","volume":"11","author":"Nardelli","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"975","DOI":"10.3201\/eid2703.202284","article-title":"COVID-19\u2013Associated Fusobacterium nucleatum Bacteremia, Belgium","volume":"27","author":"Wolff","year":"2021","journal-title":"Emerg. Infect. Dis."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1080\/21645515.2020.1849516","article-title":"Pneumococcal carriage in children with COVID-19","volume":"17","author":"Aykac","year":"2021","journal-title":"Hum. Vaccines Immunother."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s12575-021-00148-6","article-title":"Nasopharyngeal Microbiota in SARS-CoV-2 Positive and Negative Patients","volume":"23","author":"Engen","year":"2021","journal-title":"Biol. Proced. Online"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Merenstein, C., Liang, G., Whiteside, S.A., Cobi\u00e1n-G\u00fcemes, A.G., Merlino, M.S., Taylor, L.J., Glascock, A., Bittinger, K., Tanes, C., and Graham-Wooten, J. (medRxiv, 2021). Signatures of COVID-19 severity and immune response in the respiratory tract microbiome, medRxiv, Preprint.","DOI":"10.1101\/2021.04.02.21254514"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e01969-20","DOI":"10.1128\/mBio.01969-20","article-title":"Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients","volume":"11","author":"Mostafa","year":"2020","journal-title":"MBio"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s12575-020-00131-7","article-title":"Nasopharyngeal Microbiota Profiling of SARS-CoV-2 Infected Patients","volume":"22","author":"Posteraro","year":"2020","journal-title":"Biol. Proced. Online"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"6262","DOI":"10.1128\/AEM.01051-12","article-title":"Upper Respiratory Tract Microbial Communities, Acute Otitis Media Pathogens, and Antibiotic Use in Healthy and Sick Children","volume":"78","author":"Pettigrew","year":"2012","journal-title":"Appl. Environ. Microbiol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/7\/1521\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:49:05Z","timestamp":1760140145000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/7\/1521"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,12]]},"references-count":43,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,7]]}},"alternative-id":["v14071521"],"URL":"https:\/\/doi.org\/10.3390\/v14071521","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,7,12]]}}}