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Crucianelli S, Mariano A, Valeriani F, Cocomello N, Gianfranceschi G, Conrado AB, Moretti F, Scotto d'Abusco A, Mennuni G, Fraioli A, Ben MD, Spica VR, Fontana M. Effects of Sulfur Thermal Water inhalations in long-COVID syndrome: spa-centred, double-blinded, randomised case-control pilot study. Clin Med (Lond) 2024:100251. [PMID: 39370044 DOI: 10.1016/j.clinme.2024.100251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 09/09/2024] [Accepted: 09/26/2024] [Indexed: 10/08/2024]
Abstract
BACKGROUND The long-COVID syndrome is characterised by a plethora of symptoms. Given its social and economic impact, many studies have stressed the urgency of proposing innovative strategies other than hospital settings. In this double-blind randomised case-control trial, we investigate the effects of sulfur thermal water inhalations, rich in H2S, compared to distilled water inhalations on symptoms, inflammatory markers, nasal microbiome in long-COVID patients. METHODS 30 outpatients aged 18-75, with positive diagnosis for long-COVID were randomised in two groups undergoing 12 consecutive days of inhalations. The active Group (STW) received sulfur thermal water inhalations whereas the placebo group received inhalations of sterile distilled non-pyrogenic water (SDW). Each participant was tested prior treatment at day 1 (T0), after the inhalations at day 14 (T1) and at 3 months follow-up (T2). At each time point, blood tests, nasal swabs for microbiome sampling, pulmonary functionality tests (PFTs) and pro-inflammatory marker measure were performed. RESULTS The scores obtained in the administered tests (6MWT, Borg score, and SGRQ) at T0, showed a significant variation in STW group, at T1 and T2. Serum cytokine levels and other inflammatory biomarkers reported a statistically significant decrease. Some specific parameters of PFT's showed ameliorations in STW group only. Changes in the STW nasopharyngeal microbiota composition were noticed, especially from T0 to T2. CONCLUSIONS Inhalations of sulfur thermal water exerted objective and subjective improvements on subjects affected by long-COVID. Significant reduction of inflammatory markers, dyspnea scores and quantitative and qualitative changes in the nasopharyngeal microbiome were also assessed.
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Affiliation(s)
- Serena Crucianelli
- School of Thermal Medicine, Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Alessia Mariano
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Federica Valeriani
- Laboratory of Epidemiology and Biotechnologies, Department of Movement Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135, Rome, Italy
| | - Nicholas Cocomello
- School of Thermal Medicine, Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Gianluca Gianfranceschi
- Laboratory of Epidemiology and Biotechnologies, Department of Movement Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135, Rome, Italy
| | | | - Ferdinando Moretti
- School of Thermal Medicine, Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anna Scotto d'Abusco
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Gioacchino Mennuni
- School of Thermal Medicine, Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Antonio Fraioli
- School of Thermal Medicine, Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Maria Del Ben
- Department of Clinical, Internal Medicine, Anesthesiological and Cardiovascular Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Vincenzo Romano Spica
- Laboratory of Epidemiology and Biotechnologies, Department of Movement Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135, Rome, Italy
| | - Mario Fontana
- School of Thermal Medicine, Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy; Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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2
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Drigot ZG, Clark SE. Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia. Curr Opin Microbiol 2024; 77:102428. [PMID: 38277901 PMCID: PMC10922932 DOI: 10.1016/j.mib.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
The respiratory tract microbiome (RTM) is a microbial ecosystem inhabiting different niches throughout the airway. A critical role for the RTM in dictating lung infection outcomes is underlined by recent efforts to identify community members benefiting respiratory tract health. Obligate anaerobes common in the oropharynx and lung such as Prevotella and Veillonella are associated with improved pneumonia outcomes and activate several immune defense pathways in the lower airway. Colonizers of the nasal cavity, including Corynebacterium and Dolosigranulum, directly impact the growth and virulence of lung pathogens, aligning with robust clinical correlations between their upper airway abundance and reduced respiratory tract infection risk. Here, we highlight recent work identifying respiratory tract bacteria that promote airway health and resilience against disease, with a focus on lung infections and the underlying mechanisms driving RTM-protective benefits.
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Affiliation(s)
- Zoe G Drigot
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA
| | - Sarah E Clark
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA.
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3
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Cai L, Xu H, Cui Z. Factors Limiting the Translatability of Rodent Model-Based Intranasal Vaccine Research to Humans. AAPS PharmSciTech 2022; 23:191. [PMID: 35819736 PMCID: PMC9274968 DOI: 10.1208/s12249-022-02330-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/09/2022] [Indexed: 12/19/2022] Open
Abstract
The intranasal route of vaccination presents an attractive alternative to parenteral routes and offers numerous advantages, such as the induction of both mucosal and systemic immunity, needle-free delivery, and increased patient compliance. Despite demonstrating promising results in preclinical studies, however, few intranasal vaccine candidates progress beyond early clinical trials. This discrepancy likely stems in part from the limited predictive value of rodent models, which are used frequently in intranasal vaccine research. In this review, we explored the factors that limit the translatability of rodent-based intranasal vaccine research to humans, focusing on the differences in anatomy, immunology, and disease pathology between rodents and humans. We also discussed approaches that minimize these differences and examined alternative animal models that would produce more clinically relevant research.
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Affiliation(s)
- Lucy Cai
- University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, USA
| | - Haiyue Xu
- The University of Texas at Austin, College of Pharmacy, Division of Molecular Pharmaceutics and Drug Delivery, 2409 University Ave., A1900, Austin, Texas, 78712, USA
| | - Zhengrong Cui
- The University of Texas at Austin, College of Pharmacy, Division of Molecular Pharmaceutics and Drug Delivery, 2409 University Ave., A1900, Austin, Texas, 78712, USA.
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4
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Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, Rotta AT, Turner NA, Pfeiffer TS, Gurley TC, Moody MA, Denny TN, Rawls JF, Clark JS, Woods CW, Kelly MS. Age-Related Changes in the Nasopharyngeal Microbiome Are Associated With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and Symptoms Among Children, Adolescents, and Young Adults. Clin Infect Dis 2022; 75:e928-e937. [PMID: 35247047 PMCID: PMC8903463 DOI: 10.1093/cid/ciac184] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Children are less susceptible to SARS-CoV-2 infection and typically have milder illness courses than adults, but the factors underlying these age-associated differences are not well understood. The upper respiratory microbiome undergoes substantial shifts during childhood and is increasingly recognized to influence host defense against respiratory pathogens. Thus, we sought to identify upper respiratory microbiome features associated with SARS-CoV-2 infection susceptibility and illness severity. METHODS We collected clinical data and nasopharyngeal swabs from 285 children, adolescents, and young adults (<21 years) with documented SARS-CoV-2 exposure. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and evaluated for age-adjusted associations between microbiome characteristics and SARS-CoV-2 infection status and respiratory symptoms. RESULTS Nasopharyngeal microbiome composition varied with age (PERMANOVA, P < .001; R2 = 0.06) and between SARS-CoV-2-infected individuals with and without respiratory symptoms (PERMANOVA, P = .002; R2 = 0.009). SARS-CoV-2-infected participants with Corynebacterium/Dolosigranulum-dominant microbiome profiles were less likely to have respiratory symptoms than infected participants with other nasopharyngeal microbiome profiles (OR: .38; 95% CI: .18-.81). Using generalized joint attributed modeling, we identified 9 bacterial taxa associated with SARS-CoV-2 infection and 6 taxa differentially abundant among SARS-CoV-2-infected participants with respiratory symptoms; the magnitude of these associations was strongly influenced by age. CONCLUSIONS We identified interactive relationships between age and specific nasopharyngeal microbiome features that are associated with SARS-CoV-2 infection susceptibility and symptoms in children, adolescents, and young adults. Our data suggest that the upper respiratory microbiome may be a mechanism by which age influences SARS-CoV-2 susceptibility and illness severity.
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Affiliation(s)
| | | | - Jhoanna N Aquino
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Javier Rodriguez
- Children’s Clinical Research Unit, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Sarah M Heston
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Debra J Lugo
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandre T Rotta
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas A Turner
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Trevor S Pfeiffer
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thaddeus C Gurley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - M Anthony Moody
- Division of Infectious Diseases, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA,Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USAand
| | - James S Clark
- Nicholas School of the Environment, Duke University, Durham, North Carolina, USA
| | - Christopher W Woods
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Matthew S Kelly
- Correspondence: M. S. Kelly, 2301 Erwin Road, Durham, NC 27710 USA ()
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5
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Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP. Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. mSystems 2021; 6:e0042521. [PMID: 34546072 PMCID: PMC8547433 DOI: 10.1128/msystems.00425-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.
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Affiliation(s)
| | - Silvio D. Brugger
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Isabel Fernandez Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Sean L. Cotton
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Sara M. Eslami
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tommy H. Tran
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Dakota S. Jones
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Samuel Minot
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christopher D. Johnston
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Section of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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6
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Abstract
Microbes in the 21st century are understood as symbionts ‘completing’ the human ‘superorganism’ (Homo sapiens plus microbial partners-in-health). This paper addresses a significant paradox: despite the vast majority of our genes being microbial, the lack of routine safety testing for the microbiome has led to unintended collateral side effects from pharmaceuticals that can damage the microbiome and inhibit innate ‘colonization resistance’ against pathobionts. Examples are discussed in which a Microbiome First Medicine approach provides opportunities to ‘manage our microbes’ holistically, repair dysbiotic superorganisms, and restore health and resilience in the gut and throughout the body: namely, managing nosocomial infections for Clostridioides difficile and Staphylococcus aureus and managing the gut and neural systems (gut–brain axis) in autism spectrum disorder. We then introduce a risk analysis tool: the evidence map. This ‘mapping’ tool was recently applied by us to evaluate evidence for benefits, risks, and uncertainties pertaining to the breastmilk ecosystem. Here, we discuss the potential role of the evidence map as a risk analysis methodology to guide scientific and societal efforts to: (1) enhance ecosystem resilience, (2) ‘manage our microbes’, and (3) minimize the adverse effects of both acute and chronic diseases.
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7
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Zhao N, Khamash DF, Koh H, Voskertchian A, Egbert E, Mongodin EF, White JR, Hittle L, Colantuoni E, Milstone AM. Low Diversity in Nasal Microbiome Associated With Staphylococcus aureus Colonization and Bloodstream Infections in Hospitalized Neonates. Open Forum Infect Dis 2021; 8:ofab475. [PMID: 34651052 PMCID: PMC8507450 DOI: 10.1093/ofid/ofab475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a leading cause of infectious morbidity and mortality in neonates. Few data exist on the association of the nasal microbiome and susceptibility to neonatal S. aureus colonization and infection. METHODS We performed 2 matched case-control studies (colonization cohort-neonates who did and did not acquire S. aureus colonization; bacteremia cohort-neonates who did [colonized neonates] and did not [controls] acquire S. aureus colonization and neonates with S. aureus bacteremia [bacteremic neonantes]). Neonates in 2 intensive care units were enrolled and matched on week of life at time of colonization or infection. Nasal samples were collected weekly until discharge and cultured for S. aureus, and the nasal microbiome was characterized using 16S rRNA gene sequencing. RESULTS In the colonization cohort, 43 S. aureus-colonized neonates were matched to 82 controls. At 1 week of life, neonates who acquired S. aureus colonization had lower alpha diversity (Wilcoxon rank-sum test P < .05) and differed in beta diversity (omnibus MiRKAT P = .002) even after adjusting for birth weight (P = .01). The bacteremia cohort included 10 neonates, of whom 80% developed bacteremia within 4 weeks of birth and 70% had positive S. aureus cultures within a few days of bacteremia. Neonates with bacteremia had an increased relative abundance of S. aureus sequences and lower alpha diversity measures compared with colonized neonates and controls. CONCLUSIONS The association of increased S. aureus abundance and decrease of microbiome diversity suggest the need for interventions targeting the nasal microbiome to prevent S. aureus disease in vulnerable neonates.
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Affiliation(s)
- Ni Zhao
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Dina F Khamash
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hyunwook Koh
- Deptartment of Applied Mathematics & Statistics, The State University of New York, Korea (SUNY Korea), Incheon, South Korea
| | - Annie Voskertchian
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emily Egbert
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | | | - Elizabeth Colantuoni
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Aaron M Milstone
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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8
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Roghmann MC, Lydecker AD, Shardell M, DeBoy RT, Johnson JK, Zhao L, Hittle LL, Mongodin EF. Effect of mupirocin for Staphylococcus aureus decolonization on the microbiome of the nose and throat in community and nursing home dwelling adults. PLoS One 2021; 16:e0252004. [PMID: 34101737 PMCID: PMC8186807 DOI: 10.1371/journal.pone.0252004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/28/2021] [Indexed: 12/26/2022] Open
Abstract
Objective To characterize the microbial communities of the anterior nares (nose) and posterior pharynx (throat) of adults dwelling in the community and in nursing homes before and after treatment with intranasal mupirocin. Methods Staphylococcus aureus-colonized adults were recruited from the community (n = 25) and from nursing homes (n = 7). S. aureus colonization was confirmed using cultures. Participants had specimens taken from nose and throat for S. aureus quantitation using quantitative PCR for the nuc gene and bacterial profiling using 16S rRNA gene sequencing over 12 weeks. After two baseline study visits 4 weeks apart, participants received intranasal mupirocin for 5 days with 3 further visits over a 8 week follow-up period. Results We found a decrease in the absolute abundance of S. aureus in the nose for 8 weeks after mupirocin (1693 vs 141 fg/ul, p = 0.047). Mupirocin caused a statistically significant disruption in bacterial communities of the nose and throat after 1 week, which was no longer detected after 8 weeks. Bacterial community profiling demonstrated that there was a decrease in the relative abundance of S. aureus (8% vs 0.3%, p<0.01) 8 weeks after mupirocin and a transient decrease in the relative abundance of Staphylococcus epidermidis in the nose (21% vs 5%, p<0.01) 1 week after mupirocin. Conclusions Decolonization with mupirocin leads to a sustained effect on absolute and relative abundance of S. aureus but not for other bacteria in the nose. This demonstrates that a short course of mupirocin selectively decreases S. aureus in the nose for up to 8 weeks.
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Affiliation(s)
- Mary-Claire Roghmann
- Geriatrics Research Education and Clinical Center, VA Maryland Health Care System, Baltimore, Maryland, United States of America
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Alison D. Lydecker
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Michelle Shardell
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Robert T. DeBoy
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - J. Kristie Johnson
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - LiCheng Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Lauren L. Hittle
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Emmanuel F. Mongodin
- Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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9
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Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, Rotta AT, Turner NA, Pfeiffer TS, Gurley TC, Moody MA, Denny TN, Rawls JF, Woods CW, Kelly MS. Age-related changes in the upper respiratory microbiome are associated with SARS-CoV-2 susceptibility and illness severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.20.21252680. [PMID: 33791716 PMCID: PMC8010748 DOI: 10.1101/2021.03.20.21252680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Children are less susceptible to SARS-CoV-2 and typically have milder illness courses than adults. We studied the nasopharyngeal microbiomes of 274 children, adolescents, and young adults with SARS-CoV-2 exposure using 16S rRNA gene sequencing. We find that higher abundances of Corynebacterium species are associated with SARS-CoV-2 infection and SARS-CoV-2-associated respiratory symptoms, while higher abundances of Dolosigranulum pigrum are present in SARS-CoV-2-infected individuals without respiratory symptoms. We also demonstrate that the abundances of these bacteria are strongly, and independently, associated with age, suggesting that the nasopharyngeal microbiome may be a potentially modifiable mechanism by which age influences SARS-CoV-2 susceptibility and severity. SUMMARY Evaluation of nasopharyngeal microbiome profiles in children, adolescents, and young adults with a SARS-CoV-2-infected close contact identified specific bacterial species that vary in abundance with age and are associated with SARS-CoV-2 susceptibility and the presence of SARS-CoV-2-associated respiratory symptoms.
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10
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Tay CJX, Ta LDH, Ow Yeong YX, Yap GC, Chu JJH, Lee BW, Tham EH. Role of Upper Respiratory Microbiota and Virome in Childhood Rhinitis and Wheeze: Collegium Internationale Allergologicum Update 2021. Int Arch Allergy Immunol 2021; 182:265-276. [PMID: 33588407 DOI: 10.1159/000513325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
There is emerging evidence that the respiratory microbiota influences airway health, and there has been intense research interest in its role in respiratory infections and allergic airway disorders. This review aims to summarize current knowledge of nasal microbiome and virome and their associations with childhood rhinitis and wheeze. The healthy infant nasal microbiome is dominated by Corynebacteriaceae and Staphylococcaceae. In contrast, infants who subsequently develop respiratory disorders are depleted of these microbes and are instead enriched with Proteobacteria spp. Although human rhinovirus and human respiratory syncytial virus are well-documented major viral pathogens that trigger rhinitis and wheezing disorders in infants, recent limited data indicate that bacteriophages may have a role in respiratory health. Future work investigating the interplay between commensal microbiota, virome, and host immunological responses is an important step toward understanding the dynamics of the nasal community in order to develop a strategical approach to combat these common childhood respiratory disorders.
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Affiliation(s)
- Carina Jing Xuan Tay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Le Duc Huy Ta
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yu Xiang Ow Yeong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gaik Chin Yap
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Elizabeth Huiwen Tham
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore, .,Khoo Teck Puat- National University Children's Medical Institute, National University Health System, Singapore, Singapore, .,Human Potential Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore,
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Accorsi EK, Franzosa EA, Hsu T, Joice Cordy R, Maayan-Metzger A, Jaber H, Reiss-Mandel A, Kline M, DuLong C, Lipsitch M, Regev-Yochay G, Huttenhower C. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol 2020; 21:301. [PMID: 33308267 PMCID: PMC7731505 DOI: 10.1186/s13059-020-02209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/19/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life. RESULTS We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated with S. aureus in infants and mothers. In gene content-based strain profiling, infant S. aureus strains are more similar to maternal strains. CONCLUSIONS This improved understanding of S. aureus colonization is an important first step toward the development of novel, ecological therapies for controlling S. aureus carriage.
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Affiliation(s)
- Emma K. Accorsi
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Eric A. Franzosa
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
| | - Tiffany Hsu
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
| | - Regina Joice Cordy
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Wake Forest University, 1834 Wake Forest Rd., Winston-Salem, NC 27109 USA
| | - Ayala Maayan-Metzger
- Sackler Faculty of Medicine, Tel Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | - Hanaa Jaber
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | | | - Madeleine Kline
- Harvard Medical School, 25 Shattuck St., Boston, MA 02115 USA
| | - Casey DuLong
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Marc Lipsitch
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Gili Regev-Yochay
- Sackler Faculty of Medicine, Tel Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | - Curtis Huttenhower
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
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Aldrich ML, LaTuga MS. 50 Years Ago in TheJournalofPediatrics: The Evolution of Health-Care Associated Infections in the Neonatal Intensive Care Unit. J Pediatr 2020; 221:180. [PMID: 32446477 DOI: 10.1016/j.jpeds.2019.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Margaret L Aldrich
- Department of Pediatrics, Children's Hospital at Montefiore, Albert Einstein College of Medicine, The Bronx, New York
| | - M Susan LaTuga
- Department of Pediatrics, Children's Hospital at Montefiore, Albert Einstein College of Medicine, The Bronx, New York
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