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Sepúlveda-Pachón IT, Dunne EM, Hanquet G, Baay M, Menon S, Jodar L, Gessner BD, Theilacker C. Effect of Pneumococcal Conjugate Vaccines on Viral Respiratory Infections: A Systematic Literature Review. J Infect Dis 2024; 230:e657-e667. [PMID: 38462672 PMCID: PMC11420806 DOI: 10.1093/infdis/jiae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND In addition to preventing pneumococcal disease, emerging evidence indicates that pneumococcal conjugate vaccines (PCVs) might indirectly reduce viral respiratory tract infections (RTIs) by affecting pneumococcal-viral interactions. METHODS We performed a systematic review of interventional and observational studies published during 2000-2022 on vaccine efficacy/adjusted effectiveness (VE) and overall effect of PCV7, PCV9, PCV10, or PCV13 against viral RTIs. RESULTS Sixteen of 1671 records identified were included. Thirteen publications described effects of PCVs against viral RTIs in children. VE against influenza ranged between 41% and 86% (n = 4), except for the 2010-2011 influenza season. In a randomized controlled trial, PCV9 displayed efficacy against any viral RTI, human seasonal coronavirus, parainfluenza, and human metapneumovirus. Data in adults were limited (n = 3). PCV13 VE was 4%-25% against viral lower RTI, 32%-35% against coronavirus disease 2019 outcomes, 24%-51% against human seasonal coronavirus, and 13%-36% against influenza A lower RTI, with some 95% confidence intervals spanning zero. No protection was found against adenovirus or rhinovirus in children or adults. CONCLUSIONS PCVs were associated with protection against some viral RTI, with the strongest evidence for influenza in children. Limited evidence for adults was generally consistent with pediatric data. Restricting public health evaluations to confirmed pneumococcal outcomes may underestimate the full impact of PCVs.
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Affiliation(s)
| | - Eileen M Dunne
- Global Vaccines and Antivirals, Pfizer Inc, Collegeville, Pennsylvania
| | - Germaine Hanquet
- Epidemiology Department, P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Marc Baay
- Epidemiology Department, P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Sonia Menon
- Epidemiology Department, P95 Epidemiology and Pharmacovigilance, Leuven, Belgium
| | - Luis Jodar
- Global Vaccines and Antivirals, Pfizer Inc, Collegeville, Pennsylvania
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Tsirigotaki M, Galanakis E. Impact of vaccines on Staphylococcus aureus colonization: A systematic review and meta-analysis. Vaccine 2023; 41:6478-6487. [PMID: 37777451 DOI: 10.1016/j.vaccine.2023.09.034] [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: 01/21/2023] [Revised: 08/17/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Concerns regarding vaccine effects on microbial ecology have led to interest in the non-targeted effects of vaccinations. OBJECTIVES To systematically review the literature related to the impact of vaccines on S. aureus carriage. METHODS We conducted a systematic search of MEDLINE, Scopus and clinical trials.gov for studies that assessed vaccine effects on S. aureus carriage in children and adults using predefined inclusion and exclusion criteria. Generic inverse variance meta-analysis was done using random-effects models. RESULTS Of 1,686 studies screened, 34 were eligible for inclusion, of which 22 were observational and 12 randomized controlled studies (RCTs). 88.2% (30/34) provided data on pneumococcal conjugate vaccines (PCV), 23.5% on influenza vaccines (8/34), 6% on other vaccines (2/34) and 20.6% on more than one vaccine (7/34). Most studies tested nasopharyngeal specimens (82.3%, 28/34). Among children aged more than 18-24 months, evidence suggested no effect of PCV on S. aureus colonization [2 RCTs, pooled OR 1.09 (95% CI 0.94-1.25), p 0.25; 7 observational studies, pooled OR: 1.02 (95% CI 0.83-1.25), p 0.86]. A transient increase in S. aureus carriage in PCV-vaccinated infants 9-15 months was shown [2 RCTs, pooled OR 1.11 (95% CI 1.00-1.23), p 0.06; 4 observational studies, pooled OR 1.64 (95% CI 1.00-2.68), p 0.05]. A reduction in S. aureus carriage was observed after influenza vaccination [4 observational studies; OR 0.85 (95% CI 0.78-0.94), p 0.0001]. Based on the Grading of Recommendations Assessment, Development and Evaluation, the quality of evidence was considered low for randomized and very low for non-randomized trials. CONCLUSION Evidence did not suggest long-term effects of pneumococcal vaccinations on S. aureus nasopharyngeal carriage in children, however transient niche changes may occur in infants. Influenza vaccination was related to decreased rates of S. aureus carriage. Data regarding other vaccines is scarce. Further research and ongoing surveillance are needed to monitor colonization changes.
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3
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Claassen-Weitz S, Gardner-Lubbe S, Xia Y, Mwaikono KS, Mounaud SH, Nierman WC, Workman L, Zar HJ, Nicol MP. Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort. MICROBIOME 2023; 11:127. [PMID: 37271810 PMCID: PMC10240772 DOI: 10.1186/s40168-023-01563-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/30/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Bacteria colonizing the nasopharynx play a key role as gatekeepers of respiratory health. Yet, dynamics of early life nasopharyngeal (NP) bacterial profiles remain understudied in low- and middle-income countries (LMICs), where children have a high prevalence of risk factors for lower respiratory tract infection. We investigated longitudinal changes in NP bacterial profiles, and associated exposures, among healthy infants from low-income households in South Africa. METHODS We used short fragment (V4 region) 16S rRNA gene amplicon sequencing to characterize NP bacterial profiles from 103 infants in a South African birth cohort, at monthly intervals from birth through the first 12 months of life and six monthly thereafter until 30 months. RESULTS Corynebacterium and Staphylococcus were dominant colonizers at 1 month of life; however, these were rapidly replaced by Moraxella- or Haemophilus-dominated profiles by 4 months. This succession was almost universal and largely independent of a broad range of exposures. Warm weather (summer), lower gestational age, maternal smoking, no day-care attendance, antibiotic exposure, or low height-for-age z score at 12 months were associated with higher alpha and beta diversity. Summer was also associated with higher relative abundances of Staphylococcus, Streptococcus, Neisseria, or anaerobic gram-negative bacteria, whilst spring and winter were associated with higher relative abundances of Haemophilus or Corynebacterium, respectively. Maternal smoking was associated with higher relative abundances of Porphyromonas. Antibiotic therapy (or isoniazid prophylaxis for tuberculosis) was associated with higher relative abundance of anerobic taxa (Porphyromonas, Fusobacterium, and Prevotella) and with lower relative abundances of health associated-taxa Corynebacterium and Dolosigranulum. HIV-exposure was associated with higher relative abundances of Klebsiella or Veillonella and lower relative abundances of an unclassified genus within the family Lachnospiraceae. CONCLUSIONS In this intensively sampled cohort, there was rapid and predictable replacement of early profiles dominated by health-associated Corynebacterium and Dolosigranulum with those dominated by Moraxella and Haemophilus, independent of exposures. Season and antibiotic exposure were key determinants of NP bacterial profiles. Understudied but highly prevalent exposures prevalent in LMICs, including maternal smoking and HIV-exposure, were associated with NP bacterial profiles. Video Abstract.
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Affiliation(s)
- Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Faculty of Economic and Management Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Yao Xia
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Center for Artificial Intelligence and Machine Learning, School of Science, Edith Cowan University, Joondalup, Australia
| | - Kilaza S. Mwaikono
- Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Department of Science and Laboratory Technology, Dar Es Salaam Institute of Technology, Dar Es Salaam, Tanzania
| | | | | | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
- SAMRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P. Nicol
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
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Shahid S, Nisar MI, Jehan F, Ahmed S, Kabir F, Hotwani A, Muneer S, Qazi MF, Muhammad S, Ali A, Zaidi AK, Iqbal NT. Co-carriage of Staphylococcus aureus and Streptococcus pneumoniae among children younger than 2 years of age in a rural population in Pakistan. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2023; 21:None. [PMID: 37337613 PMCID: PMC10276771 DOI: 10.1016/j.cegh.2023.101293] [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: 12/19/2022] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Objectives Staphylococcus aureus and Streptococcus pneumoniae are common colonizers of the human nasopharynx. In this study, we describe S. aureus nasopharyngeal carriage and evaluate its association with S. pneumoniae carriage post-10-valent pneumococcal conjugate vaccine (PCV10) introduction in Pakistan. Methods A serial cross-sectional study was undertaken from 2014 to 2018, children <2 years were randomly selected, and nasopharyngeal swabs were collected using standard WHO guidelines. S. aureus and S. pneumoniae isolates were identified using standard methods and tested for antimicrobial susceptibility by the standard Kirby-Bauer disk-diffusion method as per Clinical & Laboratory Standards Institute (CLSI) recommendations. Regression analysis was used to determine predictors associated with S. aureus carriage. Results We enrolled 3140 children. S. aureus carriage prevalence was 5.6% (176/3140), and 50.1% (81/176) of the isolates were methicillin-resistant S. aureus (MRSA). S. aureus carriage was higher in the absence of pneumococcus compared to isolates in which pneumococcus was present (7.5% vs 5.0%). S. aureus carriage was negatively associated with pneumococcal carriage, being in 3rd and 4th year of enrollment, and vaccination with two and three PCV10 doses, in addition, fast breathing, ≥2 outpatients visits, and rainy season were positively associated. The following resistance rates were observed: 98.9% for penicillin, 74.4% for fusidic acid, and 23.3% for gentamicin, 10.2% for erythromycin, and 8.5% for cotrimoxazole. All isolates were susceptible to amikacin. Conclusions Overall S. aureus carriage prevalence was low, PCV10 vaccine was protective against the carriage. The proportion of MRSA carriage and antimicrobial resistance was high in this community warranting continuous monitoring for invasive infections.
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Affiliation(s)
- Shahira Shahid
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fyezah Jehan
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sheraz Ahmed
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sahrish Muneer
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Sajid Muhammad
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Asad Ali
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita K.M. Zaidi
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Najeeha T. Iqbal
- Department of Pediatric and Child Health, Aga Khan University, Karachi, Pakistan
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Aggarwal N, Kitano S, Puah GRY, Kittelmann S, Hwang IY, Chang MW. Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies. Chem Rev 2023; 123:31-72. [PMID: 36317983 PMCID: PMC9837825 DOI: 10.1021/acs.chemrev.2c00431] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 01/12/2023]
Abstract
The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.
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Affiliation(s)
- Nikhil Aggarwal
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Shohei Kitano
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ginette Ru Ying Puah
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - Sandra Kittelmann
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Singapore
Institute of Technology, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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6
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Recurrent Acute Otitis Media Environmental Risk Factors: A Literature Review from the Microbiota Point of View. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2030046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Acute otitis media (AOM) constitutes a multifactorial disease, as several host and environmental factors contribute to its occurrence. Prevention of AOM represents one of the most important goals in pediatrics, both in developing countries, in which complications, mortality, and deafness remain possible consequences of the disease, compared to in developed countries, in which this condition has an important burden in terms of medical, social, and economical implications. The strategies for AOM prevention are based on reducing the burden of risk factors, through the application of behavioral, environmental, and therapeutic interventions. The introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, providing novel insights into the pathogenesis of middle ear diseases through the identification of potential protective bacteria. The upper respiratory tract (URT) is a pivotal region in AOM pathogenesis, as it could act as a source of pathogens than of protective microorganisms for the middle ear (ME). Due to its direct connection with the external ambient, the URT is particularly exposed to the influence of environmental agents. The aim of this review was to evaluate AOM environmental risk factors and their impact on URT microbial communities, and to investigate AOM pathogenesis from the microbiota perspective.
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O'Connor D. The omics strategy: the use of systems vaccinology to characterise immune responses to childhood immunisation. Expert Rev Vaccines 2022; 21:1205-1214. [PMID: 35786291 DOI: 10.1080/14760584.2022.2093193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Vaccines have had a transformative impact on child health. Despite this impact the immunological processes involved in protective responses are not entirely understood and vaccine development has been largely empirical. Recent technological advances offer the opportunity to reveal the immunology underlying vaccine response at an unprecedented resolution. These data could revolutionise the way vaccines are developed and tested and further augment their role in securing the health of children around the world. AREAS COVERED Systems level information and the tools are now being deployed by vaccinologists at all stages of the vaccine development pathway; however, this review will specifically describe some of the key findings that have be gleaned from multi-omics datasets collected in the context of childhood immunisation. EXPERT OPINION Despite the success of vaccines there remains hard-to-target pathogens, refractory to current vaccination strategies. Moreover, zoonotic diseases with pandemic potential are a threat to global health, as recently illustrated by COVID-19. Systems vaccinology holds a great deal of promise in revealing a greater understanding of vaccine responses and consequently modernising vaccinology. However, there is a need for future studies -particularly in vulnerable populations that are targets for vaccination programmes - if this potential is to be fulfilled.
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Affiliation(s)
- Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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8
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Hirschhorn A, Averbuch D, Michaan N, Adler A, Grisaru-Soen G. Invasive Fusobacterium Infections in Children: A Retrospective Multicenter Study. Pediatr Infect Dis J 2022; 41:517-523. [PMID: 35363651 DOI: 10.1097/inf.0000000000003514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The past decade has witnessed a rise in Fusobacterium infections. This study aimed to describe the epidemiology, clinical and demographic characteristics and outcomes associated with Fusobacterium infections in hospitalized children in central Israel. METHODS We retrospectively analyzed the medical records of children <18 years old who had been admitted with a diagnosis of invasive Fusobacterium infection (IFI) between January 2010 and April 2020. Clinical, laboratory and microbiologic data were retrieved. IFI diagnosis was based upon microbiological identification in any specimen by culture or by 16S ribosomal RNA polymerase chain reaction. RESULTS Fifty-one children (26 boys) with a median age of 3 years (range, 5-16 years) were included. Hospitalizations for IFI increased from 19 of 100,000 admissions between 2010 and 2015 to 50 of 100,000 between 2016 and 2020, representing a 2.5-fold increase. Most of the infections were from an otogenic source (n = 28, 55%) followed by an oropharyngeal/respiratory source (n = 21, 41%). The most common complications were subperiosteal and epidural abscesses (41% and 37%, respectively). Thrombosis was diagnosed in 11 children, 10 of whom had sinus vein thrombosis. All had an otogenic source. Children with otogenic compared with all other infection sources were significantly younger (median age of 1.9 vs. 3 years; P < 0.001). Forty-seven children (92%) underwent a surgical intervention. All patients survived, one with neurologic sequelae. CONCLUSIONS The admissions for IFI in children increased 2.5-fold during the last decade. The most common source is otogenic, especially among younger children, and it is associated with high complication rates. Current management, including combinations of antibiotics and surgical interventions, leads to favorable outcome.
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Affiliation(s)
- Adi Hirschhorn
- From the Pediatric Infectious Disease Unit, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Diana Averbuch
- Paediatric Infectious Diseases, Paediatric Division, Hadassah Medical Center, Jerusalem, Israel, affiliated to the Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nadav Michaan
- Microbiology Laboratory
- Department of Obstetrics and Gynecology, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Galia Grisaru-Soen
- From the Pediatric Infectious Disease Unit, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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9
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Kielbik K, Pietras A, Jablonska J, Bakiera A, Borek A, Niedzielska G, Grzegorczyk M, Grywalska E, Korona-Glowniak I. Impact of Pneumococcal Vaccination on Nasopharyngeal Carriage of Streptococcus pneumoniae and Microbiota Profiles in Preschool Children in South East Poland. Vaccines (Basel) 2022; 10:vaccines10050791. [PMID: 35632547 PMCID: PMC9143411 DOI: 10.3390/vaccines10050791] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022] Open
Abstract
In 2017, Poland introduced the 10-valent pneumococcal conjugate vaccine (PCV) into its national immunization schedule. This prospective study was conducted between March and June 2020 to determine the impact of vaccination on prevalence of the nasopharyngeal carriage of S. pneumoniae in 176 healthy children and to determine how conjugate vaccines indirectly affect colonization of nasopharyngeal microbiota. Pneumococcal isolates were analyzed by serotyping and antimicrobial resistance tests. Nasopharyngeal microbiota were detected and identified using the culture method and real-time PCR amplification primers and hydrolysis-probe detection with the 16S rRNA gene as the target. In the vaccinated group of children, colonization was in 24.2% of children, compared to 21.4% in the unvaccinated group. Serotypes 23A and 23B constituted 41.5% of the isolates. Serotypes belonging to PCV10 and PCV13 constituted 4.9% and 17.1% of the isolates, respectively. S. pneumoniae isolates were resistant to penicillin (34.1%), erythromycin (31.7%), and co-trimoxazole (26.8%). Microbial DNA qPCR array correlated to increased amounts of Streptococcus mitis and S. sanguinis in vaccinated children, with reduced amounts of C. pseudodiphtericum, S. aureus, and M. catarrhalis. Introduction of PCV for routine infant immunization was associated with significant reductions in nasopharyngeal carriage of PCV serotypes and resistant strains amongst vaccine serotypes, yet carriage of non-PCV serotypes increased modestly, particularly serotype 23B.
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Affiliation(s)
- Karolina Kielbik
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
- Correspondence: (K.K.); (I.K.-G.)
| | - Aleksandra Pietras
- Department of Pediatric Otolaryngology, Phoniatrics and Audiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.P.); (J.J.); (G.N.)
| | - Joanna Jablonska
- Department of Pediatric Otolaryngology, Phoniatrics and Audiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.P.); (J.J.); (G.N.)
| | - Adrian Bakiera
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
| | - Anna Borek
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
| | - Grazyna Niedzielska
- Department of Pediatric Otolaryngology, Phoniatrics and Audiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.P.); (J.J.); (G.N.)
| | - Michal Grzegorczyk
- Department of Rehabilitation and Physiotherapy, Medical University of Lublin, 20-081 Lublin, Poland;
| | - Ewelina Grywalska
- Department of Experimental Immunology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Izabela Korona-Glowniak
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.B.)
- Correspondence: (K.K.); (I.K.-G.)
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10
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Kelly MS, Plunkett C, Yu Y, Aquino JN, Patel SM, Hurst JH, Young RR, Smieja M, Steenhoff AP, Arscott-Mills T, Feemster KA, Boiditswe S, Leburu T, Mazhani T, Patel MZ, Rawls JF, Jawahar J, Shah SS, Polage CR, Cunningham CK, Seed PC. Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy. THE ISME JOURNAL 2022; 16:655-665. [PMID: 34511605 PMCID: PMC8857224 DOI: 10.1038/s41396-021-01108-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023]
Abstract
Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0-6 months of age) or bimonthly (6-12 months of age) from 179 mother-infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.
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Affiliation(s)
- Matthew S. Kelly
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Catherine Plunkett
- grid.16753.360000 0001 2299 3507Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Yahe Yu
- grid.40803.3f0000 0001 2173 6074Department of Mathematics, North Carolina State University, Raleigh, NC USA
| | - Jhoanna N. Aquino
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Sweta M. Patel
- grid.26009.3d0000 0004 1936 7961Division of Pulmonary Allergy, and Critical Care Medicine, Duke University, Durham, NC USA
| | - Jillian H. Hurst
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Rebecca R. Young
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Marek Smieja
- grid.25073.330000 0004 1936 8227Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Andrew P. Steenhoff
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.239552.a0000 0001 0680 8770Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Tonya Arscott-Mills
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana ,grid.239552.a0000 0001 0680 8770Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Kristen A. Feemster
- grid.239552.a0000 0001 0680 8770Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Sefelani Boiditswe
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tirayaone Leburu
- grid.7621.20000 0004 0635 5486Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Tiny Mazhani
- grid.7621.20000 0004 0635 5486University of Botswana School of Medicine, Gaborone, Botswana
| | - Mohamed Z. Patel
- grid.7621.20000 0004 0635 5486University of Botswana School of Medicine, Gaborone, Botswana
| | - John F. Rawls
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke University, Durham, NC USA
| | - Jayanth Jawahar
- grid.26009.3d0000 0004 1936 7961Department of Molecular Genetics and Microbiology, Duke University, Durham, NC USA
| | - Samir S. Shah
- grid.239573.90000 0000 9025 8099Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Christopher R. Polage
- grid.26009.3d0000 0004 1936 7961Department of Pathology, Duke University, Durham, NC USA
| | - Coleen K. Cunningham
- grid.26009.3d0000 0004 1936 7961Division of Pediatric Infectious Diseases, Duke University, Durham, NC USA
| | - Patrick C. Seed
- grid.16753.360000 0001 2299 3507Division of Pediatric Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
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11
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Henares D, Rocafort M, Brotons P, de Sevilla MF, Mira A, Launes C, Cabrera-Rubio R, Muñoz-Almagro C. Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease. Front Cell Infect Microbiol 2021; 11:744727. [PMID: 34712623 PMCID: PMC8546175 DOI: 10.3389/fcimb.2021.744727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
Introduction Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children’s nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children’s health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure. Methods We investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene. Results Main epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3–6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics. Conclusion Our results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.
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Affiliation(s)
- Desiree Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Muntsa Rocafort
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Alex Mira
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Health and Genomics, Center for Advanced Research in Public Health, Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre (TEAGASC), Moorepark, Fermoy, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
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12
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Henares D, Brotons P, de Sevilla MF, Fernandez-Lopez A, Hernandez-Bou S, Perez-Argüello A, Mira A, Muñoz-Almagro C, Cabrera-Rubio R. Differential nasopharyngeal microbiota composition in children according to respiratory health status. Microb Genom 2021; 7. [PMID: 34699345 PMCID: PMC8627214 DOI: 10.1099/mgen.0.000661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Acute respiratory infections (ARIs) constitute one of the leading causes of antibiotic administration, hospitalization and death among children <5 years old. The upper respiratory tract microbiota has been suggested to explain differential susceptibility to ARIs and modulate ARI severity. The aim of the present study was to investigate the relation of nasopharyngeal microbiota and other microbiological parameters with respiratory health and disease, and to assess nasopharyngeal microbiota diagnostic utility for discriminating between different respiratory health statuses. We conducted a prospective case-control study at Hospital Sant Joan de Deu (Barcelona, Spain) from 2014 to 2018. This study included three groups of children <18 years with gradual decrease of ARI severity: cases with invasive pneumococcal disease (IPD) (representative of lower respiratory tract infections and systemic infections), symptomatic controls with mild viral upper respiratory tract infections (URTI), and healthy/asymptomatic controls according to an approximate case-control ratio 1:2. Nasopharyngeal samples were collected from participants for detection, quantification and serotyping of pneumococcal DNA, viral DNA/RNA detection and 16S rRNA gene sequencing. Microbiological parameters were included on case-control classification models. A total of 140 subjects were recruited (IPD=27, URTI=48, healthy/asymptomatic control=65). Children's nasopharyngeal microbiota composition varied according to respiratory health status and infection severity. The IPD group was characterized by overrepresentation of Streptococcus pneumoniae, higher frequency of invasive pneumococcal serotypes, increased rate of viral infection and underrepresentation of potential protective bacterial species such as Dolosigranulum pigrum and Moraxella lincolnii. Microbiota-based classification models differentiated cases from controls with moderately high accuracy. These results demonstrate the close relationship existing between a child's nasopharyngeal microbiota and respiratory health, and provide initial evidence of the potential of microbiota-based diagnostics for differential diagnosis of severe ARIs using non-invasive samples.
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Affiliation(s)
- Desiree Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, Barcelona, Spain
| | | | | | | | - Alex Mira
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO, Valencia, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre (TEAGASC), Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, County Cork, Ireland
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13
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Paediatric otogenic cerebral venous sinus thrombosis: a multidisciplinary approach. The Journal of Laryngology & Otology 2021; 136:3-7. [PMID: 34698003 DOI: 10.1017/s0022215121003145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Paediatric otogenic cerebral venous sinus thrombosis is a rare, heterogeneous and life-threatening condition, with possible otological, neurological and ophthalmological sequelae. Its course and outcomes can be widely variable. The publications available often consider individual aspects of paediatric otogenic cerebral venous sinus thrombosis management. The condition itself and the nature of the currently available guidance can lead to uncertainties when holistically managing patients with paediatric otogenic cerebral venous sinus thrombosis. OBJECTIVES Clear recommendations for the comprehensive assessment and management of paediatric otogenic cerebral venous sinus thrombosis are presented, along with the literature review upon which they are based. Its clinical and radiological assessment are discussed. CONCLUSION A multidisciplinary approach to assessment and management is recommended, inclusive of infectious diseases, ENT surgery, neurology, ophthalmology and haematology. On balance, anticoagulation is recommended for three months. Follow-up imaging is not recommended in the absence of clinical concern. Follow up by ENT surgery, neurology and ophthalmology departments is recommended.
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14
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McNeil JC, Sommer LM, Dunn JJ, Hulten KG, Kaplan SL, Vallejo JG. Molecular Epidemiology of Contemporary Invasive Haemophilus influenzae Isolates in Texas Children. Pediatr Infect Dis J 2021; 40:852-855. [PMID: 34260499 DOI: 10.1097/inf.0000000000003188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Although vaccination has reduced the incidence of Haemophilus influenzae type b, nontypeable H. influenzae and other encapsulated types remain a health threat. Little is known regarding the contemporary molecular epidemiology of these organisms. We conducted multilocus sequence typing on invasive H. influenzae during a period of increasing incidence.
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Affiliation(s)
- J Chase McNeil
- From the Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Lauren M Sommer
- From the Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - James J Dunn
- Department of Pathology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Kristina G Hulten
- From the Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Sheldon L Kaplan
- From the Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Jesus G Vallejo
- From the Department of Pediatrics, Section of Infectious Diseases, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
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15
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de Steenhuijsen Piters WAA, Binkowska J, Bogaert D. Early Life Microbiota and Respiratory Tract Infections. Cell Host Microbe 2021; 28:223-232. [PMID: 32791114 DOI: 10.1016/j.chom.2020.07.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/02/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022]
Abstract
Over the last decade, it has become clear that respiratory and intestinal tract microbiota are related to pathogenesis of respiratory tract infections (RTIs). Host and environmental factors can drive respiratory microbiota maturation in early life, which in turn is related to consecutive susceptibility to RTIs. Moreover, during RTIs, including viral bronchiolitis, the local microbiome appears to play an immunomodulatory role through complex interactions, though causality has not yet been fully demonstrated. The microbiota is subsequently associated with recovery after RTIs and can be related to persistent or long-term sequelae. In this Review, we explore the epidemiological evidence supporting these associations and link to mechanistic insights. The long-term consequences of childhood RTIs and the comprehensive role of the microbiota at various stages in RTI pathogenesis call for early life preventative and therapeutic interventions to promote respiratory health.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Justyna Binkowska
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
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16
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de Sévaux JL, Venekamp RP, Lutje V, Hak E, Schilder AG, Sanders EA, Damoiseaux RA. Pneumococcal conjugate vaccines for preventing acute otitis media in children. Cochrane Database Syst Rev 2020; 11:CD001480. [PMID: 33231293 PMCID: PMC8096893 DOI: 10.1002/14651858.cd001480.pub6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Prior to introducing pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae was most commonly isolated from the middle ear fluid of children with acute otitis media (AOM). Reducing nasopharyngeal colonisation of this bacterium by PCVs may lead to a decline in AOM. The effects of PCVs deserve ongoing monitoring since studies from the post-PCV era report a shift in causative otopathogens towards non-vaccine serotypes and other bacteria. This updated Cochrane Review was first published in 2002 and updated in 2004, 2009, 2014, and 2019. OBJECTIVES To assess the effect of PCVs in preventing AOM in children up to 12 years of age. SEARCH METHODS We searched CENTRAL, MEDLINE, Embase, CINAHL, LILACS, Web of Science, and two trials registers, ClinicalTrials.gov and WHO ICTRP, to 11 June 2020. SELECTION CRITERIA Randomised controlled trials of PCV versus placebo or control vaccine. DATA COLLECTION AND ANALYSIS We used the standard methodological procedures expected by Cochrane. The primary outcomes were frequency of all-cause AOM and adverse effects. Secondary outcomes included frequency of pneumococcal AOM and frequency of recurrent AOM (defined as three or more AOM episodes in six months or four or more in one year). We used GRADE to assess the certainty of the evidence. MAIN RESULTS We included 15 publications of 11 trials (60,733 children, range 74 to 37,868 per trial) of 7- to 11-valent PCVs versus control vaccines (meningococcus type C vaccine in three trials, and hepatitis A or B vaccine in eight trials). We included one additional publication of a previously included trial for this 2020 update. We did not find any relevant trials with the newer 13-valent PCV. Most studies were funded by pharmaceutical companies. Overall, risk of bias was low. In seven trials (59,415 children), PCVs were administered in early infancy, whilst four trials (1318 children) included children aged one year and over who were either healthy or had a history of respiratory illness. There was considerable clinical heterogeneity across studies, therefore we reported results from individual studies. PCV administered in early infancy PCV7 The licenced 7-valent PCV with CRM197 as carrier protein (CRM197-PCV7) was associated with a 6% (95% confidence interval (CI) -4% to 16%; 1 trial; 1662 children) and 6% (95% CI 4% to 9%; 1 trial; 37,868 children) relative risk reduction (RRR) in low-risk infants (moderate-certainty evidence), but was not associated with a reduction in all-cause AOM in high-risk infants (RRR -5%, 95% CI -25% to 12%). PCV7 with the outer membrane protein complex of Neisseria meningitidis serogroup B as carrier protein (OMPC-PCV7) was not associated with a reduction in all-cause AOM (RRR -1%, 95% CI -12% to 10%; 1 trial; 1666 children; low-certainty evidence). CRM197-PCV7 and OMPC-PCV7 were associated with 20% (95% CI 7% to 31%) and 25% (95% CI 11% to 37%) RRR in pneumococcal AOM, respectively (2 trials; 3328 children; high-certainty evidence), and CRM197-PCV7 with 9% (95% CI -12% to 27%) and 10% (95% CI 7% to 13%) RRR in recurrent AOM (2 trials; 39,530 children; moderate-certainty evidence). PHiD-CV10/11 The effect of a licenced 10-valent PCV conjugated to protein D, a surface lipoprotein of Haemophilus influenzae, (PHiD-CV10) on all-cause AOM in healthy infants varied from 6% (95% CI -6% to 17%; 1 trial; 5095 children) to 15% (95% CI -1% to 28%; 1 trial; 7359 children) RRR (low-certainty evidence). PHiD-CV11 was associated with 34% (95% CI 21% to 44%) RRR in all-cause AOM (1 trial; 4968 children; moderate-certainty evidence). PHiD-CV10 and PHiD-CV11 were associated with 53% (95% CI 16% to 74%) and 52% (95% CI 37% to 63%) RRR in pneumococcal AOM (2 trials; 12,327 children; high-certainty evidence), and PHiD-CV11 with 56% (95% CI -2% to 80%) RRR in recurrent AOM (1 trial; 4968 children; low-certainty evidence). PCV administered at a later age PCV7 We found no evidence of a beneficial effect on all-cause AOM of administering CRM197-PCV7 in children aged 1 to 7 years with a history of respiratory illness or frequent AOM (2 trials; 457 children; moderate-certainty evidence) and CRM197-PCV7 combined with a trivalent influenza vaccine in children aged 18 to 72 months with a history of respiratory tract infections (1 trial; 597 children; moderate-certainty evidence). CRM197-PCV9 In 1 trial including 264 healthy daycare attendees aged 1 to 3 years, CRM197-PCV9 was associated with 17% (95% CI -2% to 33%) RRR in parent-reported all-cause otitis media (very low-certainty evidence). Adverse events Nine trials reported on adverse effects (77,389 children; high-certainty evidence). Mild local reactions and fever were common in both groups, and occurred more frequently in PCV than in control vaccine groups: redness (< 2.5 cm): 5% to 20% versus 0% to 16%; swelling (< 2.5 cm): 5% to 12% versus 0% to 8%; and fever (< 39 °C): 15% to 44% versus 8% to 25%. More severe redness (> 2.5 cm), swelling (> 2.5 cm), and fever (> 39 °C) occurred less frequently (0% to 0.9%, 0.1% to 1.3%, and 0.4% to 2.5%, respectively) in children receiving PCV, and did not differ significantly between PCV and control vaccine groups. Pain or tenderness, or both, was reported more frequently in PCV than in control vaccine groups: 3% to 38% versus 0% to 8%. Serious adverse events judged to be causally related to vaccination were rare and did not differ significantly between groups, and no fatal serious adverse event judged causally related to vaccination was reported. AUTHORS' CONCLUSIONS Administration of the licenced CRM197-PCV7 and PHiD-CV10 during early infancy is associated with large relative risk reductions in pneumococcal AOM. However, the effects of these vaccines on all-cause AOM is far more uncertain based on low- to moderate-certainty evidence. We found no evidence of a beneficial effect on all-cause AOM of administering PCVs in high-risk infants, after early infancy, and in older children with a history of respiratory illness. Compared to control vaccines, PCVs were associated with an increase in mild local reactions (redness, swelling), fever, and pain and/or tenderness. There was no evidence of a difference in more severe local reactions, fever, or serious adverse events judged to be causally related to vaccination.
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Affiliation(s)
- Joline Lh de Sévaux
- Department of Emergency Medicine, Ziekenhuis St Jansdal, Harderwijk, Netherlands
- Department of Internal Medicine, Ziekenhuis Gelderse Vallei, Ede, Netherlands
| | - Roderick P Venekamp
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Vittoria Lutje
- Cochrane Infectious Diseases Group, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Eelko Hak
- Groningen Research Institute of Pharmacy, University Groningen, 9713 AV Groningen, Netherlands
| | - Anne Gm Schilder
- evidENT, Ear Institute, University College London, London, UK
- Julius Center for Health Sciences and Primary Care & Department of Otorhinolaryngology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- National Institute of Health Research, University College London Hospitals Biomedical Research Centre, London, UK
| | - Elisabeth Am Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Center for Infectious Diseases, The National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Roger Amj Damoiseaux
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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17
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Folino F, Ruggiero L, Capaccio P, Coro I, Aliberti S, Drago L, Marchisio P, Torretta S. Upper Respiratory Tract Microbiome and Otitis Media Intertalk: Lessons from the Literature. J Clin Med 2020; 9:jcm9092845. [PMID: 32887458 PMCID: PMC7563526 DOI: 10.3390/jcm9092845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Otitis media (OM) is one of the most common diseases occurring during childhood. Microbiological investigations concerning this topic have been primarily focused on the four classical otopathogens (Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pyogenes) mainly because most of the studies have been conducted with culture-dependent methods. In recent years, the introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, leading to a better comprehension of the role of resident flora in health and disease. The upper respiratory tract (URT) is a region of major interest in otitis media pathogenesis, as it could serve as a source of pathogens for the middle ear (ME). Studies conducted with culture-independent methods in the URT and ME have provided novel insights on the pathogenesis of middle ear diseases through the identification of both possible new causative agents and of potential protective bacteria, showing that imbalances in bacterial communities could influence the natural history of otitis media in children. The aim of this review is to examine available evidence in microbiome research and otitis media in the pediatric age, with a focus on its different phenotypes: acute otitis media, otitis media with effusion and chronic suppurative otitis media.
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Affiliation(s)
- Francesco Folino
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Correspondence:
| | - Luca Ruggiero
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Pasquale Capaccio
- Department of Otolaryngology and Head and Neck Surgery, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (P.C.); (S.T.)
- Department of Biomedical Surgical Dental Science, University of Milan, 20122 Milan, Italy
| | - Ilaria Coro
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Stefano Aliberti
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Internal Medicine Department, Respiratory Unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Lorenzo Drago
- Laboratory of Clinical Microbiology, Department of Biomedical Science for Health, University of Milan, 20122 Milan, Italy;
| | - Paola Marchisio
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (I.C.); (S.A.); (P.M.)
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Sara Torretta
- Department of Otolaryngology and Head and Neck Surgery, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (P.C.); (S.T.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
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18
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Ramos-Sevillano E, Wade WG, Mann A, Gilbert A, Lambkin-Williams R, Killingley B, Nguyen-Van-Tam JS, Tang CM. The Effect of Influenza Virus on the Human Oropharyngeal Microbiome. Clin Infect Dis 2020; 68:1993-2002. [PMID: 30445563 PMCID: PMC6541733 DOI: 10.1093/cid/ciy821] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/04/2018] [Indexed: 12/27/2022] Open
Abstract
Background Secondary bacterial infections are an important cause of morbidity and mortality associated with influenza infections. As bacterial disease can be caused by a disturbance of the host microbiome, we examined the impact of influenza on the upper respiratory tract microbiome in a human challenge study. Methods The dynamics and ecology of the throat microbiome were examined following an experimental influenza challenge of 52 previously-healthy adult volunteers with influenza A/Wisconsin/67/2005 (H3N2) by intranasal inoculation; 35 healthy control subjects were not subjected to the viral challenge. Serial oropharyngeal samples were taken over a 30-day period, and the V1-V3 region of the bacterial 16S ribosomal RNA sequences were amplified and sequenced to determine the composition of the microbiome. The carriage of pathogens was also detected. Results Of the 52 challenged individuals, 43 developed proven influenza infections, 33 of whom became symptomatic. None of the controls developed influenza, although 22% reported symptoms. The diversity of bacterial communities remained remarkably stable following the acquisition of influenza, with no significant differences over time between individuals with influenza and those in the control group. Influenza infection was not associated with perturbation of the microbiome at the level of phylum or genus. There was no change in colonization rates with Streptococcus pneumoniae or Neisseria meningitidis. Conclusions The throat microbiota is resilient to influenza infection, indicating the robustness of the upper-airway microbiome.
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Affiliation(s)
| | | | - Alex Mann
- hVIVO Services Limited, Queen Mary BioEnterprises Innovation Centre, United Kingdom
| | - Anthony Gilbert
- hVIVO Services Limited, Queen Mary BioEnterprises Innovation Centre, United Kingdom
| | | | - Ben Killingley
- Department of Infection and Acute Medicine, University College London Hospital, United Kingdom
| | | | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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Rosenthal A, Gans H, Schwenk HT. A 10-Month-Old Female With Complicated Mastoiditis Due to Fusobacterium necrophorum: A Case Report and Literature Review. J Pediatric Infect Dis Soc 2020; 9:399-401. [PMID: 32531061 DOI: 10.1093/jpids/piaa059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 04/16/2020] [Indexed: 11/14/2022]
Affiliation(s)
- Ayelet Rosenthal
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Hayley Gans
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Hayden T Schwenk
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
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Welp AL, Bomberger JM. Bacterial Community Interactions During Chronic Respiratory Disease. Front Cell Infect Microbiol 2020; 10:213. [PMID: 32477966 PMCID: PMC7240048 DOI: 10.3389/fcimb.2020.00213] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic respiratory diseases including chronic rhinosinusitis, otitis media, asthma, cystic fibrosis, non-CF bronchiectasis, and chronic obstructive pulmonary disease are a major public health burden. Patients suffering from chronic respiratory disease are prone to persistent, debilitating respiratory infections due to the decreased ability to clear pathogens from the respiratory tract. Such infections often develop into chronic, life-long complications that are difficult to treat with antibiotics due to the formation of recalcitrant biofilms. The microbial communities present in the upper and lower respiratory tracts change as these respiratory diseases progress, often becoming less diverse and dysbiotic, correlating with worsening patient morbidity. Those with chronic respiratory disease are commonly infected with a shared group of respiratory pathogens including Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis, among others. In order to understand the microbial landscape of the respiratory tract during chronic disease, we review the known inter-species interactions among these organisms and other common respiratory flora. We consider both the balance between cooperative and competitive interactions in relation to microbial community structure. By reviewing the major causes of chronic respiratory disease, we identify common features across disease states and signals that might contribute to community shifts. As microbiome shifts have been associated with respiratory disease progression, worsening morbidity, and increased mortality, these underlying community interactions likely have an impact on respiratory disease state.
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Affiliation(s)
- Allison L. Welp
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
- Graduate Program in Microbiology and Immunology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
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Complications of Otitis Media and Sinusitis Caused by Streptococcus anginosus Group Organisms in Children. Pediatr Infect Dis J 2020; 39:108-113. [PMID: 31738321 DOI: 10.1097/inf.0000000000002514] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND The Streptococcus anginosus group (SAG, S. anginosus, S. intermedius and S. constellatus) are often associated with severe disease and abscess formation. In our institution, we observed an apparent increase in frequency of intraorbital and intracranial infections resulting from SAG at Texas Children's Hospital. We undertook a retrospective review to describe the frequency and clinical features of these infections. METHODS We reviewed the database of the microbiology laboratory at Texas Children's Hospital from 2011 to 2018 for SAG-positive cultures. Cases included were those associated with (1) either otitis media or sinusitis and (2) Pott's puffy tumor, orbital abscesses, mastoiditis, epidural abscesses, subdural empyema, brain parenchymal abscesses or dural enhancement by imaging. The number of overall diagnoses were determined using diagnostic codes and used to estimate the proportion of disease caused by SAG. RESULTS Ninety-five cases were identified meeting inclusion criteria. The median age of patients was 11.4 years, and 75.8% were previously healthy. S. intermedius was most commonly isolated (80%) followed by S. constellatus (12.6%) and S. anginosus (7.4%); 50.5% of cases were polymicrobial. Among polymicrobial cases, Staphylococcus aureus was most frequently isolated. All patients underwent surgical intervention. 8.4% of patients experienced persistent neurologic deficits. We observed a significant increase in disease incidence during the study period; in addition, the overall proportion of all intracranial infections caused by SAG increased. CONCLUSIONS Complications of otitis media and sinusitis caused by SAG are associated with substantial morbidity. These infections are becoming increasingly common at our center although the precise reason for this temporal trend is unclear.
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Coudert A, Fanchette J, Regnier G, Delmas J, Truy E, Nicollas R, Akkari M, Couloignier V, Ayari-Khalfallah S. Fusobacterium necrophorum, a major provider of sinus thrombosis in acute mastoiditis: A retrospective multicentre paediatric study. Clin Otolaryngol 2019; 45:182-189. [PMID: 31746543 DOI: 10.1111/coa.13478] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/22/2019] [Accepted: 11/09/2019] [Indexed: 01/31/2023]
Abstract
OBJECTIVE To evaluate in children the clinical severity and evolution of otogenic lateral sinus thrombosis (OLST) due to Fusobacterium necrophorum compared with other bacterial otogenic thrombosis and propose a specific management flowchart for Fusobacterium OLST. DESIGN A retrospective multicentre cohort study. SETTINGS Four French ENT paediatric departments. PARTICIPANTS A total of 260 under 18 years old admitted for acute mastoiditis were included. Initial imaging was reviewed to focus on complicated mastoiditis and 52 OLST were identified. Children were then divided into two groups according to bacteriological results: 28 in the "OLST Fusobacterium group" and 24 in the "OLST other bacteria group". RESULTS There was a significant association between F necrophorum and OLST (P < .001). When compared to the OLST other bacteria group, children in the OLST Fusobacterium group were significantly younger (61 months vs 23 months, P < .01) and had a more severe clinical presentation: higher CRP (113 mg/L vs 175.7 mg/L, P = .02) and larger subperiosteal abscess (14 mm vs 21 mm, P < .01). Medical management was also more intensive in the OLST Fusobacterium group than in the OLST other bacteria group: increased number of conservative surgeries (66.7% vs 92.9%, P = .03) and longer hospital stay (13.7 days vs 19.8 days, P = .02). At the end of follow-up, the clinical course was good in both groups without any neurological sequelae. CONCLUSIONS Thrombotic complications are very frequent in case of Fusobacterium mastoiditis and clinicians should be aware of the initial severity of the clinical presentation. Under appropriate management, the clinical course of Fusobacterium OLST is as good as that of other bacterial otogenic thrombosis.
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Affiliation(s)
- Aurélie Coudert
- Service d'ORL Pédiatrique, Hôpital Femme Mère Enfants, Hospices Civils de Lyon, Lyon, France
| | - Julia Fanchette
- Service d'ORL Pédiatrique, Hôpital Necker, Centre Hospitalier et Universitaire, Paris, France
| | - Gaëlle Regnier
- Service d'ORL Pédiatrique, Hôpital Gui de Chauliac, Centre Hospitalier et Universitaire, Montpellier, France
| | - Justine Delmas
- Service d'ORL Pédiatrique, Hôpital de la Timone, Centre Hospitalier et Universitaire, Marseille, France
| | - Eric Truy
- Service d'ORL Pédiatrique, Hôpital Femme Mère Enfants, Hospices Civils de Lyon, Lyon, France
| | - Richard Nicollas
- Service d'ORL Pédiatrique, Hôpital de la Timone, Centre Hospitalier et Universitaire, Marseille, France
| | - Mohamed Akkari
- Service d'ORL Pédiatrique, Hôpital Gui de Chauliac, Centre Hospitalier et Universitaire, Montpellier, France
| | - Vincent Couloignier
- Service d'ORL Pédiatrique, Hôpital Necker, Centre Hospitalier et Universitaire, Paris, France
| | - Sonia Ayari-Khalfallah
- Service d'ORL Pédiatrique, Hôpital Femme Mère Enfants, Hospices Civils de Lyon, Lyon, France
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23
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Gonçalves VM, Kaneko K, Solórzano C, MacLoughlin R, Saleem I, Miyaji EN. Progress in mucosal immunization for protection against pneumococcal pneumonia. Expert Rev Vaccines 2019; 18:781-792. [PMID: 31305196 DOI: 10.1080/14760584.2019.1643719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: Lower respiratory tract infections are the fourth cause of death worldwide and pneumococcus is the leading cause of pneumonia. Nonetheless, existing pneumococcal vaccines are less effective against pneumonia than invasive diseases and serotype replacement is a major concern. Protein antigens could induce serotype-independent protection, and mucosal immunization could offer local and systemic immune responses and induce protection against pneumococcal colonization and lung infection. Areas covered: Immunity induced in the experimental human pneumococcal carriage model, approaches to address the physiological barriers to mucosal immunization and improve delivery of the vaccine antigens, different strategies already tested for pneumococcal mucosal vaccination, including live recombinant bacteria, nanoparticles, bacterium-like particles, and nanogels as well as, nasal, pulmonary, sublingual and oral routes of vaccination. Expert opinion: The most promising delivery systems are based on nanoparticles, bacterial-like particles or nanogels, which possess greater immunogenicity than the antigen alone and are considered safer than approaches based on living cells or toxoids. These particles can protect the antigen from degradation, eliminating the refrigeration need during storage and allowing the manufacture of dry powder formulations. They can also increase antigen uptake, control release of antigen and trigger innate immune responses.
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Affiliation(s)
| | - Kan Kaneko
- b School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University James Parsons Building , Liverpool , UK
| | - Carla Solórzano
- c Department of Clinical Sciences, Liverpool School of Tropical Medicine , Liverpool , UK
| | - Ronan MacLoughlin
- d Science Department and Clinical Department, Aerogen Ltd., IDA Business Park , Galway , Ireland
| | - Imran Saleem
- b School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University James Parsons Building , Liverpool , UK
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24
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Boelsen LK, Dunne EM, Mika M, Eggers S, Nguyen CD, Ratu FT, Russell FM, Mulholland EK, Hilty M, Satzke C. The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji. MICROBIOME 2019; 7:106. [PMID: 31311598 PMCID: PMC6636143 DOI: 10.1186/s40168-019-0716-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 06/24/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Streptococcus pneumoniae is a significant global pathogen that colonises the nasopharynx of healthy children. Pneumococcal conjugate vaccines, which reduce nasopharyngeal colonisation of vaccine-type S. pneumoniae, may have broader effects on the nasopharyngeal microbiota; however, data are limited. In Fiji, nasopharyngeal carriage prevalence of S. pneumoniae and other colonising species differ between the two main ethnic groups. Here, we examined the association between the 7-valent pneumococcal conjugate vaccine (PCV7) and the nasopharyngeal microbiota of children in Fiji, including for each of the two main ethnic groups-indigenous Fijians (iTaukei) and Fijians of Indian descent (FID). METHOD The nasopharyngeal microbiota of 132 Fijian children was examined using nasopharyngeal swabs collected from 12-month-old iTaukei and FID children who were vaccinated (3 doses PCV7) or unvaccinated in infancy as part of a phase II randomised controlled trial. Microbiota composition was determined by sequencing the V4 region of the 16S rRNA gene. Species-specific carriage of S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Staphylococcus aureus was determined using real-time quantitative PCR. Associations between microbiota composition and other host and environmental factors were considered in the analysis. RESULTS PCV7 had no overall impact on microbial diversity or composition. However, ethnic differences were observed in both diversity and composition with iTaukei children having higher relative abundance of Moraxella (p = 0.004) and Haemophilus (p = 0.004) and lower relative abundance of Staphylococcus (p = 0.026), Dolosigranulum (p = 0.004) and Corynebacterium (p = 0.003) compared with FID children. Further, when we stratified by ethnicity, associations with PCV7 could be detected: vaccinated iTaukei children had a lower relative abundance of Streptococcus and Haemophilus compared with unvaccinated iTaukei children (p = 0.022 and p = 0.043, respectively); and vaccinated FID children had a higher relative abundance of Dolosigranulum compared with unvaccinated FID children (p = 0.037). Children with symptoms of an upper respiratory tract infection (URTI) had a significantly different microbiota composition to children without symptoms. The microbiota composition of iTaukei children without URTI symptoms was most similar to the microbiota composition of FID children with URTI symptoms. CONCLUSIONS Associations between PCV7 and nasopharyngeal microbiota differed within each ethnic group. This study highlights the influence that ethnicity and URTIs have on nasopharyngeal microbiota.
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Affiliation(s)
- Laura K. Boelsen
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria Australia
| | - Eileen M. Dunne
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria Australia
| | - Moana Mika
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Stefanie Eggers
- Translational Genomics Unit, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria Australia
| | - Cattram D. Nguyen
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria Australia
| | | | - Fiona M. Russell
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria Australia
- Centre for International Child Health, Department of Paediatrics, The University of Melbourne, Parkville, Victoria Australia
| | - E. Kim Mulholland
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria Australia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria Australia
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria Australia
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de Steenhuijsen Piters WAA, Jochems SP, Mitsi E, Rylance J, Pojar S, Nikolaou E, German EL, Holloway M, Carniel BF, Chu MLJN, Arp K, Sanders EAM, Ferreira DM, Bogaert D. Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine. Nat Commun 2019; 10:2981. [PMID: 31278315 PMCID: PMC6611866 DOI: 10.1038/s41467-019-10814-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is the main bacterial pathogen involved in pneumonia. Pneumococcal acquisition and colonization density is probably affected by viral co-infections, the local microbiome composition and mucosal immunity. Here, we report the interactions between live-attenuated influenza vaccine (LAIV), successive pneumococcal challenge, and the healthy adult nasal microbiota and mucosal immunity using an experimental human challenge model. Nasal microbiota profiles at baseline are associated with consecutive pneumococcal carriage outcome (non-carrier, low-dense and high-dense pneumococcal carriage), independent of LAIV co-administration. Corynebacterium/Dolosigranulum-dominated profiles are associated with low-density colonization. Lowest rates of natural viral co-infection at baseline and post-LAIV influenza replication are detected in the low-density carriers. Also, we detected the fewest microbiota perturbations and mucosal cytokine responses in the low-density carriers compared to non-carriers or high-density carriers. These results indicate that the complete respiratory ecosystem affects pneumococcal behaviour following challenge, with low-density carriage representing the most stable ecological state.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Simon P Jochems
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Esther L German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mark Holloway
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Beatriz F Carniel
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands.
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom.
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Dubourg G, Edouard S, Raoult D. Relationship between nasopharyngeal microbiota and patient's susceptibility to viral infection. Expert Rev Anti Infect Ther 2019; 17:437-447. [PMID: 31106653 DOI: 10.1080/14787210.2019.1621168] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: The burden of respiratory viral infections is a global public health concern with significant mortality, morbidity, and economic impact. While Koch's postulate led to considering only the etiological agent, numerous works have demonstrated that commensal microbes could contribute to both the susceptibility and the severity of these infections, in particular those of the nasopharynx. Areas covered: Herein, we first propose to briefly recall the historical background that led to considering microbes inhabiting the nasopharyngeal microbiota as a potential contributor to human viral infections. We describe the evolution of the normal nasopharyngeal microbiota composition over time, especially during the first year of life. We aimed to resume the changes of the nasopharyngeal microbiota during viral respiratory infections. We also develop how nasopharyngeal microbiota could contribute to the acquisition of respiratory viral infections. We finally provide the potential therapeutic perspectives deriving from these findings. Expert opinion: Prospective studies focusing on children have identified that nasopharyngeal microbiota composition is associated with predisposition to acute respiratory illness and bronchiolitis, while data are scarce regarding adults. For the latter, further works are needed, in particular as a part of the multi-OMICS approach that should probably be performed in conjunction with gut microbiota studies.
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Affiliation(s)
- Grégory Dubourg
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
| | - Sophie Edouard
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a IRD, Assistance Publique Hôpitaux de Marseille (APHM), Microbes, Evolution, Phylogeny and Infection (MEPHI) , Aix Marseille University , Marseille , France.,b IHU-Méditerranée Infection , Marseille , France
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27
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Abstract
Community-acquired pneumonia (CAP) is a leading cause of morbidity and mortality worldwide. Despite broad literature including basic and translational scientific studies, many gaps in our understanding of host-pathogen interactions remain. In this review, pathogen virulence factors that drive lung infection and injury are discussed in relation to their associated host immune pathways. CAP epidemiology is considered, with a focus on Staphylococcus aureus and Streptococcus pneumoniae as primary pathogens. Bacterial factors involved in nasal colonization and subsequent virulence are illuminated. A particular emphasis is placed on bacterial pore-forming toxins, host cell death, and inflammasome activation. Identified host-pathogen interactions are then examined by linking pathogen factors to aberrant host response pathways in the context of acute lung injury in both primary and secondary infection. While much is known regarding bacterial virulence and host immune responses, CAP management is still limited to mostly supportive care. It is likely that improvements in therapy will be derived from combinatorial targeting of both pathogen virulence factors and host immunomodulation.
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Fortanier AC, Venekamp RP, Boonacker CWB, Hak E, Schilder AGM, Sanders EAM, Damoiseaux RAMJ. Pneumococcal conjugate vaccines for preventing acute otitis media in children. Cochrane Database Syst Rev 2019; 5:CD001480. [PMID: 31135969 PMCID: PMC6537667 DOI: 10.1002/14651858.cd001480.pub5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Prior to introducing pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae was most commonly isolated from middle ear fluid of children with acute otitis media (AOM). Reducing nasopharyngeal colonisation of this bacterium by PCVs may lead to a decline in AOM. The effects of PCVs deserve ongoing monitoring since studies from the post-PCV era report a shift in causative otopathogens towards non-vaccine serotypes and other bacteria. This updated Cochrane Review was first published in 2002 and updated in 2004, 2009, and 2014. The review title was changed (to include the population, i.e. children) for this update. OBJECTIVES To assess the effect of PCVs in preventing AOM in children up to 12 years of age. SEARCH METHODS We searched CENTRAL, MEDLINE, Embase, CINAHL, LILACS, Web of Science, and trials registers (ClinicalTrials.gov and WHO ICTRP) to 29 March 2019. SELECTION CRITERIA Randomised controlled trials of PCV versus placebo or control vaccine. DATA COLLECTION AND ANALYSIS We used the standard methodological procedures expected by Cochrane. The primary outcomes were frequency of all-cause AOM and adverse effects. Secondary outcomes included frequency of pneumococcal AOM and frequency of recurrent AOM (defined as three or more AOM episodes in six months or four or more in one year). We used GRADE to assess the quality of the evidence. MAIN RESULTS We included 14 publications of 11 trials (60,733 children, range 74 to 37,868 per trial) of 7- to 11-valent PCVs versus control vaccines (meningococcus type C vaccine in three trials, and hepatitis A or B vaccine in eight trials). We included two additional trials for this update. We did not find any relevant trials with the newer 13-valent PCV. Most studies were funded by pharmaceutical companies. Overall, risk of bias was low. In seven trials (59,415 children) PCVs were administered in early infancy, while four trials (1318 children) included children aged one year and over who were either healthy or had a history of respiratory illness. There was considerable clinical heterogeneity across studies, therefore we did not perform meta-analyses.Adverse eventsNine trials reported on adverse effects (77,389 children; high-quality evidence). Mild local reactions and fever were common in both groups, and occurred more frequently in PCV than in control vaccine groups: redness (< 2.5 cm): 5% to 20% versus 0% to 16%; swelling (< 2.5 cm): 5% to 12% versus 0% to 8%; and fever (< 39 °C): 15% to 44% versus 8% to 25%. More severe redness (> 2.5 cm), swelling (> 2.5 cm), and fever (> 39 °C) occurred less frequently (0% to 0.9%, 0.1% to 1.3%, and 0.4% to 2.5%, respectively in children receiving PCV) and did not differ significantly between PCV and control vaccine groups. Pain or tenderness, or both was reported more frequently in PCV than in control vaccine groups: 3% to 38% versus 0% to 8%. Serious adverse events judged causally related to vaccination were rare and did not differ significantly between groups, and no fatal serious adverse event judged causally related to vaccination was reported.PCV administered in early infancyPCV7The effect of a licenced 7-valent PCV with CRM197 as carrier protein (CRM197-PCV7) on all-cause AOM varied from -5% (95% confidence interval (CI) -25% to 12%) relative risk reduction (RRR) in high-risk infants (1 trial; 944 children; moderate-quality evidence) to 6% (95% CI -4% to 16%; 1 trial; 1662 children) and 6% (95% CI 4% to 9%; 1 trial; 37,868 children) RRR in low-risk infants (high-quality evidence). PCV7 with the outer membrane protein complex of Neisseria meningitidis serogroup B as carrier protein (OMPC-PCV7), was not associated with a reduction in all-cause AOM (RRR -1%, 95% CI -12% to 10%; 1 trial; 1666 children; high-quality evidence).CRM197-PCV7 and OMPC-PCV7 were associated with 20% (95% CI 7% to 31%) and 25% (95% CI 11% to 37%) RRR in pneumococcal AOM, respectively (2 trials; 3328 children; high-quality evidence) and CRM197-PCV7 with 9% (95% CI -12% to 27%) to 10% (95% CI 7% to 13%) RRR in recurrent AOM (2 trials; 39,530 children; high-quality evidence).PHiD-CV10/11The effect of a licenced 10-valent PCV conjugated to protein D, a surface lipoprotein of Haemophilus influenzae, (PHiD-CV10) on all-cause AOM varied from 6% (95% CI -6% to 17%; 1 trial; 5095 children) to 15% (95% CI -1% to 28%; 1 trial; 7359 children) RRR in healthy infants (moderate-quality evidence). PHiD-CV11 was associated with 34% (95% CI 21% to 44%) RRR in all-cause AOM (1 trial; 4968 children; high-quality evidence).PHiD-CV10 and PHiD-CV11 were associated with 53% (95% CI 16% to 74%) and 52% (95% CI 37% to 63%) RRR in pneumococcal AOM (2 trials; 12,327 children; high-quality evidence) and PHiD-CV11 with 56% (95% CI -2% to 80%) RRR in recurrent AOM (1 trial; 4968 children; moderate-quality evidence).PCV administered at later agePCV7We found no evidence of a beneficial effect on all-cause AOM of administering CRM197-PCV7 in children aged 1 to 7 years with a history of respiratory illness or frequent AOM (2 trials; 457 children; high-quality evidence) and CRM197-PCV7 combined with a trivalent influenza vaccine in children aged 18 to 72 months with a history of respiratory tract infections (1 trial; 597 children; high-quality evidence).CRM197-PCV9In 1 trial including 264 healthy day-care attendees aged 1 to 3 years, CRM197-PCV9 was associated with 17% (95% CI -2% to 33%) RRR in parent-reported all-cause OM (low-quality evidence). AUTHORS' CONCLUSIONS Administration of the licenced CRM197-PCV7 and PHiD-CV10 during early infancy is associated with large relative risk reductions in pneumococcal AOM. However, the effects of these vaccines on all-cause AOM is far more uncertain. We found no evidence of a beneficial effect on all-cause AOM of administering PCVs in high-risk infants, after early infancy (i.e. in children one year and above), and in older children with a history of respiratory illness. Compared to control vaccines, PCVs were associated with an increase in mild local reactions (redness, swelling), fever, and pain and/or tenderness. We found no evidence of a difference in more severe local reactions, fever, or serious adverse events judged causally related to vaccination.
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Affiliation(s)
- Alexandre C Fortanier
- University Medical Center Utrecht, Utrecht UniversityJulius Center for Health Sciences and Primary CareHP: Str. 6.131PO Box 85500UtrechtNetherlands3508 GA
| | - Roderick P Venekamp
- University Medical Center Utrecht, Utrecht UniversityJulius Center for Health Sciences and Primary CareHP: Str. 6.131PO Box 85500UtrechtNetherlands3508 GA
| | - Chantal WB Boonacker
- University Medical Center Utrecht, Utrecht UniversityJulius Center for Health Sciences and Primary CareHP: Str. 6.131PO Box 85500UtrechtNetherlands3508 GA
| | - Eelko Hak
- University GroningenGroningen Research Institute of PharmacyA. Deuslinglaan 19713 AV GroningenNetherlands
| | - Anne GM Schilder
- University College LondonevidENT, Ear Institute330 Grays Inn RoadLondonUKWC1X 8DA
- University Medical Center Utrecht, Utrecht UniversityJulius Center for Health Sciences and Primary Care & Department of OtorhinolaryngologyUtrechtNetherlands
| | - Elisabeth AM Sanders
- Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht UniversityDepartment of Pediatric Immunology and Infectious DiseasesPO Box 85090UtrechtNetherlands3508 AB
- The National Institute for Public Health and the EnvironmentCenter for Infectious DiseasesBilthovenNetherlands
| | - Roger AMJ Damoiseaux
- University Medical Center Utrecht, Utrecht UniversityJulius Center for Health Sciences and Primary CareHP: Str. 6.131PO Box 85500UtrechtNetherlands3508 GA
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Microbiome as a tool and a target in the effort to address antimicrobial resistance. Proc Natl Acad Sci U S A 2019; 115:12902-12910. [PMID: 30559176 DOI: 10.1073/pnas.1717163115] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.
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In silico epitope identification of unique multidrug resistance proteins from Salmonella Typhi for vaccine development. Comput Biol Chem 2019; 78:74-80. [DOI: 10.1016/j.compbiolchem.2018.11.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/14/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
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Nontypeable Haemophilus influenzae Invasive Blood Isolates Are Mainly Phosphorylcholine Negative and Show Decreased Complement-Mediated Killing That Is Associated with Lower Binding of IgM and CRP in Comparison to Colonizing Isolates from the Oropharynx. Infect Immun 2019; 87:IAI.00604-18. [PMID: 30455196 DOI: 10.1128/iai.00604-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/09/2018] [Indexed: 11/20/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) bacteria express various molecules that contribute to their virulence. The presence of phosphocholine (PCho) on NTHi lipooligosaccharide increases adhesion to epithelial cells and is an advantage for the bacterium, enabling nasopharyngeal colonization, as measured in humans and animal models. However, when PCho is expressed on the lipooligosaccharide, it is also recognized by the acute-phase protein C-reactive protein (CRP) and PCho-specific antibodies, both of which are potent initiators of the classical pathway of complement activation. In this study, we show that blood isolates, which are exposed to CRP and PCho-specific antibodies in the bloodstream, have a higher survival in serum than oropharyngeal isolates, which was associated with a decreased presence of PCho. PCholow strains showed decreased IgM, CRP, and complement C3 deposition, which was associated with increased survival in human serum. Consistent with the case for the PCholow strains, removal of PCho expression by licA gene deletion decreased IgM, CRP, and complement C3 deposition, which increased survival in human serum. Complement-mediated killing of PChohigh strains was mainly dependent on binding of IgM to the bacterial surface. These data support the hypothesis that a PCholow phenotype was selected in blood during invasive disease, which increased resistance to serum killing, mainly due to lowered IgM and CRP binding to the bacterial surface.
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Abstract
BACKGROUND Recent reports have reported an increase in the incidence of acute mastoiditis because of Fusobacterium necrophorum. However, the crude incidence and the specific clinical and laboratory characteristics of F. necrophorum mastoiditis in children have not been described. Our aim was to describe these features to identify high-risk patients. METHODS The electronic medical records of all children with acute mastoiditis at a tertiary medical center between July 2011 and December 2015 were analyzed. Using a stepwise logistic regression to identify independent risk factors for F. necrophorum, we formulated a predictive model. RESULTS F. necrophorum was identified in 13% (19/149) of mastoiditis cases with an identifiable agent. Its incidence increased 7-fold from 2.8% in 2012 to 20.4% in 2015 (P = 0.02). F. necrophorum infection had unique clinical, laboratory and prognostic features. The vast majority had complications and underwent surgical intervention. The predictive model used 4 parameters to define high-risk patients for F. necrophorum infection at admission: females, winter/spring season, prior antibiotic treatment and a C-reactive protein value >20 mg/dL (area under receiver operating characteristic curve 0.929). CONCLUSIONS Clinicians should be aware of the increasing incidence of F. necrophorum mastoiditis and consider anaerobic cultures and specific anaerobic coverage in high-risk patients.
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Nisar MI, Nayani K, Akhund T, Riaz A, Irfan O, Shakoor S, Muneer S, Muslim S, Hotwani A, Kabir F, Whitney C, Kim L, Srinivasan V, Ali A, Zaidi AKM, Jehan F. Nasopharyngeal carriage of Streptococcus pneumoniae in children under 5 years of age before introduction of pneumococcal vaccine (PCV10) in urban and rural districts in Pakistan. BMC Infect Dis 2018; 18:672. [PMID: 30563483 PMCID: PMC6299586 DOI: 10.1186/s12879-018-3608-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 12/10/2018] [Indexed: 11/10/2022] Open
Abstract
Background Benefits of pneumococcal conjugate vaccine programs have been linked to the vaccine’s ability to disrupt nasopharyngeal carriage and transmission. The 10-valent pneumococcal vaccine (PCV10) was included in the Expanded Program on Immunization (EPI) in Sindh, Pakistan in February 2013. This study was carried out immediately before PCV10 introduction to establish baseline pneumococcal carriage and prevalent serotypes in young children and to determine if carriage differed in urban and rural communities. Methods Nasopharyngeal specimens were collected from a random sample of children 3-11 and 12-59 months of age in an urban community (Karachi) and children 3-11 months of age in a rural community (Matiari). Samples were processed in a research laboratory in Karachi. Samples were transported in STGG media, enriched in Todd Hewitt broth, rabbit serum and yeast extract, cultured on 5% sheep blood agar, and serotyped using the CDC standardized sequential multiplex PCR assay. Serotypes were categorized into PCV10-type and non-vaccine types. Results We enrolled 670 children. Pneumococci were detected in 73.6% and 79.5 % of children in the infant group in Karachi and Matiari, respectively, and 78.2% of children 12 to 59 months of age in Karachi. In infants, 38.9% and 33.5% of those carrying pneumococci in Karachi and Matiari, respectively, had PCV10 types. In the older age group in Karachi, the proportion was 30.7%, not significantly different from infants. The most common serotypes were 6A, 23F, 19A, 6B and 19F. Conclusion We found that about 3 of 4 children carried pneumococci, and this figure did not vary with age group or urban or rural residence. Planned annual surveys in the same communities will inform change in carriage of PCV10 serotype pneumococci after the introduction and uptake of PCV10 in these communities Electronic supplementary material The online version of this article (10.1186/s12879-018-3608-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Kanwal Nayani
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Tauseef Akhund
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Atif Riaz
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Omar Irfan
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sehrish Muneer
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Sana Muslim
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | | | - Lindsay Kim
- Centre for Disease Control and Prevention, Atlanta, USA
| | | | - Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan
| | - Anita K M Zaidi
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan.,Bill & Melinda Gates Foundation, Seattle, USA
| | - Fyezah Jehan
- Department of Pediatrics and Child Health, Aga Khan University, Stadium Road, Karachi, 74800, Pakistan.
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Morales M, Ludwig G, Ercibengoa M, Esteva C, Sanchez-Encinales V, Alonso M, Muñoz-Almagro C, Marimón JM. Changes in the serotype distribution of Streptococcus pneumoniae causing otitis media after PCV13 introduction in Spain. PLoS One 2018; 13:e0209048. [PMID: 30562385 PMCID: PMC6298674 DOI: 10.1371/journal.pone.0209048] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/27/2018] [Indexed: 11/19/2022] Open
Abstract
One of the beneficial effects of pneumococcal conjugate vaccines (PCVs) has been a decrease in the incidence of non-invasive infections, such as otitis media (OM) caused by vaccine serotypes. In this study, we analyzed the epidemiology of pneumococcal OM before and after PCV13 introduction in 2010. Between 2008 and 2016, the middle ear exudates from 2653 children under 14 years of age with OM were studied in two Spanish provinces (Gipuzkoa and Barcelona), and S. pneumoniae was isolated in 235 (8.9%) of cases. The 204 available isolates were serotyped and distributed in three 3-year periods: one before and two after PCV13 introduction (early and late post-PCV13). A significant decrease in the rate of OM caused by S. pneumoniae was observed mainly due to a decrease in infections caused by all PCV13 serotypes, although exceptions were observed including the persistence of serotype 3 in Gipuzkoa and a weak re-emergence of serotype 19F in both regions. The rate and diversity of non-PCV13 serotypes increased in both regions and an emerging clone causing OM was detected in each region: serotype 23B ST2372 in Gipuzkoa and serotype 11A ST838/ST6521 in Barcelona. The introduction of PCV13 has been followed by a change in the epidemiology of pneumococcal OM, with a decrease in the rate of vaccine serotypes accompanied by an increase in the diversity of non-vaccine serotype and the clonal spreading of different single clones in each region.
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Affiliation(s)
- María Morales
- Donostia University Hospital–Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Guillermo Ludwig
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, Sant Joan de Déu University Hospital, Barcelona, Spain
| | - Maria Ercibengoa
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Preventive Medicine and Health Public Department, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
| | - Cristina Esteva
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, Sant Joan de Déu University Hospital, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Marta Alonso
- Donostia University Hospital–Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Molecular Microbiology Department, Institut de Recerca Sant Joan de Déu, Sant Joan de Déu University Hospital, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - José Maria Marimón
- Donostia University Hospital–Biodonostia Health Research Institute, Donostia-San Sebastian, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
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Cleary DW, Devine VT, Morris DE, Osman KL, Gladstone RA, Bentley SD, Faust SN, Clarke SC. Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae. Microb Genom 2018; 4. [PMID: 30080135 PMCID: PMC6202451 DOI: 10.1099/mgen.0.000209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The implementation of pneumococcal conjugate vaccines (PCVs) has led to a decline in vaccine-type disease. However, there is evidence that the epidemiology of non-typeable Haemophilus influenzae (NTHi) carriage and disease can be altered as a consequence of PCV introduction. We explored the epidemiological shifts in NTHi carriage using whole genome sequencing over a 5-year period that included PCV13 replacement of PCV7 in the UK’s National Immunization Programme in 2010. Between 2008/09 and 2012/13 (October to March), nasopharyngeal swabs were taken from children <5 years of age. Significantly increased carriage post-PCV13 was observed and lineage-specific associations with Streptococcus pneumoniae were seen before but not after PCV13 introduction. NTHi were characterized into 11 discrete, temporally stable lineages, congruent with current knowledge regarding the clonality of NTHi. The increased carriage could not be linked to the expansion of a particular clone and different co-carriage dynamics were seen before PCV13 implementation when NTHi co-carried with vaccine serotype pneumococci. In summary, PCV13 introduction has been shown to have an indirect effect on NTHi epidemiology and there exists both negative and positive, distinct associations between pneumococci and NTHi. This should be considered when evaluating the impacts of pneumococcal vaccine design and policy.
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Affiliation(s)
- David W Cleary
- 1Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,2NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Vanessa T Devine
- 3Northern Ireland Centre for Stratified Medicine and Clinical Translational Research Innovation Centre, Londonderry, UK
| | - Denise E Morris
- 1Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Karen L Osman
- 1Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | | | | | - Saul N Faust
- 1Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,5NIHR Southampton Clinical Research Facility, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Stuart C Clarke
- 2NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,1Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,6Global Health Research Institute, University of Southampton, Southampton, UK
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Dai W, Wang H, Zhou Q, Feng X, Lu Z, Li D, Yang Z, Liu Y, Li Y, Xie G, Shen K, Yang Y, Zheng Y, Li S. The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia. Emerg Microbes Infect 2018; 7:92. [PMID: 29789582 PMCID: PMC5964150 DOI: 10.1038/s41426-018-0097-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/12/2022]
Abstract
In recent years, the morbidity of Mycoplasma pneumoniae pneumonia (MPP) has dramatically increased in China. An increasing number of studies indicate that an imbalance in the respiratory microbiota is associated with respiratory infection. We selected 28 hospitalized patients infected with M. pneumoniae and 32 healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from healthy children, whereas NP, OP and bronchoalveolar lavage (BAL) specimens were collected from patients. Microbiota analysis was performed on all microbial samples using 16 S ribosomal RNA (16 S rRNA) sequencing. The NP microbial samples in healthy children were divided into two groups, which were dominated by either Staphylococcus or mixed microbial components. The respiratory microbiota in pneumonia patients harbored a lower microbial diversity compared to healthy children, and both the NP and OP microbiota of patients differed significantly from that of healthy children. Hospitalized MPP children with a higher abundance of Mycoplasma in the BAL fluid (BALF) microbiota tended to suffer longer hospitalization lengths and higher peak fevers and serum C-reactive protein levels. Concordance analysis explained the succession of imbalanced NP microbiota to the OP and lung in diseased children. However, the association of the abundance of Mycoplasma in BALF microbiota with that in NP or OP microbiota varied among individuals, which suggested the sensitivity of BALF in MPP diagnostics, mirroring MPP severity.
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Affiliation(s)
- Wenkui Dai
- Department of Computer Science, City University of Hong Kong, 999077, Hong Kong, China
| | - Heping Wang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Qian Zhou
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Xin Feng
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Zhiwei Lu
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Dongfang Li
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China.,Institute of Statistics, NanKai University, No. 94 Weijin Road, 300071, Tianjin, China
| | - Zhenyu Yang
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Yanhong Liu
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Yinhu Li
- Department of Microbial Research, WeHealthGene Institute, 3C19, No. 19 Building, 518000, Dayun Software Town, Shenzhen, China
| | - Gan Xie
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Kunling Shen
- Department of Respiratory Diseases, Beijing Children's Hospital, 100045, Beijing, China
| | - Yonghong Yang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019, Yitian Road, 518026, Futian District, Shenzhen, China.
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, 999077, Hong Kong, China.
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Hakansson AP, Orihuela CJ, Bogaert D. Bacterial-Host Interactions: Physiology and Pathophysiology of Respiratory Infection. Physiol Rev 2018; 98:781-811. [PMID: 29488821 PMCID: PMC5966719 DOI: 10.1152/physrev.00040.2016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
It has long been thought that respiratory infections are the direct result of acquisition of pathogenic viruses or bacteria, followed by their overgrowth, dissemination, and in some instances tissue invasion. In the last decades, it has become apparent that in contrast to this classical view, the majority of microorganisms associated with respiratory infections and inflammation are actually common members of the respiratory ecosystem and only in rare circumstances do they cause disease. This suggests that a complex interplay between host, environment, and properties of colonizing microorganisms together determines disease development and its severity. To understand the pathophysiological processes that underlie respiratory infectious diseases, it is therefore necessary to understand the host-bacterial interactions occurring at mucosal surfaces, along with the microbes inhabiting them, during symbiosis. Current knowledge regarding host-bacterial interactions during asymptomatic colonization will be discussed, including a plausible role for the human microbiome in maintaining a healthy state. With this as a starting point, we will discuss possible disruptive factors contributing to dysbiosis, which is likely to be a key trigger for pathobionts in the development and pathophysiology of respiratory diseases. Finally, from this renewed perspective, we will reflect on current and potential new approaches for treatment in the future.
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Affiliation(s)
- A P Hakansson
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
| | - C J Orihuela
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
| | - D Bogaert
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
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Lappan R, Imbrogno K, Sikazwe C, Anderson D, Mok D, Coates H, Vijayasekaran S, Bumbak P, Blyth CC, Jamieson SE, Peacock CS. A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera. BMC Microbiol 2018; 18:13. [PMID: 29458340 PMCID: PMC5819196 DOI: 10.1186/s12866-018-1154-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 02/08/2018] [Indexed: 12/15/2022] Open
Abstract
Background Recurrent acute otitis media (rAOM, recurrent ear infection) is a common childhood disease caused by bacteria termed otopathogens, for which current treatments have limited effectiveness. Generic probiotic therapies have shown promise, but seem to lack specificity. We hypothesised that healthy children with no history of AOM carry protective commensal bacteria that could be translated into a specific probiotic therapy to break the cycle of re-infection. We characterised the nasopharyngeal microbiome of these children (controls) in comparison to children with rAOM (cases) to identify potentially protective bacteria. As some children with rAOM do not appear to carry any of the known otopathogens, we also hypothesised that characterisation of the middle ear microbiome could identify novel otopathogens, which may also guide the development of more effective therapies. Results Middle ear fluids, middle ear rinses and ear canal swabs from the cases and nasopharyngeal swabs from both groups underwent 16S rRNA gene sequencing. The nasopharyngeal microbiomes of cases and controls were distinct. We observed a significantly higher abundance of Corynebacterium and Dolosigranulum in the nasopharynx of controls. Alloiococcus, Staphylococcus and Turicella were abundant in the middle ear and ear canal of cases, but were uncommon in the nasopharynx of both groups. Gemella and Neisseria were characteristic of the case nasopharynx, but were not prevalent in the middle ear. Conclusions Corynebacterium and Dolosigranulum are characteristic of a healthy nasopharyngeal microbiome. Alloiococcus, Staphylococcus and Turicella are possible novel otopathogens, though their rarity in the nasopharynx and prevalence in the ear canal means that their role as normal aural flora cannot be ruled out. Gemella and Neisseria are unlikely to be novel otopathogens as they do not appear to colonise the middle ear in children with rAOM. Electronic supplementary material The online version of this article (10.1186/s12866-018-1154-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachael Lappan
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia. .,Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.
| | - Kara Imbrogno
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Chisha Sikazwe
- Department of Microbiology, PathWest, Perth, WA, Australia
| | - Denise Anderson
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Danny Mok
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Harvey Coates
- School of Medicine, The University of Western Australia, Perth, WA, Australia
| | - Shyan Vijayasekaran
- School of Medicine, The University of Western Australia, Perth, WA, Australia.,Princess Margaret Hospital for Children, Perth, WA, Australia
| | - Paul Bumbak
- School of Medicine, The University of Western Australia, Perth, WA, Australia.,Princess Margaret Hospital for Children, Perth, WA, Australia
| | - Christopher C Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.,Department of Microbiology, PathWest, Perth, WA, Australia.,School of Medicine, The University of Western Australia, Perth, WA, Australia.,Princess Margaret Hospital for Children, Perth, WA, Australia
| | - Sarra E Jamieson
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Christopher S Peacock
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia. .,Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.
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Khamash DF, Voskertchian A, Milstone AM. Manipulating the microbiome: evolution of a strategy to prevent S. aureus disease in children. J Perinatol 2018; 38:105-109. [PMID: 29120455 PMCID: PMC5790614 DOI: 10.1038/jp.2017.155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/21/2017] [Accepted: 08/30/2017] [Indexed: 12/12/2022]
Abstract
Hospitalized infants have the highest rates of invasive Staphylococcus aureus disease of any population and infection control strategies such as decolonization have been insufficient. For decades, researchers began studying the microbiome in search of new prevention strategies. The resident microbiota was found to be closely associated with susceptibility and at times, resistance to S. aureus colonization. The evolution of nucleic acid based techniques has enhanced our understanding of the complex relationship between the nasal microbiota and S. aureus colonization. We review what is known about bacterial communities in the nasal cavity of infants and discuss how future microbiome studies may help identify novel interventions to protect high-risk infants from S. aureus disease.
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Affiliation(s)
- Dina F. Khamash
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Annie Voskertchian
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Aaron M. Milstone
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD,Department of Hospital Epidemiology and Infection Control, Johns Hopkins Hospital, Baltimore, MD
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40
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Siemens N, Oehmcke-Hecht S, Mettenleiter TC, Kreikemeyer B, Valentin-Weigand P, Hammerschmidt S. Port d'Entrée for Respiratory Infections - Does the Influenza A Virus Pave the Way for Bacteria? Front Microbiol 2017; 8:2602. [PMID: 29312268 PMCID: PMC5742597 DOI: 10.3389/fmicb.2017.02602] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial and viral co-infections of the respiratory tract are life-threatening and present a global burden to the global community. Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes are frequent colonizers of the upper respiratory tract. Imbalances through acquisition of seasonal viruses, e.g., Influenza A virus, can lead to bacterial dissemination to the lower respiratory tract, which in turn can result in severe pneumonia. In this review, we summarize the current knowledge about bacterial and viral co-infections of the respiratory tract and focus on potential experimental models suitable for mimicking this disease. Transmission of IAV and pneumonia is mainly modeled by mouse infection. Few studies utilizing ferrets, rats, guinea pigs, rabbits, and non-human primates are also available. The knowledge gained from these studies led to important discoveries and advances in understanding these infectious diseases. Nevertheless, mouse and other infection models have limitations, especially in translation of the discoveries to humans. Here, we suggest the use of human engineered lung tissue, human ex vivo lung tissue, and porcine models to study respiratory co-infections, which might contribute to a greater translation of the results to humans and improve both, animal and human health.
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Affiliation(s)
- Nikolai Siemens
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
- Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sonja Oehmcke-Hecht
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Thomas C. Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Peter Valentin-Weigand
- Center for Infection Medicine, Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
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41
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Impact of the Respiratory Microbiome on Host Responses to Respiratory Viral Infection. Vaccines (Basel) 2017; 5:vaccines5040040. [PMID: 29099809 PMCID: PMC5748607 DOI: 10.3390/vaccines5040040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 11/17/2022] Open
Abstract
Viruses are responsible for most of both upper and lower acute respiratory infections (ARIs). The microbiome—the ecological community of microorganisms sharing the body space, which has gained considerable interest over the last decade—is modified in health and disease states. Even if most of these disturbances have been previously described in relation to chronic disorders of the gastrointestinal microbiome, after a short reminder of microbiome characteristics and methods of characterization, this review will describe the impact of the microbiome (mainly respiratory) on host responses to viral ARIs. The microbiome has a direct environmental impact on the host cells but also an indirect impact on the immune system, by enhancing innate or adaptive immune responses. In microbial infections, especially in viral infections, these dramatic modifications could lead to a dramatic impact responsible for severe clinical outcomes. Studies focusing on the microbiome associated with transcriptomic analyses of the host response and deep characterization of the pathogen would lead to a better understanding of viral pathogenesis and open avenues for biomarker development and innovative therapeutics.
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Frayman KB, Armstrong DS, Grimwood K, Ranganathan SC. The airway microbiota in early cystic fibrosis lung disease. Pediatr Pulmonol 2017; 52:1384-1404. [PMID: 28815937 DOI: 10.1002/ppul.23782] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022]
Abstract
Infection plays a critical role in the pathogenesis of cystic fibrosis (CF) lung disease. Over the past two decades, the application of molecular and extended culture-based techniques to microbial analysis has changed our understanding of the lungs in both health and disease. CF lung disease is a polymicrobial disorder, with obligate and facultative anaerobes recovered alongside traditional pathogens in varying proportions, with some differences observed to correlate with disease stage. While healthy lungs are not sterile, differences between the lower airway microbiota of individuals with CF and disease-controls are already apparent in childhood. Understanding the evolution of the CF airway microbiota, and its relationship with clinical treatments and outcome at each disease stage, will improve our understanding of the pathogenesis of CF lung disease and potentially inform clinical management. This review summarizes current knowledge of the early development of the respiratory microbiota in healthy children and then discusses what is known about the airway microbiota in individuals with CF, including how it evolves over time and where future research priorities lie.
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Affiliation(s)
- Katherine B Frayman
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David S Armstrong
- Department of Respiratory Medicine, Monash Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.,Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Gold Coast, Queensland, Australia
| | - Sarath C Ranganathan
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Melbourne, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Kelly MS, Surette MG, Smieja M, Pernica JM, Rossi L, Luinstra K, Steenhoff AP, Feemster KA, Goldfarb DM, Arscott-Mills T, Boiditswe S, Rulaganyang I, Muthoga C, Gaofiwe L, Mazhani T, Rawls JF, Cunningham CK, Shah SS, Seed PC. The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana. Pediatr Infect Dis J 2017; 36:e211-e218. [PMID: 28399056 PMCID: PMC5555803 DOI: 10.1097/inf.0000000000001607] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Nearly half of child pneumonia deaths occur in sub-Saharan Africa. Microbial communities in the nasopharynx are a reservoir for pneumonia pathogens and remain poorly described in African children. METHODS Nasopharyngeal swabs were collected from children with pneumonia (N = 204), children with upper respiratory infection symptoms (N = 55) and healthy children (N = 60) in Botswana between April 2012 and April 2014. We sequenced the V3 region of the bacterial 16S ribosomal RNA gene and used partitioning around medoids to cluster samples into microbiota biotypes. We then used multivariable logistic regression to examine whether microbiota biotypes were associated with pneumonia and upper respiratory infection symptoms. RESULTS Mean ages of children with pneumonia, children with upper respiratory infection symptoms and healthy children were 8.2, 11.4 and 8.0 months, respectively. Clustering of nasopharyngeal microbiota identified 5 distinct biotypes: Corynebacterium/Dolosigranulum-dominant (23%), Haemophilus-dominant (11%), Moraxella-dominant (24%), Staphylococcus-dominant (13%) and Streptococcus-dominant (28%). The Haemophilus-dominant [odds ratio (OR): 13.55; 95% confidence interval (CI): 2.10-87.26], the Staphylococcus-dominant (OR: 8.27; 95% CI: 2.13-32.14) and the Streptococcus-dominant (OR: 39.97; 95% CI: 6.63-241.00) biotypes were associated with pneumonia. The Moraxella-dominant (OR: 3.71; 95% CI: 1.09-12.64) and Streptococcus-dominant (OR: 12.26; 95% CI: 1.81-83.06) biotypes were associated with upper respiratory infection symptoms. In children with pneumonia, HIV infection was associated with a lower relative abundance of Dolosigranulum (P = 0.03). CONCLUSIONS Pneumonia and upper respiratory infection symptoms are associated with distinct nasopharyngeal microbiota biotypes in African children. A lower abundance of the commensal genus Dolosigranulum may contribute to the higher pneumonia risk of HIV-infected children.
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Affiliation(s)
- Matthew S. Kelly
- Botswana-UPenn Partnership, Gaborone, Botswana
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | | | - Marek Smieja
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- St. Joseph’s Healthcare, Hamilton, Ontario, Canada
| | - Jeffrey M. Pernica
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Laura Rossi
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Andrew P. Steenhoff
- Botswana-UPenn Partnership, Gaborone, Botswana
- Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kristen A. Feemster
- Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - David M. Goldfarb
- Botswana-UPenn Partnership, Gaborone, Botswana
- Department of Pathology and Laboratory Medicine, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Tonya Arscott-Mills
- Botswana-UPenn Partnership, Gaborone, Botswana
- Global Health Center, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | | | - Tiny Mazhani
- University of Botswana School of Medicine, Gaborone, Botswana
| | - John F. Rawls
- Center for the Genomics of Microbial Systems, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC
| | - Coleen K. Cunningham
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Samir S. Shah
- Divisions of Hospital Medicine and Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Patrick C. Seed
- Division of Pediatric Infectious Diseases, Duke University Medical Center, Durham, NC, USA
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Mika M, Maurer J, Korten I, Allemann A, Aebi S, Brugger SD, Qi W, Frey U, Latzin P, Hilty M. Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case-control study. MICROBIOME 2017; 5:85. [PMID: 28738889 PMCID: PMC5525364 DOI: 10.1186/s40168-017-0302-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/06/2017] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bacterial colonization of the upper airways is a prerequisite for subsequent invasive disease. With the introduction of the 7- and 13-valent pneumococcal conjugate vaccines (PCV7 and PCV13), changes in pneumococcal upper airway colonization have been described. It is, however, less evident whether the vaccines lead to compositional changes of the upper airway microbiota. Here, we performed a case-control study using samples from a longitudinal infant cohort from Switzerland. We compared pneumococcal carriage and the nasal microbiota within the first year of life of healthy infants vaccinated with either PCV7 (n = 20, born in 2010) or PCV13 (n = 21, born between 2011 and 2013). Nasal swabs were collected every second week (n = 763 in total). Pneumococcal carriage was analyzed by quantitative PCR of the pneumococcal-specific lytA gene. Analysis of the bacterial core microbiota was performed based on 16S rRNA sequencing and subsequent oligotyping. We exclusively performed oligotyping of the core microbiota members, which were defined as the five most abundant bacterial families (Moraxellaceae, Streptococcaceae, Staphylococcaceae, Corynebacteriaceae, and Pasteurellaceae). Linear mixed effect (LME) and negative binomial regression models were used for statistical analyses. RESULTS We found a higher number of samples positive for pneumococcal carriage in PCV7- compared to PCV13-vaccinated infants (LME model; P = 0.01). In contrast, infants vaccinated in the PCV13 era had an increased alpha diversity as measured by the richness and the Shannon Diversity Index (LME model; P = 0.003 and P = 0.01, respectively). Accordingly, the PCV13 era was associated with clusters of a higher diversity than PCV7-associated clusters. Furthermore, infants vaccinated with PCV13 had a higher binary-based within-subject microbiota similarity, as well as a decreased Jensen-Shannon distance over time as compared to PCV7-vaccinated infants, indicating a higher microbiota stability in the PCV13 era (LME model and t test; P = 0.06 and P = 0.03, respectively). CONCLUSIONS We hypothesize that the higher diversity and stability of the upper airway microbiota in the PCV13 era is the result of the lower pneumococcal carriage rate. This seems to indicate that the nasal bacterial microbiota of infants has changed in recent years as compared to the beginning of this study.
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Affiliation(s)
- Moana Mika
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Josua Maurer
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Insa Korten
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Aurélie Allemann
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
| | - Silvio D Brugger
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Weihong Qi
- Functional Genomics Center, Swiss Federal Institute of Technology Zurich/University of Zurich, Zurich, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), Basel, Switzerland
| | - Philipp Latzin
- Division of Respiratory Medicine, Department of Pediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, 3010, Bern, Switzerland.
- Department of Infectious Diseases, University Hospital, Bern, Switzerland.
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Chonmaitree T, Jennings K, Golovko G, Khanipov K, Pimenova M, Patel JA, McCormick DP, Loeffelholz MJ, Fofanov Y. Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media. PLoS One 2017; 12:e0180630. [PMID: 28708872 PMCID: PMC5510840 DOI: 10.1371/journal.pone.0180630] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/18/2017] [Indexed: 01/21/2023] Open
Abstract
Background Interferences between pathogenic bacteria and specific commensals are known. We determined the interactions between nasopharyngeal microbial pathogens and commensals during viral upper respiratory tract infection (URI) and acute otitis media (AOM) in infants. Methods We analyzed 971 specimens collected monthly and during URI and AOM episodes from 139 infants. The 16S rRNA V4 gene regions were sequenced on the Illumina MiSeq platform. Results Among the high abundant genus-level nasopharyngeal microbiota were Moraxella, Haemophilus, and Streptococcus (3 otopathogen genera), Corynebacterium, Dolosigranulum, Staphylococcus, Acinetobacter, Pseudomonas, and Bifidobacterium. Bacterial diversity was lower in culture-positive samples for Streptococcus pneumoniae, and Haemophilus influenzae, compared to cultured-negative samples. URI frequencies were positively associated with increasing trend in otopathogen colonization. AOM frequencies were associated with decreasing trend in Micrococcus colonization. During URI and AOM, there were increases in abundance of otopathogen genera and decreases in Pseudomonas, Myroides, Yersinia, and Sphingomonas. Otopathogen abundance was increased during symptomatic viral infection, but not during asymptomatic infection. The risk for AOM complicating URI was reduced by increased abundance of Staphylococcus and Sphingobium. Conclusion Otopathogen genera played the key roles in URI and AOM occurrences. Staphylococcus counteracts otopathogens thus Staphylococcal colonization may be beneficial, rather than harmful. While Sphingobium may play a role in preventing AOM complicating URI, the commonly used probiotic Bifidobacterium did not play a significant role during URI or AOM. The role of less common commensals in counteracting the deleterious effects of otopathogens requires further studies.
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Affiliation(s)
- Tasnee Chonmaitree
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
- * E-mail:
| | - Kristofer Jennings
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Georgiy Golovko
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Kamil Khanipov
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Maria Pimenova
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Janak A. Patel
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
| | - David P. McCormick
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Michael J. Loeffelholz
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Yuriy Fofanov
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States of America
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Dorn ES, Tress B, Suchodolski JS, Nisar T, Ravindran P, Weber K, Hartmann K, Schulz BS. Bacterial microbiome in the nose of healthy cats and in cats with nasal disease. PLoS One 2017; 12:e0180299. [PMID: 28662139 PMCID: PMC5491177 DOI: 10.1371/journal.pone.0180299] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/13/2017] [Indexed: 12/22/2022] Open
Abstract
Background Traditionally, changes in the microbial population of the nose have been assessed using conventional culture techniques. Sequencing of bacterial 16S rRNA genes demonstrated that the human nose is inhabited by a rich and diverse bacterial microbiome that cannot be detected using culture-based methods. The goal of this study was to describe the nasal microbiome of healthy cats, cats with nasal neoplasia, and cats with feline upper respiratory tract disease (FURTD). Methodology/Principal findings DNA was extracted from nasal swabs of healthy cats (n = 28), cats with nasal neoplasia (n = 16), and cats with FURTD (n = 15), and 16S rRNA genes were sequenced. High species richness was observed in all samples. Rarefaction analysis revealed that healthy cats living indoors had greater species richness (observed species p = 0.042) and Shannon diversity (p = 0.003) compared with healthy cats living outdoors. Higher species richness (observed species p = 0.001) and Shannon diversity (p<0.001) were found in middle-aged cats in comparison to healthy cats in different age groups. Principal coordinate analysis revealed separate clustering based on similarities in bacterial molecular phylogenetic trees of 16S rRNA genes for indoor and outdoor cats. In all groups examined, the most abundant phyla identified were Proteobacteria, Firmicutes, and Bacteroidetes. At the genus level, 375 operational taxonomic units (OTUs) were identified. In healthy cats and cats with FURTD, Moraxella spp. was the most common genus, while it was unclassified Bradyrhizobiaceae in cats with nasal neoplasia. High individual variability was observed. Conclusion This study demonstrates that the nose of cats is inhabited by much more variable and diverse microbial communities than previously shown. Future research in this field might help to develop new diagnostic tools to easily identify nasal microbial changes, relate them to certain disease processes, and help clinicians in the decision process of antibiotic selection for individual patients.
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Affiliation(s)
- Elisabeth S. Dorn
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Barbara Tress
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tariq Nisar
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Prajesh Ravindran
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Karin Weber
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Katrin Hartmann
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
| | - Bianka S. Schulz
- Clinic of Small Animal Medicine, LMU University of Munich, Munich, Germany
- * E-mail:
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Geographic variation in pneumococcal vaccine efficacy estimated from dynamic modeling of epidemiological data post-PCV7. Sci Rep 2017; 7:3049. [PMID: 28607461 PMCID: PMC5468270 DOI: 10.1038/s41598-017-02955-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
Although mean efficacy of multivalent pneumococcus vaccines has been intensively studied, variance in vaccine efficacy (VE) has been overlooked. Different net individual protection across settings can be driven by environmental conditions, local serotype and clonal composition, as well as by socio-demographic and genetic host factors. Understanding efficacy variation has implications for population-level effectiveness and other eco-evolutionary feedbacks. Here I show that realized VE can vary across epidemiological settings, by applying a multi-site-one-model approach to data post-vaccination. I analyse serotype prevalence dynamics following PCV7, in asymptomatic carriage in children attending day care in Portugal, Norway, France, Greece, Hungary and Hong-Kong. Model fitting to each dataset provides site-specific estimates for vaccine efficacy against acquisition, and pneumococcal transmission parameters. According to this model, variable serotype replacement across sites can be explained through variable PCV7 efficacy, ranging from 40% in Norway to 10% in Hong-Kong. While the details of how this effect is achieved remain to be determined, here I report three factors negatively associated with the VE readout, including initial prevalence of serotype 19F, daily mean temperature, and the Gini index. The study warrants more attention on local modulators of vaccine performance and calls for predictive frameworks within and across populations.
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Bergenfelz C, Hakansson AP. Streptococcus pneumoniae Otitis Media Pathogenesis and How It Informs Our Understanding of Vaccine Strategies. CURRENT OTORHINOLARYNGOLOGY REPORTS 2017; 5:115-124. [PMID: 28616365 PMCID: PMC5446555 DOI: 10.1007/s40136-017-0152-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW This study aimed to review the literature regarding the mechanisms of transition from asymptomatic colonization to induction of otitis media and how the insight into the pathogenesis of otitis media has the potential to help design future otitis media-directed vaccines. RECENT FINDINGS Respiratory viruses have long been shown to predispose individuals to bacterial respiratory infections, such as otitis media. Recent information suggests that Streptococcus pneumoniae, which colonize the nasopharynx asymptomatically, can sense potentially "threatening" changes in the nasopharyngeal environment caused by virus infection by upregulating specific sets of genes involved in biofilm release, dissemination from the nasopharynx to other sites, and protection against the host immune system. Furthermore, an understanding of the transcriptional and proteomic changes occurring in bacteria during transition to infection has led to identification of novel vaccine targets that are disease-specific and will not affect asymptomatic colonization. This approach will avoid major changes in the delicate balance of microorganisms in the respiratory tract microbiome due to elimination of S. pneumoniae. SUMMARY Our recent findings are reviewed in the context of the current literature on the epidemiology and pathogenesis of otitis media. We also discuss how other otopathogens, such as Haemophilus influenzae and Moraxella catarrhalis, as well as the normal respiratory microbiome, can modulate the ability of pneumococci to cause infection. Furthermore, the unsatisfactory protection offered by the pneumococcal conjugate vaccines is highlighted and we review potential future strategies emerging to confer a more specific protection against otitis media.
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Affiliation(s)
- Caroline Bergenfelz
- Division of Experimental Infection Medicine, Department of Translational Medicine, Wallenberg Laboratory, Lund University, Inga Marie Nilsson's Street 53, 20502 Malmö, SE Sweden
| | - Anders P Hakansson
- Division of Experimental Infection Medicine, Department of Translational Medicine, Wallenberg Laboratory, Lund University, Inga Marie Nilsson's Street 53, 20502 Malmö, SE Sweden
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Barenkamp SJ, Chonmaitree T, Hakansson AP, Heikkinen T, King S, Nokso-Koivisto J, Novotny LA, Patel JA, Pettigrew M, Swords WE. Panel 4: Report of the Microbiology Panel. Otolaryngol Head Neck Surg 2017; 156:S51-S62. [PMID: 28372529 PMCID: PMC5490388 DOI: 10.1177/0194599816639028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/24/2016] [Indexed: 12/12/2022]
Abstract
Objective To perform a comprehensive review of the literature from July 2011 until June 2015 on the virology and bacteriology of otitis media in children. Data Sources PubMed database of the National Library of Medicine. Review Methods Two subpanels comprising experts in the virology and bacteriology of otitis media were created. Each panel reviewed the relevant literature in the fields of virology and bacteriology and generated draft reviews. These initial reviews were distributed to all panel members prior to meeting together at the Post-symposium Research Conference of the 18th International Symposium on Recent Advances in Otitis Media, National Harbor, Maryland, in June 2015. A final draft was created, circulated, and approved by all panel members. Conclusions Excellent progress has been made in the past 4 years in advancing our understanding of the microbiology of otitis media. Numerous advances were made in basic laboratory studies, in animal models of otitis media, in better understanding the epidemiology of disease, and in clinical practice. Implications for Practice (1) Many viruses cause acute otitis media without bacterial coinfection, and such cases do not require antibiotic treatment. (2) When respiratory syncytial virus, metapneumovirus, and influenza virus peak in the community, practitioners can expect to see an increase in clinical otitis media cases. (3) Biomarkers that predict which children with upper respiratory tract infections will develop otitis media may be available in the future. (4) Compounds that target newly identified bacterial virulence determinants may be available as future treatment options for children with otitis media.
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Affiliation(s)
- Stephen J. Barenkamp
- Department of Pediatrics, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Tasnee Chonmaitree
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Terho Heikkinen
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Samantha King
- The Research Institute at Nationwide Children’s Hospital and Ohio State University, Columbus, Ohio, USA
| | - Johanna Nokso-Koivisto
- Department of Otorhinolaryngology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Laura A. Novotny
- The Research Institute at Nationwide Children’s Hospital and Ohio State University, Columbus, Ohio, USA
| | - Janak A. Patel
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Melinda Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - W. Edward Swords
- Department of Microbiology and Immunology, Wake Forest University, Winston-Salem, North Carolina, USA
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Pérez-Losada M, Alamri L, Crandall KA, Freishtat RJ. Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma. PLoS One 2017; 12:e0170543. [PMID: 28107528 PMCID: PMC5249091 DOI: 10.1371/journal.pone.0170543] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 01/06/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The nasopharynx is a reservoir for pathogens associated with respiratory illnesses such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome of infants and adults during health and disease; less is known, however, about the composition and temporal dynamics (i.e., longitudinal variation) of microbiotas from children and adolescents. Here we use NGS technology to characterize the nasopharyngeal microbiomes of asthmatic children and adolescents (6 to 18 years) and determine their stability over time. METHODS Two nasopharyngeal washes collected 5.5 to 6.5 months apart were taken from 40 children and adolescents with asthma living in the Washington D.C. area. Sequence data from the 16S-V4 rRNA gene region (~250 bp) were collected from the samples using the MiSeq platform. Raw data were processed in mothur (SILVA123 reference database) and Operational Taxonomic Units (OTU)-based alpha- and beta-diversity metrics were estimated. Relatedness among samples was assessed using PCoA ordination and Procrustes analyses. Differences in microbial diversity and taxon mean relative proportions were assessed using linear mixed effects models. Core microbiome analyses were also performed to identify stable and consistent microbes of the nasopharynx. RESULTS AND DISCUSSION A total of 2,096,584 clean 16S sequences corresponding to an average of 167 OTUs per sample were generated. Representatives of Moraxella*, Staphylococcus*, Dolosigranulum, Corynebacterium, Prevotella, Streptococcus*, Haemophilus*, Fusobacterium* and a Neisseriaceae genus accounted for 86% of the total reads. These nine genera have been previously found in the nasopharynxes of both infants and adults, but in different proportions. OTUs from the five genera highlighted (*) above defined the nasopharyngeal core microbiome at the 95% level. No significant differences in alpha- and beta-diversity were observed between seasons, but bacterial mean relative proportions of Haemophilus, Moraxella, Staphylococcus and Corynebacterium varied significantly between summer-fall and age groups (inter-patient variation). Additionally, OTUs varied significantly within patients between time points in 35 of the 40 patients analyzed. Future cross-sectional studies should be mindful of the temporal dynamics of the nasopharyngeal microbiota.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America
- Division of Emergency Medicine, Children's National Medical Center, Washington DC, United States of America
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Lamia Alamri
- Division of Emergency Medicine, Children's National Medical Center, Washington DC, United States of America
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, Virginia, United States of America
| | - Robert J Freishtat
- Division of Emergency Medicine, Children's National Medical Center, Washington DC, United States of America
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