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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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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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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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5
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, 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
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, 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
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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Khan AA, Singh H, Bilal M, Ashraf MT. Microbiota, probiotics and respiratory infections: the three musketeers can tip off potential management of COVID-19. Am J Transl Res 2021; 13:10977-10993. [PMID: 34786037 PMCID: PMC8581851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Rapid infectivity of SARS-CoV2 with recent viral variants is posing a challenge in the development of robust therapeutic strategies. On the other hand, microbiota is debated for its involvement in SARS-CoV2 infection with varied opinions. Although ample data about the role of microbiota and probiotics in respiratory viral infections are available, their role in COVID-19 is limited albeit emerging rapidly. The utilization of probiotics for the management of COVID-19 is still under investigation in many clinical trials. Existing information coupled with recent COVID-19 related studies can suggest various ways to use microbiota modulation and probiotics for managing this pandemic. Present article indicates the role of microbiota modulation and probiotics in respiratory infections. In addition, scattered evidence was gathered to understand the potential of microbiota and probiotics in the management of SARS-CoV2. Gut-airway microbiota connection is already apparent in respiratory tract viral infections, including SARS-CoV2. Though few clinical trials are evaluating microbiota and probiotics for COVID-19 management, the safety evaluation must be given more serious consideration because of the possibility of opportunistic infections among COVID-19 patients. Nevertheless, the information about microbiota modulation using probiotics and prebiotics can be helpful to manage this outbreak and this review presents different aspects of this idea.
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Affiliation(s)
- Abdul Arif Khan
- Division of Microbiology, Indian Council of Medical Research-National AIDS Research InstitutePune, Maharashtra 411026, India
| | - HariOm Singh
- Division of Molecular Biology, Indian Council of Medical Research-National AIDS Research InstitutePune, Maharashtra 411026, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of TechnologyHuaian 223003, China
| | - Mohd Tashfeen Ashraf
- School of Biotechnology, Gautam Buddha UniversityGautam Budh Nagar, Greater Noida (UP), India
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Cleary DW, Morris DE, Anderson RA, Jones J, Alattraqchi AG, A Rahman NI, Ismail S, Razali MS, Mohd Amin R, Abd Aziz A, Esa NK, Amiruddin S, Chew CH, Simin H, Abdullah R, Yeo CC, Clarke SC. The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia. NPJ Biofilms Microbiomes 2021; 7:1. [PMID: 33402693 PMCID: PMC7785749 DOI: 10.1038/s41522-020-00173-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n = 28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n = 17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.
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Affiliation(s)
- David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, UK.
| | - Denise E Morris
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Rebecca A Anderson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Jessica Jones
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Ahmed Ghazi Alattraqchi
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Nor Iza A Rahman
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salwani Ismail
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Mohd Sayuti Razali
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Rahmah Mohd Amin
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Aniza Abd Aziz
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Nor Kamaruzaman Esa
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Salman Amiruddin
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Hafis Simin
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
- Akademi Seni Budaya dan Warisan Kebangsaan, (ASWARA), Jalan Tun Ismail, Kuala Lumpur, Malaysia
| | - Ramle Abdullah
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Chew Chieng Yeo
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Trust, Southampton, UK
- Global Health Research Institute, University of Southampton, Southampton, UK
- School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
- Centre for Translational Research, IMU Institute for Research, Development and Innovation (IRDI), Kuala Lumpur, Malaysia
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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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Marsh RL, Aho C, Beissbarth J, Bialasiewicz S, Binks M, Cervin A, Kirkham LAS, Lemon KP, Slack MPE, Smith-Vaughan HC. Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109836. [PMID: 31879084 PMCID: PMC7085411 DOI: 10.1016/j.ijporl.2019.109836] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To perform a comprehensive review of otitis media microbiome literature published between 1st July 2015 and 30th June 2019. DATA SOURCES PubMed database, National Library of Medicine. REVIEW METHODS Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members. CONCLUSIONS Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data. IMPLICATIONS FOR PRACTICE Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.
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Affiliation(s)
- Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia.
| | - Celestine Aho
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Seweryn Bialasiewicz
- The University of Queensland, Australian Centre for Ecogenomics, Queensland, Australia; Children's Health Queensland, Centre for Children's Health Research, Queensland, Australia
| | - Michael Binks
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Lea-Ann S Kirkham
- Centre for Child Health Research, University of Western Australia, Western Australia, Australia; Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Western Australia, Australia
| | - Katherine P Lemon
- Forsyth Institute (Microbiology), USA and Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Massachusetts, USA; Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology and Pediatrics, Infectious Diseases Section, Texas Children's Hospital, Baylor College of Medicine, Texas, USA
| | - Mary P E Slack
- School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
| | - Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia; School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
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Effects of 10-valent pneumococcal conjugate (PCV10) vaccination on the nasopharyngeal microbiome. Vaccine 2020; 38:1436-1443. [DOI: 10.1016/j.vaccine.2019.11.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023]
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11
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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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12
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Salter SJ, Scott P, Page AJ, Tracey A, de Goffau MC, Cormie C, Ochoa-Montaño B, Ling CL, Tangmanakit J, Turner P, Parkhill J. 'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs. Microb Genom 2019; 5. [PMID: 30720420 PMCID: PMC6421346 DOI: 10.1099/mgen.0.000247] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
'Candidatus Ornithobacterium hominis' represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys of people from South-East Asia, Africa and Australia. It frequently colonizes the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42 % of nasopharyngeal swabs from 12-month-old children in the Maela refugee camp in Thailand. The species, a Gram-negative bacillus, has not yet been cultured, but the cells can be identified in mixed samples by fluorescent hybridization. Here, we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9 Mb, sharing 62 % average amino acid identity with the only other member of the genus, the bird pathogen Ornithobacterium rhinotracheale. The draft genomes encode multiple antibiotic-resistance genes, competition factors, Flavobacterium johnsoniae-like gliding motility genes and a homologue of the Pasteurella multocida mitogenic toxin. Intra- and inter-host genome comparison suggests that colonization with this bacterium is both persistent and strain exclusive.
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Affiliation(s)
| | - Paul Scott
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Andrew J Page
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK.,†Present address: Quadram Institute Bioscience, Norwich, UK
| | - Alan Tracey
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | | | - Claire Cormie
- 1Pathogen Genomics, Wellcome Sanger Institute, Hinxton, UK
| | - Bernardo Ochoa-Montaño
- 2Department of Biochemistry, University of Cambridge, Cambridge, UK.,‡Present address: Illumina Cambridge Ltd, Little Chesterford, UK
| | - Clare L Ling
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jiraporn Tangmanakit
- 3Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Paul Turner
- 4Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,5Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
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13
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Abstract
The microbiome is defined as the total of cellular microorganisms of baczerial, viral or e. g., parasite origin living on the surface of a body. Within the anatomical areas of otorhinolaryngology, a significant divergence and variance can be demonstrated. For ear, nose, throat, larynx and cutis different interactions of microbiome and common factors like age, diet and live style factors (e. g., smoking) have been detected in recent years. Besides, new insights hint at a passible pathognomic role of the microbiome towards diseases in the ENT area. This review article resumes the present findings of this rapidly devloping scientific area.
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Affiliation(s)
- Achim G Beule
- HNO-Uniklinik Münster.,Klinik und Poliklinik für Hals-Nasen-Ohrenkrankheiten der Universitätsmedizin Greifswald
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14
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Salter SJ, Turner C, Watthanaworawit W, de Goffau MC, Wagner J, Parkhill J, Bentley SD, Goldblatt D, Nosten F, Turner P. A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children. PLoS Negl Trop Dis 2017; 11:e0005975. [PMID: 28968382 PMCID: PMC5638608 DOI: 10.1371/journal.pntd.0005975] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/12/2017] [Accepted: 09/19/2017] [Indexed: 11/19/2022] Open
Abstract
A longitudinal study was undertaken in infants living in the Maela refugee camp on the Thailand-Myanmar border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The bacterial 16S rRNA gene profiles of 544 swabs from 21 infants were analysed to see how the microbiota changes with age, respiratory infection, antibiotic consumption and pneumococcal acquisition. The nasopharyngeal microbiota is a somewhat homogenous community compared to that of other body sites. In this cohort it is dominated by five taxa: Moraxella, Streptococcus, Haemophilus, Corynebacterium and an uncharacterized Flavobacteriaceae taxon of 93% nucleotide similarity to Ornithobacterium. Infant age correlates with certain changes in the microbiota across the cohort: Staphylococcus and Corynebacterium are associated with the first few months of life while Moraxella and the uncharacterised Flavobacteriaceae increase in proportional abundance with age. Respiratory illness and antibiotic use often coincide with an unpredictable perturbation of the microbiota that differs from infant to infant and in different illness episodes. The previously described interaction between Dolosigranulum and Streptococcus was observed in these data. Monthly sampling demonstrates that the nasopharyngeal microbiota is in flux throughout the first two years of life, and that in this refugee camp population the pool of potential bacterial colonisers may be limited. The nasopharynx hosts a community of microbes that first colonise us during infancy and that changes as we grow. Colonisation with certain species is a risk factor for developing respiratory infections such as pneumonia, while other species can have a protective influence. In this study we use molecular methods to identify the bacteria present in nasopharyngeal swabs taken regularly from children in a refugee camp in Thailand. The microbiota develops with age, with early colonisers such as Corynebacterium or Staphylococcus being eventually outgrown by Moraxella and an uncultured taxon described here as unclassified Flavobacteriaceae I. There is evidence in the cohort of Streptococcus pneumoniae being frequently carried and transmitted throughout the first two years of life. We found that the microbiota profiles were not unique or distinguishable between individuals in this study, which is unlike studies in high income, low density populations.
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Affiliation(s)
- Susannah J. Salter
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Josef Wagner
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Julian Parkhill
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Stephen D. Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - David Goldblatt
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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15
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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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16
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Kwambana-Adams B, Hanson B, Worwui A, Agbla S, Foster-Nyarko E, Ceesay F, Ebruke C, Egere U, Zhou Y, Ndukum M, Sodergren E, Barer M, Adegbola R, Weinstock G, Antonio M. Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology. Sci Rep 2017; 7:8127. [PMID: 28811633 PMCID: PMC5557800 DOI: 10.1038/s41598-017-08717-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/13/2017] [Indexed: 01/07/2023] Open
Abstract
There is growing concern that interventions that alter microbial ecology can adversely affect health. We characterised the impact of the seven-valent pneumococcal conjugate vaccine (PCV7) on pneumococcal carriage and the bacterial component of the nasopharyngeal microbiome during infancy. Newborns were recruited into three groups as follows: Group1 (n = 33) was the control group and comprised infants who received PCV7 after 6 months and came from unvaccinated communities. Group 2 (n = 30) came from unvaccinated communities and Group 3 (n = 39) came from vaccinated communities. Both group 2 and 3 received PCV7 at 2, 3 and 4 months. Culture and 16 S rRNA gene sequencing were performed on nasopharyngeal specimens collected at regular intervals from infants. Nasopharyngeal carriage of PCV7 serotypes in Group 1 was significantly higher than in Group 2 and 3 (p < 0.01). However, pneumococcal carriage remained comparable due to an expansion of non-vaccine serotypes in Groups 2 and 3. Determination of phylogenetic dis(similarities) showed that the bacterial community structures were comparable across groups. A mixed effects model showed no difference in community richness (p = 0.15) and Shannon α-diversity (p = 0.48) across the groups. Immediate replacement of pneumococcal vaccine serotypes with non-vaccine serotypes may mitigate the impact of PCV7 on nasopharyngeal bacterial community structure and ecology.
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Affiliation(s)
- Brenda Kwambana-Adams
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia.
- London School of Hygiene and Tropical Medicine, London, UK.
| | - Blake Hanson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Archibald Worwui
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia
| | - Schadrac Agbla
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia
- London School of Hygiene and Tropical Medicine, London, UK
| | - Ebenezer Foster-Nyarko
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia
| | - Fatima Ceesay
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia
| | - Chinelo Ebruke
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia
- London School of Hygiene and Tropical Medicine, London, UK
| | - Uzochukwu Egere
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Maze Ndukum
- The Genome Instituted (Washington University in St Louis), St. Louis, Missouri, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Michael Barer
- Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | | | - George Weinstock
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia (MRCG), Fajara, The Gambia
- London School of Hygiene and Tropical Medicine, London, UK
- Division of Microbiology & Immunity, Warwick Medical School, University Of Warwick, Coventry, UK
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17
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Harris TM, Rumaseb A, Beissbarth J, Barzi F, Leach AJ, Smith-Vaughan HC. Culture of non-typeable Haemophilus influenzae from the nasopharynx: Not all media are equal. J Microbiol Methods 2017; 137:3-5. [PMID: 28342745 DOI: 10.1016/j.mimet.2017.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/19/2017] [Accepted: 03/19/2017] [Indexed: 10/19/2022]
Abstract
The efficacy of chocolate agar, versus bacitracin, vancomycin, clindamycin, chocolate agar (BVCCA) for the isolation of non-typeable Haemophilus influenzae (NTHi) from nasopharyngeal swabs was determined. BVCCA cultured NTHi from 97.3% of NTHi-positive swabs, compared to 87.1% for chocolate agar. To maximise culture sensitivity, the use of both media is recommended.
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Affiliation(s)
- Tegan M Harris
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Angela Rumaseb
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Federica Barzi
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; School of Medicine, Griffith University, Gold Coast, Queensland, Australia.
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18
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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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19
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Kwambana-Adams BA, Asiedu-Bekoe F, Sarkodie B, Afreh OK, Kuma GK, Owusu-Okyere G, Foster-Nyarko E, Ohene SA, Okot C, Worwui AK, Okoi C, Senghore M, Otu JK, Ebruke C, Bannerman R, Amponsa-Achiano K, Opare D, Kay G, Letsa T, Kaluwa O, Appiah-Denkyira E, Bampoe V, Zaman SMA, Pallen MJ, D'Alessandro U, Mwenda JM, Antonio M. An outbreak of pneumococcal meningitis among older children (≥5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana. BMC Infect Dis 2016; 16:575. [PMID: 27756235 PMCID: PMC5070171 DOI: 10.1186/s12879-016-1914-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND An outbreak of pneumococcal meningitis among non-infant children and adults occurred in the Brong-Ahafo region of Ghana between December 2015 and April 2016 despite the recent nationwide implementation of a vaccination programme for infants with the 13-valent pneumococcal conjugate vaccine (PCV13). METHODS Cerebrospinal fluid (CSF) specimens were collected from patients with suspected meningitis in the Brong-Ahafo region. CSF specimens were subjected to Gram staining, culture and rapid antigen testing. Quantitative PCR was performed to identify pneumococcus, meningococcus and Haemophilus influenzae. Latex agglutination and molecular serotyping were performed on samples. Antibiogram and whole genome sequencing were performed on pneumococcal isolates. RESULTS Eight hundred eighty six patients were reported with suspected meningitis in the Brong-Ahafo region during the period of the outbreak. In the epicenter district, the prevalence was as high as 363 suspected cases per 100,000 people. Over 95 % of suspected cases occurred in non-infant children and adults, with a median age of 20 years. Bacterial meningitis was confirmed in just under a quarter of CSF specimens tested. Pneumococcus, meningococcus and Group B Streptococcus accounted for 77 %, 22 % and 1 % of confirmed cases respectively. The vast majority of serotyped pneumococci (80 %) belonged to serotype 1. Most of the pneumococcal isolates tested were susceptible to a broad range of antibiotics, with the exception of two pneumococcal serotype 1 strains that were resistant to both penicillin and trimethoprim-sulfamethoxazole. All sequenced pneumococcal serotype 1 strains belong to Sequence Type (ST) 303 in the hypervirulent ST217 clonal complex. CONCLUSION The occurrence of a pneumococcal serotype 1 meningitis outbreak three years after the introduction of PCV13 is alarming and calls for strengthening of meningitis surveillance and a re-evaluation of the current vaccination programme in high risk countries.
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Affiliation(s)
- Brenda Anna Kwambana-Adams
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | | | | | | | | | | | - Ebenezer Foster-Nyarko
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | | | | | - Archibald Kwame Worwui
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Catherine Okoi
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Madikay Senghore
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Jacob Kweku Otu
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Chinelo Ebruke
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia
| | - Richard Bannerman
- Brong Ahafo Regional Health Directorate, Sunyani, Brong Ahafo, Ghana
| | | | - David Opare
- National Public Health Reference Laboratory, Ghana Health Service, Accra, Ghana
| | - Gemma Kay
- Microbiology and Infection Unit, Warwick Medical School, Warwick, UK
| | - Timothy Letsa
- Brong Ahafo Regional Health Directorate, Sunyani, Brong Ahafo, Ghana
| | | | | | | | - Syed M A Zaman
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, Warwick, UK
| | - Umberto D'Alessandro
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia.,London School of Hygiene and Tropical Medicine, London, UK.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Jason M Mwenda
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | - Martin Antonio
- Vaccines and Immunity Theme, The Medical Research Council Unit The Gambia, P.O Box 273, Banjul, Fajara, The Gambia. .,Microbiology and Infection Unit, Warwick Medical School, Warwick, UK. .,London School of Hygiene and Tropical Medicine, London, UK.
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Marsh RL, Kaestli M, Chang AB, Binks MJ, Pope CE, Hoffman LR, Smith-Vaughan HC. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. MICROBIOME 2016; 4:37. [PMID: 27388563 PMCID: PMC4936249 DOI: 10.1186/s40168-016-0182-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/24/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Invasive methods requiring general anaesthesia are needed to sample the lung microbiota in young children who do not expectorate. This poses substantial challenges to longitudinal study of paediatric airway microbiota. Non-invasive upper airway sampling is an alternative method for monitoring airway microbiota; however, there are limited data describing the relationship of such results with lung microbiota in young children. In this study, we compared the upper and lower airway microbiota in young children to determine whether non-invasive upper airway sampling procedures provide a reliable measure of either lung microbiota or clinically defined differences. RESULTS The microbiota in oropharyngeal (OP) swabs, nasopharyngeal (NP) swabs and bronchoalveolar lavage (BAL) from 78 children (median age 2.2 years) with and without lung disease were characterised using 16S rRNA gene sequencing. Permutational multivariate analysis of variance (PERMANOVA) detected significant differences between the microbiota in BAL and those in both OP swabs (p = 0.0001, Pseudo-F = 12.2, df = 1) and NP swabs (p = 0.0001; Pseudo-F = 21.9, df = 1) with the NP and BAL microbiota more different than the OP and BAL, as indicated by a higher Pseudo-F value. The microbiota in combined OP and NP data (upper airways) provided a more comprehensive representation of BAL microbiota, but significant differences between the upper airway and BAL microbiota remained, albeit with a considerably smaller Pseudo-F (PERMANOVA p = 0.0001; Pseudo-F = 4.9, df = 1). Despite this overall difference, paired BAL and upper airway (OP and NP) microbiota were >50 % similar among 69 % of children. Furthermore, canonical analysis of principal coordinates (CAP analysis) detected significant differences between the microbiota from clinically defined groups when analysing either BAL (eigenvalues >0.8; misclassification rate 26.5 %) or the combined OP and NP data (eigenvalues >0.8; misclassification rate 12.2 %). CONCLUSIONS Upper airway sampling provided an imperfect, but reliable, representation of the BAL microbiota for most children in this study. We recommend inclusion of both OP and NP specimens when non-invasive upper airway sampling is needed to assess airway microbiota in young children who do not expectorate. The results of the CAP analysis suggest lower and upper airway microbiota profiles may differentiate children with chronic suppurative lung disease from those with persistent bacterial bronchitis; however, further research is needed to confirm this observation.
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Affiliation(s)
- R. L. Marsh
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
| | - M. Kaestli
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
- />Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT Australia
| | - A. B. Chang
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
- />Queensland Children’s Medical Research Institute, Queensland University of Technology, Brisbane, QLD Australia
| | - M. J. Binks
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
| | - C. E. Pope
- />Department of Pediatrics, University of Washington, Seattle, WA USA
- />Department of Microbiology, University of Washington, Seattle, WA USA
| | - L. R. Hoffman
- />Department of Pediatrics, University of Washington, Seattle, WA USA
- />Department of Microbiology, University of Washington, Seattle, WA USA
| | - H. C. Smith-Vaughan
- />Menzies School of Health Research, Charles Darwin University, PO Box 41096, Casuarina, Darwin, NT 0810 Australia
- />School of Medicine, Griffith University, Gold Coast, QLD Australia
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21
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Pérez-Losada M, Crandall KA, Freishtat RJ. Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children. MICROBIOME 2016; 4:25. [PMID: 27306800 PMCID: PMC4910261 DOI: 10.1186/s40168-016-0170-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/06/2016] [Indexed: 05/24/2023]
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 during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known about spatial variation (biogeography) in nasal microenvironments and how sampling techniques may capture that microbial diversity. FINDINGS We used targeted 16S rRNA MiSeq sequencing and two different sampling strategies [nasal washes (NW) and nasal brushes (NB)] to characterize the nasopharyngeal microbiota in 30 asthmatic children. Nasal brushing is more abrasive than nasal washing and targeted the inner portion of the inferior turbinate. This region is expected to be different from other nasal microenvironments. Nasal washing is not spatially specific. Our 30 × 2 nasal microbiomes generated 1,474,497 sequences, from which we identified an average of 157 and 186 OTUs per sample in the NW and NB groups, respectively. Microbiotas from NB showed significantly higher alpha-diversity than microbiotas from NW. Similarly, both nasal microbiotas were distinct from each other (PCoA) and significantly differed in their community composition and abundance in at least 9 genera (effective size ≥1 %). CONCLUSIONS Nasopharyngeal microenvironments in asthmatic children contain microbiotas with different diversity and structure. Nasal washes and brushes capture that diversity differently. Future microbial studies of the nasopharynx need to be aware of potential spatial variation (biogeography).
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA, 20147, USA.
- Division of Emergency Medicine, Children's National Medical Center, Washington, DC, 20010, USA.
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal.
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA, 20147, USA
| | - Robert J Freishtat
- Division of Emergency Medicine, Children's National Medical Center, Washington, DC, 20010, USA
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Pickering JL, Prosser A, Corscadden KJ, de Gier C, Richmond PC, Zhang G, Thornton RB, Kirkham LAS. Haemophilus haemolyticus Interaction with Host Cells Is Different to Nontypeable Haemophilus influenzae and Prevents NTHi Association with Epithelial Cells. Front Cell Infect Microbiol 2016; 6:50. [PMID: 27242968 PMCID: PMC4860508 DOI: 10.3389/fcimb.2016.00050] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/18/2016] [Indexed: 02/02/2023] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that resides in the upper respiratory tract and contributes to a significant burden of respiratory related diseases in children and adults. Haemophilus haemolyticus is a respiratory tract commensal that can be misidentified as NTHi due to high levels of genetic relatedness. There are reports of invasive disease from H. haemolyticus, which further blurs the species boundary with NTHi. To investigate differences in pathogenicity between these species, we optimized an in vitro epithelial cell model to compare the interaction of 10 H. haemolyticus strains with 4 NTHi and 4 H. influenzae-like haemophili. There was inter- and intra-species variability but overall, H. haemolyticus had reduced capacity to attach to and invade nasopharyngeal and bronchoalveolar epithelial cell lines (D562 and A549) within 3 h when compared with NTHi. H. haemolyticus was cytotoxic to both cell lines at 24 h, whereas NTHi was not. Nasopharyngeal epithelium challenged with some H. haemolyticus strains released high levels of inflammatory mediators IL-6 and IL-8, whereas NTHi did not elicit an inflammatory response despite higher levels of cell association and invasion. Furthermore, peripheral blood mononuclear cells stimulated with H. haemolyticus or NTHi released similar and high levels of IL-6, IL-8, IL-10, IL-1β, and TNFα when compared with unstimulated cells but only NTHi elicited an IFNγ response. Due to the relatedness of H. haemolyticus and NTHi, we hypothesized that H. haemolyticus may compete with NTHi for colonization of the respiratory tract. We observed that in vitro pre-treatment of epithelial cells with H. haemolyticus significantly reduced NTHi attachment, suggesting interference or competition between the two species is possible and warrants further investigation. In conclusion, H. haemolyticus interacts differently with host cells compared to NTHi, with different immunostimulatory and cytotoxic properties. This study provides an in vitro model for further investigation into the pathogenesis of Haemophilus species and the foundation for exploring whether H. haemolyticus can be used to prevent NTHi disease.
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Affiliation(s)
- Janessa L Pickering
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia
| | - Amy Prosser
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia
| | - Karli J Corscadden
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia Perth, WA, Australia
| | - Camilla de Gier
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia; Department of Paediatrics, Princess Margaret Hospital for ChildrenPerth, WA, Australia
| | - Guicheng Zhang
- School of Public Health, Curtin University Perth, WA, Australia
| | - Ruth B Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia
| | - Lea-Ann S Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia
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Pérez-Losada M, A. Crandall K, J. Freishtat R. Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.2.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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24
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Nasopharyngeal carriage of Streptococcus pneumoniae and other bacteria in the 7th year after implementation of the pneumococcal conjugate vaccine in the Netherlands. Vaccine 2015; 34:531-539. [PMID: 26667610 DOI: 10.1016/j.vaccine.2015.11.060] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/20/2015] [Accepted: 11/21/2015] [Indexed: 01/02/2023]
Abstract
After introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in the infant national immunization program (NIP) in the Netherlands in 2006, Streptococcus pneumoniae strains of the non-vaccine serotype 19A emerged and became the dominant serotype in carriage in children and their parents. Similar patterns were observed in other European countries and the United States. Increases in carriage rates of Staphylococcus aureus and non-typeable (NT) Haemophilus influenzae were also observed. After switching of PCV7 to 10-valent vaccine (PCV10) in 2011, a new carriage surveillance study was performed in the winter of 2012/2013. Nasopharyngeal carriage of S. pneumoniae, H. influenzae, S. aureus, and Moraxella catarrhalis was determined by conventional culture in 330 PCV10-vaccinated 11-month-old children, 330 PCV7-vaccinated 24-month-old children, and their parents. Carriage prevalence was compared with similar carriage studies conducted in 2005, 2009, and 2010/2011. Although serotype 19A remained the most frequently carried pneumococcal serotype in children, prevalence of 19A significantly declined in PCV7-vaccinated 24-month-old children (14% to 8%, p=0.01), but less in PCV10-vaccinated 11-month-old children (12% to 9%, p=0.31). Carriage of H. influenzae remained stable at an elevated level (65% in 11-month-olds and 69% in 24-month-olds), while the carriage of S. aureus returned to pre-PCV7 levels in 11-month-old children (14% in 2010/2011 to 7% in 2012/2013), but not in 24-month-olds (remained at 7%). Our results might indicate a new balance between replacing non-vaccine pneumococcal serotypes and other potential pathogenic bacteria in nasopharyngeal carriage. Carriage studies are valuable tools in assessing vaccine effects on pathogens circulating in the population, for evaluation of PCV impact, and in predicting changes in respiratory and invasive disease.
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