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Measuring the Possibility of Middle Ear Discharge for COVID-19 Test Material. Interdiscip Perspect Infect Dis 2022; 2022:7207846. [PMID: 35464252 PMCID: PMC9020411 DOI: 10.1155/2022/7207846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 pandemic is still ongoing, and new variants continue to emerge. Various examination methods and sampling specimens are continuously being developed and published. The standard for sampling is in the nasopharynx. However, in children, this is often uncomfortable and at risk of eliciting complications. Therefore, it is necessary to look for other alternative sampling sites such as fluid from the middle ear. Scientific evidence shows that the middle ear can be a place for the attachment and growth of the SARS-CoV-2 virus. Currently, to the best of the author's knowledge, there have been no publications on middle ear discharge as a sample for the determination of the diagnosis of COVID-19. Based on this, the authors would like to explore the possibility of middle ear discharge for COVID-19 test material. A narrative review on the use of middle ear discharge as a potential diagnostic specimen for COVID-19 was conducted. The searches were conducted in the PubMed and ProQuest databases.
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Ngo CC, Massa HM, McMonagle BA, Perry CF, Nissen MD, Sloots TP, Thornton RB, Cripps AW. Predominant Bacterial and Viral Otopathogens Identified Within the Respiratory Tract and Middle Ear of Urban Australian Children Experiencing Otitis Media Are Diversely Distributed. Front Cell Infect Microbiol 2022; 12:775535. [PMID: 35360096 PMCID: PMC8963760 DOI: 10.3389/fcimb.2022.775535] [Citation(s) in RCA: 6] [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: 09/14/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background Otitis media (OM) is one of the most common infections in young children, arising from bacterial and/or viral infection of the middle ear. Globally, Streptococcus pneumoniae and non-typeable Haemophilus influenzae (NTHi) are the predominant bacterial otopathogens. Importantly, common upper respiratory viruses are increasingly recognized contributors to the polymicrobial pathogenesis of OM. This study aimed to identify predominant bacteria and viruses in the nasopharynx, adenoids and middle ears of peri-urban/urban South-East Queensland Australian children, with and without clinical history of chronic otitis media with effusion (COME) and/or recurrent acute otitis media (RAOM). Methods Sixty children, 43 diagnosed with OM and 17 controls with no clinical history of OM from peri-urban/urban South-East Queensland community were recruited to the study. Respiratory tract bacterial and viral presence were examined within nasopharyngeal swabs (NPS), middle ear effusions (MEE) and adenoids, using real-time polymerase chain reaction (RT-PCR) and bacterial culture. Results At least one otopathogen present was observed in all adenoid samples, 86.1% and 82.4% of NPS for children with and without OM, respectively, and 47.1% of the MEE from the children with OM. NTHi was the most commonly detected bacteria in both the OM and control cohorts within the adenoids (90.0% vs 93.8%), nasopharynx (67.4% vs 58.8%) respectively, and in the MEE (OM cohort 25.9%). Viruses were detected in all adenoid samples, 67.4% vs 47.1% of the NPS from the OM and control cohorts, respectively, and 37% of the MEE. Rhinovirus was the predominant virus identified in the adenoids (85.0% vs 68.8%) and nasopharynx (37.2% vs 41.2%) from the OM and control cohorts, respectively, and the MEE (19.8%). Conclusions NTHi and rhinovirus are predominant otopathogens within the upper respiratory tract of children with and without OM from peri-urban and urban South-East Queensland, Australia. The presence of bacterial otopathogens within the middle ear is more predictive of concurrent URT infection than was observed for viruses, and the high otopathogen carriage within adenoid tissues confirms the complex polymicrobial environment in children, regardless of OM history.
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Affiliation(s)
- Chinh C. Ngo
- John Curtin School of Medical Research, College of Health and Medicine, Australian National University, Canberra, ACT, Australia
| | - Helen M. Massa
- School of Pharmacy and Medical Sciences, Griffith University, Gold Coast, QLD, Australia
- *Correspondence: Helen M. Massa,
| | - Brent A. McMonagle
- School of Medicine and Dentistry, Griffith University, Gold Coast, QLD, Australia
- Pindara Private Hospital, Ramsay Health Care, Gold Coast, QLD, Australia
| | - Christopher F. Perry
- School of Clinical Medicine, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Otolaryngology, Head and Neck Surgery Department, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Michael D. Nissen
- Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Theo P. Sloots
- Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Ruth B. Thornton
- Centre for Child Health Research, University of Western Australia, Perth, WA, Australia
- Wesfarmers Centre of Vaccines and Infectious Disease, Telethon Kids Institute, Perth, WA, Australia
| | - Allan W. Cripps
- School of Medicine and Dentistry, Griffith University, Gold Coast, QLD, Australia
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Beissbarth J, Smith-Vaughan HC, Cheng AC, Morris PS, Leach AJ. BIGDATA: A Protocol to Create and Extend a 25-Year Clinical Trial and Observational Data Asset to Address Key Knowledge Gaps in Otitis Media and Hearing Loss in Australian Aboriginal and Non-Aboriginal Children. Front Pediatr 2022; 10:804373. [PMID: 35498792 PMCID: PMC9047683 DOI: 10.3389/fped.2022.804373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION Otitis media (OM) is a common childhood illness, often resolving without intervention and acute and long-term complications are rare. However, Australian Aboriginal and Torres Strait Islander infants and children experience a high burden of OM and are at high risk of complications (tympanic membrane perforation and chronic infections). Bacterial OM is commonly associated with Streptococcus pneumoniae, non-typeable Haemophilus influenzae, and Moraxella catarrhalis. BIGDATA is a data asset combining over 25 years of microbiology and OM surveillance research from the Ear Health Research Program at Menzies School of Health Research (Northern Territory, Australia), including 11 randomized controlled trials, four cohort studies, eight surveys in over 30 remote communities (including data from Western Australia), and five surveys of urban childcare centers including Aboriginal and Torres Strait Islander and non-Indigenous children. Outcome measures include clinical examinations (focusing on OM), antibiotic prescriptions, pneumococcal vaccination, modifiable risk factors such as smoking and household crowding, and nasopharyngeal and ear discharge microbiology including antimicrobial resistance testing. METHODS AND ANALYSIS The initial series of projects are planned to address the following key knowledge gaps: (i) otitis media prevalence and severity over pre pneumococcal conjugate vaccines (PCVs) and three eras of increasing PCV valency; (ii) impact of increasing valency PCVs on nasopharyngeal carriage dynamics of pneumococcal serotypes, and antimicrobial resistance; (iii) impact of increasing valency PCVs on nasopharyngeal carriage dynamics and antimicrobial resistance of other otopathogens; and (iv) serotype specific differences between children with acute OM and OM with effusion or without OM. These data will be utilized to identify research gaps, providing evidence-based prioritization for ongoing research. ETHICS AND DISSEMINATION Data asset creation and priority analyses were approved by the Human Research Ethics Committee of Northern Territory Department of Health and Menzies School of Health Research (EC00153, 18-3281), the Child and Adolescent Health Service Human Research Ethics Committee and Western Australian Aboriginal Health Ethics Committee. Dissemination will be through peer review publication and conference presentations.
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Affiliation(s)
- Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia.,Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, VIC, Australia
| | - Peter S Morris
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.,Royal Darwin Hospital, Darwin, NT, Australia
| | - Amanda J Leach
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
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Kang HM, Kang JH. Effects of nasopharyngeal microbiota in respiratory infections and allergies. Clin Exp Pediatr 2021; 64:543-551. [PMID: 33872488 PMCID: PMC8566799 DOI: 10.3345/cep.2020.01452] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/02/2021] [Indexed: 11/27/2022] Open
Abstract
The human microbiome, which consists of a collective cluster of commensal, symbiotic, and pathogenic microorganisms living in the human body, plays a key role in host health and immunity. The human nasal cavity harbors commensal bacteria that suppress the colonization of opportunistic pathogens. However, dysbiosis of the nasal microbial community is associated with many diseases, such as acute respiratory infections including otitis media, sinusitis and bronchitis and allergic respiratory diseases including asthma. The nasopharyngeal acquisition of pneumococcus, which exists as a pathobiont in the nasal cavity, is the initial step in virtually all pneumococcal diseases. Although the factors influencing nasal colonization and elimination are not fully understood, the adhesion of opportunistic pathogens to nasopharyngeal mucosa receptors and the eliciting of immune responses in the host are implicated in addition to bacterial microbiota properties and colonization resistance dynamics. Probiotics or synbiotic interventions may show promising and effective roles in the adjunctive treatment of dysbiosis; however, more studies are needed to characterize how these interventions can be applied in clinical practice in the future.
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Affiliation(s)
- Hyun Mi Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin Han Kang
- Division of Pediatric Infectious Diseases, Departments of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Lappan R, Jamieson SE, Peacock CS. Reviewing the Pathogenic Potential of the Otitis-Associated Bacteria Alloiococcus otitidis and Turicella otitidis. Front Cell Infect Microbiol 2020; 10:51. [PMID: 32117817 PMCID: PMC7033548 DOI: 10.3389/fcimb.2020.00051] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/27/2020] [Indexed: 12/20/2022] Open
Abstract
Alloiococcus otitidis and Turicella otitidis are common bacteria of the human ear. They have frequently been isolated from the middle ear of children with otitis media (OM), though their potential role in this disease remains unclear and confounded due to their presence as commensal inhabitants of the external auditory canal. In this review, we summarize the current literature on these organisms with an emphasis on their role in OM. Much of the literature focuses on the presence and abundance of these organisms, and little work has been done to explore their activity in the middle ear. We find there is currently insufficient evidence available to determine whether these organisms are pathogens, commensals or contribute indirectly to the pathogenesis of OM. However, building on the knowledge currently available, we suggest future approaches aimed at providing stronger evidence to determine whether A. otitidis and T. otitidis are involved in the pathogenesis of OM. Such evidence will increase our understanding of the microbial risk factors contributing to OM and may lead to novel treatment approaches for severe and recurrent disease.
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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
| | - 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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Marsh RL, Smith-Vaughan HC, Chen AC, Marchant JM, Yerkovich ST, Gibson PG, Pizzutto SJ, Hodge S, Upham JW, Chang AB. Multiple Respiratory Microbiota Profiles Are Associated With Lower Airway Inflammation in Children With Protracted Bacterial Bronchitis. Chest 2019; 155:778-786. [DOI: 10.1016/j.chest.2019.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 12/01/2022] Open
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Coleman A, Wood A, Bialasiewicz S, Ware RS, Marsh RL, Cervin A. The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media. MICROBIOME 2018; 6:199. [PMID: 30396360 PMCID: PMC6219068 DOI: 10.1186/s40168-018-0577-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic review of the literature exploring the upper airway and middle ear microbiota in relation to OM in indigenous children. METHODS Papers targeting microbiota in relation to OM in children < 18 years indigenous to Australia, New Zealand, North America, and Greenland were sought. MEDLINE, CINAHL, EMBASE, Cochrane Library, and Informit databases were searched using key words. Two independent reviewers screened titles, abstracts, and then full-text papers against inclusion criteria according to PRISMA guidelines. RESULTS Twenty-five papers considering indigenous Australian, Alaskan, and Greenlandic children were included. There were high rates of nasopharyngeal colonization with the three main otopathogens (Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis) in indigenous children with OM. Middle ear samples had lower rates of otopathogen detection, although detection rates increased when molecular methods were used. Pseudomonas aeruginosa and Staphylococcus aureus were commonly detected in middle ear discharge of children with chronic suppurative OM. There was a significant heterogeneity between studies, particularly in microbiological methods, which were largely limited to culture-based detection of the main otopathogens. CONCLUSIONS There are high rates of otopathogen colonization in indigenous children with OM. Chronic suppurative OM appears to be associated with a different microbial profile. Beyond the main otopathogens, the data are limited. Further research is required to explore the entire upper respiratory tract/middle ear microbiota in relation to OM, with the inclusion of healthy indigenous peers as controls.
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Affiliation(s)
- Andrea Coleman
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland Australia
- Queensland Pediatric Infectious Disease Laboratory, Centre for Children’s Health Research, Children’s Health Queensland Hospital, Queensland University of Technology, Child Health Research Centre, The University of Queensland, 62 Graham Street, South Brisbane, Queensland 4101 Australia
| | - Amanda Wood
- The Deadly Ears Program, Children’s Health Queensland Hospital and Health Service, Brisbane, Queensland Australia
| | - Seweryn Bialasiewicz
- Queensland Pediatric Infectious Disease Laboratory, Centre for Children’s Health Research, Children’s Health Queensland Hospital, Queensland University of Technology, Child Health Research Centre, The University of Queensland, 62 Graham Street, South Brisbane, Queensland 4101 Australia
| | - Robert S. Ware
- Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland Australia
| | - Robyn L. Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory Australia
| | - Anders Cervin
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland Australia
- Head & Neck Surgery, Department of Otolaryngology, Royal Brisbane and Women’s Hospital, Brisbane, Queensland Australia
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8
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Boers SA, de Zeeuw M, Jansen R, van der Schroeff MP, van Rossum AMC, Hays JP, Verhaegh SJC. Characterization of the nasopharyngeal and middle ear microbiota in gastroesophageal reflux-prone versus gastroesophageal reflux non-prone children. Eur J Clin Microbiol Infect Dis 2018; 37:851-857. [PMID: 29404836 PMCID: PMC5916997 DOI: 10.1007/s10096-017-3178-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/25/2017] [Indexed: 12/21/2022]
Abstract
Otitis media (OM) is one of the most common pediatric infections worldwide, but the complex microbiology associated with OM is poorly understood. Previous studies have shown an association between OM and gastroesophageal reflux (GER) in children. Therefore, in order to bridge the gap in our current understanding of the interaction between GER and OM, we investigated the nasopharyngeal and middle ear microbiota of children suffering from GER-associated OM and OM only, using culture-independent 16S rRNA gene sequencing. Middle ear fluid, nasopharyngeal swabs, and clinical data were collected as part of a prospective pilot study conducted at the Department of Otorhinolaryngology of the Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands. A total of 30 children up to 12 years of age who suffered from recurrent acute otitis media (AOM) (5), chronic otitis media with effusion (OME) (23), or both (2), and who were listed for tympanostomy tube placement, were included in the study. Nine children were included in the GER-associated OM cohort and 21 in the OM-only cohort. We found no obvious effect of GER on the nasopharyngeal and middle ear microbiota between the two groups of children. However, our results highlight the need to assess the true role of Alloiococcus spp. and Turicella spp. in children presenting with a high prevalence of recurrent AOM and chronic OME.
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Affiliation(s)
- Stefan A Boers
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marjolein de Zeeuw
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Ruud Jansen
- Department of Molecular Biology, Regional Laboratory of Public Health, Haarlem, The Netherlands
| | - Marc P van der Schroeff
- Department of Otorhinolaryngology, Erasmus MC-Sophia Children's Hospital, University Medical Center, Rotterdam, The Netherlands
| | - Annemarie M C van Rossum
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, Erasmus MC-Sophia Children's Hospital, University Medical Center, Rotterdam, The Netherlands
| | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Suzanne J C Verhaegh
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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9
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Chan CL, Richter K, Wormald PJ, Psaltis AJ, Vreugde S. Alloiococcus otitidis Forms Multispecies Biofilm with Haemophilus influenzae: Effects on Antibiotic Susceptibility and Growth in Adverse Conditions. Front Cell Infect Microbiol 2017; 7:344. [PMID: 28824879 PMCID: PMC5539592 DOI: 10.3389/fcimb.2017.00344] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/14/2017] [Indexed: 11/13/2022] Open
Abstract
Otitis media with effusion (OME) is a biofilm driven disease and commonly accepted otopathogens, such as Haemophilus influenzae, Streptococcus pneumonia, and Moraxella catarrhalis, have been demonstrated to form polymicrobial biofilms within the middle ear cleft. However, Alloiococcus otitidis (A. otitidis), which is one of the most commonly found bacteria within middle ear aspirates of children with OME, has not been described to form biofilms. The aim of this study was to investigate whether A. otitidis can form biofilms and investigate the impact on antibiotic susceptibility and survivability in polymicrobial biofilms with H. influenzae in vitro. The ability of A. otitidis to form single-species and polymicrobial biofilms with H. influenzae was explored. Clinical and commercial strains of A. otitidis and H. influenzae were incubated in brain heart infusion with and without supplementation. Biofilm was imaged using confocal laser scanning microscopy and scanning electron microscopy. Quantification of biofilm biomass and viable bacterial number was assessed using crystal violet assays and viable cell counting in both optimal growth conditions and in adverse growth conditions (depleted media and sub-optimal growth temperature). Antimicrobial susceptibility and changes in antibiotic resistance of single-species and multi-species co-culture were assessed using a microdilution method to assess minimal bactericidal concentration and E-test for amoxicillin and ciprofloxacin. A. otitidis formed single-species and polymicrobial biofilms with H. influenzae. Additionally, whilst strain dependent, combinations of polymicrobial biofilms decreased antimicrobial susceptibility, albeit a small magnitude, in both planktonic and polymicrobial biofilms. Moreover, A. otitidis promoted H. influenzae survival by increasing biofilm production in depleted media and at suboptimal growth temperature. Our findings suggest that A. otitidis may play an indirect pathogenic role in otitis media by altering H. influenzae antibiotic susceptibility and enhancing growth under adverse conditions.
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Affiliation(s)
- Chun L Chan
- Department of Surgery, Otolaryngology-Head and Neck Surgery, Adelaide UniversityAdelaide, SA, Australia
| | - Katharina Richter
- Department of Surgery, Otolaryngology-Head and Neck Surgery, Adelaide UniversityAdelaide, SA, Australia
| | - Peter-John Wormald
- Department of Surgery, Otolaryngology-Head and Neck Surgery, Adelaide UniversityAdelaide, SA, Australia
| | - Alkis J Psaltis
- Department of Surgery, Otolaryngology-Head and Neck Surgery, Adelaide UniversityAdelaide, SA, Australia
| | - Sarah Vreugde
- Department of Surgery, Otolaryngology-Head and Neck Surgery, Adelaide UniversityAdelaide, SA, Australia
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Protasova IN, Per'yanova OV, Podgrushnaya TS. [Acute otitis media in the children: etiology and the problems of antibacterial therapy]. Vestn Otorinolaringol 2017; 82:84-89. [PMID: 28514373 DOI: 10.17116/otorino201782284-89] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The objective of the present review was to summarize the currently available literature data on etiology of acute otitis media in the children, the role of biofilms in the development of this pathology, and sensitivity of its principal causative factors to various antibiotic medications. The secondary objective was to elaborate the practical guidelines for the prevention of acute otitis media in the children.
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Affiliation(s)
- I N Protasova
- V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Russian Ministry of Health, Krasnoyarsk, Russia, 660022; Russian-Japanese Centre of Microbiology, Metagenomics and Infectious Diseases of V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Russian Ministry of Health, Krasnoyarsk, Russia, 660022
| | - O V Per'yanova
- V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Russian Ministry of Health, Krasnoyarsk, Russia, 660022; Russian-Japanese Centre of Microbiology, Metagenomics and Infectious Diseases of V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Russian Ministry of Health, Krasnoyarsk, Russia, 660022
| | - T S Podgrushnaya
- V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Russian Ministry of Health, Krasnoyarsk, Russia, 660022
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Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media. mSphere 2017; 2:mSphere00006-17. [PMID: 28357413 PMCID: PMC5362748 DOI: 10.1128/msphere.00006-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/03/2017] [Indexed: 11/20/2022] Open
Abstract
Although S. pneumoniae, H. influenzae, and M. catarrhalis have been long established as the most important pathogens in acute otitis media using culture and specific PCR assays, the knowledge of their mutual quantitative relations and possible roles of other bacteria is incomplete. The advent of unbiased bacteriome 16S rRNA gene profiling has allowed the detection of nearly all bacteria present in the sample, and it helps in depicting their mutual quantitative ratios. Due to the difficulties in performing mass sequencing in low-volume samples, only a few bacteriome-profiling studies of otitis media have been published, all limited to cases of chronic otitis media. Here, we present a study on samples obtained from young children with acute otitis media, successfully using a strategy of nested PCR coupled with mass sequencing, and demonstrate that the method can confer quantitative information hardly obtainable by other methods. The aim of the study was to analyze the bacteriome of acute otitis media with a novel modification of next-generation sequencing techniques. Outpatient children with acute otitis media were enrolled in the study, and middle ear fluids were collected during 90 episodes from 79 subjects aged 5 to 42 months (median age, 19 months). The bacteriome profiles of middle ear fluid samples were determined by a nested-PCR amplification of the 16S rRNA gene (V4 region), followed by mass sequencing. The profiling results were compared to the results of specific PCR assays targeting selected prevalent pathogens. Bacteriome profiling using nested amplification of low-volume samples was aided by a bioinformatic subtraction of signal contaminants from the recombinant polymerase, achieving a sensitivity slightly lower than that of specific PCR detection. Streptococcus pneumoniae was detected in 28 (31%) samples, Haemophilus influenzae in 24 (27%), Moraxella catarrhalis in 18 (20%), Staphylococcus spp. in 21 (23%), Turicella otitidis in 5 (5.6%), Alloiococcus otitidis in 3 (3.3%), and other bacteria in 14 (16%) using bacteriome profiling. S. pneumoniae was the dominant pathogen in 14 (16%) samples, H. influenzae in 15 (17%), M. catarrhalis in 5 (5.6%), T. otitidis in 2, and Staphylococcus auricularis in 2. Weaker signals of Prevotella melaninogenica, Veillonella dispar, and Veillonella montpellierensis were noted in several samples. Fourteen samples (16%) were not explainable by bacterial pathogens; novel causative agents were not detected. In conclusion, unbiased bacteriome profiling helped in depicting the true mutual quantitative ratios of ear bacteria, but at present, its complicated protocol impedes its routine clinical use. IMPORTANCE Although S. pneumoniae, H. influenzae, and M. catarrhalis have been long established as the most important pathogens in acute otitis media using culture and specific PCR assays, the knowledge of their mutual quantitative relations and possible roles of other bacteria is incomplete. The advent of unbiased bacteriome 16S rRNA gene profiling has allowed the detection of nearly all bacteria present in the sample, and it helps in depicting their mutual quantitative ratios. Due to the difficulties in performing mass sequencing in low-volume samples, only a few bacteriome-profiling studies of otitis media have been published, all limited to cases of chronic otitis media. Here, we present a study on samples obtained from young children with acute otitis media, successfully using a strategy of nested PCR coupled with mass sequencing, and demonstrate that the method can confer quantitative information hardly obtainable by other methods.
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12
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Microbiology of otitis media in Indigenous Australian children: review. The Journal of Laryngology & Otology 2017; 131:S2-S11. [DOI: 10.1017/s0022215116009294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractObjectives:To review research addressing the polymicrobial aetiology of otitis media in Indigenous Australian children in order to identify research gaps and inform best practice in effective prevention strategies and therapeutic interventions.Methods:Literature review.Results:Studies of aspirated middle-ear fluid represented a minor component of the literature reviewed. Most studies relied upon specimens from middle-ear discharge or the nasopharynx. Culture-based middle-ear discharge studies have found that non-typeableHaemophilus influenzaeandStreptococcus pneumoniaepredominate, withMoraxella catarrhalis, Staphylococcus aureusandStreptococcus pyogenesisolated in a lower proportion of samples.Alloiococcus otitidiswas detected in a number of studies; however, its role in otitis media pathogenesis remains controversial. Nasopharyngeal colonisation is a risk factor for otitis media in Indigenous infants, and bacterial load of otopathogens in the nasopharynx can predict the ear state of Indigenous children.Conclusion:Most studies have used culture-based methods and specimens from middle-ear discharge or the nasopharynx. Findings from these studies are consistent with international literature, but reliance on culture may incorrectly characterise the microbiology of this condition. Advances in genomic technologies are now providing microbiologists with the ability to analyse the entire mixed bacterial communities (‘microbiomes’) of samples obtained from Indigenous children with otitis media.
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13
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Molecular Microbiological Profile of Chronic Suppurative Otitis Media. J Clin Microbiol 2016; 54:2538-46. [PMID: 27487953 DOI: 10.1128/jcm.01068-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/26/2016] [Indexed: 01/13/2023] Open
Abstract
Chronic suppurative otitis media (CSOM) presents with purulent otorrhea (ear discharge), is characterized by chronic inflammation of the middle ear and mastoid cavity, and contributes to a significant disease burden worldwide. Current antibiotic therapy is guided by swab culture results. In the absence of detailed molecular microbiology studies of CSOM patients, our current understanding of the microbiota of CSOM (and indeed of the healthy ear) remains incomplete. In this prospective study, 24 patients with CSOM were recruited, along with 22 healthy controls. Culture-based techniques and 16S rRNA gene amplicon sequencing were used to profile the bacterial community for each patient. Comparisons between patients with and without cholesteatoma in the middle ear and mastoid cavity were also made. A major finding was that the middle ear of many healthy controls was not sterile, which is contradictory to the results of previous studies. However, sequencing data showed that Staphylococcus aureus, along with a range of other Gram-positive and Gram-negative organisms, were present in all subgroups of CSOM and healthy controls. Large interpatient variability in the microbiota was observed within each subgroup of CSOM and controls, and there was no bacterial community "signature" which was characteristic of either health or disease. Comparisons of the culture results with the molecular data show that culture-based techniques underestimate the diversity of bacteria found within the ear. This study reports the first detailed examination of bacterial profiles of the ear in healthy controls and patients with CSOM.
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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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15
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Chan CL, Wabnitz D, Bardy JJ, Bassiouni A, Wormald PJ, Vreugde S, Psaltis AJ. The microbiome of otitis media with effusion. Laryngoscope 2016; 126:2844-2851. [PMID: 27335217 DOI: 10.1002/lary.26128] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/26/2016] [Accepted: 05/12/2016] [Indexed: 11/08/2022]
Abstract
OBJECTIVES/HYPOTHESIS The adenoid pad has been considered a reservoir for bacteria in the pathogenesis of otitis media with effusion. This study aimed to characterize the middle ear microbiota in children with otitis media with effusion and establish whether a correlation exists between the middle ear and adenoid microbiota. STUDY DESIGN Prospective, controlled study. METHODS Middle ear aspirates adenoid pad swabs were collected from 23 children undergoing ventilation tube insertion. Adenoid swabs from patients without ear disease were controls. Samples were analyzed using 16S rRNA sequencing on the Illumina MiSeq platform. RESULTS Thirty-five middle ear samples were collected. The middle ear effusion microbiota was dominated by Alloiococcus otitidis (23% mean relative abundance), Haemophilus (22%), Moraxella (5%), and Streptococcus (5%). Alloiococcus shared an inverse correlation with Haemophilus (P = .049) and was found in greater relative abundance in unilateral effusion (P = .004). The microbiota of bilateral effusions from the same patient were similar (P < .001). However, the otitis media with effusion microbiota were found to be dissimilar to that of the adenoid (P = .01), whereas the adenoid microbiota of otitis media with effusion and control patients were similar (P > .05) (permutational multivariate analysis of the variance). CONCLUSIONS Dissimilarities between the local microbiota of the adenoid and the middle ear question the theory that the adenoid pad is a significant reservoir to the middle ear in children with otitis media with effusion. A otitidis had the greatest cumulative relative abundance, particularly in unilateral effusions, and shares an inverse correlation with the relative abundance of Haemophilus. LEVEL OF EVIDENCE NA Laryngoscope, 126:2844-2851, 2016.
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Affiliation(s)
- Chun Ling Chan
- Department of Otolaryngology-Head & Neck Surgery, Adelaide University, Adelaide, South Australia, Australia
| | - David Wabnitz
- Department of Otolaryngology-Head & Neck Surgery, The Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Jake Jervis Bardy
- Department of Otolaryngology-Head & Neck Surgery, Adelaide University, Adelaide, South Australia, Australia
| | - Ahmed Bassiouni
- Department of Otolaryngology-Head & Neck Surgery, Adelaide University, Adelaide, South Australia, Australia
| | - Peter-John Wormald
- Department of Otolaryngology-Head & Neck Surgery, Adelaide University, Adelaide, South Australia, Australia
| | - Sarah Vreugde
- Department of Otolaryngology-Head & Neck Surgery, Adelaide University, Adelaide, South Australia, Australia
| | - Alkis James Psaltis
- Department of Otolaryngology-Head & Neck Surgery, Adelaide University, Adelaide, South Australia, Australia
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16
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Slinger R, Duval M, Langill J, Bromwich M, MacCormick J, Chan F, Vaccani JP. Direct molecular detection of a broad range of bacterial and viral organisms and Streptococcus pneumoniae vaccine serotypes in children with otitis media with effusion. BMC Res Notes 2016; 9:247. [PMID: 27130295 PMCID: PMC4850712 DOI: 10.1186/s13104-016-2040-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/14/2016] [Indexed: 12/22/2022] Open
Abstract
Background Otitis media with effusion (OME) causes significant morbidity in children, but the causes of OME and methods for prevention are unclear. To look for potential infectious etiologies, we performed a pilot study using multiple-target real-time polymerase chain reaction (qPCR) for 27 infectious agents, including nine bacterial organisms and 18 respiratory viruses in middle ear fluids (MEFs) from children with OME. QPCR was also performed for the 13 Streptococcus pneumoniae serotypes contained in the current vaccine. Results Forty-eight MEF samples were obtained and qPCR detected bacterial nucleic acid (NA) in 39/48 (81 %) and viral NA in 7/48 (15 %). Alloiococcus otitidis and S. pneumoniae were both detected in 15/48 (31 %) MEFs, followed by M. catarrhalis in 14/48 (29 %), H. influenzae in 5/48 (10 %) and M. pneumoniae in 4/48 (8 %). Rhinoviruses were most common virus type detected, found in 4/48 (8 %) MEFs. Serotypes included in the current 13-serotype vaccine were detected in only 3/15 (20 %) S. pneumoniae qPCR-positive MEFs. Conclusions Bacteria may play an important role in OME, since over 80 % of MEFs contained bacterial NA. Further research into the role of A. otitidis in OME will be helpful. Serotypes of S. pneumoniae not included in the current 13-serotype vaccine may be involved in OME. Larger studies of OME S. pneumoniae serotypes are needed to help determine which additional serotypes should be included in future vaccine formulations in order to try to prevent OME.
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Affiliation(s)
- Robert Slinger
- Department of Laboratory Medicine and Pathology, Children's Hospital of Eastern Ontario, University of Ottawa, 401 Smyth Rd, Ottawa, ON, K1H 8L1, Canada.
| | - Melanie Duval
- Department of Laboratory Medicine and Pathology, Children's Hospital of Eastern Ontario, University of Ottawa, 401 Smyth Rd, Ottawa, ON, K1H 8L1, Canada
| | - Jonathan Langill
- Department of Laboratory Medicine and Pathology, Children's Hospital of Eastern Ontario, University of Ottawa, 401 Smyth Rd, Ottawa, ON, K1H 8L1, Canada
| | - Matthew Bromwich
- Department of Surgery, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Johnna MacCormick
- Department of Surgery, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Francis Chan
- Department of Laboratory Medicine and Pathology, Children's Hospital of Eastern Ontario, University of Ottawa, 401 Smyth Rd, Ottawa, ON, K1H 8L1, Canada
| | - Jean-Philippe Vaccani
- Department of Surgery, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
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17
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Ngo CC, Massa HM, Thornton RB, Cripps AW. Predominant Bacteria Detected from the Middle Ear Fluid of Children Experiencing Otitis Media: A Systematic Review. PLoS One 2016; 11:e0150949. [PMID: 26953891 PMCID: PMC4783106 DOI: 10.1371/journal.pone.0150949] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Otitis media (OM) is amongst the most common childhood diseases and is associated with multiple microbial pathogens within the middle ear. Global and temporal monitoring of predominant bacterial pathogens is important to inform new treatment strategies, vaccine development and to monitor the impact of vaccine implementation to improve progress toward global OM prevention. METHODS A systematic review of published reports of microbiology of acute otitis media (AOM) and otitis media with effusion (OME) from January, 1970 to August 2014, was performed using PubMed databases. RESULTS This review confirmed that Streptococcus pneumoniae and Haemophilus influenzae, remain the predominant bacterial pathogens, with S. pneumoniae the predominant bacterium in the majority reports from AOM patients. In contrast, H. influenzae was the predominant bacterium for patients experiencing chronic OME, recurrent AOM and AOM with treatment failure. This result was consistent, even where improved detection sensitivity from the use of polymerase chain reaction (PCR) rather than bacterial culture was conducted. On average, PCR analyses increased the frequency of detection of S. pneumoniae and H. influenzae 3.2 fold compared to culture, whilst Moraxella catarrhalis was 4.5 times more frequently identified by PCR. Molecular methods can also improve monitoring of regional changes in the serotypes and identification frequency of S. pneumoniae and H. influenzae over time or after vaccine implementation, such as after introduction of the 7-valent pneumococcal conjugate vaccine. CONCLUSIONS Globally, S. pneumoniae and H. influenzae remain the predominant otopathogens associated with OM as identified through bacterial culture; however, molecular methods continue to improve the frequency and accuracy of detection of individual serotypes. Ongoing monitoring with appropriate detection methods for OM pathogens can support development of improved vaccines to provide protection from the complex combination of otopathogens within the middle ear, ultimately aiming to reduce the risk of chronic and recurrent OM in vulnerable populations.
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Affiliation(s)
- Chinh C. Ngo
- School of Medical Science, Griffith University, Gold Coast, Queensland, Australia
- Molecular Basis of Disease, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Helen M. Massa
- School of Medical Science, Griffith University, Gold Coast, Queensland, Australia
- Molecular Basis of Disease, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- * E-mail:
| | - Ruth B. Thornton
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
- Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Allan W. Cripps
- School of Medical Science, Griffith University, Gold Coast, Queensland, Australia
- Molecular Basis of Disease, Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
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Chang AB, Smith-Vaughan H, Sloots TP, Valery PC, Whiley D, Beissbarth J, Torzillo PJ. Upper airway viruses and bacteria detection in clinical pneumonia in a population with high nasal colonisation do not relate to clinical signs. Pneumonia (Nathan) 2015; 6:48-56. [PMID: 31641578 PMCID: PMC5922338 DOI: 10.15172/pneu.2015.6/636] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/23/2015] [Indexed: 12/27/2022] Open
Abstract
Indigenous Australian children have high (up to 90%) rates of nasopharyngeal microbial colonisation and of hospitalisation for pneumonia. In Indigenous children hospitalised with pneumonia in Central Australia, we describe the nasopharyngeal detection of viruses and bacteria and assessed whether their presence related to signs of pneumonia (tachypnoea and/or chest in-drawing) on hospital admission and during subsequent days. Nasopharyngeal swabs (NPS) and data were prospectively collected from 145 children (median age = 23.5 months, interquartile range [IQR] 8.7–50) hospitalised with pneumonia at Alice Springs Hospital, Australia, between April 2001 and July 2002. The cohort was enrolled in a randomised controlled study using zinc and/or vitamin A supplementation. NPS were taken within 24 hours of hospitalisation and kept frozen at-80°C until analysed in 2014. Polymerase chain reaction (PCR) was used to detect Moraxella catarrhalis, Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Chlamydophila pneumoniae, Mycoplasma pneumoniae, and 16 respiratory viruses. Uni- and multi-variate analyses were used to examine the relationships. One or more organisms were present in 137 (94.5%) NPS; 133 (91.7%) detected ≥ 1 bacterium, 34 (37.2%) for ≥ 1 virus and 50 (34.5%) were positive for both viruses and bacteria. C. pneumoniae (n = 3) and M. pneumoniae (n = 2) were rare. In multi-variate analyses, age < 12 months (odds ratio [OR] 6.6 [95% confidence interval {CI} 1.7–25.4]) and fever (OR 4.1 [95% CI 1.7–10.4]) were associated with tachypnoea and chest in-drawing. However the presence of bacteria and/or virus type was not associated with tachypnoea and/or chest in-drawing on admission or during recovery. In children with high nasopharyngeal microbial colonisation rates, the utility of NPS in determining the diagnosis of clinical pneumonia or duration of tachypnoea or in-drawing is likely limited. Larger cohort and case-control studies are required to confirm our findings.
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Affiliation(s)
- Anne B Chang
- 17Menzies School of Health Research, Charles Darwin University, Casuarina, Australia.,27Department of Respiratory and Sleep Medicine, Queensland Children's Health Services and Queensland Children's Medical Research Institute, Queensland University of Technology, Herston, Australia.,Department of Respiratory and Sleep Medicine, Queensland Children's Hospital and Health Service, South Brisbane, Queensland 4101 Australia
| | - Heidi Smith-Vaughan
- 17Menzies School of Health Research, Charles Darwin University, Casuarina, Australia.,37School of Medicine, Griffith University, Australia
| | - Theo P Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewksi Virus Research Centre, Queensland Children's Health Services, Herston, Australia
| | - Patricia C Valery
- 17Menzies School of Health Research, Charles Darwin University, Casuarina, Australia
| | - David Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewksi Virus Research Centre, Queensland Children's Health Services, Herston, Australia
| | - Jemima Beissbarth
- 17Menzies School of Health Research, Charles Darwin University, Casuarina, Australia
| | - Paul J Torzillo
- 47Sydney Medical School, University of Sydney, Sydney, Australia.,57Royal Prince Alfred Hospital, Sydney, Australia
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19
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Jervis-Bardy J, Rogers GB, Morris PS, Smith-Vaughan HC, Nosworthy E, Leong LEX, Smith RJ, Weyrich LS, De Haan J, Carney AS, Leach AJ, O'Leary S, Marsh RL. The microbiome of otitis media with effusion in Indigenous Australian children. Int J Pediatr Otorhinolaryngol 2015; 79:1548-55. [PMID: 26228497 DOI: 10.1016/j.ijporl.2015.07.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Indigenous Australian children have a high prevalence of otitis media with effusion (OME) and associated conductive hearing loss. Only three microbiological studies of middle ear fluid (MEF) from Indigenous Australian children with OME have been reported. All of these were reliant on culture or species-specific PCR assays. The aim of this study was to characterise the middle ear fluid (MEF), adenoid and nasopharyngeal (NP) microbiomes of Indigenous Australian children, using culture-independent 16S rRNA gene sequencing. METHODS MEF, NP swabs and adenoid specimens were collected from 11 children in the Alice Springs region of Central Australia. Bacterial communities in these specimens were characterised using 16S rRNA gene sequencing. RESULTS The microbiota in MEF samples were dominated (>50% relative abundance) by operational taxonomic units (OTUs) consistent with Alloiococcus otitidis (6/11), Haemophilus influenzae (3/11) or Streptococcus sp. (specifically, Mitis group streptococci which includes Streptococcus pneumoniae) (1/11). Anatomical site selectivity was indicated by the presence of a single conserved Haemophilus OTU in 7/11 MEF samples. In comparison, there were ten distinct Haemophilus OTUs observed across the NP and adenoid samples. Despite significant differences between the MEF and NP/adenoid microbiomes, Streptococcus sp., H. influenzae and Moraxella catarrhalis OTUs were common to all sample types. Co-occurrence of classical otopathogens in paired MEF and NP/Adenoid samples is consistent with earlier culture-based studies. CONCLUSION These data highlight the need to further assess H. influenzae traits important in otitis media and to understand the role of canal flora, especially A. otitidis, in populations with a high prevalence of tympanic membrane perforation.
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Affiliation(s)
- Jake Jervis-Bardy
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; School of Medicine, Flinders University, Adelaide, SA, Australia
| | - Geraint B Rogers
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia
| | - Peter S Morris
- 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
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Lex E X Leong
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia
| | - Renee J Smith
- Infection and Immunity Theme, South Australia Health and Medical Research Institute, Adelaide, SA, Australia; School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia
| | - Jacques De Haan
- Department of Otolaryngology, Alice Springs Hospital, Alice Springs, NT, Australia
| | - A Simon Carney
- Department of Otolaryngology-Head & Neck Surgery, Flinders University, Adelaide, SA, Australia
| | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Stephen O'Leary
- Department of Otolaryngology, University of Melbourne, Melbourne, VIC, Australia
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
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Jervis-Bardy J, Leong LEX, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, Nosworthy E, Morris PS, O’Leary S, Rogers GB, Marsh RL. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. MICROBIOME 2015; 3:19. [PMID: 25969736 PMCID: PMC4428251 DOI: 10.1186/s40168-015-0083-8] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 04/03/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The rapid expansion of 16S rRNA gene sequencing in challenging clinical contexts has resulted in a growing body of literature of variable quality. To a large extent, this is due to a failure to address spurious signal that is characteristic of samples with low levels of bacteria and high levels of non-bacterial DNA. We have developed a workflow based on the paired-end read Illumina MiSeq-based approach, which enables significant improvement in data quality, post-sequencing. We demonstrate the efficacy of this methodology through its application to paediatric upper-respiratory samples from several anatomical sites. RESULTS A workflow for processing sequence data was developed based on commonly available tools. Data generated from different sample types showed a marked variation in levels of non-bacterial signal and 'contaminant' bacterial reads. Significant differences in the ability of reference databases to accurately assign identity to operational taxonomic units (OTU) were observed. Three OTU-picking strategies were trialled as follows: de novo, open-reference and closed-reference, with open-reference performing substantially better. Relative abundance of OTUs identified as potential reagent contamination showed a strong inverse correlation with amplicon concentration allowing their objective removal. The removal of the spurious signal showed the greatest improvement in sample types typically containing low levels of bacteria and high levels of human DNA. A substantial impact of pre-filtering data and spurious signal removal was demonstrated by principal coordinate and co-occurrence analysis. For example, analysis of taxon co-occurrence in adenoid swab and middle ear fluid samples indicated that failure to remove the spurious signal resulted in the inclusion of six out of eleven bacterial genera that accounted for 80% of similarity between the sample types. CONCLUSIONS The application of the presented workflow to a set of challenging clinical samples demonstrates its utility in removing the spurious signal from the dataset, allowing clinical insight to be derived from what would otherwise be highly misleading output. While other approaches could potentially achieve similar improvements, the methodology employed here represents an accessible means to exclude the signal from contamination and other artefacts.
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Affiliation(s)
- Jake Jervis-Bardy
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
- />School of Medicine, Flinders University, Bedford Park, Adelaide, SA Australia
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Lex E X Leong
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Shashikanth Marri
- />School of Medicine, Flinders University, Bedford Park, Adelaide, SA Australia
| | - Renee J Smith
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
- />School of Biological Sciences, Flinders University, Adelaide, South Australia 5001 Australia
| | - Jocelyn M Choo
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Heidi C Smith-Vaughan
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
| | - Elizabeth Nosworthy
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
| | - Peter S Morris
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
| | - Stephen O’Leary
- />Department of Otolaryngology, University of Melbourne, Melbourne, VIC Australia
| | - Geraint B Rogers
- />School of Medicine, Flinders University, Bedford Park, Adelaide, SA Australia
- />Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA Australia
| | - Robyn L Marsh
- />Menzies School of Health Research, Child Health Division, Charles Darwin University, Darwin, NT Australia
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Smith-Vaughan HC, Binks MJ, Marsh RL, Kaestli M, Ward L, Hare KM, Pizzutto SJ, Thornton RB, Morris PS, Leach AJ. Dominance of Haemophilus influenzae in ear discharge from Indigenous Australian children with acute otitis media with tympanic membrane perforation. BMC EAR, NOSE, AND THROAT DISORDERS 2013; 13:12. [PMID: 24099576 PMCID: PMC3852835 DOI: 10.1186/1472-6815-13-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/01/2013] [Indexed: 11/10/2022]
Abstract
Background Indigenous Australian children living in remote communities experience high rates of acute otitis media with tympanic membrane perforation (AOMwiP). Otitis media in this population is associated with dense nasopharyngeal colonization of three primary otopathogens; Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis. Little is known about the relative abundance of these pathogens during infection. The objective of this study was to estimate the abundance and concordance of otopathogens in ear discharge and paired nasopharyngeal swabs from children with AOMwiP (discharge of not more than 6 weeks’ duration and perforation size <2%). Methods Culture and quantitative PCR (qPCR) estimation of H. influenzae, S. pneumoniae, M. catarrhalis and total bacterial load were performed on paired nasopharyngeal and ear discharge swabs from 55 Indigenous children with AOMwiP aged 3.5 – 45.6 months and resident in remote communities. Results By culture, H. influenzae, S. pneumoniae, and M. catarrhalis were detected in 80%, 84% and 91% of nasopharyngeal swabs, and 49%, 33% and 4% of ear discharge swabs, respectively. Using qPCR, H. influenzae, S. pneumoniae, and M. catarrhalis were detected in 82%, 82%, and 93% of nasopharyngeal swabs, and 89%, 41% and 18% of ear discharge swabs, respectively. Relative abundance of H. influenzae in ear discharge swabs was 0-68% of the total bacterial load (median 2.8%); whereas S. pneumoniae and M. catarrhalis relative abundances were consistently <2% of the total bacterial load. S. pneumoniae and M. catarrhalis abundances were significantly lower in ear discharge compared with nasopharyngeal swabs (p = 0.001, p < 0.001); no significant difference was observed in H. influenzae mean abundance at the two sites. Conclusions H. influenzae was the dominant otopathogen detected in ear discharge swabs collected from children with AOMwiP. High prevalence and abundance of S. pneumoniae and M. catarrhalis in the nasopharynx did not predict ear discharge prevalence and abundances of these pathogens. PCR was substantially more sensitive than culture for ear discharge, and a necessary adjunct to standard microbiology. Quantitative methods are required to understand species abundance in polymicrobial infections and may be needed to measure accurately the microbiological impact of interventions and to provide a better understanding of clinical failure in these children.
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Affiliation(s)
- Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
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