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Defining the microbes in the middle ear and upper respiratory tract that lead to recurrent ear infections – a metagenomic study
Names of investigators
Christopher S Peacock, Sarra E Jamieson, Rachael Lappan, Timo Lassmann, Elyce Iagallo, Kara Imbrogno, Christopher Blyth, Harvey L Coates, Paul Bumbak, Lea-Ann Kirkham, Ruth Thornton, Deborah Lehmann, Richard Lipscombe, Shyan Vijayasekaran.
Otitis media (OM, or ear infection) is a very common illness of childhood. Some children will have multiple ear infections in their early years and are diagnosed with recurrent acute OM. There is a high level of complexity within the microbial community of the middle ear during an episode of OM. This project is using the latest sequencing technology to examine the microbial composition of the middle ear and the nasopharyngeal region, the site of initial colonization prior to OM. This is being compared to the same environment in children who appear resistant to recurrent ear infections but who attend daycare, a known risk factor for OM. The project has recruited 99 cases (i.e. children having grommets inserted for recurrent acute otitis media) along with an age and season matched control for each case. From case children we gained parental consent to collect any middle ear fluid present at the time of grommet insertion, a saline rinse of the middle ear, a nasopharyngeal swab and a swab of the ear canal. From control children we gained parental consent to collect a nasopharyngeal swab. From these samples we have extracted all of the microbial DNA and sequenced the 16S rRNA gene, a bacterial specific gene found in all bacterial species that can be used to identify the bacteria present in the sample. We found that the nasopharynx of the cases contains greater bacterial diversity than that of the controls, and of the middle ear. Several low-abundance genera found in the cases were absent from the controls and may have some involvement in rAOM. We also identified two genera (Corynebacterium and Dolosigranulum) that were significantly more abundant in the healthy controls compared to the cases and might be involved in resistance to rAOM. A subset of samples has been selected to undergo whole genome shotgun sequencing to identify bacteria and species and strain level, and to provide information on genes involved in pathogenesis or disease resistance. This phase of the project is currently underway.
In addition, we are currently undertaking a pilot project to look at the use of Dual RNA-Seq in furthering our understanding of host-pathogen interactions in otitis media. Dual RNA-Seq is a methodology that sequences RNA from a sample, both host and bacterial, and then looks at what genes are being expressed in these samples. This will be done in middle ear fluid collected from children undergoing grommet insertion for recurrent acute otitis media and chronic otitis media with effusion. Recruitment to this study is complete and the data is currently being analysed. In this pilot study 16 children were recruited. The use of Dual RNA-Seq has not been applied to otitis media previously so this pilot project will help us determine if this is likely to be an informative approach and potentially provide preliminary data to aid in designing a larger study. This approach is important to determine which bacteria are active in the middle ear as metagenomic sequencing can only determine the presence of bacteria (live, dead or dormant). This may help us determine whether potential novel pathogens are involved in OM or are simply bystanders.
Plain Language summary
Recurrent middle ear infections (or otitis media) are one of the most common reasons for children to visit their GP, to be prescribed antibiotics and to undergo surgery. Currently we know of several specific microbes that cause ear infections, however it is thought that are probably many more microbes that also cause ear infections. It is also likely that there are microbes normally present in the middle ear and at the back of the nose that are not responsible for causing any illness but could be considered as useful microbes that help the body to maintain its healthy state and fight off the microbes that do cause illness. To try and identify all of the microbes in the middle ear and at the back of the nose (the ones that cause illness and the ones that are useful) this project will use a new type of technology that allows us to look at the DNA (also called “the building block of life”). We hope this information will help to develop novel treatments that will reduce the number of ear infections that children in the future have.
Funders of the project
Telethon-New Children’s Hospital Research Fund
Wesfarmers Centre Seed Funding
Harvey L Coates, SPACH, PMH & UWA
Shyan Vijayasekaran, SPACH, PMH & UWA
Paul Bumbak, Princess Margaret Hospital for Children & UWA
Lea-Ann Kirkham, SPACH
Ruth Thornton, SPACH
Richard Lipscombe, Proteomics International Pty Ltd, Nedlands, WA.
Feilman Fellow; Program Head, Genetics and Rare DiseasesEmail me
Director, Wesfarmers Centre of Vaccines and Infectious Diseases; Co-Head, Infectious Diseases Epidemiology, Wesfarmers Centre of Vaccines and Infectious Diseases, Honorary and NHMRC Emerging Leadership FellowEmail me
Co-Head, Bacterial Respiratory Infectious Disease Group; Microbiology Lead, Wesfarmers Centre of Vaccines & Infectious Diseases
Co-Lead, Bacterial Respiratory Infectious Disease Group, Wesfarmers Centre of Vaccines & Infectious Diseases