Responses of the Resident Oral Microbiome of Children to Amoxicillin
Research type
Research Study
Full title
Responses of the Resident Oral Microbiome of Children to Amoxicillin Therapy
IRAS ID
241219
Contact name
Mona Alshaye
Contact email
Sponsor organisation
University of Leeds
Duration of Study in the UK
2 years, 6 months, 31 days
Research summary
Summary of Research
Dentists account for 7% to 10% of all antibiotic prescriptions, and amoxicillin is the first-line antibiotic recommended to be used by several guidelines in paediatric dentistry for management of dental abscesses. Antibiotics that are prescribed to eradicate certain pathogens will have various effects on our microbiome. Greater understanding of such effects and the amount of disturbance to the oral microbiomes is required. Therefore, we aim in our study to investigate the impact of amoxicillin administration on the oral microbiome of a group of children aged 5–10 years old. Saliva samples will be collected from 36 children who will be attending paediatric dentistry clinics at Leeds Dental Institute (LDI) and are indicated for antibiotic prescription. The researcher will obtain informed consent and assent. The participants are agreeing to answer questions about antibiotic use and medical history and to give access to their dental examination findings. The collection of saliva samples from each child will be before and after amoxicillin prescription at different time points (baseline, two weeks and three months after). Baseline samples will be collected on the day at the emergency clinic. Two-week samples will be obtained when the child visits LDI for review and treatment after the antibiotic course ends. The three-month samples will be collected at a follow-up appointment where the participant will receive prevention treatment. All saliva samples will be processed and analysed in a laboratory in the Wellcome Trust Brenner Building (WTBB), St James’s University Hospital. Analysis of the samples is to evaluate the composition of the oral microbial community and their gene expression profile in the saliva samples at different time points.Summary of Results
Title: Responses of the Resident Oral Microbiome of Children to Amoxicillin Therapy.
Background: The World Health Organisation considers antibiotic resistance an increasing global threat that creates a clinical and financial burden on healthcare systems worldwide. The British Prime Minister in July 2014 announced that antibiotic resistance is not a distant threat, with 25,000 people a year already dying from infections resistant to antibiotic drugs in Europe alone. Dentists account for 7 to 10% of all antibiotic prescriptions. Several paediatric dentistry guidelines recommend amoxicillin for the management of dental abscesses. Antibiotics undoubtedly impact our microbiome. The knowledge of the effect of antibiotic use on the oral microbiome is limited, especially in children. A better understanding of the effect of antibiotics and their disturbance to the oral microbiome is required.
Aims: This longitudinal cohort study examines the hypothesis that the oral microbiome is altered in function and in composition through amoxicillin administration to children and the oral microbiome is a reservoir for antibiotic resistance genes (ARGs) from both oral and non-oral organisms.
Method: A total of 14 children aged 4-11years old attending the Leeds Dental Hospital who were indicated for antibiotic prescription were recruited. Saliva samples and clinical information were collected from children before, two-week and three-month after amoxicillin therapy. Oral microbial profiles (taxonomic and functional) were obtained using a shotgun metagenomic and meta-transcriptomic approaches. Unique reads were annotated using blastp against the CARD database (e-value ≤ 1e-5) to characterise ARGs. Comparison analysis was used to evaluate the composition, function, and resistome of the oral microbiome at different timepoints.Summary of Results
Results: To the researcher’s best knowledge, this is the first study to characterise the salivary microbiome and resistome of children under the influence of amoxicillin using metagenomic and metatranscriptomic analyses simultaneously. The study investigated the oral microbiome composition, function, and resistome response to antibiotic administration (amoxicillin) to address the identified objectives as follows:
Changes in Composition and Function of the Oral Microbiota after Antibiotic (Amoxicillin) Administration
Oral Microbiome CompositionThe study showed that significant changes in the composition of the oral microbiome occurred at the two-week timepoint. Despite the observable compositional changes three months after antibiotic therapy, no statistically significant changes were detected at the three-month timepoint. Additionally, the characterisation of the oral microbiota differed considerably between metagenomic and metatranscriptomic studies, indicating that some taxa are more active in the oral microbiome than others. Furthermore, the ubiquitous oral microbiome was identified at the phylum, genus, and species levels at different timepoints before and after antibiotic exposure and included bacterial, fungal, archaeal, and viral components.
Oral Microbiome Function
The study found that the majority of significant changes in the function of the oral microbiome occurred at the two-week timepoint, with only a few significant changes at the three-month timepoint. The functional metagenomic and metatranscriptomic investigations of the KEGG and eggNOG analyses generally agreed, revealing that the most prevalent markers in the oral microbiome included those involved in carbohydrate metabolism, amino acid metabolism, energy metabolism, and the metabolism of cofactors and vitamins. CAZy metagenomic and metatranscriptomic analyses revealed an enrichment of the six CAZy families, with glycoside hydrolases being the most enriched family. There were great inter-individual differences in taxonomic and functional profiles.
Presence and Expression of Antibiotic Resistance Genes, Including Amoxicillin Resistance.
Oral Resistome
The study presented statistically significant changes in the oral resistome before and after amoxicillin exposure, including an increase in the ARGs number after three months compared to the baseline. In addition, thirty ARGs showed statistically significant abundance changes between the timepoints, including the ARGs conferring resistance to amoxicillin (TEM-1, OXA-85, OprM, golS, and mtrE). The findings revealed the presence of twenty-five AGRs that were ubiquitous in all the samples, supporting the concept of core resistome. Furthermore, inter-individual variations in the ARGs abundance results were evident.
Gene Expression of the Oral MicrobiomeThe metatranscriptomic investigation revealed a different pattern of transcriptome gene expression at the baseline timepoint that varied from the two-week and three-month timepoint patterns, which were almost similar. Additionally, the clustering profile of differentially expressed genes (DEGs) at the baseline timepoint showed higher gene expression levels compared to the two-week and three-month timepoints.
The Duration Needed for the Oral Microbiome to Recover after Antibiotic (Amoxicillin) Intake
The oral microbiome composition investigation showed statistically significant changes at the two-week timepoint. However, there were observable, though not statistically significant, compositional changes in the oral microbiome after three months of antibiotic therapy. While the functional profile of the oral microbiome showed significant differences at the two-week and three-month timepoints. Lastly, the oral resistome also revealed statistically significant changes in the abundance of ARGs between the timepoints (baseline, two-week, and three-month). In summary, the oral microbiome of children demonstrated resilience and the ability to recover after a short course of antibiotics therapy for dental infection, despite the fact that some compositional, functional, and resistome changes unrecovered for the duration of the study period.
The results of this study indicate a substantial but incomplete recovery of the oral microbiome three months after amoxicillin therapy. Based on the findings presented in the study, the null hypotheses, which are that there are no differences in composition and function, nor are there differences in the presence and expression of antibiotic resistance genes before and after antibiotic (amoxicillin) therapy are rejected.
Conclusion: Differences in the metagenome, metatranscriptome and resistome of children is showing following treatment with amoxicillin. The study indicates a substantial but incomplete recovery of the oral microbiome following three months of amoxicillin therapy.Please do not hesitate to contact us if you have any questions or queries:
Mrs. Mona Alshaye Dr. Thuy Do
Postgraduate student Lecturer in Microbiology
Paediatric dentistry department Oral biology department
University of Leeds University of Leeds
Address: LS2 9LU Address: LS9 7TF
Tel: +44 (0)7780099192 Tel: +44 (0)1133438936
Email: dnmmaa@ leeds.ac.uk Email: n.t.do@leeds.ac.ukProf. Bernadette Drummond
Clinical Professor in Paediatric Dentistry
Paediatric dentistry department
University of Leeds
Address: LS2 9LU
Tel: +44 (0)1133432870
Email: b.k.drummond@leeds.ac.uREC name
Yorkshire & The Humber - Leeds West Research Ethics Committee
REC reference
19/YH/0223
Date of REC Opinion
21 Aug 2019
REC opinion
Further Information Favourable Opinion