Projects

040 - Metagenomics to Medication: the effect of antibiotics on the oral resistome

• Chief Investigator A: Dr Smitha Sukumar
• Chief Investigator B: A/Prof Leanne Teoh
• Research Collaborators: Dr Fang Wang, Gina Browne, Dr Elena Martinez, Dr Christina Adler, Dr Seth Delpatchitra, Prof Michael McCullough, Prof Paul Sambrook

Introduction

Antimicrobial resistance (AMR) is predicted to result in 10 million deaths annually by 2050 without appropriate intervention. Resistance is spread via antimicrobial resistance genes (ARGs). Therefore. surveillance studies of these collections of ARGs also known as the resistome are critical to understanding the scope and spread of AMR. However, this information is more impactful when combined with prescribing practices as this provides a far more comprehensive and nuanced picture of AMR in any given population.
Our study aims to understand AMR in a dental setting by combining genomic surveillance of the oral resistome with prescribing data in patients presenting with acute dental infections.
Our methodology is unique (an Australian first) as it combines genetic and public health methodologies to better understand an intractable and “wicked” problem. This study will be impactful at a microbiological level as we know what the genetic resistance profiles of patients taking antibiotics look like. This will improve our understanding of the impact of antibiotics on the microbiome and the spread of AMR. The impact of our study may be evaluated in translational outcomes, specifically, these results may provide evidence about the genetic impacts of prescribing narrow and broad-spectrum antibiotics. This may directly translate to providing evidence for antibiotic choices for dental infections thus, informing future guideline development and antibiotic choices in dental practice.

Aim

The specific aims of this project are twofold.
1) create a genomic profile of antimicrobial resistance genes (ARGs) from the oral cavity of patients with acute odontogenic (tooth) infections
2) overlapping this genomic profile with prescribing data i.e., matching resistance map with what antibiotics patients have been given for their infection.
By addressing these aims, we provide a comprehensive picture of how direct antibiotic exposure influences the composition of the oral resistome.
This project supports eviDent’s mission, to translate oral health research into better general health for all Australians by addressing a gap in knowledge about AMR in the dental setting. Resistance is one of the most significant health burdens facing society today. It is worthwhile to consider that most medical research today investigates diseases like diabetes, hypertension, and cancers. These diseases are prevalent because of increased life spans which are due to antibiotics which has saved humanity from the ravages of infectious disease. Therefore, curbing AMR is a priority for global health if we expect to reap the rewards of medical progress into the future.
Our profession has an important role to play. As prescribing clinicians, dentists write approximately 10% of all antibiotic prescriptions globally. Alarmingly 80% of these prescriptions are inappropriate or not required. Our results provide clinicians with meaningful insight into actions of antibiotics on the microbiome, antibiotics they have prescribed. To date the impact of prescribing antibiotics has not been able to be evaluated beyond clinical outcomes such as reduction in swelling. Our project identifies ARGs present and quantifies them. The funding requested is to extend our understanding of how ARGs spread using state of the art, long read sequencing. A subset population will be investigated further to ascertain the definitive relationship between the species which carries ARGs and how its transferred. This has not been done before in the oral resistome. This requires upgrading the existing bioinformatics pipeline which may have translational potential as public health diagnostic tools in the future as next generation sequencing technologies become cheaper and more widely available.

Methodology

This is a prospective, clinical, surveillance study which will be conducted at dental hospitals in Melbourne (ethics pending see attachment) and Adelaide. All samples collected will be sent to Sydney, where the microbial genomics work will be undertaken.
Our study population (n=45) will be allocated equally to one of three groups
- Group 1/control patients do not require antibiotics.
- Group 2 includes patients that do require antibiotics and have never been prescribed them before for this infection.
- Group 3 patients who have been previously prescribed antibiotics for this infection and require another course of antibiotics.
Two samples will be taken for each patient by the treating clinician who will record the antibiotic choice(s) and regimen(s) with additional patient data (age, medical history). The clinician will take an oral plaque sample prior to undertaking treatment at the first appointment (this will be a pre-antibiotic sample for Group 2 and 3). The second sample will be collected at the review appointment (post antibiotic sample for Group 2 and 3).
Collected samples will be stored in -80oC storage and shipped to The Charles Perkins Centre, The University of Sydney where the DNA will be extracted and undergo whole genome sequencing (subcontracted to Ramaciotti Centre for Genomics at UNSW). Of the 90 samples collected, eight samples will undergo both short and long read metagenomic sequencing.
To date there is a paucity of studies using long read sequencing method due to cost (almost 7.5 times the cost of short read sequencing per sample). Thus, the priority of this project and the requested funding is specifically for long read metagenomics. Due to budgetary constraints long reading sequencing is limited to about 1% of the samples (representative samples from each group) which will provide baseline data about the relationship between ARG, bacteria and MGE. The sequenced data will run through bioinformatics pipeline developed by the CIA and team of bioinformaticians to identify and quantify ARGs and the species these genes live in. The genetic profiles will then be analysed with the metadata collected about prescribing practice.

What are the expected outcomes?

The expected outcomes of the project and anticipated benefits to practitioners and their patients are in the broadest terms curbing the spread of AMR by reducing the use of antibiotics.
This will be achieved using public health campaigns in two populations
1. Patients: Create a dental specific public health initiative about use and impacts of antibiotics on the human microbiome to increase awareness of AMR in a hospital setting. This can be measured using qualitative measures such as surveys and focus groups. This initiative has the potential to be expanded into private setting based on impact of initial program.
2. Practitioners: Targeted antimicrobial stewardship programs for clinicians involved in the studies and then extrapolated for institution specific programs. This will demonstrate the impact of the grant funding as we will be able to gather data about prescribing practice before and after education intervention.