Identifying selective cofactors that contribute to the role of the intestinal microbiome as a reservoir of multiple resistance genes transmissible to pathogenic bacteria
Project Lead
Challenges
One of the critical challenges for veterinary and human medicine is the evolution of pathogens resistant to multiple drugs and antimicrobials previously used to treat them. The problem is compounded by the carriage of antimicrobial resistance (AMR) genes on mobile DNA. Transfer of these genes between distinct bacteria from different sources contributes to the environmental spread of AMR. For example, we have found that Campylobacter isolates from animals carry identical tetracycline resistance genes to human commensal bacteria, located on the same mobile DNA. This provides strong evidence for the spread of genes between diverse bacteria from diverse environments.
The concern is that zoonotic pathogens and emerging bacterial diseases may carry multiple drug resistance genes that can spread between livestock and human commensal microbiota, and be acquired by other pathogens. Such transfer of AMR genes between bacteria is impacted by environmental factors including antimicrobial use, the presence of heavy metals and other biocides. It is crucial to understand the effects of external factors on gene evolution and transfer, which allows us to identify risk factors affecting transmission of genes, and the bacteria carrying them, between the environment, animals, and humans.
We do not know:
- Whether the commensal microbiome - the community of gut microbes living in our intestine - is a reservoir of transferable AMR genes
- Whether the same resistance genes and bacteria, are widely distributed in samples obtained from diverse environments
- The frequencies and mechanisms by which AMR genes transfer in both directions between gut, environmental and pathogenic bacteria
- The transmission pathways of AMR genes between bacteria
- How co-selection factors including antimicrobials and heavy metals influence the co-carriage and spread of multiple resistance genes
Questions
- What strategies can reduce the spread of resistance genes and bacteria to protect public health, animal health and reduce the environmental spread of antimicrobial resistance in Scotland?
Solutions
It is vital to understand the contribution of resident intestinal bacteria to the environmental flow of antimicrobial resistance genes. It is also important to understand the role of the environment in determining carriage of AMR in intestinal bacteria.
We are isolating resistant commensal bacteria from diverse sources (cattle, sheep, pigs, deer, wild geese). This allows us to compare the presence of identical resistance genes between non-harmful and pathogenic bacteria isolated from different hosts and different locations. In collaboration with other SEFARI scientists we will determine whether different farming practices affect prevalence, evolution and transfer of AMR bacteria and genes. We will also determine whether the same genes are also present in soil and water samples collected by other SEFARI scientists.
The main objectives of this project are:
- Compare the distribution of identical AMR genes in diverse bacterial species from diverse environmental samples.
- Understand the prevalence of multiple AMR genes within members of the commensal gut microbiota.
- Develop a searchable database containing all available information on individual bacterial isolates to assess linkages between specific genes and distinct bacteria from diverse hosts and environments.
- Determine the role of the commensal microbiome as a reservoir of potentially transferable resistance genes.
- Determine the impact of external environmental factors on carriage of AMR.
- Assess the incidence of gene transfer between pathogenic and commensal bacteria in experiments mimicking conditions in the gastrointestinal tract.
Overall, we are providing information about the reservoirs of transferable multiple drug resistance genes within diverse commensal gut microbiomes. Co-selectable marker genes may increase spread of AMR and lead to the emergence of multiple drug resistant pathogenic bacteria. These findings will provide insights to help reduce the distribution and spread of resistance genes through the environment.
Project Partners
Progress
In the first year we focussed on building our collection of resistant bacteria. Collaborations with other SEFARI researchers enabled us to isolate bacteria from samples that were being investigated in various different ways, maximising the information obtained. For instance the sheep samples were obtained from a study that also collected soil and water samples from the same fields the sheep were grazing in, which will enable us to investigate the contribution of the environment to the prevalence of resistance in the sheep. Samples from deer, sheep, and wild geese were collected, transported to the Rowett Institute and viable multi-drug resistant anaerobic bacterial strains were cultured and identified. Many different species of obligately anaerobic bacteria were isolated from deer and sheep samples while isolates from geese samples were mainly facultative bacteria, able to grow in the presence of oxygen. From three separate deer isolations between 10% and 35% of bacterial colonies grown were obligately anaerobic. Out of 1295 colonies re-purified, 160 anaerobic bacteria resistant to various combinations of tetracycline, erythromycin and streptomycin were isolated from deer samples cultured on selective anaerobic plates. These isolates have been identified based on partial 16S rRNA gene sequences and comprise 28 different bacterial genera, including four novel isolates with no database homologues. The antimicrobial resistance profile of a subset of isolates was determined, showing that several are resistant to multiple antimicrobials including ampicillin, chloramphenicol, ciprofloxacin and amoxicillin.
Publications and other outputs
Leaflet showcasing the work on Antimicrobial Resistance by various Scottish Institutes at the Royal Highland Show (June 2022)
Organised the International Gut Microbiology conference in Aberdeen (June 2023) weblink - https://www.abdn.ac.uk/events/conferences/gutmicro2023/ . The conference included session on use of the microbiome to reduce infectious disease in animals.
Presentations, reports, and other information
A report on AMR in the environment was sent to RESAS for dissemination to external stakeholders (October 2022).
Podcast entitled ‘The Pros and Cons of Antibiotics’ released during Antibiotic Awareness week (Nov 2022).
Weblink - https://www.abdn.ac.uk/events/resources/cafe-connect-1650.php.
During the past year we continued to assemble the culture collection and now have more than 300 obligately anaerobic bacteria isolated from faecal samples collected from deer, cattle, pig, sheep and geese, plus an additional 51 facultative isolates. These bacteria were selected based on resistance to at least one antimicrobial (tetracycline, ampicillin or erythromycin). Most of the bacteria cultured from geese samples were in fact aerobic, with only about 1% able to grow under anaerobic conditions. The geese samples also contained fewest resistant isolates while pig samples contained the highest proportions of resistant bacteria. Further analysis of some deer, pig and sheep isolates revealed that most (28/29 isolates tested) were resistant to two or more antimicrobials. On average deer isolates were resistant to 6 of the 12 antimicrobials tested, while sheep isolates were resistant to 8 out of 12. The level of resistance also varied, with some strains only resistant to very low antimicrobial concentrations (<1µg/ml) and others resistant to high concentrations (>256 µg/ml). Sequence analysis determined that these strains consisted of 81 unique species, including 11 novel, previously unknown species. We are in the process of a more detailed comparison of different isolates from different host species to compare the presence of identical resistance genes across these anaerobic bacteria. The genes present will also be compared to those identified in pathogenic bacteria isolated from the same animal samples by other SEFARI researchers. This data will then tell us about the possible spread of genes through these environments.
Publications and other outputs
Poster presentation at the International Gut Microbiology Symposium (13-15th June 2023).
Guest appearance on Inside Matters podcast with James Mcilroy [ What is a Healthy Gut Microbiome? ]
The Rowett Institute’s Gut Microbiology Group, which include PI Karen Scott, were runners up in the Global grants Award for the research group with greatest impact on Gut Microbiome Research (April 2023). They also gained the UoA Principle’s Award for Excellence (Research Team) in June 2023.
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