Identification of our collection of 575 bacterial isolates (based on 16S rRNA gene sequencing) indicates we have isolates from 123 different species, including 24 potentially novel species. Whole genome sequence (WGS) information has been obtained for 132 isolates, including representatives of all unique species and the potentially novel isolates. This data will be analysed in year 4. Initial analysis of the first 25 isolates shows that they contain 32 different known antimicrobial resistance (AMR) genes. Nine different tetracycline resistance genes were present and five isolates contained two, and one isolate four, separate tetracycline resistance genes. These isolates were all different bacterial species, isolated from either sheep or deer showing the wide distribution of the same genes in different bacteria. We are continuing to screen this data to identify heavy metal resistance genes and investigate whether these genes are found together in the genomes. Detection of the same genes in different bacterial species, from different animal hosts and ecosystems, provides evidence for the spread of these genes through the environment.

We have so far not detected any transfer of specific resistance genes in lab experiments. Whether this is because gene transfer is not occurring, or because it only occurs at very low frequencies that we cannot detect is unclear. Further analysis of the WGS data of the isolates to identify which resistance genes are located on mobile pieces of DNA, and the distribution of these sequences in our samples will be an alternative way to assess the incidence of gene transfer events. The AMR genes present will also be compared to those identified on pathogenic bacteria isolated by other SEFARI researchers from the same animal samples. This data will be used to model gene transfer through the farm environment. The project is on track to deliver important information on the links between antimicrobial exposure and bacterial resistance and spread through the environment.

Project Impact:

Policy: The antimicrobial resistance work was presented at the Shaping the Science for Scotland’s Food Future conference (April 2024). There were 160 attendees including Scottish Government representatives, policy makers, stakeholders and scientists from Scottish research institutes. The presentation highlighted the collaborative nature of this project that will provide greater impact for all the projects.

Industry, Public and Professional: Samples from pigs had the highest numbers of culturable resistant bacteria, even when farms currently used low amounts of antimicrobials. Sequence analysis indicates that the same resistance genes are present in different bacterial species, isolated from different hosts. This confirms that resident gut bacteria are indeed an important source of resistance genes, and that antimicrobial applications have a lasting legacy.

A few cattle and deer isolates will be included in the global collaborative RUMEN Gateway project led by Queens University, Belfast. This project aims to assemble a freely available sequenced culture collection of the most important rumen anaerobic bacteria. Contribution of our novel isolates adds an important resource and facilitates wider use of these cultures and raises the profile of the project in the scientific community.

Knowledge exchange and other outputs:

This project featured in an episode of the OnFARM Scottish Farming Podcast, in partnership with SERAFI. The episode [Farming and AMR (anti-microbial resistance) https://www.on-farm.co.uk/] highlighted research on AMR in farming, raising awareness among farmers about sustainable livestock management and responsible antimicrobial use (May 2024).

A SEFARI blog Exploiting beneficial bacterial strains to reduce the incidence of pathogens in animals and to promote One Health, has had over 1000 views 

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 (13-15^th 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.

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. 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. In total, 160 anaerobic bacteria resistant to various combinations of tetracycline, erythromycin and streptomycin were purified 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.