Antimicrobial resistance transmission in the environment: the role of soil as a reservoir and conduit in the transmission of AMR

Antimicrobial resistance (AMR) is an on-going global health threat; and similar to the SARS-CoV-2 pandemic, has a significant impact on public health and the global economy. If no action is taken, an estimated 10 million deaths per annum will arise from infections caused by resistant microorganisms by 2050^1,2. It is now widely recognised that global efforts to control the spread of resistant microorganisms must utilise a One Health-based approach. This approach permits a collaborative examination of how resistant pathogens can spread between humans, animals and the environment³.

The contamination of the environment, specifically water bodies and soil, by antimicrobials, including antibiotic resistant bacteria (ABR) and antibiotic resistance genes (ARG), is attributable to human activity⁴. These include the disposal of human and animal waste^5,6, pharmaceutical manufacturing waste⁷, and use of antimicrobials as pesticides in crops^8,9.

The presence of ABR and ABG in the environment increases the potential for onwards dissemination, colonisation and establishment of infection in human and animal populations⁴.

Many bacteria which are implicated in important, and recalcitrant human and animal infections have been isolated in water bodies and the soil¹⁰. Amongst these are Enterobacteriaceae, which are ubiquitous and members are commensal and/or pathogenic gut dwellers (enteric bacteria). Species such as E. coli and Klebsiella spp. are commonly associated with important resistance genes, including extended spectrum  b-lactamase (ESBLs) and carbapenemases (CPEs) that confer resistance to third generation cephalosporins and the carbapenem antibiotics, respecively¹¹. Although there is ample evidence-based information on the global spread of these clinically important resistant enteric bacteria in human^12,13 and animal populations^14,15, the potential for soil as an environmental reservoir is understudied. There are gaps in our understanding of the impact of ABR and ABGs in the soil and the risk this poses to human and animal health¹⁶. Thus, more research is needed to address these knowledge gaps and evaluate the risks to human, animal and environmental health¹⁷.

Therefore, this PhD project will use a multi-method approach to evaluate the importance of the soil as a reservoir and conduit for the transmission of antibiotic selected resistant enteric bacteria and selected b-lactamase genes (including ESBLs and CPEs). Specifically, the student will receive training in the use of a selection of culture- and PCR-based profiling, 16sRNA, single-genome and metagenome sequencing and analyses to answer the research questions.

Testable hypothesis -The project will test the hypothesis that soil stratification/structure facilitates the persistence of ABR and the ARGs they carry. On perturbation, this persistence effect is reduced, potentiating the loss and subsequent spread of ARGs via host ARB.

This will be achieved by using an in vitro soil strata model and soil and water samples obtained from large commercial farms to evaluate the following:

1. How effective is soil as a reservoir for AMR?
   1. Does AMR persist in the soil?
   2. Does AMR spread from the soil to the wider environment, and onwards to humans and animals?
   3. What components of soil are important for AMR transmission?
2. The role in facilitating onward transmission to humans and animals?
   1. How does perturbation affect distribution of AMR in the soil?
   2. Does (a) above induce dissemination/how does transmission occur?

This project will equip you with key microbiology, molecular biology and bioinformatics (bacterial genome analyses and metagenomics skills). You will be part of large research groups jointly working on antimicrobial resistance across the Schools of Biosciences and Medicine and Veterinary Medicine and you will have the opportunity to make an impact on a project that has an international and interdisciplinary outlook.

First Class or Upper Second-class BSc or in Master’s level degree (or international equivalent, merit or disntnction) in Microbiology, Molecular Biology, Biomedical Sciences, Veterinary Biosciences or related fields.

Prior experience in research or industry may also be acceptable.

IELTS Academic: 6.5 or above (or equivalent) with 6 in each individual category.

Dr Chinyere Okoro

Professor Roberto La Ragione