The need for environmental AMR surveillance

Human and animal pathogens exist both within hosts and within the environments that these hosts live in, including hospitals, veterinary centres, farms and within the community. There is a greater risk of becoming infected (requiring treatment) with a multi-drug resistant organism (MDRO) if a human/animal host has been previously asymptomatically colonised. MDROs such as Carbapenem resistant Enterobacteriales (CREs) and extended spectrum β-lactamase (ESBL) producers, methicillin resistant Staphylococci (including S. aureus (MRSA) and S. pseudointermedius (MRSP)) confer resistance to multiple, important antibiotic groups. Globally, MDROs commonly cause hospital acquired infections (HAIs) and are increasingly being isolated from animals and the environment. AMR was associated with 4.95 million human deaths in 2019. 

Globally, many people live in close proximity to animals. Over half of the world's population is believed to own a pet and many rural and urban families live alongside their farm animals. Over 500 million pastoralists rely on their livestock for food and income. Scientists are becoming more aware of how the relationships between humans, animals and the environment enable the spread of antimicrobial resistant (AMR) organisms. These linkages, often collectively refered to as 'One Health', are vital for researchers to consider when trying to unpick how AMR spreads. Read about how to develop a One Health project here.

Currently there are no standardised tools/guidelines for genomic surveillance of environmental pathogens and AMR genes. To combat this, the Centre for Clinical Microbiology at UCL, led by Dr Linzy Elton, alongside partner sites such as the Royal Free London NHS Foundation Trust, HerpeZ in Zambia led by Dr John Tembo and the Institute for Endemic Diseases in Sudan led by Professor Muzamil Mahdi Abdel Hamid, have been developing the Environmental AMR Genomic Surveillance (EARGS) tool, that incorporates whole genome sequencing (WGS) of clinical and environmental isolates, as well as metagenomics for direct sampling of clinical and veterinary environments. EARGS aims to agnostically identify AMR genes, plasmids and transmission patterns for MDROs across One Health settings.  

So far we have deployed parts of the EARGS pipeline in multiple surveillance studies:

  • A study in Lusaka, Zambia, and Khartoum, Sudan, identified that COVID-19 patients have a greater risk of contracting an MDRO hospital acquired infection (HAI) (Elton et al. 2023). More information about this project can be found on our AMR:COVID page here.
  • A study of hospitalised UK COVID-19 patients showed an increased risk of certain AMR HAIs amongst patients hospitalised with COVID-19 (publication pending).
  • A study taking clinical and environmental WGS and environmental metagenomic samples showed evidence of patient-patient and patient-environment transmission of MDRO resistance genes in hospital settings (publication pending approval).
  • A study identifying AMR genes related to companion animal infections, in a UK veterinary environment using metagenomics (publication pending).

The EARGS pipeline 

We have been developing each section of the EARGS pipeline and aim to Open Access publish the protocol here soon. The pipeline consists of multiple parts:

Sample collection

We have been assessing how best to collect samples to ensure sensitivity and accuracy. For whole genome sequencing of clinical and environmental isolates, we have tested out different sample types (e.g. rectal swabs, nasal swabs, wound swabs) and culturing techniques, such as liquid and selective agar plates. For metagenomic sampling, we have compared surface swabbing with water samples for sensitivity. 

Nucleic acid extraction

We have been testing different extraciton kits. This has been expecially important when it comes to metagenomics, to ensure that the proportions of DNA/RNA we get out represents the proportion of organisms in the original environmental sample (some organisms, such as the Mycobacteria, can be very difficult to extract DNA from, and are therefore often under-represented in metagenomic samples).

Library preparation and sequencing

This pipeline has been developed using Oxford Nanopore Technologies (ONT) MinION device. As well as having a small laboratory footprint and low set up costs (making it a practical choice for resource constrained laboratories), it is also a portable and versatile platform, making it compatible with the One Health surveillance tool we want EARGS to be. You can view tutorial videos we developed as part of the pipeline on our 'sequencing tutorial' pages.

Bioinformatics and data analysis tools

We have been testing out different bioinformatics tools to identify different data analysis pipelines. This is important to ensure data acuracy. The identification of different aspects of AMR (such as the transmission of MDROs) requires different programmes and optimisation.  

Training

So far, the Centre for Clinical Microbiology have trained scientists in the UK, Zambia and Sudan on the EARGS pipeline and some of the videos can be found on our 'sequencing tutorial' pages. We are in the process of developing the complete training materials and will upload them here soon.