Skip to main navigationSkip to main content
The University of Southampton
Biological Sciences

Research project: Occurrence and horizontal gene transfer of carbapenemase and ESBL genes in soil microbiomes

Currently Active: 

To investigate antibiotic resistance in soil microcosms and gene transfer between the soil microbiomes and pathogenic bacteria.

Rhizosphere of rice plants
Rhizosphere of rice plants

This project aims to understand the potential of environmental reservoirs and transmission of antimicrobial resistance in members of soil microbiomes and between transient human and animal pathogens entering the environment. It also seeks to understand if horizontal gene transfer (HGT) occurs successfully between potential pathogens in the various soil microbiomes and complex matrices encompassing clay, loam and sandy soils.

The work will utilize modern molecular biology and genomics to screen microbiome populations and defined third generation extended spectrum beta lactamase ESBL and fourth generation carbapenemase Escherichia coli and Klebsiella pneumoniae donor strains, with an E. coli sensitive strain as the recipient. This study will help identify the specific environmental drivers of the HGT and beta lactamase selection processes including implications for both anthropogenic (animal husbandry, human wastewater disposal) and non-anthropogenic (wild animal and bird faecal ingress) drivers.

Cultivation approaches have identified identical ARGs in both soil microbes and clinical pathogens (Forsberg et al. 2012. Science 337: 1107–1111), indicating that transfer occurs between commensal and pathogenic bacteria. The direction of transfer is not known, so the question remains if pathogens have obtained the ARGs from soil microbes or vice versa. In contrast, a cultivation-independent approach showed that the majority of ARGs in soil are distinct from those found in pathogens and are associated with specific bacterial phyla, indicating they are not typically mobile (Forsberg et al. 2014. Nature 509: 612–616.). The contrast between cultivation and cultivation-independent studies highlights a cultivation bias and a need for alternative methods to investigate AMR in soil.

Detection of bla CTX-M-15 in possible transconjugants
Detection of bla CTX-M-15 in possible transconjugants

Stable isotope probing (SIP) is a cultivation-independent approach to target specific microorganisms in environmental samples. These techniques are necessary since currently only the minority of microbial species can be grown and isolated on laboratory media. The principle behind SIP is to add an artificial growth substrate labelled with a stable isotope to the environmental sample (e.g. (13C); only those microorganisms that use the substrate will become labelled by metabolising the substrate and incorporating the isotope into their biomolecules. Labelled nucleic acids ([13C]DNA or ([13C]RNA) can be separated from the unlabelled community DNA/RNA by buoyant density ultracentrifugation and then sequenced to identify the target microorganisms.

Principle Investigator & Supervisor: Professor Bill Keevil
Funding provider: NERC
Funding duration: September 2016-June 2018

Affiliated research group

Institute for Life Sciences (IfLS)
Network for Anti-Microbial Resistance and Infection Prevention (NAMRIP)


E. coli  CTX-M plasmid Gołębiewski et al. 2007
E. coli CTX-M plasmid Gołębiewski et al. 2007
K. pneumoniae NDM-1 plasmid Yohei Doi et al
K. pneumoniae NDM-1 plasmid Yohei Doi et al

Related research groups

Environmental Biosciences
Share this research project Share this on Facebook Share this on Twitter Share this on Weibo
Privacy Settings