The SPARK (Spread of Population-wide Antibiotic Resistance in Klebsiella) project, funded by the JPIAMR instrument of the European Union H2020 programme, seeks to address the complex issue of transmission of antimicrobial resistance genes and strains of Klebsiella pneumoniae between reservoirs and humans. The project is coordinated by Prof Ed Feil (Bath University, UK).
Klebsiella pneumoniae (Kp) is a leading cause of multidrug resistant hospital-acquired infections
globally, and is responsible for an increasing public health burden in the community. In order to control the spread of Kp through targeted surveillance and intervention policies, it is necessary to identify the sources of emergent community and health-care associated infection from the interlinked and varied niches encompassing “the environment”.
To address this, we will sample from multiple clinical, community, agricultural, veterinary and
environmental settings in and around a single town, Pavia, in Northern Italy, and supplement these data with matched samples from France and elsewhere. We will use whole genome sequencing of community (mixed-colony) samples to assay accessory gene abundance and distribution.
This contrasts with the more common approach based on phylogenetic analysis of single colonies, which would be of limited utility over broad environmental scales due to the complexity of transmission chains, environmental dormancy, and high rates of recombination. In contrast, our gene-centric approach provides a much more efficient means to understand ecological adaptation, the distribution of resistance and virulence genes, and to identify key environmental reservoirs from which clinical clones emerge. A key deliverable of this project will be the establishment of a pan-genome database (‘pangenomium’) that will integrate with both existing Kp genome community resources established by project partners (BIGSdb-kp, and wgsa.net).