Sewage surveillance

We believe sewage surveillance can be a resource-efficient complement to traditional, clinical surveillance as the latter requires analyses of a very large number of individual patient samples. The potential value is particularly apparent in many low- and middle-income countries where clinical resistance surveillance is scarce or even absent. Still, also in countries with well-developed clinical surveillance systems, sewage surveillance can play a role as it has a greater potential to detect rare resistance factors. With adapted approaches, sewage surveillance also allows the discovery of resistance factors that already circulates in pathogens in the clinics but has passed unnoticed by the clinical community.

Quantitative sewage surveillance can be based on either analyses of gene abundances (metagenomics, qPCR) or analyses of isolates. We do both, but have a focus on the latter as it has a much greater potential to e.g. link resistance to a specific bacterial species. We are now in a phase where we are exploring the possibility to expand isolate-based surveillance to other species than E coli. Also, we are also increasing our work in sub-Saharan Africa where we intend to benchmark sewage surveillance with regional clinical surveillance of antibiotic resistance. Most of our work on quantitative sewage surveillance is led by Associate Professor Carl-Fredrik Flach, while Larsson leads the work on discovering new forms of resistance.

Examples of recent papers

Larsson DGJ, Flach C-F. (2021). Antibiotic resistance in the environment. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-021-00649-x  Read-only link: https://rdcu.be/cAQBC.

Flach C-F, Hutinel M, Razavi M, Åhrén C, Larsson DGJ. (2021). Monitoring of hospital sewage shows both promise and limitations as an early-warning system for carbapenemase-producing Enterobacterales in a low-prevalence setting. Water Research. Vol 200:117261. https://doi.org/10.1016/j.watres.2021.117261

Karkman A, Berglund F, Flach C-F, Kristiansson E, Larsson DGJ. (2020) Predicting clinical resistance prevalence using sewage metagenomic data. Communications Biology. 3:711 https://doi.org/10.1038/s42003-020-01439-6

Huijbers PMSC, Larsson DGJ, Flach C-F. (2020). Surveillance of antibiotic resistant Escherichia coli in human populations through urban wastewater in ten European countries. Environmental Pollution. 261:114200.  https://doi.org/10.1016/j.envpol.2020.114200.

Böhm M-E, Razavi M, Marathe NP, Flach C-F, Larsson DGJ. (2020). Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities. Microbiome. 8:41. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00814-z.

Hutinel M, Huijbers PMC, Fick J, Åhrén C, Larsson DGJ, Flach CF. (2019). Population-level surveillance of antibiotic resistance in Escherichia coli through sewage analysis. Euro Surveill. 24(37). pii=1800497. https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2019.24.37.1800497

Huijbers PMC, Flach C-F, Larsson DGJ. (2019). A conceptual framework for the environmental surveillance of antibiotics and antibiotic resistance. Environ Int. 130:104880. DOI: https://doi.org/10.1016/j.envint.2019.05.074