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Pandemic Preparedness Capabilities

Pandemic preparedness against antimicrobial resistance through wastewater monitoring


PI(s)/Head responsible for the resource:

Sanna Koskiniemi

Host organisation(s):

Uppsala University

Resource description:

The increasing spread of antimicrobial resistance (AMR) is a serious threat to human and animal health, and a OneHealth approach is needed to reduce the transmission of AMR microorganisms. AMR monitoring is considered essential to assess: (i) the overall AR status in a human population or community; (ii) the risks that AMR evolves and spread across One-Health compartments; (iii) the risk of AMR transmission to humans. The difficulties in global monitoring of AMR are many; ranging from ethical issues regarding human samples to lack of comparable methods available across nations. Recently, wastewater sampling has emerged as an excellent means of monitoring AMR as well as other pandemics. Clear benefits associated with wastewater sampling compared to clinical samples is that arising problems can be detected early and that it reduces bias as monitoring occurs on the whole population rather than a few individual patients. Here we suggest to set up a platform that will allow us to monitor prevalence of AMR in wastewater samples and by adapting computational modelling set up during the Covid-19 pandemic amongst others, we will develop models that will allow us to determine when the prevalence in wastewater reaches levels that indicates elevated risk for the spread of AMR in the clinic. This knowledge at regional and national levels will give the health care indications before the problem arises, allowing preparedness against potential epidemic outbreaks. In the long run, we hope to establish cheap and non-laborious techniques that can be used world-wide, allowing global awareness of upcoming potential problem clones and providing information for decision makers regarding protection of at-risk groups, changes in treatment regimens to avoid selection, increased screening in the clinic etc. The platform will also be an important tool to follow up the effects of interventions. Global AMR monitoring will require international cooperation and coordinated action and here we plan to use the channels of ReAct and Uppsala antibiotic center to implement the techniques in the world. The aim for this project is to set up a platform that will be integrated into the Microbial single cell sequencing platform at the end of the period. The techniques will be developed to increase pandemic preparedness against the silent AMR pandemic, but they will also be of use for many scientific projects regarding microbial evolution and epidemiology that struggle with the same type of problems to connect genes with species.

Research findings:

Sustainable use of antibiotics requires up-to-date information on local prevalence of antibiotic-resistant disease-causing bacteria, here referred to as pathogens. Only with such information can health-care professionals make informed treatment choices and be prepared for emerging pathogens. In this project we have developed a method that allows for early detection of emerging antibiotic resistant pathogens. In our proof-of-principal, we detected pathogenic E. coli bacteria encoding resistance to a last resort antibiotic (carbapenem) in wastewater from Uppsala. Very similar resistant strains were isolated at the Uppsala university hospital during the same time period, suggesting that our method can be used to monitor the presence of pathogenic, resistant bacteria in a population through wastewater. This information can be used to detect when new pathogens and/or resistant bacteria emerge in different regions in Sweden. Thus, the developed platform could be used for early warnings to hospitals and primary care units of arising problems that require new treatment regimens.

During development of the bioinformatic pipeline used in this project, we identified numerous problems with existing metagenomic pipelines. These existing pipelines are used by most researchers in the field today, which could be problematic. The pipeline could for example not identify species correctly, either due to incomplete databases or due to problems with the algorithms. This is problematic, if you intend to use the pipeline to determine which species are present and if these are resistant to a specific antibiotic and pathogen. Thus, even though the output from the pipeline looks correct, the conclusions drawn from this data will be wrong. The problems became obvious in our project as we performed traditional growth- based methodology in parallel with metagenomics, which is not done in most projects. We believe that our findings are important for researchers using these existing pipelines, as well as governmental authorities, as both need to be aware of these methodological problems to not act on false conclusions.

Finally, we unexpectedly found a critical risk for Colistin resistance development among Gram-negative bacteria in the Uppsala region. Colistin is a last resort antibiotic used for Gram-negative bacterial infections when no other options remain. We detected presence of E. coli encoding the mcr Colistin resistance gene in Uppsala wastewater in 2024 and onward. This was unexpected, as no reports regarding Colistin resistance had been made from the clinic. We were able to confirm that Colistin resistant E. coli were and are indeed present in the wastewater by traditional methods and whole genome sequencing. The mcr resistance gene is typically encoded on transferrable plasmids, meaning that the resistance can easily be transferred to pathogens upon changes in selection pressure. For example, if the use of Colistin is suddenly required because of an increased prevalence of multi-drug resistant Klebsiella or Acinetobacter as during the Uppsala university hospital outbreak in 2005-2010, this will rapidly select for Colistin resistant pathogens. Such pathogens, are likely already to begin with multi-drug resistant and by acquiring Colistin resistance, they likely become untreatable. Thus, we believe that our results support the use of wastewater-based epidemiology in identification of potential risks regionally.

Taken together, we believe that this pilot-project has shown the importance of performing wastewater-based monitoring of antibiotic resistance and bacterial pathogens regionally in Sweden. Our pipeline allows for creating a “now-cast” of the implied clinical risk at site, which could help health care professionals and regional authorities to take important decisions regarding treatment choices and screening efforts. Our results also urge for the development of better bioinformatic methods for analysis of metagenomic data as well as more comprehensive databases of bacterial genomes, to reduce wrongful conclusions regarding emerging threats. Our pilot-project focused on one problematic pathogen, in one particular region, and we believe that future work should focus on setting up pipelines for other emerging bacterial threats in other regions of Sweden.

Impact on prepardness for future pandemics:

Antimicrobial resistance (AMR) is a growing global health issue. Modern health care depends on the availability of efficient antibiotics, not only for direct treatment of bacterial infections, but to ensure the safety of complicated medical interventions, including advanced surgery, cancer chemotherapy, and pre-term delivery of neonates. Sustainability of antibiotic usage is contingent on up-to-date information on local epidemiology of AMR, enabling informed treatment choices and preparedness for emergent pathogens.

The dissemination of AMR and emergence of novel types of resistance are facilitated by environmental contamination of antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes, all emerging environmental pollutants, recognized as an immediate public health concern. Therefore, monitoring across all One Health-compartments is essential to truly estimate future risks of AMR pathogens. However, the direct hazard constituted by these pollutants is difficult to quantify and clinical risks, in both short- and long-term, are essentially unknown. Implementation of our AMR surveillance method will provide guidelines and incentives for reducing AMR across one Health Settings while aiding healthcare preparedness for emerging AMR.

Our pilot clearly shows that wastewater-based monitoring can be used to detect emerging threats as well as for an overview of the prevalence of AMR pathogens across One Health compartments. A standardized, global wastewater-based method would be a valuable tool for monitoring and understanding the clinical impact of AMR in different regions. In the long- term, we need cheap, non-laborious, standardized techniques that can be used worldwide, for global awareness of upcoming high-risk pathogens. Such information could then guide decision-makers regarding protection of at-risk groups, changes in treatment regimens to avoid selection and treatment failure, and increased targeted screening in the clinics. For example, our findings that the Uppsala population is a reservoir for transferrable Colistin resistance could be used for decisions regarding where to hospitalize patients suffering from multi-drug resistant infections that require Colistin treatment. Or, it could be used for screening efforts among hospital staff to prevent transmission to patients that require Colistin treatment. Importantly, we did not intend to look for Colistin resistance specifically as there have been no reports of Colistin resistance in the clinic. Thus, our findings support that this pipeline can be used for detection of novel threats, not yet emerged in the region.

The prevalence of Colistin resistant strains is likely not restricted to Uppsala. Thus, this information should be used to monitor other regions, to get a comprehensive view of the arising threat of Colistin resistance in the Swedish ecosystem. Having a national monitoring pipeline set up will allow us to determine when the prevalence in wastewater reaches levels that indicates elevated risk for the spread of AMR in the clinic. This knowledge at regional and national levels will give the health care indications before the problem arises, allowing preparedness against potential epidemic outbreaks. In the long run, the platform will also be an important tool to follow up the effects of interventions. Finally, wastewater-based monitoring of AMR is also well in line with the recent decision in the EU parliament, which calls on member states to set up national facilities to screen for AMR bacteria in wastewater, refer here. Of importance here is also the problems identified with existing metagenomic pipelines, which could drive researchers, health care workers as well as governmental authorities to reach the wrong conclusions regarding the current situation. Our results are important for developing the next generation of metagenomic pipelines for wastewater-based monitoring that are essential for an efficient global preparedness for emerging pandemics across One Health compartments.

Contact information:

Sanna Koskiniemi
Associate Professor
Email: sanna.koskiniemi@icm.uu.se