Periodic Reporting for period 1 - REPARES (Research platform on antibiotic resistance spread through wastewater treatment plants) Reporting period: 2019-10-01 to 2020-12-31 Summary of the context and overall objectives of the project In the last decades, we have observed progressively reduced efficacy of antibiotic treatment of common bacterial infectious diseases. This is mainly due to the increased presence of bacteria resistant to antibiotics (ARB). Pathogenic bacteria can acquire antibiotic resistance through random gene mutations under the stress caused by exposure to antibiotics or other antimicrobial agents such as disinfectants, UV light etc. Otherwise, antibiotic resistance can be spread by horizontal gene transfer, i.e. the transfer of genetic information (antibiotic-resistant genes – ARGs) between individual bacteria cells.Municipal wastewater treatment plants receive ARB and ARGs in the wastewater from hospitals, residential, industrial, and agricultural areas. They also receive great loads of antibiotics and other pharmaceuticals, because between 50 and 90% of antibiotics dispensed to humans or animals are excreted intact or in metabolite forms via urine and feces. The additional load comes from excessive consumption and disposal of unused antibiotics. The presence of pharmaceuticals promotes the selection of resistant bacteria strains occurring in the activated sludge (i.e. mixed bacteria culture used for biological wastewater treatment) and may later be released to the environment.The World Health Organization qualified the antibiotic resistance development to the major global threats to society and advised to identify and control the hot spots (such as wastewater treatment plants) causing antibiotic resistance spread. However, due to methodological inconsistencies, the monitoring of ARB performed by different groups around the world cannot be easily compared which jeopardizes the global efforts to mitigate antibiotic resistance development.REPARES aims to:• Increase collaboration and knowledge exchange among different stakeholders in the field of antibiotic resistance (academic institutions, industries, governmental agencies, policymakers etc.) through establishing web-based communication platforms (https://repares.vscht.cz/).• Harmonize the methodological approaches (standard operational procedures, “golden standards”) for ARGs measurement in wastewater and sewage sludge and organize inter-laboratory comparative study.• Improve the access of other researchers to the genomic data related to ARB occurring in wastewater through establishing a publicly available database embedded into a globally renowned MiDAS database developed by one consortium member (Aalborg University).• Utilize the expertise of world-leading research groups involved in the project (TU Delft, Wetsus, Catholic University of Porto, Aalborg University, and the University of Warsaw) to train junior researchers mainly at UCT Prague (project coordinator). Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far Currently, we are preparing 4 papers within the REPARES project. These papers are based on the short secondments carried out by junior researchers and on the work done during Seminar 1 on PCR methodology. Two short research visits from UCT were organized in the first period of the REPARES project. Aleksandra Milobedzka did her short research visit at UCP with prof. Célia M. Manaia and Dana Vejmelkova did her short research visit at Wetsus. These visits, even though taking place largely during the first period of COVID-19-related restrictions, will fruit in at least two joined papers and for Dana Vejmelkova started further cooperation that continued by virtual soft-skills training as she until now participates in Wetsus team meetings and performs further research.In the first reporting period, one seminar was organized - Seminar 1 - Impact of DNA Extraction on DNA Quality and Molecular Analytical Outputs was organized at TU Delft (in M4, January 2020). By the time of writing this periodic report, Seminars 3 and 4 were already organized by UCT in January 2021.Organizing the shadowing visits has been challenging under the COVID-19 restrictions. However, Dana Vejmelkova is currently undergoing online soft-skills training as she participates once or twice a week at the video meetings of the Wetsus team. Similar online training is currently being organized for Sabina Purkrtova (UCT) at TUD.Summer school on transferable skills was partially organized in November 2020 (M14). Since it needed to be online due to COVID-19, only half of the seminar was done in November and the second half was done in April 2021 (M19). So far, two international research projects were submitted within the consortium: project WISE@ARC within the framework of JPI Aquatic pollutants and project CHEMBIOSE within the framework of European Green Deal H2020 RIA LC-GD-8-2-2020 (TUD, UW, UCP, and UCT involved, submitted on January 26, 2021). The submission of these projects was already an intensive training of UCT’s researchers involved (mainly Jan Bartacek and Sabina Purkrtová) in project submission. Still, a dedicated workshop on proposal submission is planned for August 2021.During Seminar 1, one company participated (Future Genomics Technologies, Leiden, Netherlands) by giving a lecture. In joined seminars 3 and 4 (that took place in January 2021), again one non-academic institution (NIPH CZ - National Institute for Health Protection) was actively involved through lecturing.We performed the first phase of an inter-laboratory study based on standard methodology established within the consortium at a joint workshop in December 2019 (M3) in Porto. The second phase of the study is currently being planned and its outcome will be a standard methodology for ARG’s detection in wastewater.The online database embedded in the MiDAS platform has been established and put into operation by a joint effort of UCT and AAU see https://midas.programming.cool/guide/antibiotic-resistance.The promoting activities (open summer school, papers publishing, operation, and promotion of the database) are mainly planned for the second part of the project. But we already established the web-based platform (https://repares.vscht.cz/) and we produced two newsletters where we actively inform about new ARG-related events and researches taking place. We also published 1 educational YouTube video in Czech and English mutations (https://www.youtube.com/channel/UCNkFASNumnK-wSxtwkgN0Mw) Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) REPARES aims at advancing the European community‘s know-how on antibiotic resistance across sanitation waterways, namely improving methodology so that data published worldwide are better comparable. Also, we aim to offer better accessibility of metagenomic data through operating the MiDAS-based database. REPARES acts as an essential vector to disseminate information on antimicrobial resistance spread within European WWTPs beyond science and technology in order to reach the non-academic community by means of open events, popularization publications, and operation of the REPARES web platform. Factsheet of REPARES
