CARE: Cross-sectoral framework for quality Assurance Resources for countries in the European Union
Proficiency testing (PT), or external quality assurance (EQA) schemes, is an integrated part of quality assurance management for laboratories within the field of human, food, and animal microbiology. Reference materials (RM) for microbiological analyses on zoonotic pathogens are available in the context of reference laboratories (e.g. EURL’s) but no mechanisms are in place at EU level combining the reference collections linked to specific reference functions and sectors. Similarly, the culture collections and microbial Biological Resources Centres (mBRCs) and associated data is highly fragmented among the Member States. At EU or national level, risk assessment and management are highly dependent on the availability and quality of data on animal populations, food and feed consumption. The quality and availability of the demographic data including those for food consumption for risk assessment differs between countries.
Thus, the CARE project focused on developing new One Health concepts for PT of laboratories, reference materials and quality/availability of demographic data. The CARE project developed new proficiency testing schemes that can be used cross-sectorally and thereby used to evaluate the capacity to manage foodborne problems from a One Health perspective. Furthermore, the project provided insight into available and desirable RM, identifying sources of both strains and genomic data, including the field of antimicrobial resistance, provided by reference laboratories and other relevant sources such as online repositories and national collections. There was a focus on the visibility of the reference material and data associated with the scientific community. The emphasis was placed on the availability and sustainability of this reference collection in order to contribute to the long-term needs of European research. CARE will also aim to disseminate more widely the information about the accessibility not only of the reference collection but also of CARE partner microbial collections. Lastly, CARE further assessed the quality and availability of the demographic data and focused on how to improve and make the data better by raising awareness of EU authorities collecting and organising demographic data.
In CARE, three new partners, ISCIII in Spain, BIOR in Latvia, and RUOKA in Finland joined the CARE consortium in 2021 and were active and included in the CARE activities contributing to this report.
The work in WP1 focused on the three PT/EQA trials conducted and provided individual feedback to all participants. The final EQA reports of W1-T2-ST1, W1-T2-ST2, and W1-T2-ST3 were finalised and W1-T2-ST1 submitted a scientific journal.
A template for planning, execution, and evaluation of cross-sectoral PTs was developed by WP1. The template covers all aspects to comply with ISO/IEC 17043 conformity assessment – general requirements for PT providers. The template contains guidance on the general considerations that should be taken before PT is executed. The template was evaluated using pilots from current project as examples.
The work in WP2/ WP3 focused on the extended analysis of the identified genomes for AMR, virulence and other typing regimes. A Web catalogue dashboard was developed to ensure visibility and accessibility of the reference materials. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) reference spectra were produced for Campylobacter, Yersinia and Salmonella strains in order to set up and share reference libraries. A sustainable development plan for the CARE collection was developed to ensure accessibility of reference material after the closure of CARE.
A risk assessment survey on relevant (meta-)data in relation to quantitative microbial risk assessments was conducted by WP4 shared with WP2 and WP3 and stakeholders to assist by increasing the accessibility of data but also to avoid duplication. Thus, feeding into the quantitative microbial risk assessment analysis on data originating from the last five years and provided by 19 OHEJP members or stakeholders including those from ORION and RADAR. In addition, a user guide for accessing relevant data for risk assessment was developed as a R software tool “rStainSelect” to ease the process of selecting suitable reference strains based on exposure and risks. Thus, the User guide and R software contribute to and support the developed strategy by EU authorities to raise the awareness of relevant reference material microbial risk assessment analysis.
- A large collection of well-characterised reference strains of food-borne pathogens (>2500 strains) available for scientists and laboratories to use.
- The three distributions of well-characterised WGS data from clustering and non-clustering Campylobacter, Listeria monocytogenes, and Salmonella isolates can be used to evaluate cluster detection pipelines in the future.
- Guidance on cross-sectorial proficiency tests/external quality assurance.
- Guide for accessing relevant data and models for quantitative microbial risk assessment available here
Guillier, L., Palma, F., Fritsch, L. (2022). Taking account of genomics in quantitative microbial risk assessment: what methods? what issues? Current Opinion in Food Science. 48, 100922. DOI: https://doi.org/10.1016/j.cofs.2022.100922
Mistou, M-Y. (2022). OHEJP CARE: foodborne pathogens collection and cross-sectoral PT. Oral presentation at 17th EURL- Campylobacter Annual meeting, Sigtuna, Sweden. 27 September 2022.
Lahti, E. (2022). CARE Pilot Proficiency Test/External Quality Assessment on detection and characterization of bacterial foodborne pathogens. (2022). Oral presentation at 17th EURL- Campylobacter Annual meeting, Sigtuna, Sweden. 27 September 2022.
Boel, J., Mistou, M-Y., Guillier, L. (2022). Oral presentation at OHEJP JIPs CARE, MATRIX, OH-HARMONY-CAP closing meeting, Copenhagen Denmark. 20 September 2022.
Brisabois. (2022). Presentation of the OHEJP CARE project with a focus on the inventory of reference materials and database at the Anses internal reference meeting, Maisons-Alfort, France. 19 May 2022.
Shah, F., Boniotti, M-B., Brisabois, A., Chesneau, O., Clermont, D., Helloin, E., Hendriksen, R., Michelacci, V., Mistou, M-Y. and the OH-EJP CARE consortium. (2022). The CARE collection, an open panel of microbiological reference materials dedicated to zoonotic and foodborne bacterial pathogens. Poster presentation at OHEJP ASM, Orvieto, Italy. 11-13 April 2022.
Boel, J., Hallam, S., Marzęta, M. L., Johnson, P., Torpdahl, M. (2022). Cross-sectorial one health proficiency test for cluster detection of Campylobacter, Salmonella, and Listeria monocytogenes based on whole genome sequencing. Poster presentation at OHEJP ASM, Orvieto, Italy. 11-13 April 2022.
Lahti, E., Blom, L., Riedel, H., Karamehmedovic, N., Heydecke, A., Garcia Fernandez, A., Lucarelli, C., Delibato, E., Sjögren, I., Ring, I., Boel, J., Lundin, K., Veldman, K., Wijnands, L., Ugarte Ruiz, M., Denis, M., Torpdahl, M., Kwit, R., Hendriksen, R., Jernberg, C. (2022). A cross-sectional pilot proficiency test/external quality assessment on detection and characterisation of food-borne pathogens. Poster presentation at OHEJP ASM, Orvieto, Italy. 11-13 April 2022.
De Oliveira Mota, J., Aarts, H., Guillier, L., Desvignes, V., editors. (2021). Identification of data currently used in quantitative microbial risk assessment. Poster presentation at OHEJP ASM, Copenhagen and online. 9-11 June 2021.
De Oliveira Mota, J., Redondo, H. G., Bergis, H., Poisson, S., Dubuisson, C., Sanaa, M., et al., editors. (2021). The Third French Individual and National Food Consumption (INCA3) Survey 2014–2015 and data for microbiological risk assessment: Models for domestic refrigerator temperatures. Oral presentation at 16th Agro-Industry and Statistical Methods Congress (Agrostat eConference 2021). 14-15 September 2021.