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# DMP of project "Decontamination measures to restore facilities and the environment after a natural or deliberate re-lease of pathogenic microorganisms"

Jean-Claude Manuguerra

► To cite this version:

Jean-Claude Manuguerra. DMP of project "Decontamination measures to restore facilities and the environment after a natural or deliberate re-lease of pathogenic microorganisms". Institut Pasteur. 2025. pasteur-05201924v2

HAL Id: pasteur-05201924

https://pasteur.hal.science/pasteur-05201924v2

Submitted on 6 Aug 2025

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# DMP of project "Decontamination measures to restore facilities and the environment after a natural or deliberate re-lease of pathogenic microorganisms"

Plan de gestion de données créé à l'aide de DMP OPIDoR, basé sur le modèle "ANR - DMP template (english)" fourni par Agence nationale de la recherche (ANR).

## Plan Details

**Plan title** DMP of project "Decontamination measures to restore facilities and the environment after a natural or deliberate re-lease of pathogenic microorganisms"

**Version** First version

**Fields of science and technology (from OECD classification)** Biological sciences

**Language** eng

**Creation date** 2022-02-28

**Last modification date** 2025-08-06

**Identifier**

**Identifier type** HAL Id

## Project Details

**Project title** Decontamination measures to restore facilities and the environment after a natural or deliberate re-lease of pathogenic microorganisms

**Acronym** DEFERM

**Abstract** The aim of the project is work along different case scenarios in order to address concrete procedures and processes of first responders with actual political focus based on threats caused by pathogenic microorganisms. The scenarios include accidental, deliberate or natural release. This focus grants us the possibility to draw on German and French expertise on first responder side and harmonize procedures between the first responders. We will address one of the capability challenges mentioned frequently after exercises and also in EU projects such as FIRE-IN (www.fire-in.eu). First responders are in the spotlight of this project. Main focus will be on the recovery phase including decontamination measures to restore facilities and the environment, an aspect that is important but still a bottle neck in operations. So far, no clear recommendations or standard operational procedures have been developed for such scenarios in Europe. In order to fit that goal, the project addresses two interconnected issues: the improvement of operational processes and the (further) development of technical methods or devices for detection and decontamination. The operational processes themselves will be explored in two directions. On the one hand, based on the two scenarios, their embedding in institutional and legal structures of biological emergency response will be examined in a Franco-German comparison (referring to
responsibilities, internal alarm chains, population warning, reporting channels, deployment of the operational organisation etc.). At the other hand the safety culture of the responsible first responders will be investigated. Referring to the technological developments in automated detection, mirofluidic cartridges based on nucleic acid analysis will allow for rapid, sensitive and specific identification and quantification of the pathogens. This enables the development and evaluation of whole procedures and technical processes focussed on the operational tactical part and the approach in a societal dimension. For the operational tactical level to pave the ground for a larger test scale on a joint French-German exercise, learning about procedures, basic investigations will be performed in small up to large work space. The work will be focused on the relevant procedures for the CBRNE scenarios "technical accident during transportation of pathogens" and "accidental release of pathogens from a production facility". The aim is to identify relevant parameters for the development of operational process data. This will help to elaborate a parameter map for decontamination processes, in order to respond adequately to biological threats. Additionally, procedures for special decontamination requirements, like different materials in sensitive rooms to be recovered, as well as vehicle decontamination (here we use existing equipment) will be developed and evaluated in a test environment. Finally, a scale-up to a large room will be investigated, and procedures will also be developed and evaluated in a test environment in order to develop recommendations to be applied in possible scenarios posing biological threats.

## Funding

* French National Research Agency : ANR-20-SEBM-0005

* French National Research Agency : ANR-20-SEBM-0005

**Start date** 2020

**End date** 2024-12-31

## Partners

* Institut Pasteur

* CEA CENTRE VALRHO

* CETEP

* ADEMTECH

* Bouches-du-Rhône Fire department

* Centre de sociologie de l'innovation (i3)

* Institut Pasteur

* CEA CENTRE VALRHO

* CETEP

* ADEMTECH

* Bouches-du-Rhône Fire department

* Centre de sociologie de l'innovation (i3)

## Research outputs :

1. WPC - Simulation with Bacterial and Viral Pathogens (Dataset)

2. WPA - Conception - Scenario development (Dataset)

3. WPB - Detection System (Dataset)

4. WPF - Decontamination Procedures and Evaluation (Dataset)

5. WP G - Operational and Tactical System Evaluation (Dataset)
## Contributors

<table><thead><tr><td>Name</td><td>Affiliation</td><td>Roles</td></tr></thead><tbody><tr><td>BORSELLI Diane</td><td>SDIS13</td><td><ul><li>Personne contact pour les données (Workpackage A)</li></ul></td></tr><tr><td>GABOYARD Manuel</td><td>ADEMTECH</td><td><ul><li>Personne contact pour les données (Workpackage B)</li></ul></td></tr><tr><td>GAS Fabienne</td><td>CEA</td><td><ul><li>Personne contact pour les données (Workpackage F)</li></ul></td></tr><tr><td>GUY Charlotte</td><td>Institut Pasteur</td><td></td></tr><tr><td>MANUGUERRA Jean-Claude -<br><a href="https://orcid.org/0000-0002-5202-6531">https://orcid.org/0000-0002-5202-6531</a></td><td>Institut Pasteur</td><td><ul><li>DMP manager</li><li>Personne contact pour les données (Workpackage C)</li><li>Project coordinator</li><li>Project coordinator</li></ul></td></tr><tr><td>MEYER Morgan</td><td>Mines-Paristech</td><td><ul><li>Personne contact pour les données (Workpackage G)</li></ul></td></tr></tbody></table>
# DMP of project "Decontamination measures to restore facilities and the environment after a natural or deliberate re-lease of pathogenic microorganisms"

## WPC - Simulation with Bacterial and Viral Pathogens

### 1. Data description and collection or re-use of existing data

#### 1a. How will new data be collected or produced and/or how will existing data be re-used?

Laboratory experiments will be realized to describe the sensitivity of model microorganisms against various decontamination methods. Virus/bacteria stocks will first be produced, aliquoted and stored until use.

Infectious titers data are measured with different methods adapted to each microorganism:

* Impedance measurement with a XCELLigence DP system and a RTCA software

* TCID50

* Plate counting (colonies/lysis plaques)

Data are acquired and registered on computer or first recorded in laboratory notebooks before replication in computer files.

Excel will be used for data management, graph representations and data analysis.

#### 1b. What data (for example the kind, formats, and volumes), will be collected or produced?

The data collected or produced are:

* textual data (pdf, doc, txt format) describing experimental settings

* tabulated numerical data d (xls, csv format) describing decontamination efficacy

* pictures or videos (jpg, png, pdf, mp4 format) of decontamination devices and procedures

The expected volume of this datased is 2 Gb.

### 2. Documentation and data quality

#### 2a. What metadata and documentation (for example the methodology of data collection and way of organising data) will accompany the data?

The following metadata will be provided:

* Date

* Experimenter name

* Bacteria/virus stock identifier

* Environmental conditions (temperature, hygrometry, material to be decontaminated)

* Dose of disinfectant (concentration or fluence or other suitable unit)

* Exposure duration or contact time

* Sampling method

* Purification method

* Infectivity measurement method

A documentation describing in detail the methods of sampling, purification and titration will be provided.

The data will be organized in two main files:
* "Methods" containing all operating procedures

* "Results" declined in subfolders, each related to a decontamination method.

Each file is named with: date and name of the microorganism and decontamination method. All info is separated by underscore.

**2b. What data quality control measures will be used?**

In order to guarantee the quality of the data, various measures are implemented:

- Biological (distinct samples) and technical (repeated measurements) replicates

- Regular review of data with co-investigators

**3. Storage and backup during the research process**

**3a. How will data and metadata be stored and backed up during the research?**

During the research project, data and metadata will be stored in secure internal Pasteur servers in a storage space dedicated to the project and accessible to all collaborators of the unit involved in the project.

**3b. How will data security and protection of sensitive data be taken care during the research**

All collaborators of the Pasteur Institute involved in the project will have access to the data. As this dataset is not confidential, it does not need to be protected in a secure repository

**4. Legal and ethical requirements, code of conduct**

**4a. If personal data are processed, how will compliance with legislation on personal data and on security be ensured?**

Not applicable

**4b. How will other legal issues, such as intellectual property rights and ownership, be managed? What legislation is applicable?**

Results are owned by the Party that generates them. Joint ownership is governed as described in the consortium agreement.

During the Project and for a period of 1 year after the end of the Project, the dissemination of own results by one or several Parties shall be governed by the Grant Notifications subject to provisions described in the consortium agreement.

**4c. What ethical issues and codes of conduct are there, and how will they be taken into account?**
All the partners are comminted to ensure the quality, the independence, transparency and neutrality of the results in accordance with French and German legislations and with international ethical standards, specifically with the european code of conduct for research integrity.

# 5. Data sharing and long-term preservation

**5a. How and when will data be shared? Are there possible restrictions to data sharing or embargo reasons?**

Until publication and sharing, raw data and dataset will be accessible only to the partners.
At the end of the project data will be deposited in a data repository (such as Zenodo) with restricted or open access.

**5b. How will data for preservation be selected, and where data will be preserved long-term (for example a data repository or archive)?**

Data will be stored during the maximum allowed by the Institut Pasteur storage allowance capacity and the repository chosen to publish the data.

**5c. What methods or software tools are needed to access and use data?**

The data will be either accessible via a repository or requests handled directly. The data are in open formats and therefore interoperable.

**5d. How will the application of a unique and persistent identifier (such as a Digital Object Identifier (DOI)) to each data set be ensured?**

A DOI will be automatically assigned to each dataset if the Zenodo repository is chosen at the end of the project to share and preserve the data.

# 6. Data management responsibilities and resources

**6a. Who (for example role, position, and institution) will be responsible for data management (i.e. the data steward)?**

Not applicable

**6b. What resources (for example financial and time) will be dedicated to data management and ensuring that data will be FAIR (Findable, Accessible, Interoperable, Re-usable)?**

Not applicable
# WPA - Conception - Scenario development

## 1. Data description and collection or re-use of existing data

**1a. How will new data be collected or produced and/or how will existing data be re-used?**

The development of the expected scenarios was based on the literature of past accidents in Europe.

The final proposal is the result of a collaborative work between the German and French first responders (Dortmund firemen, THW and SDIS 13) during the WP A.

The data will be reused for scenario implementation during WP G (Operational and Tactical Systems Evaluation).

**1b. What data (for example the kind, formats, and volumes), will be collected or produced?**

The data produced are two scenarios of biological contamination. A first one at small scale and a second one at large scale.

## 2. Documentation and data quality

**2a. What metadata and documentation (for example the methodology of data collection and way of organising data) will accompany the data?**

Not applicable

**2b. What data quality control measures will be used?**

Not applicable

## 3. Storage and backup during the research process

**3a. How will data and metadata be stored and backed up during the research?**

During the research project, data and metadata will be stored in secure internal SDIS 13 servers in a storage space dedicated to the project and accessible to all collaborators of the unit involved in the project.

**3b. How will data security and protection of sensitive data be taken care during the research?**
As this dataset is not confidential, it does not need to be protected in a secure repository.

## 4. Legal and ethical requirements, code of conduct

4a. If personal data are processed, how will compliance with legislation on personal data and on security be ensured?

Not applicable

4b. How will other legal issues, such as intellectual property rights and ownership, be managed? What legislation is applicable?

Not applicable

4c. What ethical issues and codes of conduct are there, and how will they be taken into account?

Not applicable

## 5. Data sharing and long-term preservation

5a. How and when will data be shared? Are there possible restrictions to data sharing or embargo reasons?

Until publication and sharing, raw data and dataset will be accessible only to the partners.

At the end of the project data will be deposited in a data repository (such as Zenodo) with restricted or open access.

5b. How will data for preservation be selected, and where data will be preserved long-term (for example a data repository or archive)?

Data will be stored during the maximum allowed by the Institut Pasteur storage allowance capacity and the repository chosen to publish the data.

5c. What methods or software tools are needed to access and use data?

The data will be either accessible via a repository or requests handled directly. The data are in open formats and therefore interoperable.
**5d. How will the application of a unique and persistent identifier (such as a Digital Object Identifier (DOI)) to each data set be ensured?**

A DOI will be automatically assigned to each dataset if the Zenodo repository is chosen at the end of the project to share and preserve the data.

# 6. Data management responsibilities and resources

**6a. Who (for example role, position, and institution) will be responsible for data management (i.e. the data steward)?**

Not applicable

**6b. What resources (for example financial and time) will be dedicated to data management and ensuring that data will be FAIR (Findable, Accessible, Interoperable, Re-usable)?**

Not applicable

# WPB - Detection System

## 1. Data description and collection or re-use of existing data

**1a. How will new data be collected or produced and/or how will existing data be re-used?**

Experiments will be performed to develop, optimize and finally characterize the detection system and its embedded reagents.

Specificity and sensitivity data will be measured using (RT-)qPCR reactions and plate counting.

Raw data will be acquired using specific software (e.g. CFX Maestro / pcrd files) and registered on computer or in laboratory notebooks.

Xlsx and pptx files will be used for data management, graph representations and data analysis.

**1b. What data (for example the kind, formats, and volumes), will be collected or produced?**

The collected/produced data are:

* Experimental descriptions (pdf, docx, txt format)

* Experimental raw data results (xlsx format, prcd format)

* Pictures (jpg, png, pdf, mp4 format)

The expected volume of this dataset is less than 1 Gb.
## 2. Documentation and data quality

**2a. What metadata and documentation (for example the methodology of data collection and way of organising data) will accompany the data?**

The main metadata accompanying the data will be:

* Date

* User name

* Objectives

* Type of sample

* Equipment Id

* Reagents Id (Lot#)

* Consummables Id

**2b. What data quality control measures will be used?**

Not applicable

## 3. Storage and backup during the research process

**3a. How will data and metadata be stored and backed up during the research?**

The data will be stored on a secured server.

**3b. How will data security and protection of sensitive data be taken care during the research?**

The access of data will be protected using unique user login and password.

## 4. Legal and ethical requirements, code of conduct

**4a. If personal data are processed, how will compliance with legislation on personal data and on security be ensured?**

Not applicable

**4b. How will other legal issues, such as intellectual property rights and ownership, be managed? What legislation is applicable?**
Results are owned by the Party that generates them. Joint ownership is governed as described in the consortium agreement.

4c. What ethical issues and codes of conduct are there, and how will they be taken into account?

Not applicable

## 5. Data sharing and long-term preservation

5a. How and when will data be shared? Are there possible restrictions to data sharing or embargo reasons?

Until publication and sharing, raw data and dataset will be accessible only to the partners.

At the end of the project data will be deposited in a data repository (such as Zenodo) with restricted or open access.

5b. How will data for preservation be selected, and where data will be preserved long-term (for example a data repository or archive)?

Data will be stored during the maximum allowed by the Institut Pasteur storage allowance capacity and the repository chosen to publish the data.

5c. What methods or software tools are needed to access and use data?

The data will be either accessible via a repository or requests handled directly. The data are in open formats and therefore
interoperable.

5d. How will the application of a unique and persistent identifier (such as a Digital Object Identifier (DOI)) to each data set be ensured?

A DOI will be automatically assigned to each dataset if the Zenodo repository is chosen at the end of the project to share and preserve the data.

## 6. Data management responsibilities and resources

6a. Who (for example role, position, and institution) will be responsible for data management (i.e. the data steward)?

Not applicable
**6b. What resources (for example financial and time) will be dedicated to data management and ensuring that data will be FAIR (Findable, Accessible, Interoperable, Re-usable)?**

Not applicable

# WPF - Decontamination Procedures and Evaluation

## 1. Data description and collection or re-use of existing data

**1a. How will new data be collected or produced and/or how will existing data be re-used?**

The data collected for decontamination assays will be noted on excel or power point and will be used for data management, graph representations and data analysis.

**1b. What data (for example the kind, formats, and volumes), will be collected or produced?**

The collected/produced data are:

* Experimental descriptions (pdf, docx, txt format)

* Experimental raw data results (xlsex format, prcd format)

* Pictures (jpg, png, pdf, mp4 format)

The expected volume of this datased is less than 1 Gb.

## 2. Documentation and data quality

**2a. What metadata and documentation (for example the methodology of data collection and way of organising data) will accompany the data?**

not applicable

**2b. What data quality control measures will be used?**

not applicable

## 3. Storage and backup during the research process
3a. How will data and metadata be stored and backed up during the research?

The data will be stored on a secured server.

3b. How will data security and protection of sensitive data be taken care during the research

The access of data will be protected by unique user login and password.

4. Legal and ethical requirements, code of conduct

4a. If personal data are processed, how will compliance with legislation on personal data and on security be ensured?

not applicable

4b. How will other legal issues, such as intellectual property rights and ownership, be managed? What legislation is applicable?

Results are owned by the Party that generates them. Joint ownership is governed as described in the consortium agreement.

4c. What ethical issues and codes of conduct are there, and how will they be taken into account?

Not applicable

5. Data sharing and long-term preservation

5a. How and when will data be shared? Are there possible restrictions to data sharing or embargo reasons?

Until publication and sharing, raw data and dataset will be accessible only to the partners.

At the end of the project data will be deposited in a data repository (such as Zenodo) with restricted or open access.

5b. How will data for preservation be selected, and where data will be preserved long-term (for example a data repository or archive)?
Data will be stored during the maximum allowed by the Institut Pasteur storage allowance capacity and the repository chosen to publish the data.

**5c. What methods or software tools are needed to access and use data?**

The data will be either accessible via a repository or requests handled directly. The data are in open formats and therefore interoperable.

**5d. How will the application of a unique and persistent identifier (such as a Digital Object Identifier (DOI)) to each data set be ensured?**

A DOI will be automatically assigned to each dataset if the Zenodo repository is chosen at the end of the project to share and preserve the data.

# 6. Data management responsibilities and resources

**6a. Who (for example role, position, and institution) will be responsible for data management (i.e. the data steward)?**

Not applicable

**6b. What resources (for example financial and time) will be dedicated to data management and ensuring that data will be FAIR (Findable, Accessible, Interoperable, Re-usable)?**

Not applicable

# WP G - Operational and Tactical System Evaluation

## 1. Data description and collection or re-use of existing data

**1a. How will new data be collected or produced and/or how will existing data be re-used?**

Question sans réponse.

**1b. What data (for example the kind, formats, and volumes), will be collected or produced?**
Question sans réponse.

## 2. Documentation and data quality

**2a. What metadata and documentation (for example the methodology of data collection and way of organising data) will accompany the data?**

Question sans réponse.

**2b. What data quality control measures will be used?**

Question sans réponse.

## 3. Storage and backup during the research process

**3a. How will data and metadata be stored and backed up during the research?**

Question sans réponse.

**3b. How will data security and protection of sensitive data be taken care during the research?**

Question sans réponse.

## 4. Legal and ethical requirements, code of conduct
4a. If personal data are processed, how will compliance with legislation on personal data and on security be ensured?

Question sans réponse.

4b. How will other legal issues, such as intellectual property rights and ownership, be managed? What legislation is applicable?

Question sans réponse.

4c. What ethical issues and codes of conduct are there, and how will they be taken into account?

Question sans réponse.

## 5. Data sharing and long-term preservation

5a. How and when will data be shared? Are there possible restrictions to data sharing or embargo reasons?

Until publication and sharing, raw data and dataset will be accessible only to the partners.

At the end of the project data will be deposited in a data repository (such as Zenodo) with restricted or open access.

5b. How will data for preservation be selected, and where data will be preserved long-term (for example a data repository or archive)?

Data will be stored during the maximum allowed by the Institut Pasteur storage allowance capacity and the repository chosen to publish the data.

5c. What methods or software tools are needed to access and use data?

The data will be either accessible via a repository or requests handled directly. The data are in open formats and therefore interoperable.

5d. How will the application of a unique and persistent identifier (such as a Digital Object Identifier (DOI)) to each
data set be ensured?

A DOI will be automatically assigned to each dataset if the Zenodo repository is chosen at the end of the project to share and preserve the data.

# 6. Data management responsibilities and resources

6a. Who (for example role, position, and institution) will be responsible for data management (i.e. the data steward)?

Not applicable

6b. What resources (for example financial and time) will be dedicated to data management and ensuring that data will be FAIR (Findable, Accessible, Interoperable, Re-usable)?

Not applicable