PIRSES-GA-2013-612309 AEDnet Project Mid-Term Report December 2014

ANNEX 1: MID-TERM REPORT

Marie Curie Actionsseventh framework programme

Marie Curie Actions – International Fellowships

Project n°: _PIRSES-GA-2013-612309________
Project Acronym: ___AEDnet_________
Project Full Name: __Anthrax Environmental Decontamination Network___
Marie Curie Actions
IRSES Mid-term Report
Period covered: from ___01.01.14_________ to ____31.12.16____
Period number: _______1_____
Start date of project: _____1st Jan 2014_______
Project coordinator name: ___Prof Les Baillie_________
Project coordinator organisation name: __Cardiff University UK__________
Date of preparation: ____24th Dec 2014________
Date of submission (SESAM): ___24th Dec 2014_________
Duration: ____12 months________
Version: _____1______

1. GENERAL PROGRESS OF THE PROJECT
Please indicate if the project:
a) has fully achieved its objectives and technical goals for the period;
b) has achieved most of its objectives and technical goals for the period with relatively minor deviations;
c) has failed to achieve critical objectives and/or is not at all on schedule.

If you answered b) or c) please include a detailed description of the modifications in the report
While the project has achieved all of its deliverables, we have not completed all of the planned secondments. On reflection, front loading the distribution of the secondments to the first 12 months (50 months in total) of the project was unrealistic. We were not helped by the fact that it took several months to complete the contractual arrangements between the project coordinator and the individual partners. It also took some time for all of the partners to fully understand the process and their respective responsibilities. Finally the on going problems in Ukraine meant that only 5 of the planned 13 secondments from that institution took place.
It is our intention to re-arrange the missed secondments so that they are completed during the lifetime of the project. A summary of the planned and completed secondments is shown in the attached GNATT chart.

Qualitative indicators of progress and success in line with workplan and milestones (description of progress towards the milestones and deliverables)
The project has met all but one of its 6 deliverables within the 12 month period and the 6th deliverable, the Month 12 meeting of the Project Management Group will be completed early in the new year.

D1.1, Month 12: A standardised method for the isolation of B.anthracis specific bacteriophages- (see attached).

D4.1, Month 3: Meeting of the Project Management Group
Held at the project meeting at the Anthrax workshop in Cardiff in March 2014. At this meeting, the contractual arrangements between the partners and Cardiff University were explained, as was the process by which funds would be transmitted to all the institutes. The reporting requirements were also explained. Due to the unrest in Ukraine, our colleagues from NSC IECVM were unable to attend the meeting in Cardiff. Information with transmitted to them via email.

We held a second informal project meeting in Tbilisi, Georgia in June 2104, to coincide with a congress on Chemical, Biological, Radiological, Nuclear and explosives (CBRNe) Science and Consequence Management which was attended by a number of the partners.

D4.2, Month 6: First Internal technical report- see attached

D4.3, Month 6: Establish project website- A project website was established and can be viewed at https://aednetproject.wordpress.com/ We are still waiting for all of the partners to provide information about their institutions which we will post on the site.
D4.4. Month 12: Internal technical report- see attached

D4.5. Month 12: Meeting of the Project Management Group- This meeting is yet to be held and will be hosted in the new year by Cardiff via Skype. The meeting will address the problem of identifying staff willing to go on secondment and will identify how the secondments which were not completed in the first 12 months are reassigned across the rest of the project period.

D4.6, Month 12: Preparation of mid- term review report to the EU Commission
Completed and submitted to EU- completed

2. PROJECT ACHIEVEMENTS
Scientific highlights and research achievements
1. With support from researchers from CU, KAU and EIG we developed A standardised method for the isolation of B.anthracis-specific bacteriophages

2. We have isolated novel B.anthracis-specific bacteriophages which will be assessed for their suitability as potential decontamination agents

3. As a consequence of the interaction between KAU and NCDC, and with support from CU, we have established a new project which started in Nov 2014 and is funded by the US Biological Engagement Program to genetically type the pathogenic strains of B.anthracis which cause anthrax in Georgia and Turkey. The project will reinforce the link formed as part of this EU funded project and will provide a foundation for future joint research efforts. The project aims to provide short-term training by WRAIR and NCDC Lugar Center collaborators to Turkish personnel in the areas of bacterial DNA extraction and molecular analysis of anthrax isolates.

Transfer of knowledge and Training activities (workshops…)
Secondment activities
WP1- Development and characterisation of phage-based decontamination agents: Nino Modebadze, Ketevan Sidamonidze from NCDC visited the group at CU for 1 month for training in the isolation and characterization of B.anthracis specific bacteriophages (task 1.2). They isolated phages form soil and observed the effect of different phages on a vaccine strain of B.anthracis. As part of this process, they employed a number of different methods which included enrichment from soil, propagation of phage in liquid broth, determination of bacteriophage titre and purification of bacteriophage.
Ms Aleksandra Nakonieczna, from WiHe visited the group at EIG for 2 months for training in the isolation and characterisation of B.anthracis-specific bacteriophages (task 1.1). During the visit she worked in a Molecular Biology laboratory led by Dr. Mzia Kutateladze. The aim of this exchange was to share and extend the knowledge about bacteriophages, including B. anthracis phages. During the secondment she took part in bacteriophage isolation from sewage samples, purification and propagation of bacteriophages, phage DNA isolation, DNA restriction analysis, PFGE analysis, phage characterization assays (adsorbtion rate, one step growth experiments, phage host range), phage adaptation according to the Appelman’s method, media preparation, and API testing.

WP2- Development of methods to enhance the activity and stability of sporicidal agents: Dr Ekaterine Tevdoradze from EIG visited the group at CU for 1 month for training in how to develop a standardised soil microcosm with which to assess germinant efficacy (Task 2.1). Studies suggested that we need to optimise the ratio of phage to target bacteria to achieve effective killing of the pathogen in soil.
Ekaterine Khmaladze, Mariam Zakalashv from NCDC visited the group at CU for 1 month for training in how to develop a standardised soil microcosm with which to assess germinant efficacy (Task 2.1). The were introduced to the method that shows the effect of germinants alone on spore reduction in soil and the principle of adding germinants to soil to trigger the conversion of spores to vegetative form. They observed that B. anthracis failed to persist in vegetative form after it had been introduced to germinate.
WP3- Field trials, efficacy testing and assessment of environmental impact
Dr Andriy Buzun from NSC IECVM visited the group at KAU for 1 month to receive training in the identification and characterisation of potential anthrax spore decontamination test sites (task 3.1). He visited a number of potential decontamination sites in Turkey with a view to identifying similar sites in Ukraine.

Dr Fatih Buyuk, Ms Aliye Gulmez and Ms Elif Tazegul from KAU visited the group at NCDC for 1 month to receive training in characterization of the genetic diversity of B.anthracis isolates (task 3.2) and safely working with B.anthracis biosafety 2 and 3 (task 3.5). During the visit they spent two weeks in the Genome Laboratory where they were introduced to sequencing methods and the platform which is used at NCDC to genotype bacterial isolates. The final two weeks were spent visiting the biosafetly level 2 and 3 facilities for training in the various aspects of operating safely in such faciltities.

Dr Leila Kvachadze from EIG visited the group at CU for 1 month for training in how to work safely in a UK containment level 2 laboratory (task 3.5).

The following researchers Dr Anatoliy Paliy,Dr Olena Kolchyk, Dr Oleksandr Rula and Mr Mykola Kalashnyk from NSC IECVM visited IZSPB Italy for one month for training in the following topics: characterization of the genetic diversity of B. anthracis (genotyping by 15 loci Multi Locus VNTR Analysis -MLVA) isolates from environmental samples via G.A.B.R.I. technique (task 3.2) and training on safely working with B. anthracis in laboratory Biosafety Level 3. (task 3.5).

Dissemination of results (conferences, publications)
To date, we have not disseminated the results of our work outside of the network. It is our intention to disseminate our results and activities to the wider scientific community and to advertise our activities on the project website at https://aednetproject.wordpress.com/
3. PROJECT MANAGEMENT
Overview of the activities carried out by the partnership, identification of problems encountered and corrective action taken.
This project involves the co-ordination of 9 institutions, five based in EU member or associate states, three based on Georgia and one based in Ukraine. Co-ordination and control of such a disparate group is a challenge. The project coordinator has been greatly assisted by the efforts of a part time project administrator who in addition to coordinating details of secondments, is also responsible for managing the project website.

We held a kickoff meeting of the Project Management Group in Cardiff in march 2014. A second informal project meeting was held in Tbilisi, Georgia in June 2104 and was attended by representatives of the majority of the groups. Our 12 month meeting is yet to be held and will be hosted in the new year by Cardiff via Skype. The meeting will address the problem of identifying staff willing to go on secondment and will identify how the secondments which were not completed in the first 12 months will be reassigned across the rest of the project period.
4. ADDITIONAL INFORMATION
Please indicate any additional information, which may be considered useful to assess the work done during the reporting period. The socio-economic aspects of the project may be addressed in this section.
Ethical issues
As stated in the proposal, no exchange of viable strains of pathogens between laboratories and between countries has or will take place (monitoring safety issues).

Also there have been no anthrax cases in the environment of the research sites.

All of the research which has been undertaken as part of this project complies with the ethical standards and guidelines of the European Union.

There is no intension to transport samples containing B.anthracis from Georgia or the Ukraine.

Statements from members of the external, independent Advisory Board stating that the project has not created any concerns with regards to bioterrorism, misuse and dual use are attached.
Appendix A: D4.2. Month 6: First Internal technical report- delayed- will be same as phage report
Appendix B: D4.4. Month 12: Internal technical report- summary of project reports
Visits to date
Attachment: Deliverable 1.1.A standardised method for the isolation of B.anthracis-specific bacteriophages

Person in charge of the project for the beneficiary/consortium
Name: Les Baillie
Date 24th Dec 2014
Signature

Appendix A: D4.2. Month 6: First Internal technical report- delayed- will be same as phage report

For administrative reason there was a delay in completing the contractual arrangements between the institution of the project coordinator and the individual partners. It also took some time for all of the partners to fully understand the process and their respective responsibilities. As a consequence, there was a delay in the start of the secondments.

In the first six month there were secondments between EIG and Cardiff and KAU and NCDC.

Dr Ekaterine Tevdoradze from EIG visited the group at CU for 1 month for training in how to develop a standardised soil microcosm with which to assess germinant efficacy (Task 2.1). Studies suggested that we need to optimise the ratio of phage to target bacteria to achieve efficient killing of the pathogen in soil.

Dr Leila Kvachadze from EIG visited the group at CU for 1 month for training in how to work safely in a UK containment level 2 laboratory (task 3.5).

Dr Fatih Buyuk, Ms Aliye Gulmez and Ms Elif Tazegul from KAU visited the group at NCDC for 1 month to receive training in characterization of the genetic diversity of B.anthracis isolates (task 3.2) and safely working with B.anthracis biosafety 2 and 3 (task 3.5). During the visit they spent two weeks in the Genome Laboratory were they were introduced to sequencing methods and the platform which is used at NCDC to genotype bacterial isolates. The final two weeks were spent visiting the biosafetly level 2 and 3 facilities for training in the various aspects of operating safely in such faciltities.

Appendix B: D4.4. Month 12: Internal technical report- summary of project reports visits to date

WP1- Development and characterisation of phage based decontamination agents

Isolation of B.anthracis specific phages using the Sterne vaccine strain of B.anthracis

1. The group at CU with help from colleagues from EIG and NCDC isolated novel B.anthracis specific phages from environmental samples and determine there biological activity. Electron microscopy images of the phages can be seen below.

micro 1micro 2micro 3
2. Ms Aleksandra Nakonieczna, from WiHe with support form the the group at EIG isolated and characterisation B.anthracis specific bacteriophages

Researchers from NCDC received training in the isolation and characterisation of B.anthracis specific bacteriophages (task 1.2) and as a consequence should be better equipped to isolate bacteriophages from there own B.anthracis contaminated sites.
WP2- Develop of methods to enhance the activity and stability of sporicidal agents

Researchers from Georgia have received training in how to set up and run soil microscosms. They were introduced to the method that shows the effect of germinants on spore reduction in soil and the principle of adding germinants to soil to trigger the conversion of spores to vegetative form. They observed that B. anthracis failed to persist in vegetative form after it had been introduced to germinate.
WP3- Field trials, efficacy testing and assessment of environmental impact
Dr Andriy Buzun from NSC IECVM visited the group at KAU for 1 month to receive training in the identification and characterisation of potential anthrax spore decontamination test sites with a view to identifying similar sites in Ukraine.

Researchers from KAU in Turkey visited the group at NCDC in Georgia for training in the use of molecular methods to characterize the genetic diversity of B.anthracis. Researchers from NSC IECVM in Ukriane underwent similar molecular characterization training at IZSPB Italy in the method of genotyping using 15 loci Multi Locus VNTR Analysis –MLVA.

Researchers from NCDC, EIG, KAU and NSC IECVM received training in how to operate safely 8in Biosafety level 2 and 3 facilities

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