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FAPIC Report Summary

Project ID: 634137
Funded under: H2020-EU.3.1.

Periodic Reporting for period 1 - FAPIC (Fast Assay for Pathogen Identification and Characterisation)

Reporting period: 2015-05-01 to 2016-10-31

Summary of the context and overall objectives of the project

The need for fast diagnostic tests characterising pathogens is high and only those avoiding the time-consuming bacteria growing step can meet the customers’ requirements. A few multiplex assays analysing patient samples directly are already available on the market (e.g. SeptiFast®, Roche). However, they require laborious handling and are considerably limited regarding the number of target genes (<20), because they are based only on molecular biology techniques such as RT- or QC-PCR. The laborious handling can be avoided if the protocols are automated. The challenge in the automatization process lies in the successful implementation of a wide range of different sample materials. Blood, swabs or urine require a specialised sample processing due to the varying physical and biological parameters.
In the project FAPIC, will be developed two very fast, automated and cost-effective diagnostic systems for the identification and characterisation of infectious diseases pathogens. The two systems are based on an innovative nucleotide probe concept and a novel highly sensitive DNA assay. The systems will significantly improve the diagnosis of infectious diseases, the subsequent patient’s antibiotic treatment and the monitoring of multidrug-resistant pathogens including their dissemination paths. The two testing systems as shown in Figure 1 are
i) a low-cost point-of-care testing (POCT) device (Patho-Stick) for a limited range of pathogens but fast and reliable diagnostics including resistance patterns for doctor’s offices and local ambulatories for a variety of sample types
ii) a high-throughput automated test system (Patho-Robot) for centralised clinical laboratories with the main advantage of broad spectrum and quantitative determination of pathogens from a variety of sample types

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During this first period of the FAPIC project, the following hardware were implemented:
- A low-cost point-of-care testing (POCT) device named Patho-doc with a fully automated approach both for sample treatment and assay analysis
- A high-throughput automated test system for routine used
Then, at the scientific level, tools were developed to:
- Automatically select and generate complex reagent compositions, required for the implementation of highly multiplex (ultraplex) assays using molecular biology
- Enable the extraction of DNA from complex samples
- A concept assay module in which one sample shall be treated and assayed

Detailed description of these achievements are presented below.

The Patho-doc is a bench-top apparatus with the capacity of handling blood sample, run a DNA extraction from it, amplify the genes of interest and identify them. Prototype of this machine was actually built during this period and the next period will be dedicated to its validation.

High-throughput system
The high-throughput system is dedicated to the routine hospital laboratories dealing with large number of samples per day. One run can handle 96 samples at a time and performed DNA extraction, amplification of the genes of interest and identification, in a fully automated manner.
The system is currently under testing and validation.

Complex reagent compositions
The high complexity of the assays performed in the FAPIC project (ultraplex) required a large number of reagents, each one specific of one particular target. This situation lead us to develop a reagent selection/design tool which is an in silico design program. Briefly, all selected targets genes are characterised by a specific sequence known and identified in a data base. The program then need to mine in this data base and select reagents with high selectivity, or the least cross reactivity.
This program is currently running and the experimental validation of the selected reagent will be the next step here.

Extraction of DNA
DNA is the core part of the sample to be analysed in the FAPIC project, since pathogens targets, resistance and virulence are coded by genes, and that these genes are the target the system is detecting. DNA isolation from sample is then one particularly important step in the development of FAPIC.
During this period, extraction protocols were developed together with hardware and disposable parts of the extraction.

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)

This first period mainly covered the development of the tools necessary to the implementation of the project.
Thus, in term of progress beyond the state of the art, the main achievements were obtained from the development of non-existing tools before the project.
These tools are, as listed above; i) a software package useful for multiplex reagents determination and choices and ii) a benchtop fully automated apparatus able to handle extraction, amplification and microarray based assay.

Related information

Record Number: 196355 / Last updated on: 2017-03-29
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