A novel fast test for antibiotic susceptibility testing for Gram positive and Gram negative bacteria

Project Information

FAST-bact

Grant agreement ID: 730713

DOI

10.3030/730713

Project closed

EC signature date 16 December 2016

Start date 1 December 2016

End date 31 May 2021

Funded under

• Horizon 2020 Framework Programme

Total cost

€ 3 675 325,01

EU contribution

€ 2 655 602,50

Coordinated by

FASTINOV SA
Portugal

Periodic Reporting for period 5 - FAST-bact (A novel fast test for antibiotic susceptibility testing for Gram positive and Gram negative bacteria)

Reporting period: 2020-12-01 to 2021-05-31

Summary of the context and overall objectives of the project

The WHO’s “Antimicrobial resistance (AMR): global report on surveillance (2014)” makes clear that resistance to common bacteria has reached alarming levels and that in some settings few, if any, of the available treatment options remain effective. Current projections include 10 million annual global deaths due to resistant microorganisms by 2030.
Hence, there is an urgent need for fast and accurate Antimicrobial Susceptibility Testing (AST) methods to drive proper treatment of infections. The novel Flow cytometry AST technology developed by the FAST-bact consortium delivers ultra-rapid results, within 2h. The FAST-bact tests will directly impact treatment of patients with bacterial infections, as well as the 400,000 patients in Europe who each year contract a multi-resistant bacterial infection. By providing faster results on the antibiotic susceptibility pattern, the FAST-bact tests will improve treatment, contribute to lowering mortality and morbidity and in the process improve the quality of life for patients and reduce the pressure for AMR.
The project aims to introduce the FAST-bact tests as product to the blood AST testing market, which includes a CE-IVD software analytical package for clinical guidance as to the interpretation of the AST results according to current CLSI and EUCAST antibiotic AST breakpoint guidelines. The consortium aims for clinical validation of the 3 assay kits (FAST grampos, FAST gramneg, FAST mar), and envisions the production of the IVD AST kits on a large-scale and regulatory compliant process, addressing both present and future EU IVD-guidelines, that will be implemented in Europe during the project.

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

Protocols for the 3 kits were optimized and validated. The kits were produced and frozen at -20ºC. In order to have room-temperature stable kits lyophilization was tried at FASTinov and transferred to the industrial partner, Clonit (former Euroclone). However, for some of the drugs, stability was compromised. Very extensive efforts were undertaken by project partners in close collaboration with external experts to optimize lyophilization conditions. After lyophilizaion, drying down with different excipients were tried, having 6 drugs already stable for more than 2 years at room temperature. One of the stable drug was colistin that, due its importance as last line drug in critical clinical situations needs a rapid report about its susceptibility. Moreover, EUCAST invalidated most of the methods due to technical difficulties found on both manual and automated methods used on clinical labs. Considered as a strategic opportunity for FASTinov a separate kit was developed, the FASTcolistinMIC kit. The new kit was produced at Clonit, dried and validated at FASTinov and SERMAS and have been submitted to the local EU Regulatory Authority, with a dedicated software. Accelerated studies already showed a 2 years stability although, room temperature stability studys are still on going.

A pilot study with cryo-version panels produced by FASTinov team began in Oct 2018 at SERMAS. Positive Blood Culture samples were collected daily. Standard AST were performed using both MicroScan and either disk diffusion method or microdilution. Results have been interpreted using both CLSI and EUCAST breakpoints. Ninety-nine patient samples have been included in the external validation. Additionally, at FASTinov, 285 blood cultures were spiked with well-characterized bacteria and inoculated into FASTinov panels. Part of these results have been presented in different international conferences and papers are in preparation.

Meanwhile the consortium continued to look for help on finding stable panels at room temperature. A CDMO specialized in antibiotic stability drugs, was contracted to produce room temperature panels with antibiotics and probes ready to use. Several pilot lots were produced and tested with good results. In parallel, a decision was made to include in the FASTbact kits, along with the drug panels, tubes prefilled with the culture media required to resuspend the drugs and carry out the subsequent incubation. This will turn the assay much easier for the user, further standardize the method and avoid problems with flow cytometry analysis due the quality of the media used, its base fluorescence and particulate content. Optimization and manufacturing of the culture media was perfomed by Clonit. After optimization, the order of production of dried panels was made and 3 validation lots produced regarding FASTgramneg and FASTgrampos. Non-clinical performance was completed at FASTinov regarding the 3 dried kits (FASTgramneg, FASTgrampos and FASTcolistinMIC) and clinical performance took place at FASTinov (using spiked blood cultures) and at SERMAS.

Partners were trained by Profess to set-up a fail-proof QA system. QA-requirements implemented at FASTinov and μRoboptics are in line with current legislation for in vitro diagnostic tools and accompanying software packages. The software package, bioFAST, for data analysis of FAST-bact kits and routine methods has been finalized and is ready to be used by clients during the commercialization phase either as a stand-alone, integrated or web application.

Since November 2020, clinical validation with dehydrated plates was achieved at SERMAS evaluating FASTgramneg and FASTgrampos kits at the same time. A total of 180 samples have been included in the study.

The results from the clinical validation have provided the ground for commercial success subsequent to FASTbact project conclusion.

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 project’s objective was the successful market introduction of FAST-bact kits, which serves important healthcare issues and contributes to society needs. The kits just developed provide reliable antibiotic susceptibility test within 2h. This will lead to a faster outcome on the susceptibility phenotype of the bacterial pathogen that infected a specific patient. This will allow, on-time targeted therapy, with much narrower spectrum; for example, in the case of resistant phenotypes, it will allow a more aggressive therapy in a more expedited time frame. On the other hand, it will reduce the common empirical clinical practice of treatment of patients with wide-spectrum antibiotics and will provide a much more specific way of treating the patient immediately and efficiently using the appropriate antibiotic. The benefits of a quicker report will also contribute to the safety of the public health system by allowing timely isolation of patients infected with AMR strains, avoiding the spread of the AMR pathogen. Technologically, the patented innovation is a platform technology that opens further developments such as applications to determine antifungal susceptibility or mechanisms of resistance of bacterial strains.

The potential commercial impact of the FAST-bact kits is being evaluated by major industrial players. The results from the clinical validation have provided the ground for commercial success subsequent to FASTbact project conclusion.

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