Intelligence for precision therapies against antimicrobial resistance: The first diagnostic panel that probes all the clinically relevant antibiotics at once

Project Information

BacterOMIC

Grant agreement ID: 881101

DOI

10.3030/881101

Project closed

EC signature date 29 October 2019

Start date 1 August 2019

End date 31 December 2021

Funded under

• INDUSTRIAL LEADERSHIP - Innovation In SMEs

Total cost

€ 2 752 387,50

EU contribution

€ 1 926 671,25

Coordinated by

BACTEROMIC SPOLKA Z OGRANICZONA ODPOWIEDZIALNOSCIA
Poland

Periodic Reporting for period 3 - BacterOMIC (Intelligence for precision therapies against antimicrobial resistance: The first diagnostic panel that probes all the clinically relevant antibiotics at once)

Reporting period: 2021-08-01 to 2021-12-31

Summary of the context and overall objectives of the project

BacterOMIC project started as a response for growing antimicrobial resistance, which is recognised by European Commission and WHO as one of the biggest threats to global health.
It is estimated that antimicrobial resistance is responsible for over 30 thousand deaths per year in the EU and 700 thousand on global scale. The experts calculated, that if we don’t stop the spread of antimicrobial resistance, it is going to cause 10 million deaths annually in 2050 and cost OECD countries EUR 2,6 trillion.
To prevent the increase of antimicrobial resistance, the overuse of antibiotics must be stopped. That’s why healthcare institutions have to switch from empirical therapy to precision targeted therapy, based on susceptibility of the particular pathogen. To conduct targeted therapy, doctors desperately need the accessible and comprehensive test, that evaluates susceptibility to all antimicrobials available.
The goal of BacterOMIC project is to address the need for precision therapy by developing the most informative automatic antimicrobial susceptibility test. The information provided by our technology is the key to overcome the antimicrobial resistance.

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

BacterOMIC company entered phase II of the project with functional prototypes of all elements of the system tested in laboratory environment. Evaluation tests showed a need for optimalisation of disposable cartridge for better ergonomics and simplicity of work. Implemented changes resulted in the necessity to redesign the devices (analyser and filling device) which operate on cartridge together with steering software.
During the first year of the project, the BacterOMIC team has designed a new cartridge which can support growth of Gram(-) and Gram(+) aerobic bacteria in 640 separated incubation chambers.
Thanks to these efforts, the cartridge elements are now ready for cost effective mass production by injection moulding. Implemented solutions ensure simplicity of laboratory procedures.
Together with the new cartridge design, a panel for antimicrobial susceptibility testing was prepared. Protocols for deposition of antibiotics were established for first antibiotic panel.
In parallel, new versions of filling device and analyser were designed. New design was prepared to meet requirements of small scale production and to be compatible with scaling up to mass production. Devices functionalities were confirmed by numerous tests in the company laboratory.
For correct determination of Antimicrobial Susceptibility Testing using the BacterOMIC system, we developed new analytical methods. Our approach is based on the use of machine learning and artificial intelligence for interpretation of results. The methods were tested on results from thousands of growth curves acquired by BacterOMIC analyser and show more than 95% agreement with reference analysis by trained microbiologist.
After successful pre-clinical trials in 2020 the company has established pilot production plants for all elements of a system. After internal evaluation of analyser and cartridges produced on designed lines the company performed clinical evaluation studies. 4 external laboratories and 1 internal laboratory took part in a study to evaluate performance of the BacterOMIC system. More than 1000 samples were tested providing results which entitled the company to register the system as in vitro diagnostic device. Analyser, Filling device and Universal Panel of 20 antibiotics for susceptibility testing of strains belonging to: Enterobacterales, Pseudomonas, Acinetobacter, Staphylococcus.
As a device for in vitro diagnostics, the BacterOMIC system has to meet strict requirements for medical device development. The company has decided to fulfil these requirements by implementing ISO13485 standards. During the first year of work, quality management system was prepared and was successfully implemented in all areas of BacterOMIC work. Correct implementation of the standard has been confirmed by an audit by a notified body and obtaining of ISO13485 certificates in area of design, manufacturing and distributions of IVD systems.

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)

It is estimated, that 70% of the pathogens causing infections in Europe are resistant to at least one antibiotic, and more and more often it turns out that it is resistant to all antimicrobials tested. To find the cure, diagnostic team has to perform costly and time-consuming additional tests, including less common or last-resort drugs. Until the test result arrives, doctors rely on empirical therapy, which become less and less effective over last years. Additional tests, unsuccessful changes of therapeutic agents, and prolonged therapy, increase the risk of side-effects and length of hospitalization. This leads to physical, emotional and financial burden for the patient and their family, and generates costs for whole society due to work absence and healthcare expenses.
Currently available automated systems are cheap and easy to use, but deliver limited information about short list of antimicrobials and often don’t provide quantitative result. On the other hand, manual methods are precise and informative, but very time-consuming and cost-ineffective.
The BacterOMIC system developed within this project, combines the precision of manual methods with the easiness and time-effectiveness of automated systems. First version of Universal Panel makes it possible to evaluate 20 antibiotics for 4 groups of pathogens (both gram(+) and gram(-)) with no need for pathogen identification prior to test.
What is more, our cooperation with healthcare professionals from several diagnostic laboratories confirmed that they found BacterOMIC system user-friendly and are eager to use it in their work.

BacterOMIC cartridge

BacterOMIC analyser operated by microbiologist

BacterOMIC Analyser and cartridge presented by microbiology specialist

BacterOMIC filling device together with cartridges and rack