BacterOMIC – development of systems for comprehensive information on antibiotic susceptibility of bacteria

Funding: Foundation for Polish Science within the TEAM TECH program POIR.04.04.00-00-2159/16-00.

Implementation period: 1.05.2017-31.12.2019


The aim of the BacterOMIC project realized in a consortium between the Institute of Physical Chemistry and Scope Fluidics sp. z o.o.  is to introduce qualitatively new possibilities in diagnostics and research on antimicrobial resistance – one of the most important current threats to the global health system.

Using microfluidic technologies, Scope Fluidics will develop a TRL6 demonstration of an automated diagnostic system delivering revolutionarily more comprehensive information than is currently available: i) true minimum inhibitory concentration values (as opposed to only break-point levels), ii) a comprehensive set of tens of antibiotics (compared to a few), and iii) information on interactions between pairs of antibiotics (no counterpart in the state of art).

The program at the Institute of Physical Chemistry will deliver i) open systems for facile generation of 2D cross-matrices of dilutions for clinical checkerboard studies of susceptibility and ii) high throughput screening of interactions between antibiotics and between antibiotics and adjuvants acting on bacteria, as a platform for research on mechanisms of resistance and in the search for effective treatment strategies.


  • Tomasz Kamiński
  • Ladislav Derzsi
  • Yurii Promovych
  • Marta Zapotoczna
  • Paweł Jankowski

PhD Students

  • Magdalena Czekalska
  • Adam Opalski
  • Łukasz Kozoń
  • Witold Postek
  • Michał Horka
  • Artur Ruszczak

MSc Students

  • Paweł Garguliński
  • Aleksandra Borkenhagen
  • Agnieszka Koszewska
  • Sara Krześniak


  • Patryk Adamczuk
  • Karol Patyrak


  1. Tomasz S. Kaminski and Piotr Garstecki (2017), Controlled droplet microfluidic systems for multistep chemical and biological assays, Chemical Society Reviews, 46, 6210 – 6226
  2. Adam S. Opalski, Tomasz S. Kaminski, Piotr Garstecki (2018), Droplet Microfluidics as a Tool for the Generation of Granular Matters and Functional Emulsions, KONA Powder and Particle Journal
  3. Witold Postek, Paweł Gargulinski, Ott Scheler, Tomasz S. Kaminski and Piotr Garstecki (2018), Microfluidic screening of antibiotic susceptibility at a single-cell level shows inoculum effect of cefotaxime in E. coli, Lab on a Chip
  4. Ott Scheler, Witold Postek, Piotr Garstecki (2018), Recent developments of microfluidics as a tool for biotechnology and microbiology, Current Opinion in Biotechnology, 55, 60–67
  5. Adam S. Opalski, Karol Makuch, Yu-Kai Lai, Ladislav Derzsi and Piotr Garstecki (2019), Grooved step emulsification systems optimize throughput of passive generation of monodisperse emulsions, Lab on a Chip, 19, 1183 – 1192
  6. Piotr Korczyk, Volkert Van Steijn, Slawomir Blonski, Damian Zaremba, David Beattie and Piotr Garstecki (2019), Accounting for corner flow unifies the understanding of droplet formation in microfluidic channels, Nature Communications 10, 2528
  7. Natalia Pacocha, Ott Scheler, Mikolaj Marcin Nowak, Ladislav Derzsi, Joanna Cichy and Piotr Garstecki (2019) Direct droplet digital PCR (dddPCR) for species specific, accurate and precise quantification of bacteria in mixed samples, Analytical Methods, 11, 5730–5735
  8. Yu-Ting Kao, Tomasz S. Kaminski, Witold Postek, Jan Guzowski, Karol Makuch, Artur Ruszczak, Felix von Stetten, Roland Zengerle and Piotr Garstecki (2020), Gravity-driven microfluidic assay for digital enumeration of bacteria and for antibiotic susceptibility testing , Lab on a Chip, 20, 54-63
  9. Adam S. Opalski, Artur Ruszczak, Yurii Promovych, Michał Horka, Ladislav Derzsi and Piotr Garstecki (2020), Combinatorial Antimicrobial Susceptibility Testing Enabled by Non-Contact Printing, Micromachines, 11, 142
  10. Ott Scheler, Karol Makuch, Pawel R. Debski, Michal Horka, Artur Ruszczak, Natalia Pacocha, Krzysztof Sozański, Olli-Pekka Smolander, Witold Postek and Piotr Garstecki, (2020), Droplet-based digital antibiotic susceptibility screen reveals single-cell clonal heteroresistance in an isogenic bacterial population, Scientific Reports, 10, 3282
  11. Adam S. Opalski, Karol Makuch, Ladislav Derzsi and Piotr Garstecki (2020), Split or slip – passive generation of monodisperse double emulsions with cores of varying viscosity in microfluidic tandem step emulsification system, RSC Advances, 10, 23058-23065
  12. Natalia Pacocha, Jakub Bogusławski, Michał Horka, Karol Makuch, Kamil Liżewski, Maciej Wojtkowski and Piotr Garstecki (2021), High-Throughput Monitoring of Bacterial Cell Density in Nanoliter Droplets: Label-Free Detection of Unmodified Gram-Positive and Gram-Negative Bacteria, Analytical Chememistry, 93, 2, 843–850
  13. Yu-Kai Lai, Adam S. Opalski, Piotr Garstecki, Ladislav Derzsi and Jan Guzowski (2022), A double-step emulsification device for direct generation of double emulsions, Soft Matter,18, 6157-6166


  1. Piotr GARSTECKI, Paweł DĘBSKI, Jarosław ZIÓŁKOWSKI, Piotr KNAP, „Microfluidic chip”, Bacteromic Sp. z o.o., European Patent Office, Patent number: EP18189586.3
  2. Piotr GARSTECKI, Jarosław ZIÓŁKOWSKI, Piotr KNAP, „Incubation segment”, Bacteromic Sp. z o.o., European Patent Office, Patent number: EP18189593.9
  3. Paweł DĘBSKI, Piotr GARSTECKI Bacteromic Sp. z o.o., “Method and system for rapidly testing antimicrobial susceptibility”, Bacteromic Sp. z o.o., European Patent Office, Patent number: EP18183741.0


Label-free and rapid optical imaging, detection and sorting of leukemia cells

Funding: Foundation for Polish Science within the TEAM NET programme (POIR.04.04.00-00-16ED/18)

Project period: 01.10.2019-31.12.2023

In this ambitious consortium project along with 5 top-notch research groups from Poland we aim to develop a state-of-the-art diagnostic device for early-stage leukemia detection and characterization by employing microfluidics coupled with stimulated Raman spectroscopy (SRS).


Leukemias are malignancies originating from hematopoietic or lymphoid precursors caused by genetic lesions leading to biochemical, proteomic and metabolomics abnormalities. Current leukemia diagnostics is based on genetic and phenotypic characterization of these changes. Due to complexity of methodologies used, the diagnostic process is often arbitrary and suffers of poor specificity (difficulties in classifying sub-types) which makes it difficult to establish the best therapeutic approach for the patients.

The RApID project (RAman Imaging for Diagnostics) aims to develop a cutting-edge Stimulated Raman Scattering (SRS) microscopic-microfluidic system for non-invasive imaging of live cells and apply it to rapid leukemia cell imaging, diagnostics and sorting. By integrating the multidisciplinary expertise from a broad range of fields (medicine, biology, (bio)chemistry, physics, engineering), consortium partners will characterize Raman spectra of leukemic cells and link them to clinico-biological features of the disease. These data will be thereafter used to design and construct a completely original, microfluidic diagnostic device utilizing SRS microscopy for label-free, rapid leukemia cell imaging, diagnostics and sorting. The device to be developed will be the first diagnostic tool exploiting this technology providing quantitative data and assisting clinicians in cost-effective early diagnostics and follow up of leukemia patients.


  • Ladislav Derzsi, PhD
  • Yurii Promovych, PhD
  • Abhay Kotnala, PhD
  • Shreyas Vasantham, MSc
  • Paweł Jankowski, PhD
  • Karol Makuch, PhD

Former team members

  • prof. Piotr Garstecki
  • Witold Postek, PhD
  • Agnieszka Koszewska, MSc
  • Łukasz Kozoń, MSc

Consortium partners

  • University of Warsaw
  • Laser Centre, Institute of Physical Chemistry, Polish Academy of Sciences
  • Jagiellonian University
  • Institute of Hematology and Transfusion Medicine
  • Medical University of Lodz


Microfluidic methods for quantitative antibiotic susceptibility assays with single cell resolution (2018/30/A/ST4/00036)

Funding: National Science Centre, Poland

Grant period: 01.10.2019-30.09.2024

Project description:

Antibiotic resistant infections continue to be one of the grimmest threats to human health. The problem can only be effectively solved by better understanding of the response of bacteria to antibiotics. It will help to avoid emergence of resistance and to guide effective treatment.

That is why the objective of our project is to develop a new set of analytical tools that will allow to characterize the complexity of how bacteria respond to antibiotics used in clinical practice. To this end we use droplet microfluidics – a set of techniques that enable generation of thousands or millions of tiny, identical droplets. These droplets may be formed of a suspension of bacteria, resulting in encapsulation of single (individual) bacterial cells, or multiple cells in the droplets. By adding antibiotics at a range of concentrations, we are able to prepare sets (libraries) of droplets, each library containing droplets with a well-defined concentration of the antibiotic and number of bacterial cells.

Team members

  • Principal Investigator: prof. Piotr Garstecki
  • Postdocs: dr Ilona Foik, dr Marcin Równicki, dr Shahab Shahryari
  • Co-investigator: dr Paweł Jankowski
  • PhD students: Shakeel Ahmad, Kinga Głuchowska

Project dissemination


Kinga Głuchowska, PhD student involved in the Maestro project, presented her research results at IChF PAN Microsympozjum. Her poster was entitled: „Quantitative, label-free and real-time monitoring of bacterial growth in nanoliter droplets”.


Artur Ruszczak, Paweł Jankowski, Shreyas Vasantham, Ott Scheler, Piotr Garstecki. Physicochemical properties predict retention of antibiotics in water in oil droplets. Analytical Chemistry January 4, 2023

Witold Postek, Natalia Pacocha, Piotr Garstecki. Microfluidics for antibiotic susceptibility testing. Lab on a Chip 2022, Advance Article, published 07 Sep 2022.

Artur Ruszczak, Simona Bartkova, Marta Zapotoczna, Ott Scheler, Piotr Garstecki. Droplet-based methods for tackling antimicrobial resistance. Current Opinion in Biotechnology, Volume 76, August 2022.

Yu-Ting Kao, Silvia Calabrese, Nadine Borst, Michael Lehnert, Yu-Kai Lai, Franziska Schlenker, Peter Juelg, Roland Zengerle, Piotr Garstecki, Felix von Stetten. Microfluidic one-pot digital droplet FISH using LNA/DNA molecular beacons for bacteria detection and absolute quantification. Biosensors 2022, 12(4), 237.

Witold Postek, Piotr Garstecki. Droplet microfluidics for high-throughput analysis of antibiotic susceptibility in bacterial cells and populations. Accounts of Chemical Research, 2022, 55, 5, 605–615.

Dominika Ogończyk, Paweł Jankowski, Piotr Garstecki. A method for simultaneous polishing and hydrophobization of polycarbonate for microfluidic applications. Polymers, 2020, 12(11), 2490.

EVOdrops: Doctoral Training Network in directed EVOlution in DROPS

The European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (813786)

  • Project manager: prof. Piotr Garstecki
  • PhD student: Francesco Nalin
  • Implementation period: 2019 – 2023

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 813786 (EVOdrops)


EVOdrops, a European training network, brings together the leading research scientists, laboratories and industries in Europe with outstanding expertise in protein engineering and microfluidics and 13 early stage researchers. We offer an extensive multi- and interdisciplinary training to ensure that they can solve these urgent and unmet challenges in biotechnology and biomedicine. We use a multidisciplinary approach combining soft matter, microfluidics and chemical biology to design solutions for the selection of new enzymes of industrial and therapeutic interest. In the future, our approaches can be generalized to challenges involving high-throughput miniaturised biochemical or cell-based assays.

EVOdrops is a translational approach for microfluidics and biochemical methods towards the engineering of proteins and systems of industrial or therapeutic interest. Two fundamental aspects of protein engineering will be effectively combined:

  1. Generation of a large and controlled genetic diversity usable as a pool of active catalysts containing unknown variants of interest.
  2. Analysis and selection at an ultra-high throughput of libraries to identify improved variants fulfilling the user-defined constraints (rate of catalysis, specificity, stability).

Project website:

From Postdoc to PI: The future leaders of ERA (PD2PI)

Project title: “The role of inter-bacteria interaction in antimicrobial resistance – droplet microfluidic approach to study urinary tract infections”. (Project no. 11)

The general aim of the project is to investigate the environmental factors affecting the emergence, development and mechanisms of antibiotic resistance in bacteria strains causing UTI.

PD2PI webpage:

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 847413.




  • Name of PD2PI fellow: dr. Ilona Paulina Foik
  • Name of mentor: Prof. dr hab. Piotr Garstecki