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Villalba MI, Gligorovski V, Rahi SJ, Willaert RG, Kasas S. A simplified version of rapid susceptibility testing of bacteria and yeasts using optical nanomotion detection. Front Microbiol 2024; 15:1328923. [PMID: 38516011 PMCID: PMC10956355 DOI: 10.3389/fmicb.2024.1328923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
We present a novel optical nanomotion-based rapid antibiotic and antifungal susceptibility test. The technique consisted of studying the effects of antibiotics or antifungals on the nanometric scale displacements of bacteria or yeasts to assess their sensitivity or resistance to drugs. The technique relies on a traditional optical microscope, a video camera, and custom-made image analysis software. It provides reliable results in a time frame of 2-4 h and can be applied to motile, non-motile, fast, and slowly growing microorganisms. Due to its extreme simplicity and low cost, the technique can be easily implemented in laboratories and medical centers in developing countries.
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Affiliation(s)
- Maria I. Villalba
- Laboratory of Biological Electron Microscopy (LBEM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Université de Lausanne, Lausanne, Switzerland
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine (NANO), Brussels, Switzerland
| | - Vojislav Gligorovski
- Laboratory of the Physics of Biological Systems (LPBS), Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sahand J. Rahi
- Laboratory of the Physics of Biological Systems (LPBS), Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ronnie G. Willaert
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine (NANO), Brussels, Switzerland
- Research Group Structural Biology Brussels, Alliance Research Group VUB-UGhent NanoMicrobiology (NAMI), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Sandor Kasas
- Laboratory of Biological Electron Microscopy (LBEM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Université de Lausanne, Lausanne, Switzerland
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine (NANO), Brussels, Switzerland
- Centre Universitaire Romand de Médecine Légale (UFAM), Université de Lausanne, Lausanne, Switzerland
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Kweku D, Villalba MI, Willaert RG, Yantorno OM, Vela ME, Panorska AK, Kasas S. Machine learning method for the classification of the state of living organisms' oscillations. Front Bioeng Biotechnol 2024; 12:1348106. [PMID: 38515626 PMCID: PMC10955466 DOI: 10.3389/fbioe.2024.1348106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
The World Health Organization highlights the urgent need to address the global threat posed by antibiotic-resistant bacteria. Efficient and rapid detection of bacterial response to antibiotics and their virulence state is crucial for the effective treatment of bacterial infections. However, current methods for investigating bacterial antibiotic response and metabolic state are time-consuming and lack accuracy. To address these limitations, we propose a novel method for classifying bacterial virulence based on statistical analysis of nanomotion recordings. We demonstrated the method by classifying living Bordetella pertussis bacteria in the virulent or avirulence phase, and dead bacteria, based on their cellular nanomotion signal. Our method offers significant advantages over current approaches, as it is faster and more accurate. Additionally, its versatility allows for the analysis of cellular nanomotion in various applications beyond bacterial virulence classification.
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Affiliation(s)
- David Kweku
- Department of Mathematics and Statistics, University of Nevada Reno, Reno, NV, United States
| | - Maria I. Villalba
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL) and University of Lausanne, Lausanne, Switzerland
- International Joint Research Group VUB-EPFL BioNanotechnology and NanoMedicine (NANO), Brussels, Switzerland
| | - Ronnie G. Willaert
- International Joint Research Group VUB-EPFL BioNanotechnology and NanoMedicine (NANO), Brussels, Switzerland
- Research Group Structural Biology Brussels, Alliance Research Group VUB-UGhent NanoMicrobiology (NAMI), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Osvaldo M. Yantorno
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI), Facultad de Ciencias Exactas, Universidad Nacional de La Plata—CONICET, Buenos Aires, Argentina
| | - Maria E. Vela
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata—CONICET, Buenos Aires, Argentina
| | - Anna K. Panorska
- Department of Mathematics and Statistics, University of Nevada Reno, Reno, NV, United States
| | - Sandor Kasas
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL) and University of Lausanne, Lausanne, Switzerland
- International Joint Research Group VUB-EPFL BioNanotechnology and NanoMedicine (NANO), Brussels, Switzerland
- Centre Universitaire Romand de Médecine Légale, Unité facultaire d’anatomie et de morphologie (UFAM), Université de Lausanne, Lausanne, Switzerland
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Villalba MI, Rossetti E, Bonvallat A, Yvanoff C, Radonicic V, Willaert RG, Kasas S. Simple optical nanomotion method for single-bacterium viability and antibiotic response testing. Proc Natl Acad Sci U S A 2023; 120:e2221284120. [PMID: 37094120 PMCID: PMC10160964 DOI: 10.1073/pnas.2221284120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Antibiotic resistance is nowadays a major public health issue. Rapid antimicrobial susceptibility tests (AST) are one of the options to fight this deadly threat. Performing AST with single-cell sensitivity that is rapid, cheap, and widely accessible, is challenging. Recent studies demonstrated that monitoring bacterial nanomotion by using atomic force microscopy (AFM) upon exposure to antibiotics constitutes a rapid and highly efficient AST. Here, we present a nanomotion detection method based on optical microscopy for testing bacterial viability. This novel technique only requires a very basic microfluidic analysis chamber, and an optical microscope equipped with a camera or a mobile phone. No attachment of the microorganisms is needed, nor are specific bacterial stains or markers. This single-cell technique was successfully tested to obtain AST for motile, nonmotile, gram-positive, and gram-negative bacteria. The simplicity and efficiency of the method make it a game-changer in the field of rapid AST.
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Affiliation(s)
- Maria I Villalba
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- International Joint Research Group Vrije Universiteit Brussel-École Polytechnique Fédérale de Lausanne NanoBiotechnology and NanoMedicine, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Eugenia Rossetti
- Centre Universitaire Romand de Médecine Légale, Unité Facultaire d'Anatomie et de Morphologie, University of Lausanne, Lausanne 1015, Switzerland
| | - Allan Bonvallat
- Centre Universitaire Romand de Médecine Légale, Unité Facultaire d'Anatomie et de Morphologie, University of Lausanne, Lausanne 1015, Switzerland
| | - Charlotte Yvanoff
- International Joint Research Group Vrije Universiteit Brussel-École Polytechnique Fédérale de Lausanne NanoBiotechnology and NanoMedicine, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Research Group Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Alliance Research Group Vrije Universiteit Brussel-UGent NanoMicrobiology, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Vjera Radonicic
- International Joint Research Group Vrije Universiteit Brussel-École Polytechnique Fédérale de Lausanne NanoBiotechnology and NanoMedicine, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Research Group Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Alliance Research Group Vrije Universiteit Brussel-UGent NanoMicrobiology, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Ronnie G Willaert
- International Joint Research Group Vrije Universiteit Brussel-École Polytechnique Fédérale de Lausanne NanoBiotechnology and NanoMedicine, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Research Group Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Alliance Research Group Vrije Universiteit Brussel-UGent NanoMicrobiology, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Sandor Kasas
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- International Joint Research Group Vrije Universiteit Brussel-École Polytechnique Fédérale de Lausanne NanoBiotechnology and NanoMedicine, Vrije Universiteit Brussel, Brussels 1050, Belgium
- Centre Universitaire Romand de Médecine Légale, Unité Facultaire d'Anatomie et de Morphologie, University of Lausanne, Lausanne 1015, Switzerland
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Villalba MI, Venturelli L, Willaert R, Vela ME, Yantorno O, Dietler G, Longo G, Kasas S. Nanomotion Spectroscopy as a New Approach to Characterize Bacterial Virulence. Microorganisms 2021; 9:microorganisms9081545. [PMID: 34442624 PMCID: PMC8398272 DOI: 10.3390/microorganisms9081545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022] Open
Abstract
Atomic force microscopy (AFM)-based nanomotion detection is a label-free technique that has been used to monitor the response of microorganisms to antibiotics in a time frame of minutes. The method consists of attaching living organisms onto an AFM cantilever and in monitoring its nanometric scale oscillations as a function of different physical-chemical stimuli. Up to now, we only used the cantilever oscillations variance signal to assess the viability of the attached organisms. In this contribution, we demonstrate that a more precise analysis of the motion pattern of the cantilever can unveil relevant medical information about bacterial phenotype. We used B. pertussis as the model organism, it is a slowly growing Gram-negative bacteria which is the agent of whooping cough. It was previously demonstrated that B. pertussis can expresses different phenotypes as a function of the physical-chemical properties of the environment. In this contribution, we highlight that B. pertussis generates a cantilever movement pattern that depends on its phenotype. More precisely, we noticed that nanometric scale oscillations of B. pertussis can be correlated with the virulence state of the bacteria. The results indicate a correlation between metabolic/virulent bacterial states and bacterial nanomotion pattern and paves the way to novel rapid and label-free pathogenic microorganism detection assays.
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Affiliation(s)
- Maria I. Villalba
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (M.I.V.); (L.V.); (G.D.)
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI), Facultad de Ciencias Exactas, Universidad Nacional de La Plata-CONICET, 1900 La Plata, Argentina;
| | - Leonardo Venturelli
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (M.I.V.); (L.V.); (G.D.)
| | - Ronnie Willaert
- Research Group Structural Biology Brussels, Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), 1050 Brussels, Belgium;
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, 1050 Brussels, Belgium
| | - Maria E. Vela
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, 1900 La Plata, Argentina;
| | - Osvaldo Yantorno
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI), Facultad de Ciencias Exactas, Universidad Nacional de La Plata-CONICET, 1900 La Plata, Argentina;
| | - Giovanni Dietler
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (M.I.V.); (L.V.); (G.D.)
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, 1050 Brussels, Belgium
| | - Giovanni Longo
- Istituto Di Struttura Della Materia–CNR, 00133 Roma, Italy;
| | - Sandor Kasas
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (M.I.V.); (L.V.); (G.D.)
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, 1050 Brussels, Belgium
- Centre Universitaire Romand de Médecine Légale, UFAM, Université de Lausanne, 1015 Lausanne, Switzerland
- Correspondence:
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Cisneros L, Cattelan N, Villalba MI, Rodriguez C, Serra DO, Yantorno O, Fadda S. Lactic acid bacteria biofilms and their ability to mitigate Escherichia coli O157:H7 surface colonization. Lett Appl Microbiol 2021; 73:247-256. [PMID: 34008189 DOI: 10.1111/lam.13509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/14/2021] [Accepted: 05/07/2021] [Indexed: 11/29/2022]
Abstract
Lactic acid bacteria (LAB) exert antagonistic activities against diverse microorganisms, including pathogens. In this work, we aimed to investigate the ability of LAB strains isolated from food to produce biofilms and to inhibit growth and surface colonization of Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 at 10°C. The ability of 100 isolated LAB to inhibit EHEC O157:H7 NCTC12900 growth was evaluated in agar diffusion assays. Thirty-seven LAB strains showed strong growth inhibitory effect on EHEC. The highest inhibitory activities corresponded to LAB strains belonging to Lactiplantibacillus plantarum, Pediococcus acidilactici and Pediococcus pentosaceus species. Eighteen out of the 37 strains that showed growth inhibitory effects on EHEC also had the ability to form biofilms on polystyrene surfaces at 10°C and 30°C. Pre-established biofilms on polystyrene of four of these LAB strains were able to reduce significantly surface colonization by EHEC at low temperature (10°C). Among these four strains, Lact. plantarum CRL 1075 not only inhibited EHEC but also was able to grow in the presence of the enteric pathogen. Therefore, this strain proved to be a good candidate for further technological studies oriented to its application in food-processing environments to mitigate undesirable surface contaminations of E. coli.
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Affiliation(s)
- L Cisneros
- Centro de Referencia para Lactobacilos (CERELA), CONICET, Tucumán, Argentina
| | - N Cattelan
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI-CONICET), Facultad de Ciencias Exactas, UNLP, Buenos Aires, Argentina.,Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - M I Villalba
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI-CONICET), Facultad de Ciencias Exactas, UNLP, Buenos Aires, Argentina
| | - C Rodriguez
- Centro de Referencia para Lactobacilos (CERELA), CONICET, Tucumán, Argentina
| | - D O Serra
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET, UNR), Predio CONICET Rosario, Ocampo y Esmeralda (2000), Rosario, Argentina
| | - O Yantorno
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI-CONICET), Facultad de Ciencias Exactas, UNLP, Buenos Aires, Argentina
| | - S Fadda
- Centro de Referencia para Lactobacilos (CERELA), CONICET, Tucumán, Argentina
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Venturelli L, Kohler AC, Stupar P, Villalba MI, Kalauzi A, Radotic K, Bertacchi M, Dinarelli S, Girasole M, Pešić M, Banković J, Vela ME, Yantorno O, Willaert R, Dietler G, Longo G, Kasas S. A perspective view on the nanomotion detection of living organisms and its features. J Mol Recognit 2020; 33:e2849. [PMID: 32227521 DOI: 10.1002/jmr.2849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 12/23/2022]
Abstract
The insurgence of newly arising, rapidly developing health threats, such as drug-resistant bacteria and cancers, is one of the most urgent public-health issues of modern times. This menace calls for the development of sensitive and reliable diagnostic tools to monitor the response of single cells to chemical or pharmaceutical stimuli. Recently, it has been demonstrated that all living organisms oscillate at a nanometric scale and that these oscillations stop as soon as the organisms die. These nanometric scale oscillations can be detected by depositing living cells onto a micro-fabricated cantilever and by monitoring its displacements with an atomic force microscope-based electronics. Such devices, named nanomotion sensors, have been employed to determine the resistance profiles of life-threatening bacteria within minutes, to evaluate, among others, the effect of chemicals on yeast, neurons, and cancer cells. The data obtained so far demonstrate the advantages of nanomotion sensing devices in rapidly characterizing microorganism susceptibility to pharmaceutical agents. Here, we review the key aspects of this technique, presenting its major applications. and detailing its working protocols.
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Affiliation(s)
- Leonardo Venturelli
- Laboratoire de Physique de la Matière Vivante, Institut de Physique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anne-Céline Kohler
- Laboratoire de Physique de la Matière Vivante, Institut de Physique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Petar Stupar
- Laboratoire de Physique de la Matière Vivante, Institut de Physique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Maria I Villalba
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI-CONICET-CCT La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Aleksandar Kalauzi
- Institute for Multidisciplinary Research, Department of Life Sciences, University of Belgrade, Belgrade, Serbia
| | - Ksenija Radotic
- Institute for Multidisciplinary Research, Department of Life Sciences, University of Belgrade, Belgrade, Serbia
| | | | - Simone Dinarelli
- Consiglio Nazionale delle Ricerche - Istituto di Struttura della Materia, CNR-ISM, Rome, Italy
| | - Marco Girasole
- Consiglio Nazionale delle Ricerche - Istituto di Struttura della Materia, CNR-ISM, Rome, Italy
| | - Milica Pešić
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković" National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jasna Banković
- Department of Neurobiology, Institute for Biological Research "Siniša Stanković" National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Maria E Vela
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA-CONICET-CCT La Plata), Universidad Nacional de La Plata, La Plata, Argentina
| | - Osvaldo Yantorno
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI-CONICET-CCT La Plata), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Ronnie Willaert
- ARG VUB-UGent NanoMicrobiology, IJRG VUB-EPFL BioNanotechnology & NanoMedicine, Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Giovanni Dietler
- Laboratoire de Physique de la Matière Vivante, Institut de Physique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Giovanni Longo
- Consiglio Nazionale delle Ricerche - Istituto di Struttura della Materia, CNR-ISM, Rome, Italy
| | - Sandor Kasas
- Laboratoire de Physique de la Matière Vivante, Institut de Physique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Centre Universitaire Romand de Médecine Légale, UFAM, Université de Lausanne, Lausanne, Switzerland
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