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Gestels Z, Baranchyk Y, Van den Bossche D, Laumen J, Abdellati S, Britto Xavier B, Manoharan-Basil SS, Kenyon C. Could traces of fluoroquinolones in food induce ciprofloxacin resistance in Escherichia coli and Klebsiella pneumoniae? An in vivo study in Galleria mellonella with important implications for maximum residue limits in food. Microbiol Spectr 2024; 12:e0359523. [PMID: 38687060 DOI: 10.1128/spectrum.03595-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
We hypothesized that the residual concentrations of fluoroquinolones allowed in food (acceptable daily intake-ADIs) could select for ciprofloxacin resistance in our resident microbiota. We developed models of chronic Escherichia coli and Klebsiella pneumoniae infection in Galleria mellonella larvae and exposed them to ADI doses of ciprofloxacin via single dosing and daily dosing regimens. The emergence of ciprofloxacin resistance was assessed via isolation of the target bacteria in selective agar plates. Exposure to as low as one-tenth of the ADI dose of the single and daily dosing regimens of ciprofloxacin resulted in the selection of ciprofloxacin resistance in K. pneumoniae but not E. coli. This resistance was associated with cross-resistance to doxycycline and ceftriaxone. Whole genome sequencing revealed inactivating mutations in the transcription repressors, ramR and rrf2, as well as mutations in gyrA and gyrB. We found that ciprofloxacin doses 10-fold lower than those classified as acceptable for daily intake could induce resistance to ciprofloxacin in K. pneumoniae. These results suggest that it would be prudent to include the induction of antimicrobial resistance as a significant criterion for determining ADIs and the associated maximum residue limits in food.IMPORTANCEThis study found that the concentrations of ciprofloxacin/enrofloxacin allowed in food can induce de novo ciprofloxacin resistance in Klebsiella pneumoniae. This suggests that it would be prudent to reconsider the criteria used to determine "safe" upper concentration limits in food.
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Affiliation(s)
- Zina Gestels
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Yuliia Baranchyk
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- UnivLyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Dorien Van den Bossche
- Clinical and Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jolein Laumen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Said Abdellati
- Clinical and Reference Laboratory, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Basil Britto Xavier
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Hospital Outbreak Support Team-HOST, Ziekenhuis Netwerk Antwerpen Middelheim, Antwerp, Belgium
| | | | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
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2
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Hansson A, Karlsen EA, Stensen W, Svendsen JSM, Berglin M, Lundgren A. Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy. ACS APPLIED MATERIALS & INTERFACES 2024; 16:6799-6812. [PMID: 38294883 PMCID: PMC10875647 DOI: 10.1021/acsami.3c16004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules' properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not function. It is particularly difficult to distinguish the influence of the AMP's molecular structure from other factors controlling the total exposure, including which type of bonds are formed between bacteria and the coating and how persistent these contacts are. Here, we combine label-free live-cell microscopy, microfluidics, and automated image analysis to study the response of surface-bound Escherichia coli challenged by the same small AMP either in solution or grafted to the surface through click chemistry. Initially after binding, the grafted AMPs inhibited bacterial growth more efficiently than did AMPs in solution. Yet, after 1 h, E. coli on the coated surfaces increased their expression of type-1 fimbriae, leading to a change in their binding mode, which diminished the coating's impact. The wealth of information obtained from continuously monitoring the growth, shape, and movements of single bacterial cells allowed us to elucidate and quantify the different factors determining the antibacterial efficacy of the grafted AMPs. We expect this approach to aid the design of elaborate antibacterial material coatings working by specific and selective actions, not limited to contact-killing. This technology is needed to support health care and food production in the postantibiotic era.
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Affiliation(s)
- Adam Hansson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Eskil André Karlsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Wenche Stensen
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - John S. M. Svendsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Mattias Berglin
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Anders Lundgren
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Centre
for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg 41346, Sweden
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3
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Zoheir AE, Stolle C, Rabe KS. Microfluidics for adaptation of microorganisms to stress: design and application. Appl Microbiol Biotechnol 2024; 108:162. [PMID: 38252163 PMCID: PMC10803453 DOI: 10.1007/s00253-024-13011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Microfluidic systems have fundamentally transformed the realm of adaptive laboratory evolution (ALE) for microorganisms by offering unparalleled control over environmental conditions, thereby optimizing mutant generation and desired trait selection. This review summarizes the substantial influence of microfluidic technologies and their design paradigms on microbial adaptation, with a primary focus on leveraging spatial stressor concentration gradients to enhance microbial growth in challenging environments. Specifically, microfluidic platforms tailored for scaled-down ALE processes not only enable highly autonomous and precise setups but also incorporate novel functionalities. These capabilities encompass fostering the growth of biofilms alongside planktonic cells, refining selection gradient profiles, and simulating adaptation dynamics akin to natural habitats. The integration of these aspects enables shaping phenotypes under pressure, presenting an unprecedented avenue for developing robust, stress-resistant strains, a feat not easily attainable using conventional ALE setups. The versatility of these microfluidic systems is not limited to fundamental research but also offers promising applications in various areas of stress resistance. As microfluidic technologies continue to evolve and merge with cutting-edge methodologies, they possess the potential not only to redefine the landscape of microbial adaptation studies but also to expedite advancements in various biotechnological areas. KEY POINTS: • Microfluidics enable precise microbial adaptation in controlled gradients. • Microfluidic ALE offers insights into stress resistance and distinguishes between resistance and persistence. • Integration of adaptation-influencing factors in microfluidic setups facilitates efficient generation of stress-resistant strains.
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Affiliation(s)
- Ahmed E Zoheir
- Department of Genetics and Cytology, Biotechnology Research Institute, National Research Centre (NRC), 33 El Buhouth St., Dokki, Cairo, 12622, Egypt
| | - Camilla Stolle
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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4
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Nguyen AV, Yaghoobi M, Zhang S, Li P, Li Q, Dogan B, Ahnrud GP, Flock G, Marek P, Simpson KW, Abbaspourrad A. Adaptive Laboratory Evolution of Probiotics toward Oxidative Stress Using a Microfluidic-Based Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2306974. [PMID: 38247174 DOI: 10.1002/smll.202306974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/28/2023] [Indexed: 01/23/2024]
Abstract
Adaptive laboratory evolution (ALE) can be used to make bacteria less susceptible to oxidative stress. An alternative to large batch scale ALE cultures is to use microfluidic platforms, which are often more economical and more efficient. Microfluidic ALE platforms have shown promise, but many have suffered from subpar cell passaging mechanisms and poor spatial definition. A new approach is presented using a microfluidic Evolution on a Chip (EVoc) design which progressively drives microbial cells from areas of lower H2 O2 concentration to areas of higher concentration. Prolonged exposure, up to 72 h, revealed the survival of adaptive strains of Lacticaseibacillus rhamnosus GG, a beneficial probiotic often included in food products. After performing ALE on this microfluidic platform, the bacteria persisted under high H2 O2 concentrations in repeated trials. After two progressive exposures, the ability of L. rhamnosus to grow in the presence of H2 O2 increased from 1 mm H2 O2 after a lag time of 31 h to 1 mm after 21 h, 2 mm after 28 h, and 3 mm after 42 h. The adaptive strains have different morphology, and gene expression compared to wild type, and genome sequencing revealed a potentially meaningful single nucleotide mutation in the protein omega-amidase.
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Affiliation(s)
- Ann V Nguyen
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Mohammad Yaghoobi
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Shiying Zhang
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Peilong Li
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Qike Li
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
| | - Belgin Dogan
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Gianna P Ahnrud
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Genevieve Flock
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Patrick Marek
- DEVCOM Soldier Center, Soldier Sustainment Directorate, Combat Feeding Division, Food Protection & Innovative Packaging Team, Natick, MA, 01760, USA
| | - Kenneth W Simpson
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, 602 Tower Rd., Ithaca, NY, 14853, USA
| | - Alireza Abbaspourrad
- Department of Food Science, College of Agricultural and Life Sciences, Cornell University, Stocking Hall, Ithaca, NY, 14853, USA
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5
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Huang C, Guo F, Wang H, Olivares J, Dalton Iii J, Belyanina O, Wattam AR, Cucinell CA, Dickerman AW, Qin QM, Han A, de Figueiredo P. An automated system for interrogating the evolution of microbial endosymbiosis. LAB ON A CHIP 2023; 23:671-683. [PMID: 36227118 DOI: 10.1039/d2lc00602b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Inter-kingdom endosymbiotic interactions between bacteria and eukaryotic cells are critical to human health and disease. However, the molecular mechanisms that drive the emergence of endosymbiosis remain obscure. Here, we describe the development of a microfluidic system, named SEER (S̲ystem for the E̲volution of E̲ndosymbiotic R̲elationships), that automates the evolutionary selection of bacteria with enhanced intracellular survival and persistence within host cells, hallmarks of endosymbiosis. Using this system, we show that a laboratory strain of Escherichia coli that initially possessed limited abilities to survive within host cells, when subjected to SEER selection, rapidly evolved to display a 55-fold enhancement in intracellular survival. Notably, molecular dissection of the evolved strains revealed that a single-point mutation in a flexible loop of CpxR, a gene regulator that controls bacterial stress responses, substantially contributed to this intracellular survival. Taken together, these results establish SEER as the first microfluidic system for investigating the evolution of endosymbiosis, show the importance of CpxR in endosymbiosis, and set the stage for evolving bespoke inter-kingdom endosymbiotic systems with novel or emergent properties.
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Affiliation(s)
- Can Huang
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Fengguang Guo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Han Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Jasmine Olivares
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - James Dalton Iii
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Olga Belyanina
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Alice R Wattam
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Clark A Cucinell
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Allan W Dickerman
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA 22904, USA
| | - Qing-Ming Qin
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX 77843, USA.
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
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6
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Adaptive Laboratory Evolution of Microorganisms: Methodology and Application for Bioproduction. Microorganisms 2022; 11:microorganisms11010092. [PMID: 36677384 PMCID: PMC9864036 DOI: 10.3390/microorganisms11010092] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Adaptive laboratory evolution (ALE) is a useful experimental methodology for fundamental scientific research and industrial applications to create microbial cell factories. By using ALE, cells are adapted to the environment that researchers set based on their objectives through the serial transfer of cell populations in batch cultivations or continuous cultures and the fitness of the cells (i.e., cell growth) under such an environment increases. Then, omics analyses of the evolved mutants, including genome sequencing, transcriptome, proteome and metabolome analyses, are performed. It is expected that researchers can understand the evolutionary adaptation processes, and for industrial applications, researchers can create useful microorganisms that exhibit increased carbon source availability, stress tolerance, and production of target compounds based on omics analysis data. In this review article, the methodologies for ALE in microorganisms are introduced. Moreover, the application of ALE for the creation of useful microorganisms as cell factories has also been introduced.
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7
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Zoheir A, Meisch L, Martín MV, Bickmann C, Kiselev A, Lenk F, Kaster AK, Rabe KS, Niemeyer CM. Macroporous Silicone Chips for Decoding Microbial Dark Matter in Environmental Microbiomes. ACS APPLIED MATERIALS & INTERFACES 2022; 14:49592-49603. [PMID: 36288792 PMCID: PMC9650684 DOI: 10.1021/acsami.2c15470] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Natural evolution has produced an almost infinite variety of microorganisms that can colonize almost any conceivable habitat. Since the vast majority of these microbial consortia are still unknown, there is a great need to elucidate this "microbial dark matter" (MDM) to enable exploitation in biotechnology. We report the fabrication and application of a novel device that integrates a matrix of macroporous elastomeric silicone foam (MESIF) into an easily fabricated and scalable chip design that can be used for decoding MDM in environmental microbiomes. Technical validation, performed with the model organism Escherichia coli expressing a fluorescent protein, showed that this low-cost, bioinert, and widely modifiable chip is rapidly colonized by microorganisms. The biological potential of the chip was then illustrated through targeted sampling and enrichment of microbiomes in a variety of habitats ranging from wet, turbulent moving bed biofilters and wastewater treatment plants to dry air-based environments. Sequencing analyses consistently showed that MESIF chips are not only suitable for sampling with high robustness but also that the material can be used to detect a broad cross section of microorganisms present in the habitat in a short time span of a few days. For example, results from the biofilter habitat showed efficient enrichment of microorganisms belonging to the enigmatic Candidate Phyla Radiation, which comprise ∼70% of the MDM. From dry air, the MESIF chip was able to enrich a variety of members of Actinobacteriota, which is known to produce specific secondary metabolites. Targeted sampling from a wastewater treatment plant where the herbicide glyphosate was added to the chip's reservoir resulted in enrichment of Cyanobacteria and Desulfobacteria, previously associated with glyphosate degradation. These initial case studies suggest that this chip is very well suited for the systematic study of MDM and opens opportunities for the cultivation of previously unculturable microorganisms.
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Affiliation(s)
- Ahmed
E. Zoheir
- Institute
for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
- Biotechnology
Research Institute, Department of Genetics and Cytology, National Research Centre (NRC), 33 El Buhouth St., Dokki, 12622 Cairo, Egypt
| | - Laura Meisch
- Institute
for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Marta Velaz Martín
- Institute
for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Christoph Bickmann
- Institute
for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Alexei Kiselev
- Institute
of Meteorology and Climate Research, Department of Atmospheric Aerosol
Research (IMK-AAF), Karlsruhe Institute
of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Florian Lenk
- Institute
for Biological Interfaces 5 (IBG-5), Biotechnology and Microbial Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344 Karlsruhe, Germany
| | - Anne-Kristin Kaster
- Institute
for Biological Interfaces 5 (IBG-5), Biotechnology and Microbial Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344 Karlsruhe, Germany
| | - Kersten S. Rabe
- Institute
for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute
for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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8
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Biofilm antimicrobial susceptibility through an experimental evolutionary lens. NPJ Biofilms Microbiomes 2022; 8:82. [PMID: 36257971 PMCID: PMC9579162 DOI: 10.1038/s41522-022-00346-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
Experimental evolution experiments in which bacterial populations are repeatedly exposed to an antimicrobial treatment, and examination of the genotype and phenotype of the resulting evolved bacteria, can help shed light on mechanisms behind reduced susceptibility. In this review we present an overview of why it is important to include biofilms in experimental evolution, which approaches are available to study experimental evolution in biofilms and what experimental evolution has taught us about tolerance and resistance in biofilms. Finally, we present an emerging consensus view on biofilm antimicrobial susceptibility supported by data obtained during experimental evolution studies.
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9
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Tang PC, Eriksson O, Sjögren J, Fatsis-Kavalopoulos N, Kreuger J, Andersson DI. A Microfluidic Chip for Studies of the Dynamics of Antibiotic Resistance Selection in Bacterial Biofilms. Front Cell Infect Microbiol 2022; 12:896149. [PMID: 35619647 PMCID: PMC9128571 DOI: 10.3389/fcimb.2022.896149] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 01/01/2023] Open
Abstract
Biofilms are arguably the most important mode of growth of bacteria, but how antibiotic resistance emerges and is selected in biofilms remains poorly understood. Several models to study evolution of antibiotic resistance have been developed, however, their usability varies depending on the nature of the biological question. Here, we developed and validated a microfluidic chip (Brimor) for studying the dynamics of enrichment of antibiotic-resistant bacteria in biofilms using real-time monitoring with confocal microscopy. In situ extracellular cellulose staining and physical disruption of the biomass confirmed Escherichia coli growth as biofilms in the chip. We showed that seven generations of growth occur in 16 h when biofilms were established in the growth chambers of Brimor, and that bacterial death and growth rates could be estimated under these conditions using a plasmid with a conditional replication origin. Additionally, competition experiments between antibiotic-susceptible and -resistant bacteria at sub-inhibitory concentrations demonstrated that the antibiotic ciprofloxacin selected for antibiotic resistance in bacterial biofilms at concentrations 17-fold below the minimal inhibitory concentration of susceptible planktonic bacteria. Overall, the microfluidic chip is easy to use and a relevant model for studying the dynamics of selection of antibiotic resistance in bacterial biofilms and we anticipate that the Brimor chip will facilitate basic research in this area.
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Affiliation(s)
- Po-Cheng Tang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Olle Eriksson
- U-Print, Uppsala University 3D-Printing Facility, Uppsala University, Uppsala, Sweden
| | | | | | - Johan Kreuger
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
- *Correspondence: Dan I. Andersson, ; Johan Kreuger,
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- *Correspondence: Dan I. Andersson, ; Johan Kreuger,
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10
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Kriukov DV, Koyuncu AH, Wong ASY. History Dependence in a Chemical Reaction Network Enables Dynamic Switching. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107523. [PMID: 35257479 DOI: 10.1002/smll.202107523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/02/2022] [Indexed: 06/14/2023]
Abstract
This work describes an enzymatic autocatalytic network capable of dynamic switching under out-of-equilibrium conditions. The network, wherein a molecular fuel (trypsinogen) and an inhibitor (soybean trypsin inhibitor) compete for a catalyst (trypsin), is kept from reaching equilibria using a continuous flow stirred tank reactor. A so-called 'linear inhibition sweep' is developed (i.e., a molecular analogue of linear sweep voltammetry) to intentionally perturb the competition between autocatalysis and inhibition, and used to demonstrate that a simple molecular system, comprising only three components, is already capable of a variety of essential neuromorphic behaviors (hysteresis, synchronization, resonance, and adaptation). This research provides the first steps in the development of a strategy that uses the principles in systems chemistry to transform chemical reaction networks into platforms capable of neural network computing.
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Affiliation(s)
- Dmitrii V Kriukov
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
| | - A Hazal Koyuncu
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
| | - Albert S Y Wong
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
- MESA+ Institute for Nanotechnology, University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
- BRAINS (Center for Brain-inspired Nano Systems), University of Twente, Drienerlolaan 5, Enschede, 7522 NH, The Netherlands
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