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Barbotin A, Billaudeau C, Sezgin E, Carballido-López R. Quantification of membrane fluidity in bacteria using TIR-FCS. Biophys J 2024; 123:2484-2495. [PMID: 38877702 PMCID: PMC11365102 DOI: 10.1016/j.bpj.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Plasma membrane fluidity is an important phenotypic feature that regulates the diffusion, function, and folding of transmembrane and membrane-associated proteins. In bacterial cells, variations in membrane fluidity are known to affect respiration, transport, and antibiotic resistance. Membrane fluidity must therefore be tightly regulated to adapt to environmental variations and stresses such as temperature fluctuations or osmotic shocks. Quantitative investigation of bacterial membrane fluidity has been, however, limited due to the lack of available tools, primarily due to the small size and membrane curvature of bacteria that preclude most conventional analysis methods used in eukaryotes. Here, we develop an assay based on total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) to directly measure membrane fluidity in live bacteria via the diffusivity of fluorescent membrane markers. With simulations validated by experiments, we could determine how the small size, high curvature, and geometry of bacteria affect diffusion measurements and correct subsequent measurements for unbiased diffusion coefficient estimation. We used this assay to quantify the fluidity of the cytoplasmic membranes of the Gram-positive bacteria Bacillus subtilis (rod-shaped) and Staphylococcus aureus (coccus) at high (37°C) and low (20°C) temperatures in a steady state and in response to a cold shock, caused by a shift from high to low temperature. The steady-state fluidity was lower at 20°C than at 37°C, yet differed between B. subtilis and S. aureus at 37°C. Upon cold shock, the membrane fluidity decreased further below the steady-state fluidity at 20°C and recovered within 30 min in both bacterial species. Our minimally invasive assay opens up exciting perspectives for the study of a wide range of phenomena affecting the bacterial membrane, from disruption by chemicals or antibiotics to viral infection or change in nutrient availability.
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Affiliation(s)
- Aurélien Barbotin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Cyrille Billaudeau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Rut Carballido-López
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
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Dubey AK, Sardana D, Verma T, Alam P, Chattopadhyay A, Nandini SS, Khamari B, Bulagonda EP, Sen S, Nandi D. Quantifying Membrane Alterations with Tailored Fluorescent Dyes: A Rapid Antibiotic Resistance Profiling Methodology. ACS Infect Dis 2024; 10:2836-2859. [PMID: 39024306 DOI: 10.1021/acsinfecdis.4c00249] [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] [Indexed: 07/20/2024]
Abstract
Accurate detection of bacterial antibiotic sensitivity is crucial for theranostics and the containment of antibiotic-resistant infections. However, the intricate task of detecting and quantifying the antibiotic-induced changes in the bacterial cytoplasmic membrane, and their correlation with other metabolic pathways leading to antibiotic resistance, poses significant challenges. Using a novel class of 4-aminophthalimide (4AP)-based fluorescent dyes with precisely tailored alkyl chains, namely 4AP-C9 and 4AP-C13, we quantify stress-mediated alterations in E. coli membranes. Leveraging the unique depth-dependent positioning and environment-sensitive fluorescence properties of these dyes, we detect antibiotic-induced membrane damage through single-cell imaging and monitoring the fluorescence peak maxima difference ratio (PMDR) of the dyes within the bacterial membrane, complemented by other methods. The correlation between the ROS-induced cytoplasmic membrane damage and the PMDR of dyes quantifies sensitivity against bactericidal antibiotics, which correlates to antibiotic-induced lipid peroxidation. Significantly, our findings largely extend to clinical isolates of E. coli and other ESKAPE pathogens like K. pneumoniae and Enterobacter subspecies. Our data reveal that 4AP-Cn probes can potentially act as precise scales to detect antibiotic-induced membrane damage ("thinning") occurring at a subnanometer scale through the quantification of dyes' PMDR, making them promising membrane dyes for rapid detection of bacterial antibiotic resistance, distinguishing sensitive and resistant infections with high specificity in a clinical setup.
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Affiliation(s)
- Ashim Kumar Dubey
- Undergraduate Programme, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Deepika Sardana
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Taru Verma
- Centre for BioSystems, Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Parvez Alam
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Avik Chattopadhyay
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Santhi Sanil Nandini
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Eswarappa Pradeep Bulagonda
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Sobhan Sen
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
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Chen J, Zhong J, Chang Y, Zhou Y, Koo SH, Tan TY, Lei H, Ai Y. Rapid and Accurate Antimicrobial Susceptibility Testing Using Label-Free Electrical Impedance-Based Microfluidic Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2303352. [PMID: 37794624 DOI: 10.1002/smll.202303352] [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: 04/20/2023] [Revised: 08/01/2023] [Indexed: 10/06/2023]
Abstract
Antimicrobial resistance has become a serious threat to the global public health. Accurate and rapid antimicrobial susceptibility testing (AST) allows evidence-based prescribing of antibiotics to improve patient care and clinical outcomes. Current culture-based AST assays are inherently limited by the doubling time of bacterial reproduction, which require at least 24 h to have a decisive result. Herein, a label-free electrical impedance-based microfluidic platform designed to expedite and streamline AST procedure for clinical practice is presented. Following a 30-min exposure of bacterial samples to antibiotics, the presented high-throughput, single-bacterium level impedance characterization platform enables a rapid 2-min AST assay. The platform facilitates accurate analysis of individual bacterial viability, as indicated by changes in electrical characteristics, thereby enabling the determination of antimicrobial resistance. Moreover, the potential clinical applicability of this platform is demonstrated by testing different E. coli strains against five antibiotics, yielding 100% categorical agreements compared to standard culture methods.
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Affiliation(s)
- Jiahong Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety/National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Yifu Chang
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Avenida da Universidade, Taipa, Macau, 999078, China
| | - Yinning Zhou
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Avenida da Universidade, Taipa, Macau, 999078, China
| | - Seok Hwee Koo
- Department of Laboratory Medicine, Changi General Hospital, Singapore, 529889, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, Singapore, 529889, Singapore
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
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Singh S, Verma T, Khamari B, Bulagonda EP, Nandi D, Umapathy S. Antimicrobial Resistance Studies Using Raman Spectroscopy on Clinically Relevant Bacterial Strains. Anal Chem 2023. [PMID: 37463121 DOI: 10.1021/acs.analchem.3c01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
There has been a steep rise in the emergence of antibiotic-resistant bacteria in the past few years. A timely diagnosis can help in initiating appropriate antibiotic therapy. However, conventional techniques for diagnosing antibiotic resistance are time-consuming and labor-intensive. Therefore, we investigated the potential of Raman spectroscopy as a rapid surveillance technology for tracking the emergence of antibiotic resistance. In this study, we used Raman spectroscopy to differentiate clinical isolates of antibiotic-resistant and -sensitive bacteria of Escherichia coli, Acinetobacter baumannii, and Enterobacter species. The spectra were collected with or without exposure to various antibiotics (ciprofloxacin, gentamicin, meropenem, and nitrofurantoin), each having a distinct mechanism of action. Ciprofloxacin- and meropenem-treated sensitive strains showed a decrease in the intensity of Raman bands associated with DNA (667, 724, 785, 1378, 1480, and 1575 cm-1) and proteins (640 and 1662 cm-1), coupled with an increase in the intensity of lipid bands (891, 960, and 1445 cm-1). Gentamicin- and nitrofurantoin-treated sensitive strains showed an increase in the intensity of nucleic acid bands (668, 724, 780, 810, 1378, 1480, and 1575 cm-1) while a decrease in the intensity of protein bands (640, 1003, 1606, and 1662 cm-1) and the lipid band (1445 cm-1). The Raman spectral changes observed in the antibiotic-resistant strains were opposite to that of antibiotic-sensitive strains. The Raman spectral data correlated well with the antimicrobial susceptibility test results. The Raman spectral dataset was used for partial least-squares (PLS) analysis to validate the biomarkers obtained from the univariate analysis. Overall, this study showcases the potential of Raman spectroscopy for detecting antibiotic-resistant and -sensitive bacteria.
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Affiliation(s)
- Saumya Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Taru Verma
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Balaram Khamari
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Eswarappa Pradeep Bulagonda
- Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Puttaparthi 515134, Andhra Pradesh, India
| | - Dipankar Nandi
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, Karnataka, India
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Crane JK, Catanzaro MN. Role of Extracellular DNA in Bacterial Response to SOS-Inducing Drugs. Antibiotics (Basel) 2023; 12:antibiotics12040649. [PMID: 37107011 PMCID: PMC10135224 DOI: 10.3390/antibiotics12040649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
The SOS response is a conserved stress response pathway that is triggered by DNA damage in the bacterial cell. Activation of this pathway can, in turn, cause the rapid appearance of new mutations, sometimes called hypermutation. We compared the ability of various SOS-inducing drugs to trigger the expression of RecA, cause hypermutation, and produce elongation of bacteria. During this study, we discovered that these SOS phenotypes were accompanied by the release of large amounts of DNA into the extracellular medium. The release of DNA was accompanied by a form of bacterial aggregation in which the bacteria became tightly enmeshed in DNA. We hypothesize that DNA release triggered by SOS-inducing drugs could promote the horizontal transfer of antibiotic resistance genes by transformation or by conjugation.
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Affiliation(s)
- John K Crane
- Division of Infectious Diseases, Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| | - Marissa N Catanzaro
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA
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Xiao C, Qiao Y, Yang G, Feng L. Antibiotics resistance evolution of isolated Vibrio parahaemolyticus from mariculture under the continuous culture of sub-inhibitory concentrations of Ulva fasciata hydroponic solution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160124. [PMID: 36372171 DOI: 10.1016/j.scitotenv.2022.160124] [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: 09/11/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The outbreak of vibriosis from Vibrio (V.) parahaemolyticus is widespread in the mariculture, and live macroalgae has been considered to be effective and eco-friendly approach for the control of vibriosis. Three V. parahaemolyticus strains with β-lactam antibiotics resistance (resistant to ampicillin (AM), amoxicillin (AMX)) were isolated from mariculture in study, and the antibiotics resistance evolution mechanism was examined at the sub-inhibitory concentration (SIC) of hydroponic solution of Ulva (U.) fasciata (HSUF). The HSUF with the highest density (20 g fresh weight U. fasciata L-1) demonstrated the strongest inhibitory rates (47.0 %-65.8 %) on the three strains during the stable phase (8-24 h) of growth curve, which indicated that the HSUF (≤20 g L-1) could be considered to be at SIC for V. parahaemolyticus strains. After continuous subculture of V. parahaemolyticus with three dilutes (1/2 (HT), 1/20 (MT) and 1/50 (LT)) of HSUF (20 g L-1), all the strains of 20th generation were still resistant to AM and AMX. However, the LT condition reduced MIC of AM (2-16 times) and AMX (0-2 times) to strains, while MT and HT showed significantly various effect of β-lactam antibiotics resistance on different strains. The biofilm formation and ROS content of V. parahaemolyticus were almost positively correlated to the concentrations of HSUF. Transcriptome sequencing analysis of a representative strain showed that the lower concentrations of HSUF caused more down-regulated DEGs of the strains, and more down-regulated (vmeA, vmeB, sapA, mrdA) DEGs of strains were related to the pathway of β-lactam antibiotics resistance at LT condition. Thus, low concentration of HSUF was seemed to have better improvement for V. parahaemolyticus strains resistant to β-lactam antibiotics, which were mainly related to the impairment of biofilm formation, ROS and efflux pump.
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Affiliation(s)
- Changyan Xiao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, People's Republic of China
| | - Yan Qiao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, People's Republic of China
| | - Guangfeng Yang
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, People's Republic of China; National-Local Joint Engineering Laboratory of Harbor Oil & Gas Storage and Transportation Technology, Zhoushan 316022, People's Republic of China
| | - Lijuan Feng
- Zhejiang Provincial Key Laboratory of Petrochemical Pollution Control, Zhejiang Ocean University, Zhoushan 316022, People's Republic of China; National-Local Joint Engineering Laboratory of Harbor Oil & Gas Storage and Transportation Technology, Zhoushan 316022, People's Republic of China.
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