151
|
Akuoko Y, Hanson RL, Harris DH, Nielsen JB, Lazalde E, Woolley AT. Rapid and simple pressure-sensitive adhesive microdevice fabrication for sequence-specific capture and fluorescence detection of sepsis-related bacterial plasmid gene sequences. Anal Bioanal Chem 2021; 413:1017-1025. [PMID: 33247338 PMCID: PMC7855688 DOI: 10.1007/s00216-020-03060-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 10/22/2022]
Abstract
Microbial resistance to currently available antibiotics poses a great threat in the global fight against infections. An important step in determining bacterial antibiotic resistance can be selective DNA sequence capture and fluorescence labeling. In this paper, we demonstrate the fabrication of simple, robust, inexpensive microfluidic devices for DNA capture and fluorescence detection of a model antibiotic resistance gene sequence. We laser micromachined polymethyl methacrylate microchannels and enclosed them using pressure-sensitive adhesive tapes. We then formed porous polymer monoliths with DNA capture probes in these microchannels and used them for sequence-specific capture, fluorescent labeling, and laser-induced fluorescence detection of picomolar (pM) concentrations of synthetic and plasmid antibiotic resistance gene targets. The relative fluorescence for the elution peaks increased with loaded target DNA concentration. We observed higher fluorescence signal and percent recovery for synthetic target DNA compared to plasmid DNA at the same loaded target concentration. A non-target gene was used for control experiments and produced < 3% capture relative to the same concentration of target. The full analysis process including device fabrication was completed in less than 90 min with a limit of detection of 30 pM. The simplicity of device fabrication and good DNA capture selectivity demonstrated herein have potential for application with processes for bacterial plasmid DNA extraction and single-particle counting to facilitate determination of antibiotic susceptibility. Graphical abstract.
Collapse
Affiliation(s)
- Yesman Akuoko
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Robert L Hanson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - David H Harris
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Jacob B Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Elaine Lazalde
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
| |
Collapse
|
152
|
Rentschler S, Kaiser L, Deigner HP. Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance. Int J Mol Sci 2021; 22:E456. [PMID: 33466437 PMCID: PMC7796476 DOI: 10.3390/ijms22010456] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023] Open
Abstract
Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.
Collapse
Affiliation(s)
- Simone Rentschler
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- EXIM Department, Fraunhofer Institute IZI (Leipzig), Schillingallee 68, 18057 Rostock, Germany
- Faculty of Science, Tuebingen University, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| |
Collapse
|
153
|
Klein AK, Dietzel A. Microfluidic Systems for Antimicrobial Susceptibility Testing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 179:291-309. [PMID: 33851232 DOI: 10.1007/10_2021_164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human health is threatened by the spread of antimicrobial resistance and resulting infections. One reason for the resistance spread is the treatment with inappropriate and ineffective antibiotics because standard antimicrobial susceptibility testing methods are time-consuming and laborious. To reduce the antimicrobial susceptibility detection time, minimize treatments with empirical broad-spectrum antibiotics, and thereby combat the further spread of antimicrobial resistance, faster and point-of-care methods are needed. This requires many different research approaches. Microfluidic systems for antimicrobial susceptibility testing offer the possibility to reduce the detection time, as small sample and reagent volumes can be used and the detection of single cells is possible. In some cases, the aim is to use human samples without pretreatment or pre-cultivation. This chapter first provides an overview of conventional detection methods. It then presents the potential of and various current approaches in microfluidics. The focus is on microfluidic methods for phenotypic antimicrobial susceptibility testing.
Collapse
Affiliation(s)
- Ann-Kathrin Klein
- Institute of Microtechnology Technische Universität Braunschweig, Braunschweig, Germany
| | - Andreas Dietzel
- Institute of Microtechnology Technische Universität Braunschweig, Braunschweig, Germany.
| |
Collapse
|
154
|
Lim T, Kim EG, Choi J, Kwon S. A high-throughput cell culture system based on capillary and centrifugal actions for rapid antimicrobial susceptibility testing. LAB ON A CHIP 2020; 20:4552-4560. [PMID: 33169754 DOI: 10.1039/d0lc00753f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance is a global threat to modern society. Rapid determination of suitable antibiotics that inhibit bacterial growth can effectively reduce antibiotic resistance and improve clinical treatment. The conventional methods of antimicrobial susceptibility testing (AST) depend on optical density measurements, which require long-time incubation. Various kinds of rapid AST systems which utilize various technologies from the field of lab on a chip have promised a great reduction in measurement time, but cannot achieve high-throughput, user-friendly testing due to the complexity of the testing system. Here, we introduce a capillary and centrifuge-based rapid AST system that reduces the time of loading the sample and culture media while achieving a high-throughput testing capacity. The capability of the proposed system is validated in a systematic analysis that includes sample loading characteristics and AST trials with standard strains. The proposed system provides a useful tool for drug testing in cell-culture systems with user-friendly and high-throughput analysis.
Collapse
Affiliation(s)
- Taegeun Lim
- QuantaMatrix Inc., Seoul National University Hospital CMI, Seoul, 03082, Republic of Korea and Department of Electrical Engineering and Computer Science, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Eun-Geun Kim
- Lowendtechnologies Co., Anyang, 14056, Republic of Korea
| | - Jungil Choi
- School of Mechanical Engineering, Kookmin University, Seoul, 02707, Republic of Korea.
| | - Sunghoon Kwon
- QuantaMatrix Inc., Seoul National University Hospital CMI, Seoul, 03082, Republic of Korea and Department of Electrical Engineering and Computer Science, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
155
|
Colistin Update on Its Mechanism of Action and Resistance, Present and Future Challenges. Microorganisms 2020; 8:microorganisms8111716. [PMID: 33147701 PMCID: PMC7692639 DOI: 10.3390/microorganisms8111716] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
Colistin has been extensively used since the middle of the last century in animals, particularly in swine, for the control of enteric infections. Colistin is presently considered the last line of defense against human infections caused by multidrug-resistant Gram-negative organisms such as carbapenemase-producer Enterobacterales, Acinetobacter baumanni, and Pseudomonas aeruginosa. Transferable bacterial resistance like mcr-genes was reported in isolates from both humans and animals. Researchers actively seek strategies to reduce colistin resistance. The definition of guidelines for colistin therapy in veterinary and human medicine is thus crucial. The ban of colistin use in swine as a growth promoter and for prophylactic purposes, and the implementation of sustainable measures in farm animals for the prevention of infections, would help to avoid resistance and should be encouraged. Colistin resistance in the human-animal-environment interface stresses the relevance of the One Health approach to achieve its effective control. Such measures should be addressed in a cooperative way, with efforts from multiple disciplines and with consensus among doctors, veterinary surgeons, and environment professionals. A revision of the mechanism of colistin action, resistance, animal and human use, as well as colistin susceptibility evaluation is debated here.
Collapse
|
156
|
Hannah S, Dobrea A, Lasserre P, Blair EO, Alcorn D, Hoskisson PA, Corrigan DK. Development of a Rapid, Antimicrobial Susceptibility Test for E. coli Based on Low-Cost, Screen-Printed Electrodes. BIOSENSORS-BASEL 2020; 10:bios10110153. [PMID: 33114106 PMCID: PMC7690799 DOI: 10.3390/bios10110153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/03/2023]
Abstract
Antibiotic resistance has been cited by the World Health Organisation (WHO) as one of the greatest threats to public health. Mitigating the spread of antibiotic resistance requires a multipronged approach with possible interventions including faster diagnostic testing and enhanced antibiotic stewardship. This study employs a low-cost diagnostic sensor test to rapidly pinpoint the correct antibiotic for treatment of infection. The sensor comprises a screen-printed gold electrode, modified with an antibiotic-seeded hydrogel to monitor bacterial growth. Electrochemical growth profiles of the common microorganism, Escherichia coli (E. coli) (ATCC 25922) were measured in the presence and absence of the antibiotic streptomycin. Results show a clear distinction between the E. coli growth profiles depending on whether streptomycin is present, in a timeframe of ≈2.5 h (p < 0.05), significantly quicker than the current gold standard of culture-based antimicrobial susceptibility testing. These results demonstrate a clear pathway to a low cost, phenotypic and reproducible antibiotic susceptibility testing technology for the rapid detection of E. coli within clinically relevant concentration ranges for conditions such as urinary tract infections.
Collapse
Affiliation(s)
- Stuart Hannah
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (A.D.); (P.L.); (E.O.B.); (D.K.C.)
- Correspondence:
| | - Alexandra Dobrea
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (A.D.); (P.L.); (E.O.B.); (D.K.C.)
| | - Perrine Lasserre
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (A.D.); (P.L.); (E.O.B.); (D.K.C.)
| | - Ewen O. Blair
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (A.D.); (P.L.); (E.O.B.); (D.K.C.)
| | - David Alcorn
- Division of Anaesthesia, Royal Alexandra Hospital, Corsebar Road, Paisley PA2 9PN, UK;
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
| | - Damion K. Corrigan
- Department of Biomedical Engineering, University of Strathclyde, 40 George Street, Glasgow G1 1QE, UK; (A.D.); (P.L.); (E.O.B.); (D.K.C.)
| |
Collapse
|
157
|
Spencer DC, Paton TF, Mulroney KT, Inglis TJJ, Sutton JM, Morgan H. A fast impedance-based antimicrobial susceptibility test. Nat Commun 2020; 11:5328. [PMID: 33087704 PMCID: PMC7578651 DOI: 10.1038/s41467-020-18902-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to develop simple and fast antimicrobial susceptibility tests (ASTs) that allow informed prescribing of antibiotics. Here, we describe a label-free AST that can deliver results within an hour, using an actively dividing culture as starting material. The bacteria are incubated in the presence of an antibiotic for 30 min, and then approximately 105 cells are analysed one-by-one with microfluidic impedance cytometry for 2-3 min. The measured electrical characteristics reflect the phenotypic response of the bacteria to the mode of action of a particular antibiotic, in a 30-minute incubation window. The results are consistent with those obtained by classical broth microdilution assays for a range of antibiotics and bacterial species.
Collapse
Affiliation(s)
- Daniel C Spencer
- Department of Electronics and Computer Science, and Institute for Life Science, University of Southampton, Hampshire, SO17 1BJ, UK
| | - Teagan F Paton
- Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA, 6009, Australia
| | - Kieran T Mulroney
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Timothy J J Inglis
- Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA, 6009, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - J Mark Sutton
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Hywel Morgan
- Department of Electronics and Computer Science, and Institute for Life Science, University of Southampton, Hampshire, SO17 1BJ, UK.
| |
Collapse
|
158
|
Jaillard M, Palmieri M, van Belkum A, Mahé P. Interpreting k-mer-based signatures for antibiotic resistance prediction. Gigascience 2020; 9:giaa110. [PMID: 33068113 PMCID: PMC7568433 DOI: 10.1093/gigascience/giaa110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/23/2020] [Accepted: 09/16/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Recent years have witnessed the development of several k-mer-based approaches aiming to predict phenotypic traits of bacteria on the basis of their whole-genome sequences. While often convincing in terms of predictive performance, the underlying models are in general not straightforward to interpret, the interplay between the actual genetic determinant and its translation as k-mers being generally hard to decipher. RESULTS We propose a simple and computationally efficient strategy allowing one to cope with the high correlation inherent to k-mer-based representations in supervised machine learning models, leading to concise and easily interpretable signatures. We demonstrate the benefit of this approach on the task of predicting the antibiotic resistance profile of a Klebsiella pneumoniae strain from its genome, where our method leads to signatures defined as weighted linear combinations of genetic elements that can easily be identified as genuine antibiotic resistance determinants, with state-of-the-art predictive performance. CONCLUSIONS By enhancing the interpretability of genomic k-mer-based antibiotic resistance prediction models, our approach improves their clinical utility and hence will facilitate their adoption in routine diagnostics by clinicians and microbiologists. While antibiotic resistance was the motivating application, the method is generic and can be transposed to any other bacterial trait. An R package implementing our method is available at https://gitlab.com/biomerieux-data-science/clustlasso.
Collapse
Affiliation(s)
| | | | | | - Pierre Mahé
- bioMérieux, Chemin de l'Orme, 69280 Marcy l'Etoile, France
| |
Collapse
|
159
|
Zhang M, Hong W, Abutaleb NS, Li J, Dong P, Zong C, Wang P, Seleem MN, Cheng J. Rapid Determination of Antimicrobial Susceptibility by Stimulated Raman Scattering Imaging of D 2O Metabolic Incorporation in a Single Bacterium. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:e2001452. [PMID: 33042757 PMCID: PMC7539191 DOI: 10.1002/advs.202001452] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/24/2020] [Indexed: 05/27/2023]
Abstract
Rapid antimicrobial susceptibility testing (AST) is urgently needed for treating infections with appropriate antibiotics and slowing down the emergence of antibiotic-resistant bacteria. Here, a phenotypic platform that rapidly produces AST results by femtosecond stimulated Raman scattering imaging of deuterium oxide (D2O) metabolism is reported. Metabolic incorporation of D2O into biomass in a single bacterium and the metabolic response to antibiotics are probed in as short as 10 min after culture in 70% D2O medium, the fastest among current technologies. Single-cell metabolism inactivation concentration (SC-MIC) is obtained in less than 2.5 h from colony to results. The SC-MIC results of 37 sets of bacterial isolate samples, which include 8 major bacterial species and 14 different antibiotics often encountered in clinic, are validated by standard minimal inhibitory concentration blindly measured via broth microdilution. Toward clinical translation, stimulated Raman scattering imaging of D2O metabolic incorporation and SC-MIC determination after 1 h antibiotic treatment and 30 min mixture of D2O and antibiotics incubation of bacteria in urine or whole blood is demonstrated.
Collapse
Affiliation(s)
- Meng Zhang
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
- Boston University Photonics CenterBostonMA02215USA
| | - Weili Hong
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
| | - Nader S. Abutaleb
- Department of Comparative PathobiologyPurdue UniversityWest LafayetteIN47907USA
| | - Junjie Li
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
- Boston University Photonics CenterBostonMA02215USA
| | - Pu‐Ting Dong
- Boston University Photonics CenterBostonMA02215USA
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
| | - Cheng Zong
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
- Boston University Photonics CenterBostonMA02215USA
| | - Pu Wang
- Vibronix Inc.West LafayetteIN47906USA
| | - Mohamed N. Seleem
- Department of Comparative PathobiologyPurdue UniversityWest LafayetteIN47907USA
- Purdue Institute of InflammationImmunology, and Infectious DiseaseWest LafayetteIN47907USA
| | - Ji‐Xin Cheng
- Department of Electrical and Computer EngineeringBoston UniversityBostonMA02215USA
- Boston University Photonics CenterBostonMA02215USA
- Department of Biomedical EngineeringBoston UniversityBostonMA02215USA
- Department of ChemistryBoston UniversityBostonMA02215USA
| |
Collapse
|
160
|
Abstract
Antimicrobial susceptibility testing (AST) is now, more than ever, a critical role of the microbiology laboratory. Several factors limit its application for patient care and antimicrobial resistance epidemiology, including time to results, requirements for pure cultures, and high starting concentration of bacteria. This review discusses the global status of AST and new phenotypic and genotypic methods in late-stage development or that are new to market.
Collapse
Affiliation(s)
- Romney M Humphries
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South C-3322 MCN, Nashville, TN 37232-2561, USA.
| |
Collapse
|
161
|
Application of Targeted Next-Generation Sequencing Assay on a Portable Sequencing Platform for Culture-Free Detection of Drug-Resistant Tuberculosis from Clinical Samples. J Clin Microbiol 2020; 58:JCM.00632-20. [PMID: 32727827 PMCID: PMC7512157 DOI: 10.1128/jcm.00632-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB). However, the complexity of sequencing platforms has limited their uptake in low-resource settings. The goal of this study was to evaluate the use of the tNGS-based DST solution Genoscreen Deeplex Myc-TB, for use on the compact, low-cost Oxford Nanopore Technologies MinION sequencer. One hundred four DNA samples extracted from smear-positive sputum sediments, previously sequenced using the Deeplex assay on an Illumina MiniSeq, were resequenced on MinION after applying a custom library preparation. MinION read quality, mapping statistics, and variant calling were computed using an in-house pipeline and compared to the reference MiniSeq data. The average percentage of MinION reads mapped to an H37RV reference genome was 90.8%, versus 99.5% on MiniSeq. The mean depths of coverage were 4,151× and 4,177× on MinION and MiniSeq, respectively, with heterogeneous distribution across targeted genes. Composite reference coverage breadth was >99% for both platforms. We observed full concordance between technologies in reporting the clinically relevant drug-resistant markers, including full gene deletions. In conclusion, we demonstrated that the workflow and sequencing data obtained from Deeplex on MinION are comparable to those for the MiniSeq, despite the higher raw error rates on MinION, with the added advantage of MinION's portability, versatility, and low capital costs. Targeted NGS on MinION is a promising DST solution for rapidly providing clinically relevant data to manage complex DR-TB cases.
Collapse
|
162
|
Kmeck A, Tancer RJ, Ventura CR, Wiedman GR. Synergies with and Resistance to Membrane-Active Peptides. Antibiotics (Basel) 2020; 9:antibiotics9090620. [PMID: 32961656 PMCID: PMC7559582 DOI: 10.3390/antibiotics9090620] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/07/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane-active peptides (MAPs) have long been thought of as the key to defeating antimicrobial-resistant microorganisms. Such peptides, however, may not be sufficient alone. In this review, we seek to highlight some of the common pathways for resistance, as well as some avenues for potential synergy. This discussion takes place considering resistance, and/or synergy in the extracellular space, at the membrane, and during interaction, and/or removal. Overall, this review shows that researchers require improved definitions of resistance and a more thorough understanding of MAP-resistance mechanisms. The solution to combating resistance may ultimately come from an understanding of how to harness the power of synergistic drug combinations.
Collapse
|
163
|
Antimicrobial resistance: the good, the bad, and the ugly. Emerg Top Life Sci 2020; 4:129-136. [PMID: 32463087 DOI: 10.1042/etls20190194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
Abstract
As the Royal Society for Biology (RSB) was forming 10 years ago, antimicrobial resistance (AMR) was being heralded as the next threat with a magnitude on a par with global warming. Just a few years later, in 2016, Jim O'Neill's report was published laying out recommendations for tackling drug-resistant infections globally. Where are we now, and what are the challenges ahead? As a slow burner, how will the impact of AMR compare against the recent rapid devastation of the COVID-19 pandemic, and how can we channel some of the good things that come from it (like the awareness and technique of effective hand hygiene) to help us combat AMR speedily and definitively?
Collapse
|
164
|
Fonseca E Silva D, Andrade FF, Gomes R, Silva-Dias A, Martins-Oliveira I, Pérez-Viso B, Ramos MH, Rodrigues AG, Cantón R, Pina-Vaz C. Ultra-rapid flow cytometry assay for colistin MIC determination in Enterobacterales, Pseudomonas aeruginosa and Acinetobacter baumannii. Clin Microbiol Infect 2020; 26:1559.e1-1559.e4. [PMID: 32835792 DOI: 10.1016/j.cmi.2020.08.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Both EUCAST and CLSI recommend broth microdilution for antimicrobial susceptibility testing of colistin, but this method is cumbersome and takes 16-24 h to give results. Our objective was to evaluate a rapid quantitative colistin MIC susceptibility assay based on flow cytometry analysis (FASTcolistin MIC) in comparison with standard broth microdilution assay. METHODS One hundred and sixteen Gram-negative bacilli (78 Enterobacterales, 28 Pseudomonas aeruginosa and 10 Acinetobacter baumannii) were studied in parallel using standard broth microdilution following EUCAST recommendations and FASTcolistin MIC kit. In the last one, a bacteria suspension (0.5 MacFarland) was prepared, diluted in Muller-Hinton broth, incubated in the susceptibility panel containing different colistin concentrations (range 0.125-64 mg/L) with a fluorescent probe and incubated 1 h at 35ºC. After that, a flow cytometry analysis using CytoFLEX (Beckmam) was performed. Using a dedicated software (BioFAST) an automated MIC result was obtained after 1.5 h. Performance evaluation was performed according to the ISO standard 20776-2. Reproducibility and repeatability, categorical (CA) and essential agreement (EA), and lot-to-lot variation and operator-to-operator variability, as well as time to results were determined. RESULTS Overall, 100% CA (CI 97-100%) and 95.7% EA (CI 90-98%) was obtained with high repeatability (100%; CI 80-100%)and reproducibility (97%; (CI 83-99%)). Absence of lot-to-lot variations or differences in the operators' performance was observed. CONCLUSIONS FASTcolistin MIC is an accurate, reliable and ultra-rapid method (1 h incubation versus 24 h) for susceptibility testing of colistin of common Gram-negative bacilli recovered in clinical laboratories.
Collapse
Affiliation(s)
- Daniela Fonseca E Silva
- Clinical Microbiology Department, Hospital and University Center of Porto, Porto, Portugal; Abel Salazar Institute of Biomedical Sciences, University of Porto, Porto, Portugal
| | - Ferdinando F Andrade
- Department of Microbiology, Faculty of Medicine of Porto University, Porto, Portugal
| | | | | | | | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Maria Helena Ramos
- Clinical Microbiology Department, Hospital and University Center of Porto, Porto, Portugal; Abel Salazar Institute of Biomedical Sciences, University of Porto, Porto, Portugal
| | - Acácio G Rodrigues
- FASTinov, SA, Porto, Portugal; Department of Microbiology, Faculty of Medicine of Porto University, Porto, Portugal
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Cidália Pina-Vaz
- FASTinov, SA, Porto, Portugal; Department of Microbiology, Faculty of Medicine of Porto University, Porto, Portugal.
| |
Collapse
|
165
|
Huang HK, Cheng HW, Liao CC, Lin SJ, Chen YZ, Wang JK, Wang YL, Huang NT. Bacteria encapsulation and rapid antibiotic susceptibility test using a microfluidic microwell device integrating surface-enhanced Raman scattering. LAB ON A CHIP 2020; 20:2520-2528. [PMID: 32542276 DOI: 10.1039/d0lc00425a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The antibiotic susceptibility test (AST) is a general laboratory procedure for bacterial identification and characterization and can be utilized to determine effective antimicrobials for individual patients. Due to the low bacterial concentration, conventional AST usually requires a prolonged bacterial culture time and a labor-intensive sample pretreatment process. Therefore, it cannot perform timely diagnosis or treatment, which results in a high mortality rate for seriously infected patients. To address this problem, we developed a microfluidic microwell device integrating surface-enhanced Raman scattering (SERS) technology, or the so called the Microwell-SERS system, to enable a rapid and high-throughput AST. Our results show that the Microwell-SERS system can successfully encapsulate bacteria in a miniaturized microwell with a greatly increased effective bacteria concentration, resulting in a shorter bacterial culture time. By attaching a microchannel onto the microwell, a smooth liquid and air exchange can purify the surrounding buffer and isolate bacteria in an individual microwell for independent SERS measurement. For proof-of-concept, we demonstrated a 2 h AST on susceptible and resistant E. coli and S. aureus with a concentration of 103 CFU mL-1 in the Microwell-SERS system, whereas the previous SERS-AST method required 108 CFU mL-1 bacterial suspension droplets dispensing on a SERS substrate. Based on the above features, we envision that the Microwell-SERS system could achieve highly sensitive, label-free, bacteria detection and rapid AST to enable timely and accurate bacterial infection disease diagnosis.
Collapse
Affiliation(s)
- Hsiu-Kang Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
| | | | | | | | | | | | | | | |
Collapse
|
166
|
Zhang K, Qin S, Wu S, Liang Y, Li J. Microfluidic systems for rapid antibiotic susceptibility tests (ASTs) at the single-cell level. Chem Sci 2020; 11:6352-6361. [PMID: 34094102 PMCID: PMC8159419 DOI: 10.1039/d0sc01353f] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Infectious diseases caused by multidrug resistant (MDR) bacterial pathogens are impending threats to global health. Since delays in identifying drug resistance would significantly increase mortality, fast and accurate antibiotic susceptibility tests (ASTs) are critical for addressing the antibiotic resistance issue. However, the conventional methods for ASTs are always labor-intensive, imprecise, complex and slow (taking 2-3 days). To address these issues, some advanced microfluidic systems have been designed for rapid phenotypic and genotypic analysis of antibiotic resistance. This review highlights the recent development of microfluidics-based ASTs at the single-cell or single-molecule level for guiding antibiotic treatment decisions and predicting therapeutic outcomes.
Collapse
Affiliation(s)
- Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Sixuan Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Yan Liang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| |
Collapse
|