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Gillespie SH, Hammond RJH. Rapid Drug Susceptibility Testing to Preserve Antibiotics. Methods Mol Biol 2024; 2833:129-143. [PMID: 38949707 DOI: 10.1007/978-1-0716-3981-8_13] [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: 07/02/2024]
Abstract
Antibiotic resistance is a global challenge likely to cost trillions of dollars in excess costs in the health system and more importantly, millions of lives every year. A major driver of resistance is the absence of susceptibility testing at the time a healthcare worker needs to prescribe an antimicrobial. The effect is that many prescriptions are unintentionally wasted and expose mutable organisms to antibiotics increasing the risk of resistance emerging. Often simplistic solutions are applied to this growing issue, such as a naïve drive to increase the speed of drug susceptibility testing. This puts a spotlight on a technological solution and there is a multiplicity of such candidate DST tests in development. Yet, if we do not define the necessary information and the speed at which it needs to be available in the clinical decision-making progress as well as the necessary integration into clinical pathways, then little progress will be made. In this chapter, we place the technological challenge in a clinical and systems context. Further, we will review the landscape of some promising technologies that are emerging and attempt to place them in the clinic where they will have to succeed.
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Affiliation(s)
- Stephen H Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, Scotland, UK.
| | - Robert J H Hammond
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, Scotland, UK
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2
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Ghoshal M, Bechtel TD, Gibbons JG, McLandsborough L. Adaptive laboratory evolution of Salmonella enterica in acid stress. Front Microbiol 2023; 14:1285421. [PMID: 38033570 PMCID: PMC10687551 DOI: 10.3389/fmicb.2023.1285421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Adaptive laboratory evolution (ALE) studies play a crucial role in understanding the adaptation and evolution of different bacterial species. In this study, we have investigated the adaptation and evolution of Salmonella enterica serovar Enteritidis to acetic acid using ALE. Materials and methods Acetic acid concentrations below the minimum inhibitory concentration (sub-MIC) were used. Four evolutionary lineages (EL), namely, EL1, EL2, EL3, and EL4, of S. Enteritidis were developed, each demonstrating varying levels of resistance to acetic acid. Results The acetic acid MIC of EL1 remained constant at 27 mM throughout 70 days, while the MIC of EL2, EL3, and EL4 increased throughout the 70 days. EL4 was adapted to the highest concentration of acetic acid (30 mM) and demonstrated the highest increase in its MIC against acetic acid throughout the study, reaching an MIC of 35 mM on day 70. The growth rates of the evolved lineages increased over time and were dependent on the concentration of acetic acid used during the evolutionary process. EL4 had the greatest increase in growth rate, reaching 0.33 (h-1) after 70 days in the presence of 30 mM acetic acid as compared to EL1, which had a growth rate of 0.2 (h-1) after 70 days with no exposure to acetic acid. Long-term exposure to acetic acid led to an increased MIC of human antibiotics such as ciprofloxacin and meropenem against the S. enterica evolutionary lineages. The MIC of ciprofloxacin for EL1 stayed constant at 0.016 throughout the 70 days while that of EL4 increased to 0.047. Bacterial whole genome sequencing revealed single-nucleotide polymorphisms in the ELs in various genes known to be involved in S. enterica virulence, pathogenesis, and stress response including phoP, phoQ, and fhuA. We also observed genome deletions in some of the ELs as compared to the wild-type S. Enteritidis which may have contributed to the bacterial acid adaptation. Discussion This study highlights the potential for bacterial adaptation and evolution under environmental stress and underscores the importance of understanding the development of cross resistance to antibiotics in S. enterica populations. This study serves to enhance our understanding of the pathogenicity and survival strategies of S. enterica under acetic acid stress.
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Affiliation(s)
- Mrinalini Ghoshal
- Department of Microbiology, University of Massachusetts, Amherst, MA, United States
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Tyler D. Bechtel
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Lynne McLandsborough
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
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Abobakr M, Uzun B, Uzun Ozsahin D, Sanlidag T, Arikan A. Assessment of UTI Diagnostic Techniques Using the Fuzzy-PROMETHEE Model. Diagnostics (Basel) 2023; 13:3421. [PMID: 37998557 PMCID: PMC10670649 DOI: 10.3390/diagnostics13223421] [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: 09/18/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023] Open
Abstract
Accurate diagnosis of urinary tract infections (UTIs) is important as early diagnosis increases treatment rates, reduces the risk of infection and disease spread, and prevents deaths. This study aims to evaluate various parameters of existing and developing techniques for the diagnosis of UTIs, the majority of which are approved by the FDA, and rank them according to their performance levels. The study includes 16 UTI tests, and the fuzzy preference ranking organization method was used to analyze the parameters such as analytical efficiency, result time, specificity, sensitivity, positive predictive value, and negative predictive value. Our findings show that the biosensor test was the most indicative of expected test performance for UTIs, with a net flow of 0.0063. This was followed by real-time microscopy systems, catalase, and combined LE and nitrite, which were ranked second, third, and fourth with net flows of 0.003, 0.0026, and 0.0025, respectively. Sequence-based diagnostics was the least favourable alternative with a net flow of -0.0048. The F-PROMETHEE method can aid decision makers in making decisions on the most suitable UTI tests to support the outcomes of each country or patient based on specific conditions and priorities.
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Affiliation(s)
- Mariam Abobakr
- Department of Medical Microbiology and Clinical Microbiology, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey
| | - Berna Uzun
- Department of Mathematics, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey
| | - Dilber Uzun Ozsahin
- Department of Medical Diagnostic Imaging, Collage of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- Operational Research Center in Healthcare, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey
| | - Tamer Sanlidag
- DESAM Research Institute, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey;
| | - Ayse Arikan
- Department of Medical Microbiology and Clinical Microbiology, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey
- DESAM Research Institute, Near East University, TRNC Mersin 10, Nicosia 99138, Turkey;
- Department of Medical Microbiology and Clinical Microbiology, Kyrenia University, TRNC Mersin 10, Kyrenia 99320, Turkey
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Poulsen JS, Nielsen CK, Pedersen NA, Wimmer R, Sondergaard TE, de Jonge N, Nielsen JL. Proteomic Changes in Methicillin-Resistant Staphylococcus aureus Exposed to Cannabinoids. JOURNAL OF NATURAL PRODUCTS 2023; 86:1690-1697. [PMID: 37411021 DOI: 10.1021/acs.jnatprod.3c00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major human pathogen that causes a wide range of infections. Its resistance to β-lactam antibiotics complicates treatment due to the limited number of antibiotics with activity against MRSA. To investigate development of alternative therapeutics, the mechanisms that mediate antibiotic resistance in MRSA need to be fully understood. In this study, MRSA cells were subjected to antibiotic stress from methicillin in combination with three cannabinoid compounds and analyzed using proteomics to assess the changes in physiology. Subjecting MRSA to nonlethal levels of methicillin resulted in an increased production of penicillin-binding protein 2 (PBP2). Exposure to cannabinoids showed antibiotic activity against MRSA, and differential proteomics revealed reduced levels of proteins involved in the energy production as well as PBP2 when used in combination with methicillin.
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Affiliation(s)
- Jan Struckmann Poulsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg East, Denmark
| | - Christina Kjærager Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg East, Denmark
| | - Nina Ahrendt Pedersen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg East, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg East, Denmark
| | - Teis Esben Sondergaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg East, Denmark
| | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg East, Denmark
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg East, Denmark
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5
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Ghoshal M, Ryu V, McLandsborough L. Evaluation of the efficacy of antimicrobials against pathogens on food contact surfaces using a rapid microbial log reduction detection method. Int J Food Microbiol 2022; 373:109699. [DOI: 10.1016/j.ijfoodmicro.2022.109699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/01/2022] [Accepted: 04/30/2022] [Indexed: 11/24/2022]
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Towards smart biomanufacturing: a perspective on recent developments in industrial measurement and monitoring technologies for bio-based production processes. J Ind Microbiol Biotechnol 2020; 47:947-964. [PMID: 32895764 PMCID: PMC7695667 DOI: 10.1007/s10295-020-02308-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/31/2020] [Indexed: 12/22/2022]
Abstract
The biomanufacturing industry has now the opportunity to upgrade its production processes to be in harmony with the latest industrial revolution. Technology creates capabilities that enable smart manufacturing while still complying with unfolding regulations. However, many biomanufacturing companies, especially in the biopharma sector, still have a long way to go to fully benefit from smart manufacturing as they first need to transition their current operations to an information-driven future. One of the most significant obstacles towards the implementation of smart biomanufacturing is the collection of large sets of relevant data. Therefore, in this work, we both summarize the advances that have been made to date with regards to the monitoring and control of bioprocesses, and highlight some of the key technologies that have the potential to contribute to gathering big data. Empowering the current biomanufacturing industry to transition to Industry 4.0 operations allows for improved productivity through information-driven automation, not only by developing infrastructure, but also by introducing more advanced monitoring and control strategies.
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Lee KS, Lee SM, Oh J, Park IH, Song JH, Han M, Yong D, Lim KJ, Shin JS, Yoo KH. Electrical antimicrobial susceptibility testing based on aptamer-functionalized capacitance sensor array for clinical isolates. Sci Rep 2020; 10:13709. [PMID: 32792573 PMCID: PMC7426404 DOI: 10.1038/s41598-020-70459-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/06/2020] [Indexed: 01/16/2023] Open
Abstract
To prescribe effective antibiotics to patients with bacterial infections in a timely manner and to avoid the misuse of antibiotics, a rapid antimicrobial susceptibility test (AST) is essential. However, conventional AST methods require more than 16 h to provide results; thus, we developed an electrical AST (e-AST) system, which provides results within 6 h. The proposed e-AST is based on an array of 60 aptamer-functionalized capacitance sensors that are comparable to currently available AST panels and a pattern-matching algorithm. The performance of the e-AST was evaluated in comparison with that of broth microdilution as the reference test for clinical strains isolated from septic patients. A total of 4,554 tests using e-AST showed a categorical agreement of 97% with a minor error of 2.2%, major error of 0.38%, and very major error of 0.38%. We expect that the proposed e-AST could potentially aid antimicrobial stewardship efforts and lead to improved patient outcomes.
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Affiliation(s)
- Kyo-Seok Lee
- Department of Physics, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sun-Mi Lee
- Nanomedical Graduate Program, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Jeseung Oh
- Proteomtech Inc., 1101 Wooree-Venture Town, Seoul, 07573, Republic of Korea
| | - In Ho Park
- Department of Microbiology, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea.,Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jun Ho Song
- Department of Physics, Yonsei University, Seoul, 03722, Republic of Korea
| | - Myeonggil Han
- Department of Microbiology, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kook Jin Lim
- Nanomedical Graduate Program, Yonsei University, Seoul, 03722, Republic of Korea.,Proteomtech Inc., 1101 Wooree-Venture Town, Seoul, 07573, Republic of Korea
| | - Jeon-Soo Shin
- Nanomedical Graduate Program, Yonsei University, Seoul, 03722, Republic of Korea. .,Department of Microbiology, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea. .,Severance Biomedical Science Institute and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Kyung-Hwa Yoo
- Department of Physics, Yonsei University, Seoul, 03722, Republic of Korea. .,Nanomedical Graduate Program, Yonsei University, Seoul, 03722, Republic of Korea.
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Vasala A, Hytönen VP, Laitinen OH. Modern Tools for Rapid Diagnostics of Antimicrobial Resistance. Front Cell Infect Microbiol 2020; 10:308. [PMID: 32760676 PMCID: PMC7373752 DOI: 10.3389/fcimb.2020.00308] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022] Open
Abstract
Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.
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Affiliation(s)
- Antti Vasala
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P. Hytönen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Olli H. Laitinen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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9
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Monitoring of drug resistance towards reducing the toxicity of pharmaceutical compounds: Past, present and future. J Pharm Biomed Anal 2020; 186:113265. [PMID: 32283481 DOI: 10.1016/j.jpba.2020.113265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022]
Abstract
Drug resistance is worldwide health care crisis which decrease drug efficacy and developing toxicities. Effective resistance detection techniques could alleviate treatment cost and mortality associated with this crisis. In this review, the conventional and modern analysis methods for monitoring of drug resistance are presented. Also, various types of emerging rapid and sensitive techniques including electrochemical, electrical, optical and nano-based methods for the screening of drug resistance were discussed. Applications of various methods for the sensitive and rapid detection of drug resistance are investigated. The review outlines existing key issues in the determination which must be overcome before any of these techniques becomes a feasible method for the rapid detection of drug resistance. In this review, the roles of nanomaterials on development of novel methods for the monitoring of drug resistance were presented. Also, limitations and challenges of conventional and modern methods were discussed.
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10
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Oh J, Ryu JS, Lee M, Jung J, Han S, Chung HJ, Park Y. Three-dimensional label-free observation of individual bacteria upon antibiotic treatment using optical diffraction tomography. BIOMEDICAL OPTICS EXPRESS 2020; 11:1257-1267. [PMID: 32206407 PMCID: PMC7075604 DOI: 10.1364/boe.377740] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 05/20/2023]
Abstract
Measuring alterations in bacteria upon antibiotic application is important for basic studies in microbiology, drug discovery, clinical diagnosis, and disease treatment. However, imaging and 3D time-lapse response analysis of individual bacteria upon antibiotic application remain largely unexplored mainly due to limitations in imaging techniques. Here, we present a method to systematically investigate the alterations in individual bacteria in 3D and quantitatively analyze the effects of antibiotics. Using optical diffraction tomography, in-situ responses of Escherichia coli and Bacillus subtilis to various concentrations of ampicillin were investigated in a label-free and quantitative manner. The presented method reconstructs the dynamic changes in the 3D refractive-index distributions of living bacteria in response to antibiotics at sub-micrometer spatial resolution.
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Affiliation(s)
- Jeonghun Oh
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology, KAIST, Daejeon 34141, South Korea
| | - Moosung Lee
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
| | - Jaehwang Jung
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
- Current Affiliation: Mechatronics R&D Center, Samsung Electronics, Hwasung 18448, South Korea
| | - SeungYun Han
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, KAIST, Daejeon 34141, South Korea
- Department of Biological Sciences, KAIST, Daejeon 34141, South Korea
| | - Yongkeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon 34141, South Korea
- Tomocube Inc., Daejeon 34051, South Korea
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Mizoguchi M, Matsumoto Y, Saito R, Sato T, Moriya K. Direct antibiotic susceptibility testing of blood cultures of gram-negative bacilli using the Drug Susceptibility Testing Microfluidic (DSTM) device. J Infect Chemother 2020; 26:554-562. [PMID: 32115345 DOI: 10.1016/j.jiac.2020.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/19/2020] [Accepted: 01/23/2020] [Indexed: 10/24/2022]
Abstract
Proper treatment of bloodstream infections requires rapid, early determination of appropriate antibiotic agents, emphasizing the need for more rapid drug susceptibility testing. The Drug Susceptibility Testing Microfluidic (DSTM) device represents a novel method in which a small amount of bacterial suspension is injected into the microchip-like device and cultured for 3 h. However, it remains unknown whether the DSTM method can directly determine antibiotic susceptibilities from positive blood cultures. Here, we developed a new approach to directly assess drug susceptibility, using the DSTM method for positive blood cultures. We compare the utility and accuracy of DSTM with those of conventional susceptibility testing methods. Fifty positive blood cultures identified as gram-negative bacilli were used herein. The outcomes of drug susceptibility and resistance assays for positive blood cultures were compared to those of conventional susceptibility testing methods to evaluate their utility and accuracy. Method agreement rates between DSTM and standard methods often exceed 90%, suggesting a high positive correlation with conventional methods. Furthermore, our results show that a combination of multiple drugs in the DSTM device helps identify extended-spectrum β-lactamase (ESBL)- and AmpC-β-lactamase (AmpC-)-producing microorganisms. In conclusion, DSTM method enables effective drug susceptibility and resistance screening within 3 h from positive blood cultures and is suitable for the rapid and personalized determination of the antimicrobial regimen.
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Affiliation(s)
- Miyuki Mizoguchi
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, 113-8655, Japan; Department of Microbiology and Immunology, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Yoshimi Matsumoto
- Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Ryoichi Saito
- Department of Microbiology and Immunology, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoaki Sato
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, 113-8655, Japan
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12
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Kapur S, Gehani M, Kammili N, Bhardwaj P, Nag V, Devara SM, Sharad S. Clinical Validation of Innovative Optical-Sensor-Based, Low-Cost, Rapid Diagnostic Test to Reduce Antimicrobial Resistance. J Clin Med 2019; 8:E2098. [PMID: 31805738 PMCID: PMC6947486 DOI: 10.3390/jcm8122098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022] Open
Abstract
The antibiotic susceptibility test determines the most effective antibiotic treatment for bacterial infection. Antimicrobial stewardship is advocated for the rational use of antibiotics to preserve their efficacy in the long term and provide empirical therapy for disease management. Therefore, rapid diagnostic tests can play a pivotal role in efficient and timely treatment. Here, we developed a novel, rapid, affordable, and portable platform for detecting uropathogens and reporting antibiogram to clinicians in just 4 h. This technology replicates the basic tenets of clinical microbiology including bacterial growth in indigenously formulated medium, and measurement of inhibition of bacterial growth in presence of antibiotic/s. Detection is based on chromogenic endpoints using optical sensors and is analyzed by a lab-developed algorithm, which reports antibiotic sensitivity to the antibiotics panel tested. To assess its diagnostic accuracy, a prospective clinical validation study was conducted in two tertiary-care Indian hospitals. Urine samples from 1986 participants were processed by both novel/index test and conventional Kirby Bauer Disc Diffusion method. The sensitivity and specificity of this assay was 92.5% and 82%, respectively (p < 0.0005). This novel technology will promote evidence-based prescription of antibiotics and reduce the burden of increasing resistance by providing rapid and precise diagnosis in shortest possible time.
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Affiliation(s)
- Suman Kapur
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India;
| | - Manish Gehani
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Hyderabad, Telangana 500078, India;
| | - Nagamani Kammili
- Department of Microbiology, Gandhi Medical College and Hospital, Hyderabad, Telangana 500003, India; (N.K.); (S.M.D.)
| | - Pankaj Bhardwaj
- All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India; (P.B.); (V.N.)
| | - Vijayalakshmi Nag
- All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India; (P.B.); (V.N.)
| | - Sudha M. Devara
- Department of Microbiology, Gandhi Medical College and Hospital, Hyderabad, Telangana 500003, India; (N.K.); (S.M.D.)
| | - Shashwat Sharad
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences and the Walter Reed National Military Medical Center, Bethesda, MD 20817, USA
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13
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Shin DJ, Andini N, Hsieh K, Yang S, Wang TH. Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:41-67. [PMID: 30939033 PMCID: PMC7369001 DOI: 10.1146/annurev-anchem-061318-115529] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.
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Affiliation(s)
- Dong Jin Shin
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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14
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Boolchandani M, D'Souza AW, Dantas G. Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet 2019; 20:356-370. [PMID: 30886350 PMCID: PMC6525649 DOI: 10.1038/s41576-019-0108-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial resistance are imperative for clinical practice to treat resistant infections and for public health efforts to limit the spread of resistance. Technologies such as next-generation sequencing are expanding our abilities to detect and study antimicrobial resistance. This Review provides a detailed overview of antimicrobial resistance identification and characterization methods, from traditional antimicrobial susceptibility testing to recent deep-learning methods. We focus on sequencing-based resistance discovery and discuss tools and databases used in antimicrobial resistance studies.
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Affiliation(s)
- Manish Boolchandani
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Alaric W D'Souza
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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15
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Shifman O, Steinberger-Levy I, Aloni-Grinstein R, Gur D, Aftalion M, Ron I, Mamroud E, Ber R, Rotem S. A Rapid Antimicrobial Susceptibility Test for Determining Yersinia pestis Susceptibility to Doxycycline by RT-PCR Quantification of RNA Markers. Front Microbiol 2019; 10:754. [PMID: 31040834 PMCID: PMC6477067 DOI: 10.3389/fmicb.2019.00754] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
Great efforts are being made to develop new rapid antibiotic susceptibility tests to meet the demand for clinical relevance versus disease progression. This is important especially in diseases caused by bacteria such as Yersinia pestis, the causative agent of plague, which grows rapidly in vivo but relatively slow in vitro. This compromises the ability to use standard growth-based susceptibility tests to obtain rapid and proper antibiotic treatment guidance. Using our previously described platform of quantifying antibiotic-specific transcriptional changes, we developed a molecular test based on changes in expression levels of doxycycline response-dependent marker genes that we identified by transcriptomic analysis. This enabled us to determine the minimal inhibitory concentration of doxycycline within 7 h compared to the 24 h required by the standard CLSI test. This assay was validated with various Y. pestis strains. Moreover, we demonstrated the applicability of the molecular test, combined with a new rapid bacterial isolation step from blood cultures, and show its relevance as a rapid test in clinical settings.
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Affiliation(s)
- Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ida Steinberger-Levy
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ronit Aloni-Grinstein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - David Gur
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Izhar Ron
- Department of Physical Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Emanuelle Mamroud
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Raphael Ber
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
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16
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Volbers D, Stierle VK, Ditzel KJ, Aschauer J, Rädler JO, Opitz M, Paulitschke P. Interference Disturbance Analysis Enables Single-Cell Level Growth and Mobility Characterization for Rapid Antimicrobial Susceptibility Testing. NANO LETTERS 2019; 19:643-651. [PMID: 30525694 DOI: 10.1021/acs.nanolett.8b02815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To support the emerging battle against antimicrobial resistance (AMR), detection methods that allow fast and accurate antimicrobial susceptibility testing (AST) are urgently needed. The early identification and application of an appropriate antibiotic treatment leads to lower mortality rates and substantial cost savings and prevents the development of resistant pathogens. In this work, we present a diffraction-based method, which is capable of quantitative bacterial growth, mobility, and susceptibility measurements. The method is based on the temporal analysis of the intensity of a light diffraction peak, which arises due to interference at a periodic pattern of gold nanostructures. The presence of bacteria disturbs the constructive interference, leading to an intensity decrease and thus allows the monitoring of bacterial growth in very low volumes. We demonstrate the direct correlation of the decrease in diffraction peak intensity with bacterial cell number starting from single cells and show the capability for rapid high-throughput AST measurements by determining the minimum inhibitory concentration for three different antimicrobials in less than 2-3 h as well as the susceptibility in less than 30-40 min. Furthermore, bacterial mobility is obtained from short-term fluctuations of the diffraction peak intensity and is shown to decrease by a factor of 3 during bacterial attachment to a surface. This multiparameter detection method allows for rapid AST of planktonic and of biofilm-forming bacterial strains in low volumes and in real-time without the need of high initial cell numbers.
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Affiliation(s)
- David Volbers
- Faculty of Physics and Center for NanoScience (CeNS) , Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz1 , München D-80539 , Germany
| | - Valentin K Stierle
- Faculty of Physics and Center for NanoScience (CeNS) , Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz1 , München D-80539 , Germany
| | - Konstantin J Ditzel
- Faculty of Physics and Center for NanoScience (CeNS) , Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz1 , München D-80539 , Germany
| | - Julian Aschauer
- Faculty of Physics and Center for NanoScience (CeNS) , Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz1 , München D-80539 , Germany
| | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience (CeNS) , Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz1 , München D-80539 , Germany
| | - Madeleine Opitz
- Faculty of Physics and Center for NanoScience (CeNS) , Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz1 , München D-80539 , Germany
| | - Philipp Paulitschke
- Faculty of Physics and Center for NanoScience (CeNS) , Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz1 , München D-80539 , Germany
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17
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Maugeri G, Lychko I, Sobral R, Roque ACA. Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends. Biotechnol J 2019; 14:e1700750. [PMID: 30024110 PMCID: PMC6330097 DOI: 10.1002/biot.201700750] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/06/2018] [Indexed: 12/16/2022]
Abstract
Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.
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Affiliation(s)
- Gaetano Maugeri
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Iana Lychko
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Rita Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Ana C A Roque
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
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18
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Leonard H, Colodner R, Halachmi S, Segal E. Recent Advances in the Race to Design a Rapid Diagnostic Test for Antimicrobial Resistance. ACS Sens 2018; 3:2202-2217. [PMID: 30350967 DOI: 10.1021/acssensors.8b00900] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Even with advances in antibiotic therapies, bacterial infections persistently plague society and have amounted to one of the most prevalent issues in healthcare today. Moreover, the improper and excessive administration of antibiotics has led to resistance of many pathogens to prescribed therapies, rendering such antibiotics ineffective against infections. While the identification and detection of bacteria in a patient's sample is critical for point-of-care diagnostics and in a clinical setting, the consequent determination of the correct antibiotic for a patient-tailored therapy is equally crucial. As a result, many recent research efforts have been focused on the development of sensors and systems that correctly guide a physician to the best antibiotic to prescribe for an infection, which can in turn, significantly reduce the instances of antibiotic resistance and the evolution of bacteria "superbugs." This review details the advantages and shortcomings of the recent advances (focusing from 2016 and onward) made in the developments of antimicrobial susceptibility testing (AST) measurements. Detection of antibiotic resistance by genomic AST techniques relies on the prediction of antibiotic resistance via extracted bacterial DNA content, while phenotypic determinations typically track physiological changes in cells and/or populations exposed to antibiotics. Regardless of the method used for AST, factors such as cost, scalability, and assay time need to be weighed into their design. With all of the expansive innovation in the field, which technology and sensing systems demonstrate the potential to detect antimicrobial resistance in a clinical setting?
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Affiliation(s)
- Heidi Leonard
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa, Israel 3200003
| | - Raul Colodner
- Laboratory of Clinical Microbiology, Emek Medical Center, Afula, Israel 18101
| | - Sarel Halachmi
- Department of Urology, Bnai Zion Medical Center, Haifa, Israel 3104800
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa, Israel 3200003
- The Russell Berrie Nanotechnology Institute, Technion − Israel Institute of Technology, Haifa, Israel, 3200003
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19
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Phenotypic antibiotic susceptibility testing of pathogenic bacteria using photonic readout methods: recent achievements and impact. Appl Microbiol Biotechnol 2018; 103:549-566. [PMID: 30443798 DOI: 10.1007/s00253-018-9505-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/12/2022]
Abstract
The development of antibiotic resistances in common pathogens is an increasing challenge for therapy of infections and especially severe complications like sepsis. To prevent administration of broad-spectrum and potentially non-effective antibiotics, the susceptibility spectrum of the pathogens underlying the infection has to be determined. Current phenotypic standard methods for antibiotic susceptibility testing (AST) require the isolation of pathogens from the patient and the subsequent culturing in the presence of antibiotics leading to results only after 24-72 h. Since the early initialization of an effective antibiotic therapy is crucial for positive treatment result in severe infections, faster methods of AST are urgently needed. A large number of different assay systems are currently tested for their practicability for fast detection of antibiotic resistance profiles. They can be divided into genotypic ones which detect the presence of certain genes or gene products associated with resistances and phenotypic assays which determine the effect of antibiotics on the pathogens. In this mini-review, we summarize current developments in fast phenotypic tests that use photonic approaches and critically discuss their status. We further outline steps that are required to bring these assays into clinical practice.
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20
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Rapid Antibiotic Susceptibility Determination for Yersinia pestis Using Flow Cytometry Spectral Intensity Ratio (SIR) Fluorescence Analysis. J Fluoresc 2018; 28:1151-1161. [PMID: 30117073 PMCID: PMC6153737 DOI: 10.1007/s10895-018-2279-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 08/09/2018] [Indexed: 12/25/2022]
Abstract
Rapid antimicrobial susceptibility tests (ASTs) are essential tool for proper treatment of patients infected by Yersinia pestis (Y. pestis), the causative agent of plague, or for post-exposure prophylaxis of a population exposed to a naturally acquired or deliberately prepared resistant variant. The standard AST of Y. pestis is based on bacterial growth and requires 24–48 h of incubation in addition to the time required for prior isolation of a bacterial culture from the clinical or environmental sample, which may take an additional 24–48 h. In this study, we present a new and rapid AST method based on a fluorescence determination of the minimum inhibitory concentration (MIC). Our method includes the incubation of bacteria with an antibiotic, followed by staining of the bacteria with oxonol dye (SynaptoGreen C4/FM1–43), which enables the rapid detection of an antibiotic’s effect on bacterial viability. We show that stained, non-viable bacteria exhibit a spectral redshift and an increase in fluorescence intensity compared to intact control bacteria. Based on these criteria, we developed a rapid flow cytometer measurement procedure and a unique spectral intensity ratio (SIR) analysis that enables determination of antibiotic susceptibility for Y. pestis within 6 h instead of the 24 to 48 h required for the standard AST. This new rapid determination of antibiotic susceptibility could be crucial for reducing mortality and preventing the spread of disease.
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21
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Schoepp NG, Schlappi TS, Curtis MS, Butkovich SS, Miller S, Humphries RM, Ismagilov RF. Rapid pathogen-specific phenotypic antibiotic susceptibility testing using digital LAMP quantification in clinical samples. Sci Transl Med 2018; 9:9/410/eaal3693. [PMID: 28978750 DOI: 10.1126/scitranslmed.aal3693] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 06/30/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022]
Abstract
Rapid antimicrobial susceptibility testing (AST) is urgently needed for informing treatment decisions and preventing the spread of antimicrobial resistance resulting from the misuse and overuse of antibiotics. To date, no phenotypic AST exists that can be performed within a single patient visit (30 min) directly from clinical samples. We show that AST results can be obtained by using digital nucleic acid quantification to measure the phenotypic response of Escherichia coli present within clinical urine samples exposed to an antibiotic for 15 min. We performed this rapid AST using our ultrafast (~7 min) digital real-time loop-mediated isothermal amplification (dLAMP) assay [area under the curve (AUC), 0.96] and compared the results to a commercial (~2 hours) digital polymerase chain reaction assay (AUC, 0.98). The rapid dLAMP assay can be used with SlipChip microfluidic devices to determine the phenotypic antibiotic susceptibility of E. coli directly from clinical urine samples in less than 30 min. With further development for additional pathogens, antibiotics, and sample types, rapid digital AST (dAST) could enable rapid clinical decision-making, improve management of infectious diseases, and facilitate antimicrobial stewardship.
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Affiliation(s)
- Nathan G Schoepp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Travis S Schlappi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Matthew S Curtis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Slava S Butkovich
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Shelley Miller
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA 90095, USA
| | - Romney M Humphries
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, 10888 Le Conte Avenue, Brentwood Annex, Los Angeles, CA 90095, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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22
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Canali C, Spillum E, Valvik M, Agersnap N, Olesen T. Real-Time Digital Bright Field Technology for Rapid Antibiotic Susceptibility Testing. Methods Mol Biol 2018; 1736:75-84. [PMID: 29322460 DOI: 10.1007/978-1-4939-7638-6_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Optical scanning through bacterial samples and image-based analysis may provide a robust method for bacterial identification, fast estimation of growth rates and their modulation due to the presence of antimicrobial agents. Here, we describe an automated digital, time-lapse, bright field imaging system (oCelloScope, BioSense Solutions ApS, Farum, Denmark) for rapid and higher throughput antibiotic susceptibility testing (AST) of up to 96 bacteria-antibiotic combinations at a time. The imaging system consists of a digital camera, an illumination unit and a lens where the optical axis is tilted 6.25° relative to the horizontal plane of the stage. Such tilting grants more freedom of operation at both high and low concentrations of microorganisms. When considering a bacterial suspension in a microwell, the oCelloScope acquires a sequence of 6.25°-tilted images to form an image Z-stack. The stack contains the best-focus image, as well as the adjacent out-of-focus images (which contain progressively more out-of-focus bacteria, the further the distance from the best-focus position). The acquisition process is repeated over time, so that the time-lapse sequence of best-focus images is used to generate a video. The setting of the experiment, image analysis and generation of time-lapse videos can be performed through a dedicated software (UniExplorer, BioSense Solutions ApS). The acquired images can be processed for online and offline quantification of several morphological parameters, microbial growth, and inhibition over time.
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Affiliation(s)
| | - Erik Spillum
- Philips BioCell A/S, Allerød, Denmark
- BioSense Solutions ApS, Farum, Denmark
| | | | | | - Tom Olesen
- Philips BioCell A/S, Allerød, Denmark
- BioSense Solutions ApS, Farum, Denmark
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23
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017; 22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.
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Affiliation(s)
- Yiyan Li
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,7 Department of Physics and Engineering, Fort Lewis College, Durango, Colorado, USA
| | | | - Weian Zhao
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,6 Department of Biological Chemistry, University of California-Irvine, Irvine, CA, USA
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24
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Leonard H, Halachmi S, Ben-Dov N, Nativ O, Segal E. Unraveling Antimicrobial Susceptibility of Bacterial Networks on Micropillar Architectures Using Intrinsic Phase-Shift Spectroscopy. ACS NANO 2017; 11:6167-6177. [PMID: 28485961 DOI: 10.1021/acsnano.7b02217] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
With global antimicrobial resistance becoming increasingly detrimental to society, improving current clinical antimicrobial susceptibility testing (AST) is crucial to allow physicians to initiate appropriate antibiotic treatment as early as possible, reducing not only mortality rates but also the emergence of resistant pathogens. In this work, we tackle the main bottlenecks in clinical AST by designing biofunctionalized silicon micropillar arrays to provide both a preferable solid-liquid interface for bacteria networking and a simultaneous transducing element that monitors the response of bacteria when exposed to chosen antibiotics in real time. We harness the intrinsic ability of the micropillar architectures to relay optical phase-shift reflectometric interference spectroscopic measurements (referred to as PRISM) and employ it as a platform for culture-free, label-free phenotypic AST. The responses of E. coli to various concentrations of five clinically relevant antibiotics are optically tracked by PRISM, allowing for the minimum inhibitory concentration (MIC) values to be determined and compared to both standard broth microdilution testing and clinic-based automated AST system readouts. Capture of bacteria within these microtopologies, followed by incubation of the cells with the appropriate antibiotic solution, yields rapid determinations of antibiotic susceptibility. This platform not only provides accurate MIC determinations in a rapid manner (total assay time of 2-3 h versus 8 h with automated AST systems) but can also be employed as an advantageous method to differentiate bacteriostatic and bactericidal antibiotics.
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Affiliation(s)
- Heidi Leonard
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Sarel Halachmi
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Nadav Ben-Dov
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Ofer Nativ
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Ester Segal
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
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25
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Fredborg M, Sondergaard TE, Wang M. Synergistic activities of meropenem double and triple combinations against carbapenemase-producing Enterobacteriaceae. Diagn Microbiol Infect Dis 2017; 88:355-360. [PMID: 28583381 DOI: 10.1016/j.diagmicrobio.2017.04.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 04/10/2017] [Accepted: 04/26/2017] [Indexed: 01/26/2023]
Abstract
The increasing emergence of carbapenemase-producing Enterobacteriaceae poses a considerable threat to global health as only limited treatment options are available and has therefore led to efforts to discover antibiotic combination regimens effective. The aim of this study was to evaluate in vitro synergistic activity of 10 meropenem double and triple combinations against the 5 most frequently encountered carbapenemases-producing Enterobacteriaceae. Broth microdilution assays showed that the meropenem and ertapenem combination was the most efficient regimen of the double combinations tested (>5-log2 fold decrease). The triple combination of meropenem, polymyxin and rifampin exhibited highest synergistic activity of the triple combinations. The divergent reports on synergistic activity of antibiotic combinations suggest that it may not be possible to predict synergy based on carbapenemase type alone. Consequently, we recommend that in vitro evaluation of synergistic activity of antibiotic combinations against carbapenemase-producing Enterobacteriaceae is performed on every isolate to ensure effective treatment regimens.
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Affiliation(s)
- Marlene Fredborg
- Department of Animal Science, Faculty of Science and Technology, Aarhus University, Blichers Allé 20, 8830 Tjele, Denmark; Department of Clinical Microbiology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark.
| | - Teis E Sondergaard
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Frederik Bajersvej 7H, 9220 Aalborg Ø, Denmark
| | - Mikala Wang
- Department of Clinical Microbiology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
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26
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Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang TH, Liao JC. New and developing diagnostic technologies for urinary tract infections. Nat Rev Urol 2017; 14:296-310. [PMID: 28248946 PMCID: PMC5473291 DOI: 10.1038/nrurol.2017.20] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.
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Affiliation(s)
- Michael Davenport
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Linda M Dairiki Shortliffe
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, California 94304 USA
| | - Tza-Huei Wang
- Departments of Mechanical and Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304 USA
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27
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Direct, rapid antimicrobial susceptibility test from positive blood cultures based on microscopic imaging analysis. Sci Rep 2017; 7:1148. [PMID: 28442767 PMCID: PMC5430693 DOI: 10.1038/s41598-017-01278-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022] Open
Abstract
For the timely treatment of patients with infections in bloodstream and cerebrospinal fluid, a rapid antimicrobial susceptibility test (AST) is urgently needed. Here, we describe a direct and rapid antimicrobial susceptibility testing (dRAST) system, which can determine the antimicrobial susceptibility of bacteria from a positive blood culture bottle (PBCB) in six hours. The positive blood culture sample is directly mixed with agarose and inoculated into a micropatterned plastic microchip with lyophilized antibiotic agents. Using microscopic detection of bacterial colony formation in agarose, the total time to result from a PBCB for dRAST was only six hours for a wide range of bacterial concentrations in PBCBs. The results from the dRAST system were consistent with the results from a standard AST, broth microdilution test. In tests of clinical isolates (n = 206) composed of 16 Gram-negative species and seven Gram-positive species, the dRAST system was accurate compared to the standard broth microdilution test, with rates of 91.11% (2613/2868) categorical agreement, 6.69% (192/2868) minor error, 2.72% (50/1837) major error and 1.45% (13/896) very major error. Thus, the dRAST system can be used to rapidly identify appropriate antimicrobial agents for the treatment of blood stream infection (BSI) and antibiotic-resistant strain infections.
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Syal K, Mo M, Yu H, Iriya R, Jing W, Guodong S, Wang S, Grys TE, Haydel SE, Tao N. Current and emerging techniques for antibiotic susceptibility tests. Theranostics 2017; 7:1795-1805. [PMID: 28638468 PMCID: PMC5479269 DOI: 10.7150/thno.19217] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/03/2017] [Indexed: 12/23/2022] Open
Abstract
Infectious diseases caused by bacterial pathogens are a worldwide burden. Serious bacterial infection-related complications, such as sepsis, affect over a million people every year with mortality rates ranging from 30% to 50%. Crucial clinical microbiology laboratory responsibilities associated with patient management and treatment include isolating and identifying the causative bacterium and performing antibiotic susceptibility tests (ASTs), which are labor-intensive, complex, imprecise, and slow (taking days, depending on the growth rate of the pathogen). Considering the life-threatening condition of a septic patient and the increasing prevalence of antibiotic-resistant bacteria in hospitals, rapid and automated diagnostic tools are needed. This review summarizes the existing commercial AST methods and discusses some of the promising emerging AST tools that will empower humans to win the evolutionary war between microbial genes and human wits.
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Affiliation(s)
- Karan Syal
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Manni Mo
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Hui Yu
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Rafael Iriya
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Wenwen Jing
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Sui Guodong
- Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Shaopeng Wang
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Thomas E. Grys
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, Arizona 85054, USA
| | - Shelley E. Haydel
- Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Nongjian Tao
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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McLaughlin HP, Gargis AS, Michel P, Sue D, Weigel LM. Optical Screening for Rapid Antimicrobial Susceptibility Testing and for Observation of Phenotypic Diversity among Strains of the Genetically Clonal Species Bacillus anthracis. J Clin Microbiol 2017; 55:959-970. [PMID: 28053211 PMCID: PMC5328465 DOI: 10.1128/jcm.02209-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/30/2016] [Indexed: 12/30/2022] Open
Abstract
During high-impact events involving Bacillus anthracis, such as the Amerithrax incident of 2001 or the anthrax outbreaks in Russia and Sweden in 2016, critical decisions to reduce morbidity and mortality include rapid selection and distribution of effective antimicrobial agents for treatment and postexposure prophylaxis. Detection of antimicrobial resistance currently relies on a conventional broth microdilution method that requires a 16- to 20-h incubation time for B. anthracis Advances in high-resolution optical screening offer a new technology to more rapidly evaluate antimicrobial susceptibility and to simultaneously assess the growth characteristics of an isolate. Herein, we describe a new method developed and evaluated as a rapid antimicrobial susceptibility test for B. anthracis This method is based on automated digital time-lapse microscopy to observe the growth and morphological effects of relevant antibiotics with an optical screening instrument, the oCelloScope. B. anthracis strains were monitored over time in the presence or absence of penicillin, ciprofloxacin, or doxycycline. Susceptibility to each antibiotic was determined in ≤4 h, 75 to 80% less than the time required for conventional methods. Time-lapse video imaging compiled from the optical screening images revealed unexpected differences in growth characteristics among strains of B. anthracis, which is considered to be a clonal organism. This technology provides a new approach for rapidly detecting phenotypic antimicrobial resistance and for documenting growth attributes that may be beneficial in the further characterization of individual strains.
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Affiliation(s)
- Heather P McLaughlin
- Biodefense Research and Development Laboratory, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amy S Gargis
- Biodefense Research and Development Laboratory, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pierre Michel
- Biodefense Research and Development Laboratory, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David Sue
- Biodefense Research and Development Laboratory, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Linda M Weigel
- Biodefense Research and Development Laboratory, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Wollenberg RD, Donau SS, Nielsen TT, Sørensen JL, Giese H, Wimmer R, Søndergaard TE. Real-time imaging of the growth-inhibitory effect of JS399-19 on Fusarium. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2016; 134:24-30. [PMID: 27914536 DOI: 10.1016/j.pestbp.2016.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/03/2016] [Accepted: 05/09/2016] [Indexed: 06/06/2023]
Abstract
Real-time imaging was used to study the effects of a novel Fusarium-specific cyanoacrylate fungicide (JS399-19) on growth and morphology of four Fusarium sp. This fungicide targets the motor domain of type I myosin. Fusarium graminearum PH-1, Fusarium solani f. sp. pisi 77-13-4, Fusarium avenaceum IBT8464, and Fusarium avenaceum 05001, which has a K216Q amino-acid substitution at the resistance-implicated site in its myosin type I motor domain, were analyzed. Real-time imaging shows that JS399-19 inhibits fungal growth but not to the extent previously reported. The fungicide causes the hypha to become entangled and unable to extend vertically. This implies that type I myosin in Fusarium is essential for hyphal and mycelia propagation. The K216Q substitution correlates with reduced susceptibility in F. avenaceum.
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Affiliation(s)
- Rasmus D Wollenberg
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark.
| | - Søren S Donau
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark
| | - Thorbjørn T Nielsen
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark
| | - Jens L Sørensen
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark
| | - Henriette Giese
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark
| | - Teis E Søndergaard
- Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark
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