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Jusková P, Schmitt S, Kling A, Rackus DG, Held M, Egli A, Dittrich PS. Real-Time Respiration Changes as a Viability Indicator for Rapid Antibiotic Susceptibility Testing in a Microfluidic Chamber Array. ACS Sens 2021; 6:2202-2210. [PMID: 33900065 PMCID: PMC8240088 DOI: 10.1021/acssensors.1c00020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Rapid identification
of a pathogen and the measurement of its antibiotic
susceptibility are key elements in the diagnostic process of bacterial
infections. Microfluidic technologies offer great control over handling
and manipulation of low sample volumes with the possibility to study
microbial cultures on the single-cell level. Downscaling the dimensions
of cultivation systems directly results in a lower number of bacteria
required for antibiotic susceptibility testing (AST) and thus in a
reduction of the time to result. The developed platform presented
in this work allows the reading of pathogen resistance profiles within
2–3 h based on the changes of dissolved oxygen levels during
bacterial cultivation. The platform contains hundreds of individual
growth chambers prefilled with a hydrogel containing oxygen-sensing
nanoprobes and different concentrations of antibiotic compounds. The
performance of the developed platform is tested using quality control Escherichia coli strains (ATCC 25922 and ATCC 35218)
in response to clinically relevant antibiotics. The results are in
agreement with values given in reference guidelines and independent
measurements using a clinical AST protocol. Finally, the platform
is successfully used for the AST of an E. coli clinical isolate obtained from a patient blood culture.
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Affiliation(s)
- Petra Jusková
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Steven Schmitt
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - André Kling
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Darius G. Rackus
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Martin Held
- Department of Biosystems Science and Engineering, Bioprocess Laboratory, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, Bioanalytics Group, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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52
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Shifman O, Aminov T, Aftalion M, Gur D, Cohen H, Bar-David E, Cohen O, Mamroud E, Levy H, Aloni-Grinstein R, Steinberger-Levy I, Rotem S. Evaluation of the European Committee on Antimicrobial Susceptibility Testing Guidelines for Rapid Antimicrobial Susceptibility Testing of Bacillus anthracis-, Yersinia pestis- and Francisella tularensis-Positive Blood Cultures. Microorganisms 2021; 9:microorganisms9051055. [PMID: 34068310 PMCID: PMC8153291 DOI: 10.3390/microorganisms9051055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Rapid determination of bacterial antibiotic susceptibility is important for proper treatment of infections. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) has recently published guidelines for rapid antimicrobial susceptibility testing (RAST) performed directly from positive blood culture vials. These guidelines, however, were only published for a limited number of common pathogenic bacteria. In this study, we evaluated the applicability of these guidelines to three Tier 1 bioterror agents (Bacillus anthracis, Yersinia pestis and Francisella tularensis) that require prompt antibiotic treatment to mitigate morbidity and mortality. We used spiked-in human blood incubated in a BACTEC™ FX40 system to determine the proper conditions for RAST using disc-diffusion and Etest assays. We found that reliable disc-diffusion inhibition diameters and Etest MIC values could be obtained in remarkably short times. Compared to the EUCAST-recommended disc-diffusion assays that will require adjusted clinical breakpoint tables, Etest-based RAST was advantageous, as the obtained MIC values were similar to the standard MIC values, enabling the use of established category breakpoint tables. Our results demonstrate the promising applicability of the EUCAST RAST for B. anthracis-, Y. pestis- or F. tularensis-positive blood cultures, which can lead to shorter diagnostics and prompt antibiotic treatment of these dangerous pathogens.
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Affiliation(s)
- Ohad Shifman
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
- Correspondence: (O.S.); (S.R.)
| | - Tamar Aminov
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - Moshe Aftalion
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - David Gur
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - Hila Cohen
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - Elad Bar-David
- The Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.B.-D.); (H.L.)
| | - Ofer Cohen
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - Emanuelle Mamroud
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - Haim Levy
- The Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (E.B.-D.); (H.L.)
| | - Ronit Aloni-Grinstein
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - Ida Steinberger-Levy
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
| | - Shahar Rotem
- The Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona 7410001, Israel; (T.A.); (M.A.); (D.G.); (H.C.); (O.C.); (E.M.); (R.A.-G.); (I.S.-L.)
- Correspondence: (O.S.); (S.R.)
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53
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Rapid antimicrobial susceptibility testing by stimulated Raman scattering metabolic imaging and morphological deformation of bacteria. Anal Chim Acta 2021; 1168:338622. [PMID: 34051990 DOI: 10.1016/j.aca.2021.338622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/16/2021] [Accepted: 05/03/2021] [Indexed: 12/19/2022]
Abstract
Methods for rapid antimicrobial susceptibility testing (AST) are urgently needed to address the emergence and spread of antimicrobial resistance. Here, we report a new method based on stimulated Raman scattering (SRS) microscopy, which measures both the metabolic activity and the morphological deformation of bacteria to determine the antimicrobial susceptibility of β-lactam antibiotics rapidly. In this approach, we quantify single bacteria's metabolic activity by the carbon-deuterium (C-D) bond concentrations in bacteria after D2O incubation. In the meantime, bacterial morphological deformation caused by β-lactam antibiotics is also measured. With these two quantifiable markers, we develop an evaluation method to perform AST of cefotaxime on 103 E. coli strains. Our method achieved a 93.2% categorical agreement and a 93.2% essential agreement with the standard reference method.
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54
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Robertson J, McGoverin C, White JR, Vanholsbeeck F, Swift S. Rapid Detection of Escherichia coli Antibiotic Susceptibility Using Live/Dead Spectrometry for Lytic Agents. Microorganisms 2021; 9:924. [PMID: 33925816 PMCID: PMC8147107 DOI: 10.3390/microorganisms9050924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance is a serious threat to public health. The empiric use of the wrong antibiotic occurs due to urgency in treatment combined with slow, culture-based diagnostic techniques. Inappropriate antibiotic choice can promote the development of antibiotic resistance. We investigated live/dead spectrometry using a fluorimeter (Optrode) as a rapid alternative to culture-based techniques through application of the LIVE/DEAD® BacLightTM Bacterial Viability Kit. Killing was detected by the Optrode in near real-time when Escherichia coli was treated with lytic antibiotics-ampicillin and polymyxin B-and stained with SYTO 9 and/or propidium iodide. Antibiotic concentration, bacterial growth phase, and treatment time used affected the efficacy of this detection method. Quantification methods of the lethal action and inhibitory action of the non-lytic antibiotics, ciprofloxacin and chloramphenicol, respectively, remain to be elucidated.
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Affiliation(s)
- Julia Robertson
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland 1023, New Zealand; (J.R.W.); (S.S.)
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
| | - Cushla McGoverin
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
- Department of Physics, The University of Auckland, Auckland 1010, New Zealand
| | - Joni R. White
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland 1023, New Zealand; (J.R.W.); (S.S.)
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
| | - Frédérique Vanholsbeeck
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Auckland 1010, New Zealand; (C.M.); (F.V.)
- Department of Physics, The University of Auckland, Auckland 1010, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland 1023, New Zealand; (J.R.W.); (S.S.)
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55
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Al-Ani RM, Al-Zubaidi MI, Lafi SA. Profile of aerobic bacteria and their antibiotic sensitivity in chronic suppurative otitis media in Al-Ramadi Teaching Hospital, Ramadi City, Iraq. Qatar Med J 2021; 2021:3. [PMID: 33868971 PMCID: PMC8024616 DOI: 10.5339/qmj.2021.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/21/2020] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Chronic suppurative otitis media (CSOM) is a common otological problem in daily clinical practice. It is crucial to know the bacterial pathogens and their antimicrobial susceptibilities in patients with CSOM to achieve a good clinical outcome. OBJECTIVES To identify the aerobic bacterial pathogens and their antibiotic sensitivities in subjects with CSOM in Al-Ramadi Teaching Hospital. MATERIALS AND METHODS A cross-sectional, descriptive study included 102 subjects with a clinical diagnosis of CSOM (aural discharge >2 weeks, eardrum perforation, and conductive deafness). Purulent discharge was obtained from the middle ear with sterile swabs and cultured for bacterial microorganisms. The sensitivity of the isolated agents to antimicrobials was evaluated by a culture and sensitivity method. SPSS version 22 was used for statistical analysis of the data. Differences were considered statistically significant at p < 0.05. RESULTS Out of 3634 outpatient subjects, 102 (2.8%) presented with active CSOM. The age range of the patients was 1-70 years (mean 28.90 ± 19.8). There were 58 females (56.9%). Out of 117 ear swab specimens, 107 (91.5%) yielded positive cultures. The majority (101, 94.4%) of the specimens yielded a single organism. There was a high statistically significant difference (p < 0.001) between gram-positive (n = 77, 68.1%) and gram-negative pathogens (n = 36, 31.9%). Pseudomonas aeruginosa in 65 (57.5%) cases and Staphylococcus aureus in 19 (16.8%) cases were the two most commonly isolated organisms. The drugs imipenem (93.8%), amikacin (86.1%), azteronam (83.1%), and ciprofloxacin (81.5%) were effective against P. aeruginosa (p < 0.001). Amikacin (100%), imipenem (94.7%), ciprofloxacin (68.4%), and gentamicin (63.1%) were the most effective antibiotics against Staph. aureus (p < 0.001). CONCLUSION The prevalence rate of active CSOM was 2.8%. Ciprofloxacin showed high effectiveness against the two most common isolated pathogens (P. aeruginosa and Staph. aureus); therefore, it could be used as empirical therapy for active CSOM cases.
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Affiliation(s)
- Raid M Al-Ani
- University of Anbar, College of Medicine, Department of Surgery/ENT, Iraq E-mail:
| | | | - Shehab A Lafi
- University of Anbar, College of Medicine, Department of Microbiology, Iraq
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56
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Henderson A, Bursle E, Stewart A, Harris PNA, Paterson D, Chatfield MD, Paul M, Dickstein Y, Rodriguez-Baño J, Turnidge JD, Kahlmeter G. A systematic review of antimicrobial susceptibility testing as a tool in clinical trials assessing antimicrobials against infections due to gram-negative pathogens. Clin Microbiol Infect 2021; 27:1746-1753. [PMID: 33813125 DOI: 10.1016/j.cmi.2021.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND Antimicrobial susceptibility testing (AST) is the standard of care for treating bacterial infections. In randomized clinical trials of new antimicrobials, AST might not be performed or reported in real time. OBJECTIVES To determine local, real-time laboratory AST performance, its usage in the trial flow, quality control (QC) of the local testing, central AST performance and the effect of using AST categorization on the trials' primary outcomes. DATA SOURCES We systematically searched PubMed, Embase, PsychINFO and Web of Science. ELIGIBILITY CRITERIA We included registered randomized controlled trials published in journals between January 2015 and December 2019. PARTICIPANTS AND INTERVENTIONS We included trials comparing different antibiotics for the treatment of infections caused predominantly by Gram-negative bacteria. METHODS Primary outcomes for different trial populations were extracted and differences between trial arms were compared for patients with infections caused by susceptible versus non-susceptible bacteria. Results are described narratively. RESULTS Of 32 randomized trials, 25 trials reported that local AST was performed, 1312 reported the local laboratory AST methods, no trial reported QC, but post-hoc referral for AST at a reference laboratory was common. Patients' outcomes were superior when patients with infections due to susceptible and non-susceptible pathogens were compared post hoc (median difference 14%, interquartile range 8%-24%) in trials allowing this comparison (seven antimicrobials), except for colistin, where 14-day mortality was 9% higher when patients were treated with colistin for colistin-susceptible versus colistin-resistant carbapenem-resistant Acinetobacter baumannii. When excluding patients with pathogens that were non-susceptible to either antimicrobial in the trials, the difference in the primary outcome between the trial arms was reduced in five out of six trials. CONCLUSIONS Trials should perform AST to guide patient inclusion or exclusion from the study and consider the impact of the central laboratory susceptibility results on the study outcomes when using post-hoc reference testing.
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Affiliation(s)
- Andrew Henderson
- Princess Alexandra Hospital, Brisbane, QLD, Australia; University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, QLD, Australia.
| | - Evan Bursle
- Princess Alexandra Hospital, Brisbane, QLD, Australia; University of Queensland, QLD, Australia; Sullivan and Nicolaides Pathology, Brisbane, QLD, Australia
| | - Adam Stewart
- University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, QLD, Australia; Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Patrick N A Harris
- University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, QLD, Australia; Pathology Queensland, Brisbane, QLD, Australia
| | - David Paterson
- University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, QLD, Australia
| | - Mark D Chatfield
- University of Queensland, Faculty of Medicine, UQ Centre for Clinical Research, QLD, Australia
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel; Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yaakov Dickstein
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel; Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jesus Rodriguez-Baño
- Hospital Universitario Virgen Macarena, Sevilla, Spain; Servicio de Enfermedades Infecciosas, Hospital Universitario Virgen Macarena, Sevilla, Spain; Departamento de Medicina, Universidad de Sevilla and Instituto de Biomedicina de Seville, Sevilla, Spain
| | - John D Turnidge
- University of Adelaide, Adelaide, SA, Australia; European Committee on Antimicrobial Susceptibility Testing (EUCAST), Adelaide, Australia
| | - Gunnar Kahlmeter
- European Committee on Antimicrobial Susceptibility Testing (EUCAST), Adelaide, Australia; European Committee on Antimicrobial Susceptibility Testing (EUCAST), Vaxjo, Sweden
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57
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Recent Development of Rapid Antimicrobial Susceptibility Testing Methods through Metabolic Profiling of Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10030311. [PMID: 33803002 PMCID: PMC8002737 DOI: 10.3390/antibiotics10030311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
Due to the inappropriate use and overuse of antibiotics, the emergence and spread of antibiotic-resistant bacteria are increasing and have become a major threat to human health. A key factor in the treatment of bacterial infections and slowing down the emergence of antibiotic resistance is to perform antimicrobial susceptibility testing (AST) of infecting bacteria rapidly to prescribe appropriate drugs and reduce the use of broad-spectrum antibiotics. Current phenotypic AST methods based on the detection of bacterial growth are generally reliable but are too slow. There is an urgent need for new methods that can perform AST rapidly. Bacterial metabolism is a fast process, as bacterial cells double about every 20 to 30 min for fast-growing species. Moreover, bacterial metabolism has shown to be related to drug resistance, so a comparison of differences in microbial metabolic processes in the presence or absence of antimicrobials provides an alternative approach to traditional culture for faster AST. In this review, we summarize recent developments in rapid AST methods through metabolic profiling of bacteria under antibiotic treatment.
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58
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Mojsoska B, Ghoul M, Perron GG, Jenssen H, Alatraktchi FA. Changes in toxin production of environmental Pseudomonas aeruginosa isolates exposed to sub-inhibitory concentrations of three common antibiotics. PLoS One 2021; 16:e0248014. [PMID: 33662048 PMCID: PMC7932067 DOI: 10.1371/journal.pone.0248014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/17/2021] [Indexed: 12/02/2022] Open
Abstract
Pseudomonas aeruginosa is an environmental pathogen that can cause severe infections in immunocompromised patients. P. aeruginosa infections are typically treated with multiple antibiotics including tobramycin, ciprofloxacin, and meropenem. However, antibiotics do not always entirely clear the bacteria from the infection site, where they may remain virulent. This is because the effective antibiotic concentration and diffusion in vitro may differ from the in vivo environment in patients. Therefore, it is important to understand the effect of non-lethal sub-inhibitory antibiotic concentrations on bacterial phenotype. Here, we investigate if sub-inhibitory antimicrobial concentrations cause alterations in bacterial virulence factor production using pyocyanin as a model toxin. We tested this using the aforementioned antibiotics on 10 environmental P. aeruginosa strains. Using on-the-spot electrochemical screening, we were able to directly quantify changes in production of pyocyanin in a measurement time of 17 seconds. Upon selecting 3 representative strains to further test the effects of sub-minimum inhibitory concentration (MICs), we found that pyocyanin production changed significantly when the bacteria were exposed to 10-fold MIC of the 3 antibiotics tested, and this was strain specific. A series of biologically relevant measured pyocyanin concentrations were also used to assess the effects of increased virulence on a culture of epithelial cells. We found a decreased viability of the epithelial cells when incubated with biologically relevant pyocyanin concentrations. This suggests that the antibiotic-induced virulence also is a value worth being enclosed in regular testing of pathogens.
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Affiliation(s)
- Biljana Mojsoska
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- PreDiagnose, Karlslunde, Denmark
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Gabriel G. Perron
- Department of Biology, Bard College, Annandale-On-Hudson, NY, United States of America
| | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
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Jackson N, Borges CA, Tarlton NJ, Resendez A, Milton AK, de Boer TR, Butcher CR, Murthy N, Riley LW. A rapid, antibiotic susceptibility test for multidrug-resistant, Gram-negative bacterial uropathogens using the biochemical assay, DETECT. J Microbiol Methods 2021; 182:106160. [PMID: 33548393 DOI: 10.1016/j.mimet.2021.106160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/04/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022]
Abstract
The increasing prevalence of extended spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases among Enterobacterales threatens our ability to treat urinary tract infections (UTIs). These organisms are resistant to most β-lactam antibiotics and are frequently multidrug-resistant (MDR). Consequently, they are often resistant to antibiotics used to empirically treat UTIs. The lack of rapid diagnostic and antibiotic susceptibility tests (AST) makes clinical management of UTIs caused by such organisms difficult, as standard culture and susceptibility assays require several days. We have adapted a biochemical detection assay, termed dual-enzyme trigger-enabled cascade technology (DETECT) for rapid detection of resistance (time-to-result of 3 h) to other antibiotics commonly used in treatment of UTIs. DETECT is activated by the presence of CTX-M and pAmpC β-lactamases. In this proof-of-concept study, the adapted DETECT assay (AST-DETECT) has been performed on pure-cultures of Klebsiella pneumoniae and Escherichia coli (48 isolates) expressing ESBL or pAmpC β-lactamases to perform AST for ciprofloxacin (sensitivity 96.9%, specificity 100%, accuracy 97.9%) nitrofurantoin (sensitivity 95.7%, specificity 91.7%, accuracy 94%) and trimethoprim/sulfamethoxazole (sensitivity 83.3%, specificity 100%, accuracy 89.4%). These results suggest that AST-DETECT may be adapted as a potential diagnostic platform to rapidly detect multidrug-resistant E. coli and K. pneumoniae that cause UTI.
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Affiliation(s)
- Nicole Jackson
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
| | - Clarissa A Borges
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Nicole J Tarlton
- Department of Microbiology, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Angel Resendez
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | | | - Tara R de Boer
- Department of Chemistry, BioAmp Diagnostics, Inc., San Carlos, CA, USA
| | - Cheyenne R Butcher
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Lee W Riley
- School of Public Health, Department of Infectious Diseases and Vaccinology, University of California Berkeley, Berkeley, CA, USA.
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60
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Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform 2021; 22:6109725. [PMID: 33483726 DOI: 10.1093/bib/bbaa403] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.
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Affiliation(s)
- Dropen Sheka
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary
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61
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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.
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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
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62
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Roncarati G, Foschi C, Ambretti S, Re MC. Rapid identification and detection of β-lactamase-producing Enterobacteriaceae from positive blood cultures by MALDI-TOF/MS. J Glob Antimicrob Resist 2021; 24:270-274. [PMID: 33401014 DOI: 10.1016/j.jgar.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/04/2020] [Accepted: 12/20/2020] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES Current evidence suggests that early diagnosis of sepsis and timely detection of antimicrobial resistance are crucial to improve mortality rates among patients. The aim of this study was to evaluate a rapid method for the identification of Gram-negative bacteria from positive blood cultures (BCs), combined with the detection of extended spectrum β-lactamases (ESβL) and carbapenemases production, by means of MALDI-TOF/MS analysis. METHODS During the study, all BCs positive for Gram-negative rods were selected. Starting from bacterial pellets obtained directly from BC broths, species identification and hydrolysis assays were achieved through MALDI-TOF/MS (Bruker). In particular, we performed a hydrolysis assays of cefotaxime (CTX) and ertapenem (ERT) for the rapid detection of resistance via ESβL and carbapenemases, respectively. These results were compared with the routine workflow, including BC subcultures and confirmation phenotypic methods. Finally, a comparison of the turnaround-time (TAT) between the two protocols was conducted. RESULTS Overall, 185 BCs positive for Enterobacteriaceae were collected. In terms of species identification, we observed a concordance of 95.9% comparing MALDI-TOF/MS results to the subculture-based method. The sensitivity and specificity for CTX hydrolysis assay were 91.1% and 92%, respectively; ERT hydrolysis assay showed a sensitivity of 96.2% and a specificity of 99.2%. The TAT of the proposed MALDI TOF/MS-based protocol was significantly lower compared with the routine workflow (P < 0.0001). CONCLUSIONS The proposed protocol can provide reliable bacterial identification and data concerning β-lactam resistance in only 3 hours, positively improving management of patients in terms of antimicrobial stewardship.
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Affiliation(s)
- Greta Roncarati
- Operative Unit of Clinical Microbiology, IRCCS S. Orsola-Malpighi University Hospital, Bologna, Italy.
| | - Claudio Foschi
- Operative Unit of Clinical Microbiology, IRCCS S. Orsola-Malpighi University Hospital, Bologna, Italy; Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - Simone Ambretti
- Operative Unit of Clinical Microbiology, IRCCS S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maria Carla Re
- Operative Unit of Clinical Microbiology, IRCCS S. Orsola-Malpighi University Hospital, Bologna, Italy; Microbiology, DIMES, University of Bologna, Bologna, Italy
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Tsang KK, Maguire F, Zubyk HL, Chou S, Edalatmand A, Wright GD, Beiko RG, McArthur AG. Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance. Microb Genom 2021; 7:mgen000500. [PMID: 33416461 PMCID: PMC8115898 DOI: 10.1099/mgen.0.000500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/08/2020] [Indexed: 11/25/2022] Open
Abstract
Diagnosing antimicrobial resistance (AMR) in the clinic is based on empirical evidence and current gold standard laboratory phenotypic methods. Genotypic methods have the potential advantages of being faster and cheaper, and having improved mechanistic resolution over phenotypic methods. We generated and applied rule-based and logistic regression models to predict the AMR phenotype from Escherichia coli and Pseudomonas aeruginosa multidrug-resistant clinical isolate genomes. By inspecting and evaluating these models, we identified previously unknown β-lactamase substrate activities. In total, 22 unknown β-lactamase substrate activities were experimentally validated using targeted gene expression studies. Our results demonstrate that generating and analysing predictive models can help guide researchers to the mechanisms driving resistance and improve annotation of AMR genes and phenotypic prediction, and suggest that we cannot solely rely on curated knowledge to predict resistance phenotypes.
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Affiliation(s)
- Kara K. Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Haley L. Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sommer Chou
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D. Wright
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew G. McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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64
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Wu J, Zhu Y, You L, Dong PT, Mei J, Cheng JX. Polymer Electrochromism Driven by Metabolic Activity Facilitates Rapid and Facile Bacterial Detection and Susceptibility Evaluation. ADVANCED FUNCTIONAL MATERIALS 2020; 30:2005192. [PMID: 33708032 PMCID: PMC7941207 DOI: 10.1002/adfm.202005192] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 05/19/2023]
Abstract
The electrochromism of a water-soluble naturally oxidized electrochromic polymer, ox-PPE, is harnessed for rapid and facile bacterial detection, discrimination, and susceptibility testing. The ox-PPE solution shows distinct colorimetric and spectroscopic changes within 30 min when mixed with live bacteria. For the underlying mechanism, it is found that ox-PPE responds to the reducing species (e.g. cysteine and glutathione) released by metabolically active bacteria. This reduction reaction is ubiquitous among various bacterial strains, with a noticeable difference that enables discrimination of Gram-negative and Gram-positive bacterial strains. Combining ox-PPE with antibiotics, methicillin-susceptible and -resistant S. aureus can be differentiated within 2.5 h. Proof-of-concept demonstration of ox-PPE for antimicrobial susceptibility testing is carried out by incubating E. coli with various antibiotics. The obtained minimum inhibition concentrations are consistent with the conventional culture-based methods, but with the procedure time significantly shortened to 3 h.
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Affiliation(s)
- Jiayingzi Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Yifan Zhu
- Department of Chemistry, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Liyan You
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Pu-Ting Dong
- Department of Chemistry, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Jianguo Mei
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Ji-Xin Cheng
- Department of Chemistry, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, USA; Department of Physics, Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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65
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Ryu JS, Im SH, Kang YK, Kim YS, Chung HJ. Ultra-fast and universal detection of Gram-negative bacteria in complex samples based on colistin derivatives. Biomater Sci 2020; 8:2111-2119. [PMID: 31967117 DOI: 10.1039/c9bm01926j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gram-negative bacteria are a significant cause of infections acquired in both hospital and community settings, resulting in a high mortality rate worldwide. Currently, a Gram-negative infection is diagnosed by symptom evaluation and is treated with empiric antibiotics which target both Gram-negative and Gram-positive bacteria. A rapid and simple diagnostic method would enable immediate and targeted treatment, while dramatically reducing antibiotic overuse. Herein, we introduce a method utilizing a fluorescent derivative of colistin (COL-FL), that can directly label the Gram-negative cell wall of live bacteria and universally detect the targets within 10 min. By using the COL-FL assay, we achieved the differential labeling of various Gram-negative pathogens related to hospital-acquired infections, which could be subsequently detected via spectrofluorometry and microscopy. Further, we determined that our method can be used for complex samples, such as combinations of multiple bacterial types; bacteria in the presence of mammalian cells; and bacteria with serum components. This assay can be integrated into a simple diagnostic platform for rapid screening tests and the stratification of Gram-negative bacterial infections in the clinic.
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Affiliation(s)
- Jea Sung Ryu
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
| | - San Hae Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Yoo Kyung Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Yang Soo Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea. and Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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Aloni-Grinstein R, Shifman O, Gur D, Aftalion M, Rotem S. MAPt: A Rapid Antibiotic Susceptibility Testing for Bacteria in Environmental Samples as a Means for Bioterror Preparedness. Front Microbiol 2020; 11:592194. [PMID: 33224128 PMCID: PMC7674193 DOI: 10.3389/fmicb.2020.592194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance of bio-threat agents holds major concerns especially in light of advances in methods for engineering pathogens with antibiotic resistance. Preparedness means for rapid identification and prompt proper medical treatment are of need to contain the event and prevent morbidity and spreading of the disease by properly treating exposed individuals before symptoms appearance. Herein, we describe a novel, rapid, simple, specific, and sensitive method named Micro-Agar-PCR-test (MAPt), which determines antibiotic susceptibility of bio-terror pathogens, directly from environmental samples, with no need for any prior isolation, quantification, or enrichment steps. As proof of concept, we have used this approach to obtain correct therapeutic antibiotic minimal inhibitory concentration (MIC) values for the Tier-1 select agents, Bacillus anthracis, Yersinia pestis, and Francisella tularensis, spiked in various environmental samples recapitulating potential bioterror scenarios. The method demonstrated efficiency for a broad dynamic range of bacterial concentrations, both for fast-growing as well as slow-growing bacteria and most importantly significantly shortening the time for accurate results from days to a few hours. The MAPt allows us to address bioterror agents-contaminated environmental samples, offering rational targeted prophylactic treatment, before the onset of morbidity in exposed individuals. Hence, MAPt is expected to provide data for decision-making personal for treatment regimens before the onset of symptoms in infected individuals.
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Affiliation(s)
- Ronit Aloni-Grinstein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ohad Shifman
- 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
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
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67
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Dhingra S, Rahman NAA, Peile E, Rahman M, Sartelli M, Hassali MA, Islam T, Islam S, Haque M. Microbial Resistance Movements: An Overview of Global Public Health Threats Posed by Antimicrobial Resistance, and How Best to Counter. Front Public Health 2020; 8:535668. [PMID: 33251170 PMCID: PMC7672122 DOI: 10.3389/fpubh.2020.535668] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Antibiotics changed medical practice by significantly decreasing the morbidity and mortality associated with bacterial infection. However, infectious diseases remain the leading cause of death in the world. There is global concern about the rise in antimicrobial resistance (AMR), which affects both developed and developing countries. AMR is a public health challenge with extensive health, economic, and societal implications. This paper sets AMR in context, starting with the history of antibiotics, including the discovery of penicillin and the golden era of antibiotics, before exploring the problems and challenges we now face due to AMR. Among the factors discussed is the low level of development of new antimicrobials and the irrational prescribing of antibiotics in developed and developing countries. A fundamental problem is the knowledge, attitude, and practice (KAP) regarding antibiotics among medical practitioners, and we explore this aspect in some depth, including a discussion on the KAP among medical students. We conclude with suggestions on how to address this public health threat, including recommendations on training medical students about antibiotics, and strategies to overcome the problems of irrational antibiotic prescribing and AMR.
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Affiliation(s)
- Sameer Dhingra
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Nor Azlina A. Rahman
- Department of Physical Rehabilitation Sciences, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Kuantan, Malaysia
| | - Ed Peile
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Motiur Rahman
- Oxford University Clinical Research Unit, Wellcome Trust Asia Programme, The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Massimo Sartelli
- Department of General and Emergency Surgery, Macerata Hospital, Macerata, Italy
| | - Mohamed Azmi Hassali
- The Discipline of Social and Administrative Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Malaysia
| | | | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
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68
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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.
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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.
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Bagudo AI, Obande GA, Harun A, Singh KKB. Advances in automated techniques to identify Acinetobacter calcoaceticus-Acinetobacter baumannii complex. ASIAN BIOMED 2020; 14:177-186. [PMID: 37551265 PMCID: PMC10373397 DOI: 10.1515/abm-2020-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Acinetobacter species, particularly those within Acinetobacter calcoaceticus-A. baumannii complex (ACB complex), have emerged as clinically relevant pathogens in hospital environments worldwide. Early and quick detection and identification of Acinetobacter infections is challenging, and traditional culture and biochemical methods may not achieve adequate levels of speciation. Moreover, currently available techniques to identify and differentiate closely related Acinetobacter species are insufficient. The objective of this review is to recapitulate the current evolution in phenotypic and automated techniques used to identify the ACB complex. Compared with other automated or semiautomated systems of bacterial identification, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrates a high level of Acinetobacter species identification and discrimination, including newly discovered species A. seifertii and A. dijkshoorniae.
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Affiliation(s)
- Ahmad Ibrahim Bagudo
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Godwin Attah Obande
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
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70
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Ransom EM, Potter RF, Dantas G, Burnham CAD. Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes! Clin Chem 2020; 66:1278-1289. [PMID: 32918462 DOI: 10.1093/clinchem/hvaa172] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/01/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) technologies are being used to predict antimicrobial resistance. The field is evolving rapidly and transitioning out of the research setting into clinical use. Clinical laboratories are evaluating the accuracy and utility of genomic resistance prediction, including methods for NGS, downstream bioinformatic pipeline components, and the clinical settings in which this type of testing should be offered. CONTENT We describe genomic sequencing as it pertains to predicting antimicrobial resistance in clinical isolates and samples. We elaborate on current methodologies and workflows to perform this testing and summarize the current state of genomic resistance prediction in clinical settings. To highlight this aspect, we include 3 medically relevant microorganism exemplars: Mycobacterium tuberculosis, Staphylococcus aureus, and Neisseria gonorrhoeae. Last, we discuss the future of genomic-based resistance detection in clinical microbiology laboratories. SUMMARY Antimicrobial resistance prediction by genomic approaches is in its infancy for routine patient care. Genomic approaches have already added value to the current diagnostic testing landscape in specific circumstances and will play an increasingly important role in diagnostic microbiology. Future advancements will shorten turnaround time, reduce costs, and improve our analysis and interpretation of clinically actionable results.
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Affiliation(s)
- Eric M Ransom
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Robert F Potter
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Gautam Dantas
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
- Departments of Pediatrics and Medicine, Washington University School of Medicine, St. Louis, MO
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71
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Likhachev IV, Kraeva LA, Samoilova AA, Rogacheva EV, Kaftyreva LA, Egorova SA, Mikhailov NV. Approbation of russian test strips for antimicrobial susceptibility testing of microorganisms by gradient diffusion method (E-test). Klin Lab Diagn 2020; 65:557-561. [PMID: 33245641 DOI: 10.18821/0869-2084-2020-65-9-557-561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The most reliable criterion for the microorganisms antibiotic susceptibility is the value of the minimum inhibitory concentration (MIC). The gradient diffusion method (epsilometric test, e-test), carried out using test strips impregnated with an antimicrobial agent, allows to obtain the quantitative value of MIC, bypassing the time-consuming steps of the traditional method of serial dilutions. We tested strips for the epsilometric test, developed at Saint-Petersburg Pasteur Institute. The quality control, carried by testing the reference strains of E. coli ATCC 25922 and S. aureus 29213, confirmed compliance of the manufacturer's declared antibiotic concentration ranges. The MIC values obtained in the study of the antibiotic susceptibility of 101 clinical isolates of microorganisms of the ESKAPE group, isolated from patients of various hospitals in St. Petersburg, were compared to 8 antimicrobial agents using tested test strips and the corresponding M.I.C. Evaluator of the Oxoid (UK). A high percentage of compliance of MIC values was demonstrated, as well as full compliance of susceptibility categories for all microorganism/antibiotic combinations. The resulting divergences in the MIC values did not exceed one step of a double serial dilution, which is permissible according to GOST R ISO 20776-1-2010. The study showed that the test strips developed at the Saint-Petersburg Pasteur Institute DNT are an acceptable alternative to import tests and, after the registration certificate will be completed, can be offered to determine the susceptibility of microorganisms to antimicrobial agents in bacteriological laboratories.
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Affiliation(s)
| | | | | | | | - L A Kaftyreva
- St. Petersburg Pasteur Institute.,State Educational Institution of the Higher Professional Education "North-Western state medical University n.a. I.I. Mechnikov" of the Ministry of Health of the Russian Federation
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72
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Durand C, Boudet A, Lavigne JP, Pantel A. Evaluation of Two Methods for the Detection of Third Generation Cephalosporins Resistant Enterobacterales Directly From Positive Blood Cultures. Front Cell Infect Microbiol 2020; 10:491. [PMID: 33014900 PMCID: PMC7516202 DOI: 10.3389/fcimb.2020.00491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
Due to the importance of a rapid determination of patients infected by multidrug resistant bacteria, we evaluated two rapid diagnostic tests for the detection of third-generation cephalosporins (3GC)-resistant Enterobacterales directly from positive blood cultures within 1 h: BL-REDTM (electrochemical method) and β-LACTATM test (chromogenic method). A panel of 150 clinical strains characterized for their resistance profiles (e.g., penicillinases, extended-spectrum beta-lactamases (ESBLs), overproduction of cephalosporinase, carbapenemases, impermeability) was tested. Approximately 100 CFU of each isolate was spiked into sterile blood culture bottles and incubated in a BD BACTECTM FX automated system (Becton Dickinson, USA). Positive blood cultures were examined to parallel testing using the BL-REDTM and β-LACTATM tests and conventional susceptibility method (disc diffusion following EUCAST recommendations). For all phenotypes combined, the sensitivity, specificity, positive predictive value, and negative predictive value in the detection of 3GC resistance were, respectively (i) with BL-REDTM: 45.7, 100, 100, and 54.2% and (ii) with β-LACTATM test: 52.2, 100, 100, and 56.9%. The positivity of tests allows to adapt antibiotic treatment whereas the negative result requires other tests. Moreover, these tests detect most Ambler class A-producing Enterobacterales (KPC, ESBL, extended-spectrum OXY) with sensitivities and specificities of 87.5 and 99% for BL-REDTM, respectively and both 100% for β-LACTATM test (47/47 isolates). These two rapid tests failed to detect AmpC overexpressed (sensitivities of 2.7% for BL-REDTM and 0% for β-LACTATM test) and Ambler class B-producing Enterobacterales (sensitivities of 40% for both tests) notably strains without ESBLs associated (sensitivities of 0% for both tests). BL-REDTM and β-LACTATM tests are easy-to-use and mainly attractive when a positive result is obtained notably to detect most of the Ambler class A-producing Enterobacterales in <1 h after the positivity of the blood culture, allowing a rapid adaptation of the antibiotic therapy in patients.
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Affiliation(s)
- Clarisse Durand
- Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Agathe Boudet
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Jean-Philippe Lavigne
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Alix Pantel
- VBMI, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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74
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Direct detection of intact Klebsiella pneumoniae carbapenemase variants from cell lysates: Identification, characterization and clinical implications. CLINICAL MASS SPECTROMETRY 2020; 17:12-21. [PMID: 34820520 DOI: 10.1016/j.clinms.2020.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022]
Abstract
Introduction Carbapenemase-producing organisms (CPOs) are a growing threat to human health. Among the enzymes conferring antibiotic resistance produced by these organisms, Klebsiella pneumoniae carbapenemase (KPC) is considered to be a growing global health threat. Reliable and specific detection of this antibiotic resistance-causing enzyme is critical both for effective therapy and to mitigate further spread. Objectives The objective of this study is to develop an intact protein mass spectrometry-based method for detection and differentiation of clinically-relevant KPC variants directly from bacterial cell lysates. The method should be specific for any variant expressed in multiple bacterial species, limit false positive results and be rapid in nature to directly influence clinical outcomes. Methods Lysates obtained directly from bacterial colonies were used for intact protein detection using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Bottom-up and top-down proteomic methods were used to characterize the KPC protein targets of interest. Comparisons between KPC-producing and KPC-non-producing isolates from a wide variety of species were also performed. Results Characterization of the mature KPC protein revealed an unexpected signal peptide cleavage site preceding an AXA signal peptide motif, modifying the molecular weight (MW) of the mature protein. Taking the additional AXA residues into account allowed for direct detection of the intact protein using top-down proteomic methods. Further validation was performed by transforming a KPC-harboring plasmid into a negative control strain, followed by MS detection of the KPC variant from the transformed cell line. Application of this approach to clearly identify clinically-relevant variants among several species is presented for KPC-2, KPC-3, KPC-4 and KPC-5. Conclusion Direct detection of these enzymes contributes to the understanding of occurrence and spread of these antibiotic-resistant organisms. The ability to detect intact KPC variants via a simple LC-MS/MS approach could have a direct and positive impact on clinical therapy, by providing both direction for epidemiological tracking and appropriate therapy.
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Key Words
- ATCC, American type culture collection
- BLAST, basic local alignment search tool
- CDC, Centers for Disease Control and Prevention
- CPO, carbapenemase-producing organisms
- CSD, charge state distribution
- Carbapenem-resistant Enterobacteriaceae
- Carbapenemase-producing organisms
- ESI, electrospray ionization
- KPC, Klebsiella pneumoniae carbapenemase
- Klebsiella pneumoniae carbapenemase
- LC, liquid chromatography
- MALDI, matrix-assisted laser desorption ionization
- MS, mass spectrometry
- MS/MS, tandem mass spectrometry
- MW, molecular weight
- Mass Spectrometry
- PCR, polymerase chain reaction
- TOF, time-of-flight
- Tandem mass spectrometry
- m/z, mass-to-charge ratio
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75
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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: 137] [Impact Index Per Article: 34.3] [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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76
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Lucena Baeza L, Hamprecht A. A profile of the GenePOC Carba C assay for the detection and differentiation of gene sequences associated with carbapenem-non-susceptibility. Expert Rev Mol Diagn 2020; 20:757-769. [PMID: 32567412 DOI: 10.1080/14737159.2020.1785287] [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] [Indexed: 12/13/2022]
Abstract
The novel GenePOC/Revogene Carba C assay (GenePOC, Québec, Canada; now Meridian Bioscience, Cincinnati, OH, USA) is a CE-IVD marked, FDA-approved qualitative in vitro diagnostic test for the detection of genes associated with carbapenem-non-susceptibility. Colonies of Enterobacterales can be directly tested without prior DNA isolation. The test consists of a fluorescent-based real-time PCR assay that runs on the centripetal microfluidic revogene platform, providing results within 70 minutes. The assay was evaluated in two studies comprising a total of 294 molecularly characterized clinical Enterobacterales isolates. The overall sensitivity for the detection of carbapenemase gene sequences with the GenePOC assay was 100% (95% CI, 98.4% to 100). Besides the common KPC, VIM, NDM and OXA-48-like carbapenemase genes, also the very variable IMP variants were all detected. The specificity of the assay was 100% (95% CI, 98.8% to 100%). In this article the performance of the GenePOC/Revogene Carba C assay is evaluated and other currently available methods for the detection of carbapenemases are reviewed.
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Affiliation(s)
- Luis Lucena Baeza
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne , Cologne, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne , Cologne, Germany.,University of Cologne , Cologne, Germany.,German Centre for Infection Research , Partner Site Bonn-Cologne, Cologne, Germany.,University of Oldenburg , Institute for Medical Microbiology and Virology, Oldenburg, Germany
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77
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Peng H, Borg RE, Nguyen ABN, Chen IA. Chimeric Phage Nanoparticles for Rapid Characterization of Bacterial Pathogens: Detection in Complex Biological Samples and Determination of Antibiotic Sensitivity. ACS Sens 2020; 5:1491-1499. [PMID: 32314570 PMCID: PMC7266372 DOI: 10.1021/acssensors.0c00654] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
Abstract
Rapid, specific, and sensitive detection of pathogenic bacteria in drink, food, and clinical samples is an important goal for public health. In addition, rapid characterization of antibiotic susceptibility could inform clinical choices and improve antibiotic stewardship. We previously reported a straightforward, inexpensive strategy to detect Gram-negative bacterial pathogens, including Pseudomonas aeruginosa, Vibrio cholerae, and Escherichia coli, taking advantage of the high affinity and specificity of phages for their bacterial hosts. Chimeric phages targeted different bacterial pathogens, and thiolation of the phages induced aggregation of gold nanoparticles (AuNPs), leading to a visible colorimetric response in the presence of at least ∼100 cells of the target bacteria. Here, we apply this strategy to complex biological samples (milk, urine, and swabs from a porcine ex vivo model of P. aeruginosa infection). We also show that this assay can be used to identify the antibiotic susceptibility profile based on detection of bacterial growth in the presence of different antibiotics. The prospect for using phage-conjugated AuNPs to detect bacterial pathogens in clinical samples and guide antibiotic choice is discussed.
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Affiliation(s)
- Huan Peng
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Raymond E. Borg
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Anna B. N. Nguyen
- Program
in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Irene A. Chen
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, Santa Barbara, California 93106, United States
- Program
in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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78
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Hahn A, Podbielski A, Meyer T, Zautner AE, Loderstädt U, Schwarz NG, Krüger A, Cadar D, Frickmann H. On detection thresholds-a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results. Acta Trop 2020; 205:105377. [PMID: 32007448 DOI: 10.1016/j.actatropica.2020.105377] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/18/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023]
Abstract
Diagnostic testing in the infectious disease laboratory facilitates decision-making by physicians at the bedside as well as epidemiological assessments and surveillance at study level. Problems may arise if test results are uncritically considered as being the same as the unknown true value. To allow a better understanding, the influence of external factors on the interpretation of test results is introduced with the example of prevalence, followed by the presentation of strengths and weaknesses of important techniques in the infectious disease laboratory like microscopy, cultural diagnostics, serology, mass spectrometry, nucleic acid amplification and hypothesis-free metagenomic sequencing with focus on basic, high-technology and potential future approaches. Special problems like multiplex testing as well as uncertainty of test evaluations, if no gold standard is available, are also stressed with a final glimpse on emerging future technologies for the infectious disease laboratory. In the conclusions, suitability for point-of-care-testing and field laboratory applications is summarized. The aim is to illustrate the limitations of diagnostic accuracy to both clinicians and study planners and to stress the importance of close cooperation with experts in laboratory disciplines so as to avoid potentially critical misunderstandings due to inappropriate interpretation of diagnostic test results.
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Affiliation(s)
- Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Andreas Podbielski
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Thomas Meyer
- Department of Dermatology, St. Josef Hospital, Bochum, Germany
| | - Andreas Erich Zautner
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Ulrike Loderstädt
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | | | - Andreas Krüger
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany; Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany.
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79
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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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80
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Emerging Designs of Electronic Devices in Biomedicine. MICROMACHINES 2020; 11:mi11020123. [PMID: 31979030 PMCID: PMC7074089 DOI: 10.3390/mi11020123] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
Abstract
A long-standing goal of nanoelectronics is the development of integrated systems to be used in medicine as sensor, therapeutic, or theranostic devices. In this review, we examine the phenomena of transport and the interaction between electro-active charges and the material at the nanoscale. We then demonstrate how these mechanisms can be exploited to design and fabricate devices for applications in biomedicine and bioengineering. Specifically, we present and discuss electrochemical devices based on the interaction between ions and conductive polymers, such as organic electrochemical transistors (OFETs), electrolyte gated field-effect transistors (FETs), fin field-effect transistor (FinFETs), tunnelling field-effect transistors (TFETs), electrochemical lab-on-chips (LOCs). For these systems, we comment on their use in medicine.
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81
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Highly specific Electrochemical Sensing of Pseudomonas aeruginosa in patients suffering from corneal ulcers: A comparative study. Sci Rep 2019; 9:18320. [PMID: 31797959 PMCID: PMC6892848 DOI: 10.1038/s41598-019-54667-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/08/2019] [Indexed: 01/12/2023] Open
Abstract
Pseudomonas aeruginosa is the most common pathogenic gram-negative bacteria causing corneal ulcers globally. In severe cases, often after trauma and eye injury, corneal destruction progresses rapidly and may be completed within 24–48 h causing blindness. In our preliminary work, we have established an ultrasensitive polyaniline (PANI)/gold nanoparticles (Au NPs)/indium tin oxide (ITO) modified sensor for rapid detection of pyocyanin (PYO) in P. aeruginosa infections with a linear range from 238 μM to 1.9 μM and a detection limit of 500 nM. In the present study, we evaluated the efficiency of the established modified electrochemical sensor in the diagnosis of P. aeruginosa in 50 samples collected from patients suffering from corneal ulcers. The obtained results were compared with the results gained by the screen-printed electrode, conventional techniques, automated identification method, and the amplification of the 16 s rRNA gene by PCR as a gold standard test for P. aeruginosa identification. We have found that the electrochemical detection of PYO by square wave voltammetry technique using PANI/Au NPs modified ITO electrode was the only technique showing 100% agreement with the molecular method in sensitivity, specificity, positive and negative predictive values when compared with the SPE, conventional and automated methods.
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82
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Welker M, van Belkum A. One System for All: Is Mass Spectrometry a Future Alternative for Conventional Antibiotic Susceptibility Testing? Front Microbiol 2019; 10:2711. [PMID: 31849870 PMCID: PMC6901965 DOI: 10.3389/fmicb.2019.02711] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
The two main pillars of clinical microbiological diagnostics are the identification of potentially pathogenic microorganisms from patient samples and the testing for antibiotic susceptibility (AST) to allow efficient treatment with active antimicrobial agents. While routine microbial species identification is increasingly performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routine AST still largely relies on conventional and molecular techniques such as broth microdilution or disk and gradient diffusion tests, PCR and automated variants thereof. However, shortly after the introduction of MALDI-TOF MS based routine identification, first attempts to perform AST on the same instruments were reported. Today, a number of different approaches to perform AST with MALDI-TOF MS and other MS techniques have been proposed, some restricted to particular microbial taxa and resistance mechanisms while others being more generic. Further, while some of the methods are in a stage of proof of principles, others are already commercialized. In this review we discuss the different principal approaches of mass spectrometry based AST and evaluate the advantages and disadvantages compared to conventional and molecular techniques. At present, the possibility that MS will soon become a routine tool for AST seems unlikely – still, the same was true for routine microbial identification a mere 15 years ago.
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Affiliation(s)
- Martin Welker
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
| | - Alex van Belkum
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
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83
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Hossain SMZ, Mansour N. Biosensors for on-line water quality monitoring – a review. ARAB JOURNAL OF BASIC AND APPLIED SCIENCES 2019. [DOI: 10.1080/25765299.2019.1691434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- S. M. Zakir Hossain
- Department of Chemical Engineering, University of Bahrain, Isa Town, Kingdom of Bahrain
| | - Noureddine Mansour
- Department of Chemical Engineering, University of Bahrain, Isa Town, Kingdom of Bahrain
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84
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García-Álvarez L, Busto H, Oteo JA. Proton nuclear magnetic resonance for antimicrobial drug susceptibility studies: why has progress been slow? Future Microbiol 2019; 14:1175-1177. [PMID: 31625445 DOI: 10.2217/fmb-2019-0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Lara García-Álvarez
- Department of Infectious Diseases, Center for Biomedical Research of La Rioja (CIBIR), San Pedro University Hospital. Logroño, 26006, Spain
| | - Héctor Busto
- Department of Chemistry, Center for Research in Chemical Synthesis (CISQ), University of La Rioja. Logroño, 26006, Spain
| | - José A Oteo
- Department of Infectious Diseases, Center for Biomedical Research of La Rioja (CIBIR), San Pedro University Hospital. Logroño, 26006, Spain
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85
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Thornhill G, David M. Endoscope-associated infections: A microbiologist's perspective on current technologies. TECHNIQUES IN GASTROINTESTINAL ENDOSCOPY 2019. [DOI: 10.1016/j.tgie.2019.150625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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86
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Leite G, Lawandi A, Cheng MP, Lee T. Stability of Biological Activity of Frozen β-lactams over Time as Assessed by Time-Lapsed Broth Microdilutions. Antibiotics (Basel) 2019; 8:antibiotics8040165. [PMID: 31557817 PMCID: PMC6963782 DOI: 10.3390/antibiotics8040165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 01/31/2023] Open
Abstract
To evaluate the antimicrobial agent's stability stored at -80 °C, six β-lactams (meropenem, ertapenem, imipenem, ceftriaxone, ceftazidime, and piperacillin-tazobactam) were studied using the broth microdilution (BMD). The minimum inhibitory concentration (MIC) remained accurate with the same amount of frozen drug for at least six months. Thereafter, there was a diminishing drug concentration due to instability. At this temperature, most β-lactams can be frozen as a stock concentration for up to six months without a significant loss in antibiotic activity.
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Affiliation(s)
- Gleice Leite
- Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada.
| | - Alexander Lawandi
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montréal, QC H4A 3J1, Canada.
| | - Matthew P Cheng
- Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada.
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montréal, QC H4A 3J1, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, McGill University, Montréal, QC H3A 1Y2, Canada.
| | - Todd Lee
- Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada.
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montréal, QC H4A 3J1, Canada.
- McGill Interdisciplinary Initiative in Infection and Immunity, McGill University, Montréal, QC H3A 1Y2, Canada.
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87
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Mahmoud B, ElMasry S, Fahim N, Abd ElSattar M, Shaker O. Detection of antibiotic susceptibility by colorimetric minimum inhibitory concentration in staphylococcal isolates. J Appl Microbiol 2019; 127:693-700. [DOI: 10.1111/jam.14347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/23/2019] [Accepted: 06/03/2019] [Indexed: 11/30/2022]
Affiliation(s)
- B.S. Mahmoud
- Faculty of Medicine Ain Shams University Cairo Egypt
| | - S.A. ElMasry
- Faculty of Medicine Ain Shams University Cairo Egypt
| | | | | | - O.A. Shaker
- Faculty of Medicine Ain Shams University Cairo Egypt
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88
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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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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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