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Yi SY, Jeong J, Kim KE, Park K, Shin YB. Staphylococcus aureus Specific FRET Probe-Based Antibacterial Susceptibility Testing (SF-AST) by Detection of Micrococcal Nuclease Activity. ACS Infect Dis 2020; 6:215-223. [PMID: 31823600 DOI: 10.1021/acsinfecdis.9b00260] [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] [Indexed: 12/22/2022]
Abstract
In this study, we describe a simple and rapid antibacterial susceptibility testing (AST) method for Staphylococcus aureus called S. aureus specific fluorescence resonance energy transfer (FRET) probe-based AST (SF-AST), which is based on an S. aureus specific FRET probe (SF probe) that detects micrococcal nuclease (MNase) activity secreted from S. aureus. The SF-AST was tested with an S. aureus quality control (QC) strain against six relevant antibiotics, and the minimum inhibitory concentration (MIC) values obtained with the broth microdilution (BMD) method were compared, as a gold standard AST. Results were obtained with high accuracy in 4-6 h. The MIC for the methicillin resistance using 20 clinical S. aureus isolates of SF-AST showed 100% sensitivity, specificity, positive predictive value, and negative predictive value, as compared to BMD. Thus, the SF-AST method is a simple, rapid, and useful antibiotic resistance test for S. aureus, and it provides a basis for clinical treatment in a short time.
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Affiliation(s)
- So Yeon Yi
- BioNano Health Guard Research Center, Daejeon 34141, Republic of Korea
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jinyoung Jeong
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kyoon Eon Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kyoungsook Park
- BioNano Health Guard Research Center, Daejeon 34141, Republic of Korea
| | - Yong Beom Shin
- BioNano Health Guard Research Center, Daejeon 34141, Republic of Korea
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
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Innovative and rapid antimicrobial susceptibility testing systems. Nat Rev Microbiol 2020; 18:299-311. [PMID: 32055026 DOI: 10.1038/s41579-020-0327-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope.
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Hassan SU, Zhang X. Microfluidics as an Emerging Platform for Tackling Antimicrobial Resistance (AMR): A Review. CURR ANAL CHEM 2020. [DOI: 10.2174/1573411015666181224145845] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background:
Antimicrobial resistance (AMR) occurs when microbes become resistant to
antibiotics causing complications and limited treatment options. AMR is more significant where antibiotics
use is excessive or abusive and the strains of bacteria become resistant to antibiotic treatments.
Current technologies for bacteria and its resistant strains identification and antimicrobial susceptibility
testing (AST) are mostly central-lab based in hospitals, which normally take days to
weeks to get results. These tools and procedures are expensive, laborious and skills based. There is
an ever-increasing demand for developing point-of-care (POC) diagnostics tools for rapid and near
patient AMR testing. Microfluidics, an important and fundamental technique to develop POC devices,
has been utilized to tackle AMR in healthcare. This review mainly focuses on the current development
in the field of microfluidics for rapid AMR testing.
Method:
Due to the limitations of conventional AMR techniques, microfluidic-based platforms have
been developed for better understandings of bacterial resistance, smart AST and minimum inhibitory
concentration (MIC) testing tools and development of new drugs. This review aims to summarize the
recent development of AST and MIC testing tools in different formats of microfluidics technology.
Results:
Various microfluidics devices have been developed to combat AMR. Miniaturization and
integration of different tools has been attempted to produce handheld or standalone devices for rapid
AMR testing using different formats of microfluidics technology such as active microfluidics, droplet
microfluidics, paper microfluidics and capillary-driven microfluidics.
Conclusion:
Current conventional AMR detection technologies provide time-consuming, costly,
labor-intensive and central lab-based solutions, limiting their applications. Microfluidics has been
developed for decades and the technology has emerged as a powerful tool for POC diagnostics of antimicrobial
resistance in healthcare providing, simple, robust, cost-effective and portable diagnostics.
The success has been reported in research articles; however, the potential of microfluidics technology
in tackling AMR has not been fully achieved in clinical settings.
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Affiliation(s)
- Sammer-ul Hassan
- Department of Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Xunli Zhang
- Department of Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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Abstract
Antimicrobial susceptibility testing (AST) technologies help to accelerate the initiation of targeted antimicrobial therapy for patients with infections and could potentially extend the lifespan of current narrow-spectrum antimicrobials. Although conceptually new and rapid AST technologies have been described, including new phenotyping methods, digital imaging and genomic approaches, there is no single major, or broadly accepted, technological breakthrough that leads the field of rapid AST platform development. This might be owing to several barriers that prevent the timely development and implementation of novel and rapid AST platforms in health-care settings. In this Consensus Statement, we explore such barriers, which include the utility of new methods, the complex process of validating new technology against reference methods beyond the proof-of-concept phase, the legal and regulatory landscapes, costs, the uptake of new tools, reagent stability, optimization of target product profiles, difficulties conducting clinical trials and issues relating to quality and quality control, and present possible solutions. This Consensus Statement presents the barriers that currently prevent the timely development and implementation of novel and rapid antimicrobial susceptibility testing platforms, including the costs involved, uptake of new tools, legal and regulatory aspects, difficulties conducting clinical trials and quality control, and presents possible solutions.
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Capturing the Resistome: a Targeted Capture Method To Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrob Agents Chemother 2019; 64:AAC.01324-19. [PMID: 31611361 PMCID: PMC7187591 DOI: 10.1128/aac.01324-19] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/01/2019] [Indexed: 12/31/2022] Open
Abstract
Identification of the nucleotide sequences encoding antibiotic resistance elements and determination of their association with antibiotic resistance are critical to improve surveillance and monitor trends in antibiotic resistance. Current methods to study antibiotic resistance in various environments rely on extensive deep sequencing or laborious culturing of fastidious organisms, both of which are heavily time-consuming operations. An accurate and sensitive method to identify both rare and common resistance elements in complex metagenomic samples is needed. Referencing the sequences in the Comprehensive Antibiotic Resistance Database, we designed a set of 37,826 probes to specifically target over 2,000 nucleotide sequences associated with antibiotic resistance in clinically relevant bacteria. Testing of this probe set on DNA libraries generated from multidrug-resistant bacteria to selectively capture resistance genes reproducibly produced higher numbers of reads on target at a greater length of coverage than shotgun sequencing. We also identified additional resistance gene sequences from human gut microbiome samples that sequencing alone was not able to detect. Our method to capture the resistome enables a sensitive means of gene detection in diverse environments where genes encoding antibiotic resistance represent less than 0.1% of the metagenome.
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A Rapid ATP Bioluminescence-based Test for Detecting Levofloxacin Resistance Starting from Positive Blood Culture Bottles. Sci Rep 2019; 9:13565. [PMID: 31578343 PMCID: PMC6775087 DOI: 10.1038/s41598-019-49358-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023] Open
Abstract
Administering appropriate antimicrobial therapy as early as possible is important for rescuing bacteremic patients. Therefore, rapid antimicrobial susceptibility tests in positive blood culture specimens have been diligently sought. Adenosine triphosphate (ATP) bioluminescence-based methods have been used for rapid antimicrobial susceptibility tests. However, blood culture specimens have not been examined in many studies, possibly due to abundant intracellular ATP in blood corpuscles resulting in false-susceptible results. In this study, we developed a rapid ATP bioluminescence-based method for detecting antibiotic resistance starting from positive blood culture. To minimize background ATP originating from blood corpuscles, specimens were centrifuged and the supernatant diluted with broth, and an ATP-eliminating reagent was then added to the bacterial suspension at the beginning of incubation. This newly devised procedure reduced the background ATP by more than five orders of magnitude. In a pilot study using levofloxacin, no false-susceptible results were observed in 15 clinical specimens. Furthermore, the results indicated that the rapid method provided additional information about bacterial activities with high resolution, in contrast to the less-thorough findings with the conventional turbidity method. Therefore, our approach will contribute to the treatment of infectious diseases as a rapid antimicrobial susceptibility test.
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Sun H, Chan CW, Wang Y, Yao X, Mu X, Lu X, Zhou J, Cai Z, Ren K. Reliable and reusable whole polypropylene plastic microfluidic devices for a rapid, low-cost antimicrobial susceptibility test. LAB ON A CHIP 2019; 19:2915-2924. [PMID: 31369010 DOI: 10.1039/c9lc00502a] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using an antimicrobial susceptibility test (AST) as an example, this work demonstrates a practical method to fabricate microfluidic chips entirely from polypropylene (PP) and the benefits for potential commercial use. Primarily caused by the misuse and abuse of antibiotics, antimicrobial resistance (AMR) is a major threat to modern medicine. The AST is a promising technique to help with the optimal use of antibiotics for reducing AMR. However, current phenotypic ASTs suffer from long turnaround time, while genotypic ASTs suffer from low reliability, and both are unaffordable for routine use. New microfluidics based AST methods are rapid but still unreliable as well as costly due to the PDMS chip material. Herein, we demonstrate a convenient method to fabricate whole PP microfluidic chips with high resolution and fidelity. Unlike PDMS chips, the whole PP chips showed better reliability due to their inertness; they are solvent-compatible and can be conveniently reused and recycled, which largely decreases the cost, and are environmentally friendly. We specially designed 3D chambers that allow for quick cell loading without valving/liquid exchange; this new hydrodynamic design satisfies the shear stress requirement for on-chip bacterial culture, which, compared to reported designs for similar purposes, allows for a simpler, more rapid, and high-throughput operation. Our system allows for reliable tracking of individual cells and acquisition of AST results within 1-3 hours, which is among the group of fastest phenotypic methods. The PP chips are more reliable and affordable than PDMS chips, providing a practical solution to improve current culture-based AST and benefiting the fight against AMR through helping doctors prescribe effective, narrow-spectrum antibiotics; they will also be broadly useful for other applications wherein a reliable, solvent-resistant, anti-fouling, and affordable microfluidic chip is needed.
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Affiliation(s)
- Han Sun
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Chiu-Wing Chan
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Yisu Wang
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Xiao Yao
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China.
| | - Xuan Mu
- Department of Biomedical Engineering, Tufts University, 4 Colby, Medford, MA 02155, USA.
| | - Xuedong Lu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jianhua Zhou
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, Department of Biomedical Engineering, School of Engineering, Sun Yat-sen University, Guangzhou, China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China. and State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Waterloo Rd, Kow-loon, Hong Kong, China
| | - Kangning Ren
- Department of Chemistry, Hong Kong Baptist University, Waterloo Rd, Kowloon, Hong Kong, China. and HKBU Institute of Research and Continuing Education, Shenzhen, China and State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Waterloo Rd, Kow-loon, Hong Kong, China
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58
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Song JH, Lee SM, Park IH, Yong D, Lee KS, Shin JS, Yoo KH. Vertical capacitance aptasensors for real-time monitoring of bacterial growth and antibiotic susceptibility in blood. Biosens Bioelectron 2019; 143:111623. [PMID: 31472413 DOI: 10.1016/j.bios.2019.111623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/29/2023]
Abstract
For the treatment of bacteremia, early diagnosis and rapid antibiotic susceptibility tests (ASTs) are necessary because survival chances decrease significantly if the proper antibiotic administration is delayed. However, conventional methods require several days from blood collection to AST as it requires three overnight cultures, including blood culture, subculture, and AST culture. Herein, we report a more rapid method of sensing bacterial growth and AST in blood based on a vertical capacitance sensor functionalized with aptamers. Owing to their vertical structure, the influence of blood cells sunk by gravity on capacitance measurements were minimized. Thus, bacterial growth in blood at 100-103 CFU/mL was monitored in real-time by measuring changes in capacitance at f = 10 kHz. Moreover, real-time capacitance measurements at f = 0.5 kHz provided information on biofilm formation induced during blood cultures. Bacterial growth and biofilm formation are inhibited above the minimal inhibitory concentration of antibiotics; therefore, we also demonstrated that vertical capacitance aptasensors could be applied to rapid AST from positive blood cultures without a need for the subculture process.
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Affiliation(s)
- Jun Ho Song
- Department of Physics, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sun-Mi Lee
- Nanomedical Graduate Program, Yonsei University, Seoul, 03722, Republic of Korea
| | - In Ho Park
- Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Severance Biomedical Science Institute, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kyo-Seok Lee
- Department of Physics, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jeon-Soo Shin
- Nanomedical Graduate Program, Yonsei University, Seoul, 03722, Republic of Korea; Department of Microbiology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea; Severance Biomedical Science Institute, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Kyung-Hwa Yoo
- Department of Physics, Yonsei University, Seoul, 03722, Republic of Korea; Nanomedical Graduate Program, Yonsei University, Seoul, 03722, Republic of Korea.
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59
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Chang KW, Cheng HW, Shiue J, Wang JK, Wang YL, Huang NT. Antibiotic Susceptibility Test with Surface-Enhanced Raman Scattering in a Microfluidic System. Anal Chem 2019; 91:10988-10995. [PMID: 31387345 DOI: 10.1021/acs.analchem.9b01027] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Antibiotic susceptibility test (AST) is essential in clinical diagnosis of serious bacterial infection, such as sepsis, while it typically takes 2-5 days for sample culture, antibiotic treatment, and reading result. Detecting metabolites secreted from bacteria with surface-enhanced Raman scattering (SERS) enables rapid determination of antibiotic susceptibility, reducing the AST time to 1-2 days. However, it still requires 1 day of culture time to obtain sufficient quantity of bacteria for sample washing, bacterial extraction, and antibiotic treatment. Additionally, the whole procedure, manually performed in open environment, often suffers from contamination and human error. To address the above problems, a microfluidic system integrating membrane filtration and the SERS-active substrate (MF-SERS) was developed to perform on-chip bacterial enrichment, metabolite collection, and in situ SERS measurements for antibiotic susceptibility test. Using Escherichia coli as the prototype bacterium, the lowest SERS detection limit of bacterial concentration of the MF-SERS system is 103 CFU/mL, which is 4 orders of magnitude lower than that using centrifugation-purification procedure, significantly shortening the bacterial culture time. The bacteria and secreted metabolites are enclosed during bacterial trapping, metabolite filtration, and SERS detection, thus minimizing possible contamination and human errors. Finally, the successful demonstration of AST on E. coli with a concentration of 103 CFU/mL is presented. Overall, the MF-SERS system with a miniature size and well-confined microenvironment allows the integration of multiple bacteria processes for bacterial enrichment, culture, and determination of AST.
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60
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Hijazi K, Joshi C, Gould IM. Challenges and opportunities for antimicrobial stewardship in resource-rich and resource-limited countries. Expert Rev Anti Infect Ther 2019; 17:621-634. [PMID: 31282277 DOI: 10.1080/14787210.2019.1640602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Inappropriate prescription practices, patient and provider knowledge and attitudes, variable availability of diagnostic and surveillance systems, and the unrestricted use of antimicrobials in animals and plants are contributory factors to the global crisis of antimicrobial resistance (AMR). Areas covered: Notwithstanding that interventions to revert AMR should be tailored to the socio-politico-economic landscape, there is a global consensus for the implementation and enhancement of antimicrobial stewardship strategies. Yet the implementation of Antimicrobial Stewardship Programs (ASPs) remains relatively limited within healthcare settings and faces complex challenges in resource-limited countries. The current review summarizes the limitations of current ASPs, translation challenges in resource-limited countries, and potential solutions. Expert opinion: Suboptimal ASP implementation in hospitals is multifactorial. Restriction of antimicrobial use should be informed by risk-benefit analyses, including the potential for substitute prescribing, and displacement of selection pressures. Thresholds in population use of antibiotics above which AMR increases may provide quantitative targets for ASPs. Horizontal and vertical collaborations involving policymakers and the general public are of paramount importance. While impactful prescribing changes require sustained engagement of the public and health-care professionals, we warn against over-estimating the benefits of behavioral interventions. We advocate for population-level stewardship interventions in addition to investment in structural factors that will aid ASP implementation.
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Affiliation(s)
- Karolin Hijazi
- a Institute of Dentistry, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen , Aberdeen , UK
| | - Chaitanya Joshi
- b Department of Medical Microbiology, Aberdeen Royal Infirmary , Aberdeen , UK
| | - Ian M Gould
- b Department of Medical Microbiology, Aberdeen Royal Infirmary , Aberdeen , UK
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61
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Song D, Liu H, Ji H, Lei Y. Whole Slide Imaging for High-Throughput Sensing Antibiotic Resistance at Single-Bacterium Level and Its Application to Rapid Antibiotic Susceptibility Testing. Molecules 2019; 24:molecules24132441. [PMID: 31277201 PMCID: PMC6651422 DOI: 10.3390/molecules24132441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/01/2023] Open
Abstract
Since conventional culture-based antibiotic susceptibility testing (AST) methods are too time-consuming (typically 24–72 h), rapid AST is urgently needed for preventing the increasing emergence and spread of antibiotic resistant infections. Although several phenotypic antibiotic resistance sensing modalities are able to reduce the AST time to a few hours or less, concerning the biological heterogeneity, their accuracy or limit of detection are limited by low throughput. Here, we present a rapid AST method based on whole slide imaging (WSI)-enabled high-throughput sensing antibiotic resistance at single-bacterium level. The time for determining the minimum inhibitory concentration (MIC) was theoretically shortest, which ensures that the growth of each individual cell present in a large population is inhibited. As a demonstration, our technique was able to sense the growth of at least several thousand bacteria at single-cell level. Reliable MIC of Enterobacter cloacae against gentamicin was obtained within 1 h, while the gold standard broth dilution method required at least 16 h for the same result. In addition, the application of our method prevails over other imaging-based AST approaches in allowing rapid and accurate determination of antibiotic susceptibility for phenotypically heterogeneous samples, in which the number of antibiotic resistant cells was negligible compared to that of the susceptible cells. Hence, our method shows great promise for both rapid AST determination and point-of-care testing of complex clinical bacteria isolates.
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Affiliation(s)
- Donghui Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Haomin Liu
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Huayi Ji
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Yu Lei
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA.
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Mishra P, Singh D, Mishra K, Kaur G, Dhull N, Tomar M, Gupta V, Kumar B, Ganju L. Rapid antibiotic susceptibility testing by resazurin using thin film platinum as a bio-electrode. J Microbiol Methods 2019; 162:69-76. [DOI: 10.1016/j.mimet.2019.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/15/2019] [Accepted: 05/15/2019] [Indexed: 01/24/2023]
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63
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Adaptable microfluidic system for single-cell pathogen classification and antimicrobial susceptibility testing. Proc Natl Acad Sci U S A 2019; 116:10270-10279. [PMID: 31068473 DOI: 10.1073/pnas.1819569116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Infectious diseases caused by bacterial pathogens remain one of the most common causes of morbidity and mortality worldwide. Rapid microbiological analysis is required for prompt treatment of bacterial infections and to facilitate antibiotic stewardship. This study reports an adaptable microfluidic system for rapid pathogen classification and antimicrobial susceptibility testing (AST) at the single-cell level. By incorporating tunable microfluidic valves along with real-time optical detection, bacteria can be trapped and classified according to their physical shape and size for pathogen classification. By monitoring their growth in the presence of antibiotics at the single-cell level, antimicrobial susceptibility of the bacteria can be determined in as little as 30 minutes compared with days required for standard procedures. The microfluidic system is able to detect bacterial pathogens in urine, blood cultures, and whole blood and can analyze polymicrobial samples. We pilot a study of 25 clinical urine samples to demonstrate the clinical applicability of the microfluidic system. The platform demonstrated a sensitivity of 100% and specificity of 83.33% for pathogen classification and achieved 100% concordance for AST.
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FRET probe-based antibacterial susceptibility testing (F-AST) by detection of bacterial nucleases released by antibiotic-induced lysis. Biosens Bioelectron 2019; 130:225-229. [DOI: 10.1016/j.bios.2019.01.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 11/21/2022]
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65
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Kim S, Masum F, Kim JK, Chung HJ, Jeon JS. On-chip phenotypic investigation of combinatory antibiotic effects by generating orthogonal concentration gradients. LAB ON A CHIP 2019; 19:959-973. [PMID: 30768106 DOI: 10.1039/c8lc01406j] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Combinatory therapy using two or more kinds of antibiotics is attracting considerable attention for inhibiting multi-drug resistant pathogenic bacteria. Although the therapy mostly leads to more powerful antimicrobial effects than using a single antibiotic (synergy), interference may arise from certain antibiotic combinations, resulting in the antimicrobial effect being suppressed (antagonism). Here, we present a microfluidic-based phenotypic screening chip to investigate combinatory antibiotic effects by automatically generating two orthogonal concentration gradients on a bacteria-trapping agarose gel. Computational simulations and fluorescence experiments together verify the simultaneous establishment of 121 concentration combinations, facilitating on-chip drug testing with stability and efficiency. Against Gram-negative bacteria, Pseudomonas aeruginosa, our chip allows the measurement of phenotypic growth levels, and enables various types of analyses for all antibiotic pairs to be conducted in 7 h. Furthermore, by providing a specific amount of susceptibility data, our chip enables the two reference models, Loewe additivity and Bliss independence, to be implemented, which classify the antibiotic interaction types into synergy or antagonism. These results suggest the efficacy of our chip as a cell-based drug screening platform for exploring the underlying pharmacological patterns of antibiotic interactions, with potential applications in guidance in clinical therapies and in screening other cell-type agents.
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Affiliation(s)
- Seunggyu Kim
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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66
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McConnell MJ. Where are we with monoclonal antibodies for multidrug-resistant infections? Drug Discov Today 2019; 24:1132-1138. [PMID: 30853568 DOI: 10.1016/j.drudis.2019.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/21/2019] [Accepted: 03/01/2019] [Indexed: 01/17/2023]
Abstract
Widespread antibiotic resistance threatens the continued efficacy of antimicrobial therapy based on small-molecule antibiotics. Infections caused by multidrug-resistant Gram-negative bacteria are particularly worrisome owing to the lack of antimicrobials retaining sufficient activity against these microorganisms. Despite the explosion in monoclonal antibody therapies that have been developed for oncologic and rheumatic indications, only three antibacterial monoclonal antibodies have been approved for clinical use. In the present review, the therapeutic potential of this drug class for treating multidrug-resistant infections is discussed, and considerations for the development of antibacterial monoclonal antibodies are presented. Finally, the state of development of monoclonal antibody therapies for some of the most problematic multidrug-resistant Gram-negative infections is summarized.
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Affiliation(s)
- Michael J McConnell
- Antimicrobial Resistance and Hospital Acquired Infections Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain.
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67
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Torres Fink I, Tormo Palop N, Borrás Salvador R, Buesa Gómez J, Gimeno Cardona C, Navarro Ortega D. Evaluation of the DNA microarray "AMR Direct Flow Chip Kit" for detection of antimicrobial resistance genes from Gram-positive and Gram-negative bacterial isolated colonies. Enferm Infecc Microbiol Clin 2019; 37:454-457. [PMID: 30857832 DOI: 10.1016/j.eimc.2018.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/16/2018] [Accepted: 12/26/2018] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The AMR Direct Flow Chip assay allows the simultaneous detection of a large variety of antibiotic resistance genetic markers. To assess this kit's performance, we use isolated colonies as starting material. The assay has been approved by the European Economic Area as a suitable device for in vitro diagnosis (CE IVD) using clinical specimens. METHODS A total of 210 bacterial isolates harbouring either one or more antimicrobial resistance genes including plasmid-encoded extended-spectrum β-lactamases (SHV, CTX-M) and carbapenemases (GES, SME, KPC, NMC/IMI, SIM, GIM, SPM, NDM, VIM, IMP, and OXA), mecA, vanA and vanB, and 30 controls were included. RESULTS The assay displayed a sensitivity and specificity of 100% for all target genes included in the array. CONCLUSION The AMR Direct Flow Chip Kit is an accurate assay for detecting genes which commonly confer resistance to β-lactams and vancomycin from isolated colonies in culture of Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Ignacio Torres Fink
- Microbiology Service, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain
| | - Nuria Tormo Palop
- Microbiology Service Consorcio Hospital General Universitario, Valencia, Spain
| | - Rafael Borrás Salvador
- Microbiology Service, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Spain
| | - Javier Buesa Gómez
- Microbiology Service, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Spain
| | - Concepción Gimeno Cardona
- Microbiology Service Consorcio Hospital General Universitario, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Spain
| | - David Navarro Ortega
- Microbiology Service, Hospital Clínico Universitario, Fundación INCLIVA, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Spain.
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68
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Mustazzolu A, Venturelli L, Dinarelli S, Brown K, Floto RA, Dietler G, Fattorini L, Kasas S, Girasole M, Longo G. A Rapid Unraveling of the Activity and Antibiotic Susceptibility of Mycobacteria. Antimicrob Agents Chemother 2019; 63:e02194-18. [PMID: 30602518 PMCID: PMC6395931 DOI: 10.1128/aac.02194-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/14/2018] [Indexed: 01/10/2023] Open
Abstract
The development of antibiotic-resistant bacteria is a worldwide health-related emergency that calls for new tools to study the bacterial metabolism and to obtain fast diagnoses. Indeed, the conventional analysis time scale is too long and affects our ability to fight infections. Slowly growing bacteria represent a bigger challenge, since their analysis may require up to months. Among these bacteria, Mycobacterium tuberculosis, the causative agent of tuberculosis, has caused more than 10 million new cases and 1.7 million deaths in 2016 only. We employed a particularly powerful nanomechanical oscillator, the nanomotion sensor, to characterize rapidly and in real time tuberculous and nontuberculous bacterial species, Mycobacterium bovis bacillus Calmette-Guérin and Mycobacterium abscessus, respectively, exposed to different antibiotics. Here, we show how high-speed and high-sensitivity detectors, the nanomotion sensors, can provide a rapid and reliable analysis of different mycobacterial species, obtaining qualitative and quantitative information on their responses to different drugs. This is the first application of the technique to tackle the urgent medical issue of mycobacterial infections, evaluating the dynamic response of bacteria to different antimicrobial families and the role of the replication rate in the resulting nanomotion pattern. In addition to a fast analysis, which could massively benefit patients and the overall health care system, we investigated the real-time responses of the bacteria to extract unique information on the bacterial mechanisms triggered in response to antibacterial pressure, with consequences both at the clinical level and at the microbiological level.
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Affiliation(s)
| | - L Venturelli
- LPMV-IPHYS, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - S Dinarelli
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - K Brown
- Molecular Immunity Unit, University of Cambridge, Cambridge, United Kingdom
| | - R A Floto
- Molecular Immunity Unit, University of Cambridge, Cambridge, United Kingdom
| | - G Dietler
- LPMV-IPHYS, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | | | - S Kasas
- LPMV-IPHYS, Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland
| | - M Girasole
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - G Longo
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche, Rome, Italy
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69
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Kim S, Lee S, Kim JK, Chung HJ, Jeon JS. Microfluidic-based observation of local bacterial density under antimicrobial concentration gradient for rapid antibiotic susceptibility testing. BIOMICROFLUIDICS 2019; 13:014108. [PMID: 30867878 PMCID: PMC6404913 DOI: 10.1063/1.5066558] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/10/2019] [Indexed: 05/09/2023]
Abstract
The need for accurate and efficient antibiotic susceptibility testing (AST) has been emphasized with respect to the emerging antimicrobial resistance of pathogenic bacteria which has increased over the recent decades. In this study, we introduce a microfluidic system that enables rapid formation of the antibiotic concentration gradient with convenient bacterial growth measurement based on color scales. Furthermore, we expanded the developed system to analyze combinatory effects of antibiotics and measured the collective antibiotic susceptibility of bacteria compared to single microfluidic AST methods. By injecting a continuous flow precisely into the channel, the system enabled the concentration gradient to be established between two parallel channels of different antibiotic concentrations within 30 min, before bacteria enter the exponential growth phase. Moreover, the local bacterial growth levels under antibiotic gradient were quantitatively determined by calculating the position-specific grayscale values from the microscopic images and were compared with the conventional optical density measurement method. We tested five antibiotic types on our platform for the pathogenic Gram-negative bacteria strain Pseudomonas aeruginosa, and we were able to determine the minimum inhibitory concentration (MIC) at which 90% to 95% of bacterial growth was inhibited. Finally, we demonstrated the efficacy of our system by showing that most of the antibiotic MICs determined in our platform show good agreement with the MIC range suggested by the Clinical and Laboratory Standards Institutes.
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Affiliation(s)
- Seunggyu Kim
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Seokhun Lee
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Ju-Kang Kim
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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70
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Maugeri G, Lychko I, Sobral R, Roque ACA. Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends. Biotechnol J 2019; 14:e1700750. [PMID: 30024110 PMCID: PMC6330097 DOI: 10.1002/biot.201700750] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/06/2018] [Indexed: 12/16/2022]
Abstract
Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.
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Affiliation(s)
- Gaetano Maugeri
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Iana Lychko
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Rita Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Ana C A Roque
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
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71
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Khan ZA, Siddiqui MF, Park S. Progress in antibiotic susceptibility tests: a comparative review with special emphasis on microfluidic methods. Biotechnol Lett 2018; 41:221-230. [PMID: 30542946 DOI: 10.1007/s10529-018-02638-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/07/2018] [Indexed: 11/25/2022]
Abstract
Antibiotic susceptibility test (AST) is an umbrella term for techniques to determine the susceptibility of bacteria to antibiotics. The antibiotic-resistant bacteria are a major threat to public health and a directed therapy based on accurate AST results is paramount in resistance control. Here we have briefly covered the progress of conventional, molecular, and automated AST tools and their limitations. Various aspects of microfluidic AST such as optical, electrochemical, colorimetric, and mechanical methods have been critically reviewed. We also address the future requirements of the microfluidic devices for AST. Cumulatively, we have outlined the overview of AST that can help to expand and improve the existing techniques and emphasize that microfluidics could be the future of AST and introduction of microtechnologies in AST will be extremely advantageous, especially for point-of-care testing.
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Affiliation(s)
- Zeeshan A Khan
- School of Mechanical Engineering, Korea University of Technology and Education, Cheonan, Chungnam, 31253, South Korea
| | - Mohd F Siddiqui
- School of Mechanical Engineering, Korea University of Technology and Education, Cheonan, Chungnam, 31253, South Korea
| | - Seungkyung Park
- School of Mechanical Engineering, Korea University of Technology and Education, Cheonan, Chungnam, 31253, South Korea.
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72
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Rohani A, Moore JH, Su YH, Stagnaro V, Warren C, Swami NS. Single-cell electro-phenotyping for rapid assessment of Clostridium difficile heterogeneity under vancomycin treatment at sub-MIC (minimum inhibitory concentration) levels. SENSORS AND ACTUATORS. B, CHEMICAL 2018; 276:472-480. [PMID: 30369719 PMCID: PMC6201234 DOI: 10.1016/j.snb.2018.08.137] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Current methods for measurement of antibiotic susceptibility of pathogenic bacteria are highly reliant on microbial culture, which is time consuming (requires > 16 hours), especially at near minimum inhibitory concentration (MIC) levels of the antibiotic. We present the use of single-cell electrophysiology-based microbiological analysis for rapid phenotypic identification of antibiotic susceptibility at near-MIC levels, without the need for microbial culture. Clostridium difficile (C. difficile) is the single most common cause of antibiotic-induced enteric infection and disease recurrence is common after antibiotic treatments to suppress the pathogen. Herein, we show that de-activation of C. difficile after MIC-level vancomycin treatment, as validated by microbiological growth assays, can be ascertained rapidly by measuring alterations to the microbial cytoplasmic conductivity that is gauged by the level of positive dielectrophoresis (pDEP) and the frequency spectra for co-field electro-rotation (ROT). Furthermore, this single-cell electrophysiology technique can rapidly identify and quantify the live C. difficile subpopulation after vancomycin treatment at sub-MIC levels, whereas methods based on measurement of the secreted metabolite toxin or the microbiological growth rate can identify this persistent C. difficile subpopulation only after 24 hours of microbial culture, without any ability to quantify the subpopulation. The application of multiplexed versions of this technique is envisioned for antibiotic susceptibility screening.
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Affiliation(s)
- Ali Rohani
- Electrical & Computer Engineering, University of Virginia
| | - John H. Moore
- Electrical & Computer Engineering, University of Virginia
| | - Yi-Hsuan Su
- Electrical & Computer Engineering, University of Virginia
| | | | - Cirle Warren
- Infectious Diseases, School of Medicine, University of Virginia
| | - Nathan S. Swami
- Electrical & Computer Engineering, University of Virginia
- Corresponding author: 351 McCormick Road, Charlottesville, VA 22904-1000;
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73
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Wang K, Li S, Petersen M, Wang S, Lu X. Detection and Characterization of Antibiotic-Resistant Bacteria Using Surface-Enhanced Raman Spectroscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2018; 8:E762. [PMID: 30261660 PMCID: PMC6215266 DOI: 10.3390/nano8100762] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 09/12/2018] [Accepted: 09/23/2018] [Indexed: 12/17/2022]
Abstract
This mini-review summarizes the most recent progress concerning the use of surface-enhanced Raman spectroscopy (SERS) for the detection and characterization of antibiotic-resistant bacteria. We first discussed the design and synthesis of various types of nanomaterials that can be used as the SERS-active substrates for biosensing trace levels of antibiotic-resistant bacteria. We then reviewed the tandem-SERS strategy of integrating a separation element/platform with SERS sensing to achieve the detection of antibiotic-resistant bacteria in the environmental, agri-food, and clinical samples. Finally, we demonstrated the application of using SERS to investigate bacterial antibiotic resistance and susceptibility as well as the working mechanism of antibiotics based on spectral fingerprinting of the whole cells.
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Affiliation(s)
- Kaidi Wang
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Shenmiao Li
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Marlen Petersen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300371, China.
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
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74
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Edmiston CE, Garcia R, Barnden M, DeBaun B, Johnson HB. Rapid diagnostics for bloodstream infections: A primer for infection preventionists. Am J Infect Control 2018; 46:1060-1068. [PMID: 29661630 DOI: 10.1016/j.ajic.2018.02.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 01/20/2023]
Abstract
Accurate and rapid antimicrobial susceptibility testing with pathogen identification in bloodstream infections is critical to life results for early sepsis intervention. Advancements in rapid diagnostics have shortened the time to results from days to hours and have had positive effects on clinical outcomes and on efforts to combat antimicrobial resistance when paired with robust antimicrobial stewardship programs. This article provides infection preventionists with a working knowledge of available rapid diagnostics for bloodstream infections.
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Affiliation(s)
| | - Robert Garcia
- Stony Brook University Medical Center, Stony Brook, NY
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75
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Rapid Antibiotic Combination Testing for Carbapenem-Resistant Gram-Negative Bacteria within Six Hours Using ATP Bioluminescence. Antimicrob Agents Chemother 2018; 62:AAC.00183-18. [PMID: 29967021 DOI: 10.1128/aac.00183-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/23/2018] [Indexed: 12/15/2022] Open
Abstract
To guide the timely selection of antibiotic combinations against carbapenem-resistant Gram-negative bacteria (CR-GNB), an in vitro test with a short turnaround time is essential. We developed an in vitro ATP bioluminescence assay to determine effective antibiotic combinations against CR-GNB within 6 h. We tested 42 clinical CR-GNB strains (14 Acinetobacter baumannii, 14 Pseudomonas aeruginosa, and 14 Klebsiella pneumoniae strains) against 74 single antibiotics and two-antibiotic combinations. Bacteria (approximately 5 log10 CFU/ml) were incubated with an antibiotic(s) at 35°C; ATP bioluminescence was measured at 6 h and 24 h; and the measurements were compared to viable counts at 24 h. Receiver operating characteristic (ROC) curves were used to determine the optimal luminescence thresholds (TRLU) for distinguishing between inhibitory and noninhibitory combinations. The areas under the 6-h and 24-h ROC curves were compared using the DeLong method. Prospective validation of the established thresholds was conducted using 18 additional CR-GNB. The predictive accuracy of TRLU for the 6-h ATP bioluminescence assay was 77.5% when all species were analyzed collectively. Predictive accuracies ranged from 73.7% to 82.7% when each species was analyzed individually. Upon comparison of the areas under the 6-h and 24-h ROC curves, the 6-h assay performed significantly better than the 24-h assay (P < 0.01). Predictive accuracy remained high upon prospective validation of the 6-h ATP assay (predictive accuracy, 79.8%; 95% confidence interval [CI], 77.6 to 81.9%), confirming the external validity of the assay. Our findings indicate that our 6-h ATP bioluminescence assay can provide guidance for prospective selection of antibiotic combinations against CR-GNB in a timely manner and may be useful in the management of CR-GNB infections.
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76
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Pereckaite L, Tatarunas V, Giedraitiene A. Current antimicrobial susceptibility testing for beta-lactamase-producing Enterobacteriaceae in clinical settings. J Microbiol Methods 2018; 152:154-164. [PMID: 30063958 DOI: 10.1016/j.mimet.2018.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 07/16/2018] [Accepted: 07/27/2018] [Indexed: 11/17/2022]
Abstract
The worldwide prevalence of beta-lactamase-producing Enterobacteriaceae (BL-E) is increasing. Bacterial infections involving ESBLs can be more difficult to treat because of antibiotic resistance, as there are fewer effective antibiotics left to be used. Moreover, treatment failure is often observed. Thus, quick and accurate identification of β-lactamases is imperative to minimize it. This review article describes most commonly used phenotypic techniques and molecular methods for the detection of ESBLs, acquired AmpC β-lactamases, and carbapenemases produced by Enterobacteriaceae. Phenotypic detection tests remain useful and relevant in clinical laboratories while molecular diagnostic methods are less affordable, more technically demanding, and not standardized. Molecular methods could be used to speed up results of bacterial antibiotic resistance or to clarify the results of phenotypic β-lactamases confirmation tests.
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Affiliation(s)
- Laura Pereckaite
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vacis Tatarunas
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Agne Giedraitiene
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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77
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Li L, Li Q, Liao Z, Sun Y, Cheng Q, Song Y, Song E, Tan W. Magnetism-Resolved Separation and Fluorescence Quantification for Near-Simultaneous Detection of Multiple Pathogens. Anal Chem 2018; 90:9621-9628. [PMID: 30001487 DOI: 10.1021/acs.analchem.8b02572] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In the modern era of molecular evidence-based medicine and advanced biomedical technologies, the rapid, sensitive and specific assay of multiple pathogens is critical to, but largely absent from, clinical practice. Therefore, to improve the current ordinary separation and collection method, we report herein a strategy of magnetism-resolved separation and fluorescence quantification for near-simultaneous detection of multiple pathogens, followed by the direct antimicrobial susceptibility testing (AST). To accomplish this strategy, we utilized aptamer-modified fluorescent-magnetic multifunctional nanoprobes (apt-FMNPs). FMNPs with intriguing different magnetic responses and excellent fluorescence quality were first self-assembled based on metal coordination interaction using (3-mercaptopropyl) trimethoxysilane, magnetic γ-Fe2O3, and fluorescent quantum dots as matrix components. Then, aptamers, which specific to target pathogens of Escherichia coli O157:H7 ( E. coli) and Salmonella typhimurium ( S. typ), were conjugated with FMNPs to yield apt-FMNPs nanoprobes for multiple pathogens assay. Based on the discrepant magnetic response of pathogen@nanoprobes complex under the identical external magnetic field, the model bacteria were fished out by magnetic adsorption at different time points and subjected to fluorescence quantification with good linear ranges and detection limits within 1h. Multiple pathogens spiked in real samples were also effectively detected by the apt-FMNPs and sequentially fished out for AST assay, which showed similar results to that for pure pathogens. The apt-FMNPs-based strategy of near-simultaneous detection of multiple pathogens shows promise for the potential application in the diagnosis and treatment of pathogen-related infectious diseases.
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Affiliation(s)
- Linyao Li
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , People's Republic of China
| | - Qingjin Li
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , People's Republic of China
| | - Ziyi Liao
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , People's Republic of China
| | - Yan Sun
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , People's Republic of China
| | - Quansheng Cheng
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , People's Republic of China
| | - Yang Song
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , People's Republic of China
| | - Erqun Song
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , People's Republic of China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Collaborative Research Center of Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , People's Republic of China.,Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , United States
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78
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79
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Tang M, Huang X, Chu Q, Ning X, Wang Y, Kong SK, Zhang X, Wang G, Ho HP. A linear concentration gradient generator based on multi-layered centrifugal microfluidics and its application in antimicrobial susceptibility testing. LAB ON A CHIP 2018; 18:1452-1460. [PMID: 29664087 DOI: 10.1039/c8lc00042e] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In almost any branch of chemistry or life sciences, it is often necessary to study the interaction between different components in a system by varying their respective concentrations in a systematic manner. Currently, many procedures for generating a series of samples of different solute concentration levels are still done manually by dilution. To address this issue, we present herein a highly automated linear concentration gradient generator based on centrifugal microfluidics. The operation of this device is based on the use of multi-layered microfluidics in which individual fluidic samples to be mixed together are stored and metered in their respective layers before finally being transferred to a mixing chamber. To demonstrate the operation of this scheme, we have used the device to conduct antimicrobial susceptibility testing (AST). Firstly, DI water, ampicillin solution and E. coli suspension were loaded into the chambers in different layers. As the device went through several rounds of spinning at different speeds, a series of metered dosages of ampicillin along a linear concentration gradient were introduced to the mixing chamber and mixed with E. coli automatically. By monitoring the spectral absorbance of the suspensions, we were able to establish the minimum inhibitory concentration (MIC) value of ampicillin against E. coli. The process took about 3 hours to complete, and the experimental results showed a strong correlation with those obtained with the standard CLSI broth dilution method. Clearly, the platform is useful for a wide range of applications such as drug discovery and personalised medicine, where concentration gradients are of concern.
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Affiliation(s)
- Minghui Tang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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80
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Dow P, Kotz K, Gruszka S, Holder J, Fiering J. Acoustic separation in plastic microfluidics for rapid detection of bacteria in blood using engineered bacteriophage. LAB ON A CHIP 2018; 18:923-932. [PMID: 29445800 DOI: 10.1039/c7lc01180f] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A more effective treatment of bacteremia requires a diagnostic platform that is both sensitive, accurate and rapid. Currently, clinical laboratory techniques require growth of bacteria prior to diagnosis, take days to complete, and leave empiric therapy and broad spectrum antibiotics as the only option at the onset of treatment. In order to bypass this growth requirement, we engineered a system that purifies bacteria from blood to improve performance in a bacteriophage-based luminescence assay. To perform the purification, we used acoustophoresis in plastic microfluidic chips, enabling future development into a low cost point-of-care system. Acoustophoresis achieves differential separation on the basis of size differences between bacteria and blood cells. We show isolation of three known pathogen species, including members of both Gram-negative and positive-bacteria from blood, and show isolation at clinically relevant concentrations. Using the device as a preparation step prior to the bacteriophage-based luminescence assay, we demonstrate a 33-fold improvement in limit of detection, compared with the unpurified sample, achieving a limit of detection of 6 bacteria.
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Affiliation(s)
- P Dow
- Draper, 555 Technology Square, Cambridge, MA 02139, USA.
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81
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Rapid and cost-effective identification and antimicrobial susceptibility testing in patients with Gram-negative bacteremia directly from blood-culture fluid. J Microbiol Methods 2018; 146:7-12. [DOI: 10.1016/j.mimet.2018.01.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 12/29/2022]
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82
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Kim JH, Kim TS, Song SH, Choi J, Han S, Kim DY, Kwon S, Lee E, Song KH, Choe PG, Bang JH, Kim ES, Park SW, Kim HB, Kim NJ, Park WB, Oh MD. Direct rapid antibiotic susceptibility test (dRAST) for blood culture and its potential usefulness in clinical practice. J Med Microbiol 2018; 67:325-331. [DOI: 10.1099/jmm.0.000678] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Jeong-Han Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sang Hoon Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | | | | | | | - Eunyoung Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyeong Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Hwan Bang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eu Suk Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sang Won Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Myoung-don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
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83
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Hong W, Karanja CW, Abutaleb NS, Younis W, Zhang X, Seleem MN, Cheng JX. Antibiotic Susceptibility Determination within One Cell Cycle at Single-Bacterium Level by Stimulated Raman Metabolic Imaging. Anal Chem 2018; 90:3737-3743. [PMID: 29461044 DOI: 10.1021/acs.analchem.7b03382] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The widespread use of antibiotics has significantly increased the number of resistant bacteria, which has also increased the urgency of rapid bacterial detection and profiling their antibiotic response. Current clinical methods for antibiotic susceptibility testing (AST) rely on culture and require at least 16 to 24 h to conduct. Therefore, there is an urgent need for a rapid method that can test the susceptibility of bacteria in a culture-free manner. Here we demonstrate a rapid AST method by monitoring the glucose metabolic activity of live bacteria at the single-cell level with hyperspectral stimulated Raman scattering (SRS) imaging. Using vancomycin-susceptible and -resistant enterococci E. faecalis as models, we demonstrate that the metabolic uptake of deuterated glucose in a single living bacterium can be quantitatively monitored via hyperspectral SRS imaging. Remarkably, the metabolic activity of susceptible bacteria responds differently to antibiotics from the resistant strain within only 0.5 h from the addition of antibiotics. Therefore, bacterial susceptibility and the minimum inhibitory concentration (MIC) of antibiotics can be determined within one cell cycle. Our metabolic imaging method is applicable to other bacteria species including E. coli, K. Pneumoniae, and S. aureus as well as different antibiotics, regardless of their mechanisms of inhibiting or killing bacteria.
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Affiliation(s)
| | | | | | | | | | | | - Ji-Xin Cheng
- Department of Biomedical Engineering and Department of Electrical and Chemical Engineering , Boston University , Boston , Massachusetts 02215 , United States
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84
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Modeling the Emergence of Antibiotic Resistance in the Environment: an Analytical Solution for the Minimum Selection Concentration. Antimicrob Agents Chemother 2018; 62:AAC.01686-17. [PMID: 29263062 DOI: 10.1128/aac.01686-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Environmental antibiotic risk management requires an understanding of how subinhibitory antibiotic concentrations contribute to the spread of resistance. We develop a simple model of competition between sensitive and resistant bacterial strains to predict the minimum selection concentration (MSC), the lowest level of antibiotic at which resistant bacteria are selected. We present an analytical solution for the MSC based on the routinely measured MIC, the selection coefficient (sc) that expresses fitness differences between strains, the intrinsic net growth rate, and the shape of the bacterial growth dose-response curve with antibiotic or metal exposure (the Hill coefficient [κ]). We calibrated the model by optimizing the Hill coefficient to fit previously reported experimental growth rate difference data. The model fit varied among nine compound-taxon combinations examined but predicted the experimentally observed MSC/MIC ratio well (R2 ≥ 0.95). The shape of the antibiotic response curve varied among compounds (0.7 ≤ κ ≤ 10.5), with the steepest curve being found for the aminoglycosides streptomycin and kanamycin. The model was sensitive to this antibiotic response curve shape and to the sc, indicating the importance of fitness differences between strains for determining the MSC. The MSC can be >1 order of magnitude lower than the MIC, typically by the factor scκ This study provides an initial quantitative depiction and a framework for a research agenda to examine the growing evidence of selection for resistant bacterial communities at low environmental antibiotic concentrations.
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85
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Huh HJ, Song DJ, Shim HJ, Kwon WK, Park MS, Ryu MR, Cho EH, Oh J, Yoo IY, Lee NY. Performance evaluation of the QMAC-dRAST for staphylococci and enterococci isolated from blood culture: a comparative study of performance with the VITEK-2 system. J Antimicrob Chemother 2018; 73:1267-1271. [DOI: 10.1093/jac/dky015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/03/2018] [Indexed: 01/15/2023] Open
Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Dong Joon Song
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hyang Jin Shim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Won Kyung Kwon
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Min-Seung Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Mi Ra Ryu
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Eun Hye Cho
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jongwon Oh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - In Young Yoo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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86
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In Vitro activity of novel glycopolymer against clinical isolates of multidrug-resistant Staphylococcus aureus. PLoS One 2018; 13:e0191522. [PMID: 29342216 PMCID: PMC5771624 DOI: 10.1371/journal.pone.0191522] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/05/2018] [Indexed: 01/15/2023] Open
Abstract
The incidence of multidrug-resistant (MDR) organisms, including methicillin-resistant Staphylococcus aureus (MRSA), is a serious threat to public health. Progress in developing new therapeutics is being outpaced by antibiotic resistance development, and alternative agents that rapidly permeabilize bacteria hold tremendous potential for treating MDR infections. A new class of glycopolymers includes polycationic poly-N (acetyl, arginyl) glucosamine (PAAG) is under development as an alternative to traditional antibiotic strategies to treat MRSA infections. This study demonstrates the antibacterial activity of PAAG against clinical isolates of methicillin and mupirocin-resistant Staphylococcus aureus. Multidrug-resistant S. aureus was rapidly killed by PAAG, which completely eradicated 88% (15/17) of all tested strains (6-log reduction in CFU) in ≤ 12-hours at doses that are non-toxic to mammalian cells. PAAG also sensitized all the clinical MRSA strains (17/17) to oxacillin as demonstrated by the observed reduction in the oxacillin MIC to below the antibiotic resistance breakpoint. The effect of PAAG and standard antibiotics including vancomycin, oxacillin, mupirocin and bacitracin on MRSA permeability was studied by measuring propidium iodide (PI) uptake by bacterial cells. Antimicrobial resistance studies showed that S. aureus developed resistance to PAAG at a rate slower than to mupirocin but similar to bacitracin. PAAG was observed to resensitize drug-resistant S. aureus strains sampled from passage 13 and 20 of the multi-passage resistance study, reducing MICs of mupirocin and bacitracin below their clinical sensitivity breakpoints. This class of bacterial permeabilizing glycopolymers may provide a new tool in the battle against multidrug-resistant bacteria.
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87
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Nguyen M, Brettin T, Long SW, Musser JM, Olsen RJ, Olson R, Shukla M, Stevens RL, Xia F, Yoo H, Davis JJ. Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. Sci Rep 2018; 8:421. [PMID: 29323230 PMCID: PMC5765115 DOI: 10.1038/s41598-017-18972-w] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics. The overall accuracy of the model, within ±1 two-fold dilution factor, is 92%. Individual accuracies are ≥90% for 15/20 antibiotics. We show that the MICs predicted by the model correlate with known antimicrobial resistance genes. Importantly, the genome-wide approach described in this study offers a way to predict MICs for isolates without knowledge of the underlying gene content. This study shows that machine learning can be used to build a complete in silico MIC prediction panel for K. pneumoniae and provides a framework for building MIC prediction models for other pathogenic bacteria.
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Affiliation(s)
- Marcus Nguyen
- Northern Illinois University, Computation Science, DeKalb, IL, 60115, USA.,University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Thomas Brettin
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Robert Olson
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Maulik Shukla
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Rick L Stevens
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA.,University of Chicago, Department of Computer Science, Chicago, IL, 60439, USA
| | - Fangfang Xia
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Hyunseung Yoo
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - James J Davis
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA. .,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA.
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88
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Kirchhoff J, Glaser U, Bohnert JA, Pletz MW, Popp J, Neugebauer U. Simple Ciprofloxacin Resistance Test and Determination of Minimal Inhibitory Concentration within 2 h Using Raman Spectroscopy. Anal Chem 2018; 90:1811-1818. [DOI: 10.1021/acs.analchem.7b03800] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Uwe Glaser
- Leibniz Institute of Photonic Technology, Jena, Germany
| | - Jürgen A. Bohnert
- Friedrich
Loeffler Institute of Medical Microbiology, Greifswald University Hospital, Greifswald, Germany
| | | | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Jena, Germany
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Research Campus InfectoGnostics Jena, Jena, Germany
| | - Ute Neugebauer
- Leibniz Institute of Photonic Technology, Jena, Germany
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
- Research Campus InfectoGnostics Jena, Jena, Germany
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89
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Domínguez CM, Ramos D, Mingorance J, Fierro JLG, Tamayo J, Calleja M. Direct Detection of OXA-48 Carbapenemase Gene in Lysate Samples through Changes in Mechanical Properties of DNA Monolayers upon Hybridization. Anal Chem 2018; 90:968-973. [PMID: 29186953 DOI: 10.1021/acs.analchem.7b04094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae have recently become an important cause of morbidity and mortality due to healthcare-associated infections. Most commonly used diagnostic methods are incompatible with fast and accurate directed therapy. We report here the direct identification of the blaOXA48 gene, which codes for the carbapenemase OXA-48, in lysate samples from Klebsiella pneumoniae. The method is PCR-free and label-free. It is based on the measurement of changes in the stiffness of DNA self-assembled monolayers anchored to microcantilevers that occur as a consequence of the hybridization. The stiffness of the DNA layer is measured through changes of the sensor resonance frequency upon hybridization and at varying relative humidity.
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Affiliation(s)
- Carmen M Domínguez
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
| | - Daniel Ramos
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz , IdiPAZ, Paseo de la Castellana, 261, Madrid, E-28046, Spain
| | - José L G Fierro
- ICP-Instituto de Catálisis y Petroleoquímica (CSIC) , Marie Curie, 2 Cantoblanco, Madrid, E-28049, Spain
| | - Javier Tamayo
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
| | - Montserrat Calleja
- IMN-Instituto de Micro y Nanotecnología (CNM-CSIC) , Isaac Newton 8, PTM, Tres Cantos, Madrid E-28760, Spain
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90
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Kim H, Jeong HY, Han S, Han S, Choi J, Jin B, Lim T, Kim EG, Kim DY, Song SH, Kim TS, Kwon S. Clinical Evaluation of QMAC-dRAST for Direct and Rapid Antimicrobial Susceptibility Test with Gram-Positive Cocci from Positive Blood Culture Bottles. ANNALS OF CLINICAL MICROBIOLOGY 2018. [DOI: 10.5145/acm.2018.21.1.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
| | - Hyun Yong Jeong
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea
- Department of Transdisciplinary Studies, Seoul National University, Seoul, Korea
| | | | | | | | | | - Taegeun Lim
- QuantaMatrix Inc., Seoul, Korea
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea
| | | | | | - Sang Hoon Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sunghoon Kwon
- QuantaMatrix Inc., Seoul, Korea
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Korea
- Department of Transdisciplinary Studies, Seoul National University, Seoul, Korea
- Seoul National University Hospital Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
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91
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Costa-de-Oliveira S, Teixeira-Santos R, Silva AP, Pinho E, Mergulhão P, Silva-Dias A, Marques N, Martins-Oliveira I, Rodrigues AG, Paiva JA, Cantón R, Pina-Vaz C. Potential Impact of Flow Cytometry Antimicrobial Susceptibility Testing on the Clinical Management of Gram-Negative Bacteremia Using the FASTinov ® Kit. Front Microbiol 2017; 8:2455. [PMID: 29312169 PMCID: PMC5733032 DOI: 10.3389/fmicb.2017.02455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/27/2017] [Indexed: 11/16/2022] Open
Abstract
Laboratory assessment of antimicrobial susceptibility is a prerequisite for adequate management of infections. The aim of this research was to evaluate the performance of the novel FASTinov® kit for antimicrobial susceptibility testing (AST) of Gram negative bacilli directly on positive blood cultures. One hundred and two positive blood cultures from patients of a Portuguese University Hospital were included. AST were performed with routine method, Vitek2, with FASTinov® kit, and with the gold standard microdilution. Bacteria directly extracted from blood cultures were used to inoculate the FASTinov® kit. Time-to-result as well as the number of patients receiving initially inappropriate therapy (and those in whom de-escalation would have been done) and length of stay (LOS) was recorded. Seventy percent of patients were over 70 years old and 18.6% were admitted in intensive care units. Regarding the isolates, 88.2% were Enterobacteriaceae, 9.8% Pseudomonas spp. and 1% Acinetobacter spp. Extended spectrum β-lactamases producing-Enterobacteriaceae were found in 7.8% of cases and 10.8% were multi-drug resistant. Fifty-one hours was the mean of time-to-result for routine test (Vitek2) vs. 2 h response regarding Fastinov® test. The overall agreement between FASTinov® and the reference microdilution method was 98%. According to the susceptibility phenotype, 16.7% of patients received initially inappropriate therapy and the mean hospital LOS of these patients was significantly higher. FASTinov® kit revealed an excellent correlation with the AST standard method and provided much earlier results than Vitek2.
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Affiliation(s)
- Sofia Costa-de-Oliveira
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal.,FASTinov, S.A., Matosinhos, Portugal
| | - Rita Teixeira-Santos
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.,FASTinov, S.A., Matosinhos, Portugal
| | - Ana P Silva
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Elika Pinho
- Department of Emergency and Intensive Care, Centro Hospitalar Sao Joao, Porto, Portugal
| | - Paulo Mergulhão
- Department of Emergency and Intensive Care, Centro Hospitalar Sao Joao, Porto, Portugal.,Department of Medicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Ana Silva-Dias
- CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal.,FASTinov, S.A., Matosinhos, Portugal
| | | | | | - Acácio G Rodrigues
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal.,FASTinov, S.A., Matosinhos, Portugal
| | - José A Paiva
- Department of Emergency and Intensive Care, Centro Hospitalar Sao Joao, Porto, Portugal.,Department of Medicine, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Cidália Pina-Vaz
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, Porto, Portugal.,FASTinov, S.A., Matosinhos, Portugal
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92
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Microfluidics for Combating Antimicrobial Resistance. Trends Biotechnol 2017; 35:1129-1139. [DOI: 10.1016/j.tibtech.2017.07.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 01/09/2023]
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93
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Kim J, Mohamed MAA, Zagorovsky K, Chan WCW. State of diagnosing infectious pathogens using colloidal nanomaterials. Biomaterials 2017; 146:97-114. [PMID: 28898761 PMCID: PMC7124370 DOI: 10.1016/j.biomaterials.2017.08.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/07/2017] [Accepted: 08/13/2017] [Indexed: 01/08/2023]
Abstract
Infectious diseases are a major global threat that accounts for one of the leading causes of global mortality and morbidity. Prompt diagnosis is a crucial first step in the management of infectious threats, which aims to quarantine infected patients to avoid contacts with healthy individuals and deliver effective treatments prior to further spread of diseases. This review article discusses current advances of diagnostic systems using colloidal nanomaterials (e.g., gold nanoparticles, quantum dots, magnetic nanoparticles) for identifying and differentiating infectious pathogens. The challenges involved in the clinical translation of these emerging nanotechnology based diagnostic devices will also be discussed.
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Affiliation(s)
- Jisung Kim
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; Terrence Donnelly Centre for Cellular and Bimolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Centre for Global Engineering, University of Toronto, Toronto, Ontario M5S 1A4, Canada
| | - Mohamed A Abdou Mohamed
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; Terrence Donnelly Centre for Cellular and Bimolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Botany and Microbiology Department, Faculty of Science, Zagazig University, Egypt
| | - Kyryl Zagorovsky
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; Terrence Donnelly Centre for Cellular and Bimolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Warren C W Chan
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada; Terrence Donnelly Centre for Cellular and Bimolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada; Department of Chemical Engineering, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Department of Materials Science and Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada.
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94
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Heather CS, Maley M. Automated direct screening for resistance of Gram-negative blood cultures using the BD Kiestra WorkCell. Eur J Clin Microbiol Infect Dis 2017; 37:117-125. [PMID: 28971266 DOI: 10.1007/s10096-017-3109-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/14/2017] [Indexed: 10/18/2022]
Abstract
Early detection of resistance in sepsis due to Gram-negative organisms may lead to improved outcomes by reducing the time to effective antibiotic therapy. Traditional methods of resistance detection require incubation times of 18 to 48 h to detect resistance. We have utilised automated specimen processing, digital imaging and zone size measurements in conjunction with direct disc susceptibility testing to develop a method for the rapid screening of Gram-negative blood culture isolates for resistance. Positive clinical blood cultures with Gram-negative organisms were prospectively identified and additional resistant mock specimens were prepared. Broth was plated and antibiotic-impregnated discs (ampicillin, ceftriaxone, piperacillin-tazobactam, meropenem, ciprofloxacin, gentamicin) were added. Plates were incubated, digitally imaged and zone sizes were measured using the BD Kiestra WorkCell laboratory automation system. Minimum, clinically useful, incubation times and optimised zone size cut-offs for resistance detection were determined. We included 187 blood cultures in the study. At 5 h of incubation, > 90% of plates yielded interpretable results. Using optimised zone size cut-offs, the sensitivity for resistance detection ranged from 87 to 100%, while the specificity ranged from 84.7 to 100%. The sensitivity and specificity for piperacillin-tazobactam resistance detection was consistently worse than for the other agents. Automated direct disc susceptibility screening is a rapid and sensitive tool for resistance detection in Gram-negative isolates from blood cultures for most of the agents tested.
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Affiliation(s)
- C S Heather
- Department of Microbiology and Infectious Diseases, NSW Health Pathology South-Liverpool, Liverpool Hospital, Corner Goulburn and Forbes Street, Liverpool, NSW, Australia.
| | - M Maley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology South-Liverpool, Liverpool Hospital, Corner Goulburn and Forbes Street, Liverpool, NSW, Australia
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95
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Fröding I, Vondracek M, Giske CG. Rapid EUCAST disc diffusion testing of MDR Escherichia coli and Klebsiella pneumoniae: inhibition zones for extended-spectrum cephalosporins can be reliably read after 6 h of incubation. J Antimicrob Chemother 2017; 72:1094-1102. [PMID: 27999046 DOI: 10.1093/jac/dkw515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/02/2016] [Indexed: 01/20/2023] Open
Abstract
Objectives The need for rapid antibiotic susceptibility testing increases with escalating levels of antimicrobial resistance in Enterobacteriaceae. Our objective was to evaluate the accuracy of reading EUCAST disc diffusion, ROSCO ESBL and carbapenemase detection kits and the Mast Carbapenemase Activity Test (CAT-ID) disc, after 6 h of incubation. Methods We used a collection of 128 isolates of Escherichia coli and Klebsiella pneumoniae with a wide variety of resistance mechanisms. Inhibition zones read from digital photo images with the BD Kiestra™ Total Lab Automation System after 6 h of incubation were compared with standard reading, after 18 h, of the same Mueller-Hinton agar plates. Results For WT isolates, zones were generally smaller at 6 h than at 18 h. Cefotaxime had excellent categorical agreement of 99%, despite the high number of challenge isolates. However, for some other antimicrobials, hetero-resistant subpopulations were commonly invisible at 6 h, which resulted in an unacceptable number of errors when using standard EUCAST breakpoints. Accurate ESBL detection was possible at 6 h for isolates lacking other β-lactamases. Carbapenemase detection was not reliable after 6 h. Conclusions Inhibition zone reading at 6 h is an accurate method for susceptibility testing of extended-spectrum cephalosporins for Enterobacteriaceae. For other antimicrobials, 6 h reading can be used for preliminary reports of clearly resistant or susceptible isolates, preferably with application of adjusted breakpoints including an area of uncertainty between susceptible and resistant values.
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Affiliation(s)
- Inga Fröding
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Vondracek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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96
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Integrated microfluidic platform for rapid antimicrobial susceptibility testing and bacterial growth analysis using bead-based biosensor via fluorescence imaging. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2492-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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97
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017; 22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.
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Affiliation(s)
- Yiyan Li
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,7 Department of Physics and Engineering, Fort Lewis College, Durango, Colorado, USA
| | | | - Weian Zhao
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,6 Department of Biological Chemistry, University of California-Irvine, Irvine, CA, USA
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98
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Smith KP, Richmond DL, Brennan-Krohn T, Elliott HL, Kirby JE. Development of MAST: A Microscopy-Based Antimicrobial Susceptibility Testing Platform. SLAS Technol 2017; 22:662-674. [PMID: 28837780 DOI: 10.1177/2472630317727721] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Antibiotic resistance is compromising our ability to treat bacterial infections. Clinical microbiology laboratories guide appropriate treatment through antimicrobial susceptibility testing (AST) of patient bacterial isolates. However, increasingly, pathogens are developing resistance to a broad range of antimicrobials, requiring AST of alternative agents for which no commercially available testing methods are available. Therefore, there exists a significant AST testing gap in which current methodologies cannot adequately address the need for rapid results in the face of unpredictable susceptibility profiles. To address this gap, we developed a multicomponent, microscopy-based AST (MAST) platform capable of AST determinations after only a 2 h incubation. MAST consists of a solid-phase microwell growth surface in a 384-well plate format, inkjet printing-based application of both antimicrobials and bacteria at any desired concentrations, automated microscopic imaging of bacterial replication, and a deep learning approach for automated image classification and determination of antimicrobial minimal inhibitory concentrations (MICs). In evaluating a susceptible strain set, 95.8% were within ±1 and 99.4% were within ±2, twofold dilutions, respectively, of reference broth microdilution MIC values. Most (98.3%) of the results were in categorical agreement. We conclude that MAST offers promise for rapid, accurate, and flexible AST to help address the antimicrobial testing gap.
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Affiliation(s)
- Kenneth P Smith
- 1 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - David L Richmond
- 2 Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Thea Brennan-Krohn
- 1 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.,3 Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Hunter L Elliott
- 2 Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - James E Kirby
- 1 Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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99
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The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives. Infect Dis Clin North Am 2017; 30:323-345. [PMID: 27208762 DOI: 10.1016/j.idc.2016.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.
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100
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Doernberg SB, Chambers HF. Antimicrobial Stewardship Approaches in the Intensive Care Unit. Infect Dis Clin North Am 2017; 31:513-534. [PMID: 28687210 DOI: 10.1016/j.idc.2017.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antimicrobial stewardship programs aim to monitor, improve, and measure responsible antibiotic use. The intensive care unit (ICU), with its critically ill patients and prevalence of multiple drug-resistant pathogens, presents unique challenges. This article reviews approaches to stewardship with application to the ICU, including the value of diagnostics, principles of empirical and definitive therapy, and measures of effectiveness. There is good evidence that antimicrobial stewardship results in more appropriate antimicrobial use, shorter therapy durations, and lower resistance rates. Data demonstrating hard clinical outcomes, such as adverse events and mortality, are more limited but encouraging; further studies are needed.
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Affiliation(s)
- Sarah B Doernberg
- Division of Infectious Diseases, Department of Medicine, University of California, 513 Parnassus Avenue, Box 0654, San Francisco, CA 94143, USA.
| | - Henry F Chambers
- Division of Infectious Diseases, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, Room 3400, Building 30, 1001 Potrero Avenue, San Francisco, CA 94110, USA
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