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Islam Sajib MS, Brunker K, Oravcova K, Everest P, Murphy ME, Forde T. Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection. J Mol Diagn 2024:S1525-1578(24)00128-4. [PMID: 38925458 DOI: 10.1016/j.jmoldx.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/05/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Bloodstream infection remains a major cause of morbidity and death worldwide. Timely and appropriate treatment can reduce mortality among critically ill patients. Current diagnostic methods are too slow to inform precise antibiotic choice, leading to the prescription of empirical antibiotics, which may fail to cover the resistance profile of the pathogen, risking poor patient outcomes. Additionally, overuse of broad-spectrum antibiotics may lead to more resistant organisms, putting further pressure on the dwindling pipeline of antibiotics, and risk transmission of these resistant organisms in the health care environment. Therefore, rapid diagnostics are urgently required to better inform antibiotic choice early in the course of treatment. Sequencing offers great promise in reducing time to microbiological diagnosis; however, the amount of host DNA compared with the pathogen in patient samples presents a significant obstacle. To address this, various host-depletion and bacterial-enrichment strategies have been used in samples, such as saliva, urine, or tissue. However, these methods have yet to be collectively integrated and/or extensively explored for rapid bloodstream infection diagnosis. Although most of these workflows possess individual strengths, their lack of analytical/clinical sensitivity and/or comprehensiveness demands additional improvements or synergistic application. Therefore, this review provides a distinctive classification system for these methods based on their working principles to guide future research, discusses their strengths and limitations, and explores potential avenues for improvement.
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Affiliation(s)
| | - Kirstyn Brunker
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom; MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Katarina Oravcova
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Paul Everest
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Michael E Murphy
- Department of Microbiology, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom; School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Taya Forde
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
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Fraticelli Guzmán NS, Badawy MW, Stockslager MA, Farrell ML, van Zyl C, Stewart S, Hu DL, Forest CR. Quantitative assessment of automated purification and concentration of E. coli bacteria. SLAS Technol 2023; 28:251-257. [PMID: 36804174 DOI: 10.1016/j.slast.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Automated methods for rapidly purifying and concentrating bacteria from environmental interferents are needed in next-generation applications for anything from water purification to biological weapons detection. Though previous work has been performed by other researchers in this area, there is still a need to create an automated system that can both purify and concentrate target pathogens in a timely manner with readily available and replaceable components that could be easily integrated with a detection mechanism. Thus, the objective of this work was to design, build, and demonstrate the effectiveness of an automated system, the Automated Dual-filter method for Applied Recovery, or aDARE. aDARE uses a custom LABVIEW program that guides the flow of bacterial samples through a pair of size-based separation membranes to capture and elute the target bacteria. Using aDARE, we eliminated 95% of the interfering beads of a 5 mL-sample volume containing 107 CFU/mL of E. coli contaminated with 2 µm and 10 µm polystyrene beads at 106 beads/mL concentration., The target bacteria were concentrated to more than twice the initial concentration in 900 µL of eluent, resulting in an enrichment ratio for the target bacteria of 42 ± 13 in 5.5 min. These results show the feasibility and effectiveness of using size-based filtration membranes to purify and concentrate a target bacterium, in this case E. coli, in an automated system.
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Affiliation(s)
- Nina Sara Fraticelli Guzmán
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Mohamed W Badawy
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Max A Stockslager
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Michael L Farrell
- Georgia Tech Research Institute, Georgia Institute of Technology, Atlanta, GA, United States
| | - Caitlin van Zyl
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA
| | - Seth Stewart
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - David L Hu
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Craig R Forest
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA.
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Needs SH, Pivetal J, Hayward J, Kidd SP, Lam H, Diep T, Gill K, Woodward M, Reis NM, Edwards AD. Moving microcapillary antibiotic susceptibility testing (mcAST) towards the clinic: unravelling kinetics of detection of uropathogenic E. coli, mass-manufacturing and usability for detection of urinary tract infections in human urine. SENSORS & DIAGNOSTICS 2023; 2:736-750. [PMID: 37216011 PMCID: PMC10197089 DOI: 10.1039/d2sd00138a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/20/2023] [Indexed: 05/24/2023]
Abstract
Innovation in infection based point-of-care (PoC) diagnostics is vital to avoid unnecessary use of antibiotics and the development of antimicrobial resistance. Several groups including our research team have in recent years successfully miniaturised phenotypic antibiotic susceptibility tests (AST) of isolated bacterial strains, providing validation that miniaturised AST can match conventional microbiological methods. Some studies have also shown the feasibility of direct testing (without isolation or purification), specifically for urinary tract infections, paving the way for direct microfluidic AST systems at PoC. As rate of bacteria growth is intrinsically linked to the temperature of incubation, transferring miniaturised AST nearer the patient requires building new capabilities in terms of temperature control at PoC, furthermore widespread clinical use will require mass-manufacturing of microfluidic test strips and direct testing of urine samples. This study shows for the first-time application of microcapillary antibiotic susceptibility testing (mcAST) directly from clinical samples, using minimal equipment and simple liquid handling, and with kinetics of growth recorded using a smartphone camera. A complete PoC-mcAST system was presented and tested using 12 clinical samples sent to a clinical laboratory for microbiological analysis. The test showed 100% accuracy for determining bacteria in urine above the clinical threshold (5 out of 12 positive) and achieved 95% categorical agreement for 5 positive urines tested with 4 antibiotics (nitrofurantoin, ciprofloxacin, trimethoprim and cephalexin) within 6 h compared to the reference standard overnight AST method. A kinetic model is presented for metabolization of resazurin, demonstrating kinetics of degradation of resazurin in microcapillaries follow those observed for a microtiter plate, with time for AST dependent on the initial CFU ml-1 of uropathogenic bacteria in the urine sample. In addition, we show for the first time that use of air-drying for mass-manufacturing and deposition of AST reagents within the inner surface of mcAST strips matches results obtained with standard AST methods. These results take mcAST a step closer to clinical application, for example as PoC support for antibiotic prescription decisions within a day.
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Affiliation(s)
- Sarah H Needs
- Reading School of Pharmacy, University of Reading Whiteknights Campus Reading RG6 6AD UK +44(0)7906014116 +44(0)118 378 4253
| | - Jeremy Pivetal
- Reading School of Pharmacy, University of Reading Whiteknights Campus Reading RG6 6AD UK +44(0)7906014116 +44(0)118 378 4253
| | - Jessica Hayward
- Reading School of Pharmacy, University of Reading Whiteknights Campus Reading RG6 6AD UK +44(0)7906014116 +44(0)118 378 4253
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust Basingstoke and North Hampshire Hospital Basingstoke RG24 9NA UK
| | - HoYin Lam
- Hampshire Hospitals NHS Foundation Trust Basingstoke and North Hampshire Hospital Basingstoke RG24 9NA UK
| | - Tai Diep
- Reading School of Pharmacy, University of Reading Whiteknights Campus Reading RG6 6AD UK +44(0)7906014116 +44(0)118 378 4253
| | - Kiran Gill
- Reading School of Pharmacy, University of Reading Whiteknights Campus Reading RG6 6AD UK +44(0)7906014116 +44(0)118 378 4253
| | - Martin Woodward
- Department of Food and Nutrition Sciences, University of Reading Whiteknights Campus Reading RG6 6DX UK
| | - Nuno M Reis
- Department of Chemical Engineering and Centre for Biosensors, Biodevices and Bioelectronics (C3Bio), University of Bath Claverton Down Bath BA2 7AY UK +44(0)1225 383 369
- Capillary Film Technology (CFT) Daux Road Billingshurst RH14 9SJ UK
| | - Alexander D Edwards
- Reading School of Pharmacy, University of Reading Whiteknights Campus Reading RG6 6AD UK +44(0)7906014116 +44(0)118 378 4253
- Capillary Film Technology (CFT) Daux Road Billingshurst RH14 9SJ UK
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Wu W, Cai G, Liu Y, Suo Y, Zhang B, Jin W, Yu Y, Mu Y. Direct single-cell antimicrobial susceptibility testing of Escherichia coli in urine using a ready-to-use 3D microwell array chip. LAB ON A CHIP 2023; 23:2399-2410. [PMID: 36806255 DOI: 10.1039/d2lc01095j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Empirical antibiotic therapies are prescribed for treating uncomplicated urinary tract infections (UTIs) due to the long turnaround time of conventional antimicrobial susceptibility testing (AST), leading to the prevalence of multi-drug resistant pathogens. We present a ready-to-use 3D microwell array chip to directly conduct comprehensive AST of pathogenic agents in urine at the single-cell level. The developed device features a highly integrated 3D microwell array, offering a dynamic range from 102 to 107 CFU mL-1, and a capillary valve-based flow distributor for flow equidistribution in dispensing channels and uniform sample distribution. The chip with pre-loaded reagents and negative pressure inside only requires the user to initiate AST by loading samples (∼3 s) and can work independently. We demonstrate an accessible sample-to-result workflow, including syringe filter-based bacteria separation and rapid single-cell AST on chip, which enables us to bypass the time-consuming bacteria isolation and pre-culture, speeding up the AST in ∼3 h from 2 days of conventional methods. Moreover, the bacterial concentration and AST with minimum inhibitory concentrations can be assessed simultaneously to provide comprehensive information on infections. With further development for multiple antibiotic conditions, the Dsc-AST assay could contribute to timely prescription of targeted drugs for better patient outcomes and mitigation of the threat of drug-resistant bacteria.
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Affiliation(s)
- Wenshuai Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
| | - Gaozhe Cai
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Yang Liu
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 102401, China
| | - Yuanjie Suo
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
| | - Boran Zhang
- Department of Hydraulic Engineering, College of Civil Engineering and Architecture, Zhejiang University, Hangzhou 310058, China
| | - Wei Jin
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
- Huzhou Institute of Zhejiang University, Huzhou 313002, China
| | - Yinghua Yu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China.
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Vancomycin-conjugated polydopamine-coated magnetic nanoparticles for molecular diagnostics of Gram-positive bacteria in whole blood. J Nanobiotechnology 2022; 20:400. [PMID: 36064405 PMCID: PMC9446563 DOI: 10.1186/s12951-022-01606-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background Sepsis is caused mainly by infection in the blood with a broad range of bacterial species. It can be diagnosed by molecular diagnostics once compounds in the blood that interfere with molecular diagnostics are removed. However, this removal relies on ultracentrifugation. Immunomagnetic separation (IMS), which typically uses antibody-conjugated silica-coated magnetic nanoparticles (Ab-SiO2-MNPs), has been widely applied to isolate specific pathogens in various types of samples, such as food and environmental samples. However, its direct use in blood samples containing bacteria is limited due to the aggregation of SiO2-MNPs in the blood and inability to isolate multiple species of bacteria causing sepsis. Results In this study, we report the synthesis of vancomycin-conjugated polydopamine-coated (van-PDA-MNPs) enabling preconcentration of multiple bacterial species from blood without aggregation. The presence of PDA and van on MNPs was verified using transmission electron microscopy, X-ray photoelectron spectroscopy, and energy disruptive spectroscopy. Unlike van-SiO2-MNPs, van-PDA-MNPs did not aggregate in the blood. Van-PDA-MNPs were able to preconcentrate several species of Gram-positive bacteria in the blood, lowering the limit of detection (LOD) to 10 colony forming units/mL by polymerase chain reaction (PCR) and quantitative PCR (qPCR). This is 10 times more sensitive than the LOD obtained by PCR and qPCR using van-SiO2-MNPs. Conclusion These results suggest that PDA-MNPs can avoid aggregation in blood and be conjugated with receptors, thereby improving the sensitivity of molecular diagnostics of bacteria in blood samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12951-022-01606-3.
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Dönmez Sİ, Needs SH, Osborn HMI, Reis NM, Edwards AD. Label-free 1D microfluidic dipstick counting of microbial colonies and bacteriophage plaques. LAB ON A CHIP 2022; 22:2820-2831. [PMID: 35792607 DOI: 10.1039/d2lc00280a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Counting viable bacterial cells and functional bacteriophage is fundamental to microbiology underpinning research, surveillance, biopharmaceuticals and diagnostics. Colony forming unit (CFU) and plaque forming unit (PFU) counting still requires slow and laborious solid culture on agar in Petri dishes or plates. Here, we show that dip-stick microfluidic strips can be used without growth indicator dye for rapid and simple CFU ml-1 and PFU ml-1 measurement. We demonstrate for the first time that fluoropolymer microcapillaries combined with digital imaging allow bacteriophage plaques to be counted rapidly in a dip-and-test format. The microfluidic length scales offer a linear 1-dimensional alternative to a 2D solid agar medium surface, with colonies or plaques clearly visible as "dashes" or "gaps". An inexpensive open source darkfield biosensor system using Raspberry Pi imaging permits label-free detection and counting of colonies or plaques within 4-8 hours in a linear, liquid matrix within ∼200 μm inner diameter microcapillaries. We obtained full quantitative agreement between 1D microfluidic colony counting in dipsticks versus conventional 2D solid agar Petri dish plates for S. aureus and E. coli, and for T2 phage and phage K, but up to 6 times faster. Time-lapse darkfield imaging permitted detailed kinetic analysis of colony growth in the microcapillaries, providing new insight into microfluidic microbiology and colony growth, not possible with Petri dishes. Surprisingly, whilst E. coli colonies appeared earlier, subsequent colony expansion was faster along the microcapillaries for S. aureus. This may be explained by the microenvironment offered for 1D colony growth within microcapillaries, linked to a mass balance between nutrient (glucose) diffusion and bacterial growth kinetics. Counting individual colonies in liquid medium was not possible for motile strains that spread rapidly along the capillary, however inclusion of soft agar inhibited spreading, making this new simple dip-and-test counting method applicable to both motile and non-motile bacteria. Label-free dipstick colony and plaque counting has potential for many analytical microbial tasks, and the innovation of 1D colony counting has relevance to other microfluidic microbiology.
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Affiliation(s)
| | - Sarah H Needs
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
| | - Nuno M Reis
- Department of Chemical Engineering and Centre for Biosensors, Biodevices and Bioelectronics (C3Bio), University of Bath, Claverton Down, Bath BA2 7AY, UK
- Capillary Film Technology Ltd, Daux Road, Billingshurst, West Sussex RH14 9SJ, UK
| | - Alexander D Edwards
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
- Capillary Film Technology Ltd, Daux Road, Billingshurst, West Sussex RH14 9SJ, UK
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Hsieh K, Mach KE, Zhang P, Liao JC, Wang TH. Combating Antimicrobial Resistance via Single-Cell Diagnostic Technologies Powered by Droplet Microfluidics. Acc Chem Res 2022; 55:123-133. [PMID: 34898173 PMCID: PMC10023138 DOI: 10.1021/acs.accounts.1c00462] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance is a global threat that if left unchecked could lead to 10 million annual mortalities by 2050. One factor contributing to the rise of multi-drug-resistant (MDR) pathogens is the reliance on traditional culture-based pathogen identification (ID) and antimicrobial susceptibility testing (AST) that typically takes several days. This delay of objective pathogen ID and AST information to inform clinical decision making results in clinicians treating patients empirically often using first-line, broad-spectrum antibiotics, contributing to the misuse/overuse of antibiotics. To combat the rise in MDR pathogens, there is a critical demand for rapid ID and AST technologies. Among the advances in ID and AST technologies in the past decade, single-cell diagnostic technologies powered by droplet microfluidics offer great promise due to their potential for high-sensitivity detection and rapid turnaround time. Our laboratory has been at the forefront of developing such technologies and applying them to diagnosing urinary tract infections (UTIs), one of the most common infections and a frequent reason for the prescription of antimicrobials. For pathogen ID, we first demonstrated the highly sensitive, amplification-free detection of single bacterial cells by confining them in picoliter-scale droplets and detection with fluorogenic peptide nucleic acid (PNA) probes that target their 16S rRNA (rRNA), a well-characterized marker for phylogenic classification. We subsequently improved the PNA probe design and enhanced detection sensitivity. For single-cell AST, we first employed a growth indicator dye and engineered an integrated device that allows us to detect growth from single bacterial cells under antibiotic exposure within 1 h, equivalent to two to three bacterial replications. To expand beyond testing a single antibiotic condition per device, a common limitation for droplet microfluidics, we developed an integrated programmable droplet microfluidic device for scalable single-cell AST. Using the scalable single-cell AST platform, we demonstrated the generation of up to 32 droplet groups in a single device with custom antibiotic titers and the capacity to scale up single-cell AST, and providing reliable pathogen categories beyond a binary call embodies a critical advance. Finally, we developed an integrated ID and AST platform. To this end, we developed a PNA probe panel that can identify nearly 90% of uropathogens and showed the quantitative detection of 16S rRNA from single bacterial cells in droplet-enabled AST after as little as 10 min of antibiotic exposure. This platform achieved both ID and AST from minimally processed urine samples in 30 min, representing one of the fastest turnaround times to date. In addition to tracing the development of our technologies, we compare them with contemporary research advances and offer our perspectives for future development, with the vision that single-cell ID and AST technologies powered by droplet microfluidics can indeed become a useful diagnostic tool for combating antimicrobial resistance.
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Affiliation(s)
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
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Needs SH, Saiprom N, Rafaque Z, Imtiaz W, Chantratita N, Runcharoen C, Thammachote J, Anun S, Peacock SJ, Ray P, Andrews S, Edwards AD. Miniaturised broth microdilution for simplified antibiotic susceptibility testing of Gram negative clinical isolates using microcapillary devices. Analyst 2022; 147:3558-3569. [DOI: 10.1039/d2an00305h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Miniaturised antibiotic susceptibility testing: 100 times smaller microcapillary broth microdilution gives equivalent result to standard microplate broth microdilution.
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Affiliation(s)
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Zara Rafaque
- Department of Microbiology, Faculty of Health Sciences, Hazara University, Mansehra, Pakistan
| | - Wajiha Imtiaz
- School of Biological Sciences, University of Reading, RG6 6DX, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Chakkaphan Runcharoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Jeeranan Thammachote
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, Thailand
| | - Suthatip Anun
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, Thailand
| | | | - Partha Ray
- The Nature Conservancy, Virginia, USA
- School of Agriculture Policy and Development, University of Reading, UK
| | - Simon Andrews
- School of Biological Sciences, University of Reading, RG6 6DX, UK
| | - Alexander D. Edwards
- School of Pharmacy, University of Reading, RG6 6DX, UK
- CFT Ltd, Daux Road, Billingshurst, RH14 9SJ, UK
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Zhang P, Kaushik AM, Hsieh K, Li S, Lewis S, Mach KE, Liao JC, Carroll KC, Wang TH. A Cascaded Droplet Microfluidic Platform Enables High-Throughput Single Cell Antibiotic Susceptibility Testing at Scale. SMALL METHODS 2022; 6:e2101254. [PMID: 35041266 DOI: 10.1002/smtd.202101254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 06/14/2023]
Abstract
The global threat of antibiotic resistance underscores critical but unmet needs for rapid antibiotic susceptibility testing (AST) technologies. To this end, droplet microfluidic-based single-cell AST offers promise by achieving unprecedented rapidity, but its potential for clinical use is marred by the capacity of testing one to few antibiotic conditions per device, which falls short from the required scale in clinically relevant scenarios. To lift the scalability constraint in rapid single-cell AST technologies, a new cascaded droplet microfluidic platform that can streamline bacteria/antibiotic mixing, single-cell encapsulation within picoliter droplets, incubation, and detection in a continuous, assembly-line-like workflow is developed. The scalability of the platform is demonstrated by generating 32 groups of ≈10 000 droplets with custom antibiotic conditions within a single device, from which a new statistics-based method is used to analyze the single cell data and produce clinically useful antibiograms with minimum inhibitory concentrations in ≈90 min for the first antibiotic, plus 2 min for each subsequent antibiotic condition. Potential clinical utility of this platform is demonstrated by testing three clinical isolates and eight urine specimens against four frequently used antibiotics, and 100% and 93.8% categorical agreements are achieved compared to laboratory-based results that became available after 48 h.
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Affiliation(s)
- Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sixuan Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shawna Lewis
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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Needs SH, Dönmez Sİ, Edwards AD. Direct microfluidic antibiotic resistance testing in urine with smartphone capture: significant variation in sample matrix interference between individual human urine samples. RSC Adv 2021; 11:38258-38263. [PMID: 35498063 PMCID: PMC9044048 DOI: 10.1039/d1ra06867a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/11/2021] [Indexed: 12/28/2022] Open
Abstract
Direct antibiotic susceptibility tests for urinary tract infections should be assessed using a wide range of individual urine samples to identify matrix interference.
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