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Wu W, Mu Y. Microfluidic technologies for advanced antimicrobial susceptibility testing. BIOMICROFLUIDICS 2024; 18:031504. [PMID: 38855477 PMCID: PMC11162290 DOI: 10.1063/5.0190112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 05/23/2024] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance is getting serious and becoming a threat to public health worldwide. The improper and excessive use of antibiotics is responsible for this situation. The standard methods used in clinical laboratories, to diagnose bacterial infections, identify pathogens, and determine susceptibility profiles, are time-consuming and labor-intensive, leaving the empirical antimicrobial therapy as the only option for the first treatment. To prevent the situation from getting worse, evidence-based therapy should be given. The choosing of effective drugs requires powerful diagnostic tools to provide comprehensive information on infections. Recent progress in microfluidics is pushing infection diagnosis and antimicrobial susceptibility testing (AST) to be faster and easier. This review summarizes the recent development in microfluidic assays for rapid identification and AST in bacterial infections. Finally, we discuss the perspective of microfluidic-AST to develop the next-generation infection diagnosis technologies.
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Affiliation(s)
- Wenshuai Wu
- Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing 210009, China
| | - Ying Mu
- Author to whom correspondence should be addressed:
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2
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Iyer V, Castro D, Malla B, Panda B, Rabson AR, Horowitz G, Heger N, Gupta K, Singer A, Norwitz ER. Culture-independent identification of bloodstream infections from whole blood: prospective evaluation in specimens of known infection status. J Clin Microbiol 2024; 62:e0149823. [PMID: 38315022 PMCID: PMC10935643 DOI: 10.1128/jcm.01498-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
Sepsis caused by bloodstream infection (BSI) is a major healthcare burden and a leading cause of morbidity and mortality worldwide. Timely diagnosis is critical to optimize clinical outcome, as mortality rates rise every hour treatment is delayed. Blood culture remains the "gold standard" for diagnosis but is limited by its long turnaround time (1-7 days depending on the organism) and its potential to provide false-negative results due to interference by antimicrobial therapy or the presence of mixed (i.e., polymicrobial) infections. In this paper, we evaluated the performance of resistance and pathogen ID/BSI, a direct-from-specimen molecular assay. To reduce the false-positivity rate common with molecular methods, this assay isolates and detects genomic material only from viable microorganisms in the blood by incorporating a novel precursor step to selectively lyse host and non-viable microbial cells and remove cell-free genomic material prior to lysis and analysis of microbial cells. Here, we demonstrate that the assay is free of interference from host immune cells and common antimicrobial agents at elevated concentrations. We also demonstrate the accuracy of this technology in a prospective cohort pilot study of individuals with known sepsis/BSI status, including samples from both positive and negative individuals. IMPORTANCE Blood culture remains the "gold standard" for the diagnosis of sepsis/bloodstream infection (BSI) but has many limitations which may lead to a delay in appropriate and accurate treatment in patients. Molecular diagnostic methods have the potential for markedly improving the management of such patients through faster turnaround times and increased accuracy. But molecular diagnostic methods have not been widely adopted for the identification of BSIs. By incorporating a precursor step of selective lysis of host and non-viable microorganisms, our resistance and pathogen ID (RaPID)/BSI molecular assay addresses many limitations of blood culture and other molecular assay. The RaPID/BSI assay has an approximate turnaround time of 4 hours, thereby significantly reducing the time to appropriate and accurate diagnosis of causative microorganisms in such patients. The short turnaround time also allows for close to real-time tracking of pathogenic clearance of microorganisms from the blood of these patients or if a change of antimicrobial regimen is required. Thus, the RaPID/BSI molecular assay helps with optimization of antimicrobial stewardship; prompt and accurate diagnosis of sepsis/BSI could help target timely treatment and reduce mortality and morbidity in such patients.
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Affiliation(s)
- Vidya Iyer
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel Castro
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Bipin Malla
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Britta Panda
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
| | - Arthur R. Rabson
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Gary Horowitz
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Nicholas Heger
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | | | - Alon Singer
- HelixBind Inc., Boxborough, Massachusetts, USA
| | - Errol R. Norwitz
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, Massachusetts, USA
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3
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Rapier-Sharman N, Hutchinson MLL, Moreno CM, Quaye A, Poole BD, Weber KS, Pitt WG, Pickett BE. A Novel Application of Spinning Disk Technology to Collect Plasma from Whole Blood Prior to Quantifying Plasma RNA. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.001007. [PMID: 38021167 PMCID: PMC10656623 DOI: 10.17912/micropub.biology.001007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
The spinning disk technology has previously been utilized to isolate bacterial components from blood in hours instead of days. We hypothesized that this platform could be applied as an alternative approach to isolating plasma RNA from a whole blood sample. We consequently tested the efficacy of the spinning disk technology to extract plasma from whole blood upstream of RNA isolation and analysis. To do so, we collected plasma using either the spinning disk or the typical two-spin centrifuge method. We found that the spinning disk method results in significantly more hemolysis during collection than the conventional two-spin centrifuge method. However, when plasma RNA recovered from both collection methods was quantified using quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), we found that the spinning disk method yielded a higher plasma RNA concentration than the two-spin centrifuge method. This suggests that the spinning disk may be an efficient alternative method to recover plasma RNA. Further work is needed to determine whether red blood cell RNA contamination is present in the plasma RNA extracted from spinning disk-processed plasma.
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Affiliation(s)
- Naomi Rapier-Sharman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Mae-Lynn L. Hutchinson
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, United States
| | - Carlos M. Moreno
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Abraham Quaye
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - Brian D. Poole
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - K. Scott Weber
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
| | - William G. Pitt
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, United States
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States
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4
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Zhao R, Shen Y, Zhao C, Wu C, Liu Y, Wan H, Lu Z. A rapid screening platform for antibiotic susceptibility testing based on a simple colorimetric method. Analyst 2023; 148:4148-4155. [PMID: 37498542 DOI: 10.1039/d3an00611e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Rapid screening platforms for antibiotic susceptibility testing (AST) are important in inhibiting bacterial resistance in clinical practice. Herein, a rapid screening platform is reported for AST, which is based on nanofiber membrane enrichment bacteria-assisted cell counting Kit-8 (CCK8) colorimetry. The absorbance of CCK8 formazan has a linear relationship with the number of bacteria. The interference of antibiotics in the absorbance of CCK8 formazan could be eliminated by separating planktonic bacteria from the culture medium using nanofiber membranes. The total detection time is 7-9 h, using the new screening platform, which is significantly shorter than that with the traditional method, and the limit of detection of this method is 10 CFU mL-1. The evaluation results of antibiotic susceptibility are identical when using the new screening method and traditional methods. This method meets the definition of "rapid testing" for antibiotic susceptibility by most microbiologists. Furthermore, the new screening platform for antibiotic susceptibility testing ability in vitro was proved using E. coli in urine and blood, and S. aureus in wound fluid as practical samples. All the results showed that the new screening platform is a promising method for rapid antibiotic susceptibility testing in vitro.
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Affiliation(s)
- Rui Zhao
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Yubin Shen
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Chenyu Zhao
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Chengfeng Wu
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Yuyang Liu
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Huakun Wan
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
| | - Zhentan Lu
- Key Laboratory of Textile Fiber and Products Ministry of Education, School of Materials Science and Engineering, Hubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials & Application, Wuhan Textile University, Wuhan, 430200, China.
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Shrestha J, Razavi Bazaz S, Ding L, Vasilescu S, Idrees S, Söderström B, Hansbro PM, Ghadiri M, Ebrahimi Warkiani M. Rapid separation of bacteria from primary nasal samples using inertial microfluidics. LAB ON A CHIP 2022; 23:146-156. [PMID: 36484411 DOI: 10.1039/d2lc00794k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Microbial populations play a crucial role in human health and the development of many diseases. These diseases often arise from the explosive proliferation of opportunistic bacteria, such as those in the nasal cavity. Recently, there have been increases in the prevalence of these opportunistic pathogens displaying antibiotic resistance. Thus, the study of the nasal microbiota and its bacterial diversity is critical in understanding pathogenesis and developing microbial-based therapies for well-known and emerging diseases. However, the isolation and analysis of these populations for clinical study complicates the already challenging task of identifying and profiling potentially harmful bacteria. Existing methods are limited by low sample throughput, expensive labeling, and low recovery of bacteria with ineffective removal of cells and debris. In this study, we propose a novel microfluidic channel with a zigzag configuration for enhanced isolation and detection of bacteria from human clinical nasal swabs. This microfluidic zigzag channel separates the bacteria from epithelial cells and debris by size differential focusing. As such, pure bacterial cell fractions devoid of large contaminating debris or epithelial cells are obtained. DNA sequencing performed on the separated bacteria defines the diversity and species present. This novel method of bacterial separation is simple, robust, rapid, and cost-effective and has the potential to be used for the rapid identification of bacterial cell populations from clinical samples.
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Affiliation(s)
- Jesus Shrestha
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Woolcock Institute of Medical Research, Respiratory Technology Group, University of Sydney, Sydney, New South Wales 2037, Australia
| | - Sajad Razavi Bazaz
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Lin Ding
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Steven Vasilescu
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney 2007, Australia
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney 2007, Australia
| | - Maliheh Ghadiri
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Woolcock Institute of Medical Research, Respiratory Technology Group, University of Sydney, Sydney, New South Wales 2037, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, New South Wales 2007, Australia
- Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow 119991, Russia
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Li JY, Chen XP, Tie YQ, Sun XL, Zhang RQ, He AN, Nie MZ, Fan GH, Li FY, Tian FY, Shen XX, Feng ZS, Ma XJ. Detection of low-load Epstein-Barr virus in blood samples by enriched recombinase aided amplification assay. AMB Express 2022; 12:71. [PMID: 35689713 PMCID: PMC9188631 DOI: 10.1186/s13568-022-01415-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
Epstein-Barr virus (EBV), a common human γ-herpesvirus, infects more than 90% of adults worldwide. The purpose of this study was to establish a novel EBV detection method by combining the recombinase aided amplification (RAA) assay with an initial enrichment step that utilizes magnetic beads coated with a recombinant human mannan-binding lectin (rhMBL, M1 protein). An M1 protein–protein A magnetic bead complex (M1 beads) was prepared and used to achieve separation and enrichment of EBV from blood. After nucleic acid extraction, DNA was amplified by RAA. Using 388 whole blood samples and 1 serum sample, we explored the specificity, sensitivity and applicability of the newly developed detection method and compared it with commercial quantitative real-time polymerase chain reaction (qPCR) following M1 bead enrichment, traditional qPCR and traditional RAA. After enrichment, the positivity rate of EBV was increased from 15.94% to 17.74% by RAA (P < 0.05) and from 7.20% to 15.17% by qPCR (P < 0.05). The viral loads after enrichment were increased by 1.13 to 23.19-fold (P < 0.05). Our data demonstrates that an RAA assay incorporating M1 bead enrichment is a promising tool for detecting low EBV viral loads in blood samples that will facilitate an early response to EBV infection. The RAA with an enrichment step that utilizes magnetic beads coated with M1 protein. A very effective method for detecting low-load virus in blood samples. The first report describing virus detection using this method.
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Affiliation(s)
- Jing-Yi Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xiao-Ping Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Yan-Qing Tie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China
| | - Xiu-Li Sun
- Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Rui-Qing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - An-Na He
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.,North China University of Science and Technology, No. 46 West Xinhua Road, Tangshan, 063009, Hebei, China
| | - Ming-Zhu Nie
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Guo-Hao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Li
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Feng-Yu Tian
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China.,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China
| | - Xin-Xin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
| | - Zhi-Shan Feng
- Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050031, Hebei, China. .,Hebei General Hospital, No. 348 West Heping Road, Shijiazhuang, 050070, Hebei, China.
| | - Xue-Jun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, No. 155, Changbai Street, Changping District, Beijing, 102206, China.
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Hoj TR, McNeely B, Webber K, Welling E, Pitt WG, Ford LC, Robison RA. A pentaplex real-time PCR assay for rapid identification of major beta-lactamase genes KPC, NDM, CTX, CMY, and OXA-48 directly from bacteria in blood. J Med Microbiol 2021; 70:001465. [PMID: 34878374 PMCID: PMC8744273 DOI: 10.1099/jmm.0.001465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction. Antibiotic resistance, particularly in cases of sepsis, has emerged as a growing global public health concern and economic burden. Current methods of blood culture and antimicrobial susceptibility testing of agents involved in sepsis can take as long as 3-5 days. It is vital to rapidly identify which antimicrobials can be used to effectively treat sepsis cases on an individual basis. Here, we present a pentaplex, real-time PCR-based assay that can quickly identify the most common beta-lactamase genes (Klebsiella pneumoniae carbapenemase (KPC); New Delhi metallo-beta-lactamase (NDM); cefotaximase-Munich (CTX-M); cephamycin AmpC beta-lactamases (CMY); and Oxacillinase-48 (OXA-48)) from pathogens derived directly from the blood of patients presenting with bacterial septicemia.Aim. To develop an assay which can rapidly identify the most common beta-lactamase genes in Carbapenem-resistant Enterobacteriaceae bacteria (CREs) from the United States.Hypothesis/Gap Statement. Septicemia caused by carbapenem-resistant bacteria has a death rate of 40-60 %. Rapid diagnosis of antibiotic susceptibility directly from bacteria in blood by identification of beta-lactamase genes will greatly improve survival rates. In this work, we develop an assay capable of concurrently identifying the five most common beta-lactamase and carbapenemase genes.Methodology. Primers and probes were created which can identify all subtypes of Klebsiella pneumoniae carbapenemase (KPC); New Delhi metallo-beta-lactamase (NDM); cefotaximase-Munich (CTX); cephamycin AmpC beta-lactamase (CMY); and oxacillinase-48 (OXA-48). The assay was validated using 13 isolates containing various PCR targets from the Centre for Disease Control Antimicrobial Resistance Isolate Bank Enterobacterales Carbapenemase Diversity Panel. Blood obtained from volunteers was spiked with CREs and bacteria were separated, lysed, and subjected to analysis via the pentaplex assay.Results. This pentaplex assay successfully identified beta-lactamase genes derived from bacteria separated from blood at concentrations of 4-8 c.f.u. ml-1.Conclusion. This assay will improve patient outcomes by supplying physicians with critical drug resistance information within 2 h of septicemia onset, allowing them to prescribe effective antimicrobials corresponding to the resistance gene(s) present in the pathogen. In addition, information supplied by this assay will lessen the inappropriate use of broad-spectrum antimicrobials and prevent the evolution of further antibiotic resistance.
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Affiliation(s)
- Taalin R. Hoj
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Bradley McNeely
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kylie Webber
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Evelyn Welling
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - William G. Pitt
- Chemical Engineering Department, Brigham Young University, Provo, UT, USA
| | - Larry C. Ford
- Infectious Diseases, Intermountain Healthcare, Provo, UT USA
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
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Krämer M, Kissmann AK, Raber HF, Xing H, Favella P, Müller I, Spellerberg B, Weil T, Kubiczek D, Sihler S, Ziener U, Rosenau F. BSA Hydrogel Beads Functionalized with a Specific Aptamer Library for Capturing Pseudomonas aeruginosa in Serum and Blood. Int J Mol Sci 2021; 22:ijms222011118. [PMID: 34681780 PMCID: PMC8537436 DOI: 10.3390/ijms222011118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022] Open
Abstract
Systemic blood stream infections are a major threat to human health and are dramatically increasing worldwide. Pseudomonas aeruginosa is a WHO-alerted multi-resistant pathogen of extreme importance as a cause of sepsis. Septicemia patients have significantly increased survival chances if sepsis is diagnosed in the early stages. Affinity materials can not only represent attractive tools for specific diagnostics of pathogens in the blood but can prospectively also serve as the technical foundation of therapeutic filtration devices. Based on the recently developed aptamers directed against P. aeruginosa, we here present aptamer-functionalized beads for specific binding of this pathogen in blood samples. These aptamer capture beads (ACBs) are manufactured by crosslinking bovine serum albumin (BSA) in an emulsion and subsequent functionalization with the amino-modified aptamers on the bead surface using the thiol- and amino-reactive bispecific crosslinker PEG4-SPDP. Specific and quantitative binding of P. aeruginosa as the dedicated target of the ACBs was demonstrated in serum and blood. These initial but promising results may open new routes for the development of ACBs as a platform technology for fast and reliable diagnosis of bloodstream infections and, in the long term, blood filtration techniques in the fight against sepsis.
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Affiliation(s)
- Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Heinz Fabian Raber
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Patrizia Favella
- Department of Life Sciences, Albstadt-Sigmaringen University of Applied Sciences, 72488 Sigmaringen, Germany; (P.F.); (I.M.)
| | - Ingrid Müller
- Department of Life Sciences, Albstadt-Sigmaringen University of Applied Sciences, 72488 Sigmaringen, Germany; (P.F.); (I.M.)
| | - Barbara Spellerberg
- Institute for Medical Microbiology and Hygiene, University Hospital Ulm, 89081 Ulm, Germany;
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max-Planck-Institute of Polymer Science, 55128 Mainz, Germany;
| | - Dennis Kubiczek
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
| | - Susanne Sihler
- Institute of Organic Chemistry III-Macromolecular Chemistry and Organic Materials, Ulm University, 89081 Ulm, Germany; (S.S.); (U.Z.)
| | - Ulrich Ziener
- Institute of Organic Chemistry III-Macromolecular Chemistry and Organic Materials, Ulm University, 89081 Ulm, Germany; (S.S.); (U.Z.)
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (M.K.); (A.-K.K.); (H.F.R.); (H.X.); (D.K.)
- Department Synthesis of Macromolecules, Max-Planck-Institute of Polymer Science, 55128 Mainz, Germany;
- Correspondence:
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9
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Armstrong CM, Lee J, Gehring AG, Capobianco JA. Flow-Through Electrochemical Biosensor for the Detection of Listeria monocytogenes Using Oligonucleotides. SENSORS 2021; 21:s21113754. [PMID: 34071528 PMCID: PMC8198859 DOI: 10.3390/s21113754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 11/29/2022]
Abstract
Consumption of food contaminated by Listeria monocytogenes can result in Listeriosis, an illness with hospitalization rates of 94% and mortality rates up to 30%. As a result, U.S. regulatory agencies governing food safety retain zero-tolerance policies for L. monocytogenes. However, detection at such low concentrations often requires strategies such as increasing sample size or culture enrichment. A novel flow-through immunoelectrochemical biosensor has been developed for Escherichia coli O157:H7 detection in 1 L volumes without enrichment. The current work further augments this biosensor’s capabilities to (1) include detection of L. monocytogenes and (2) accommodate genetic detection to help overcome limitations based upon antibody availability and address specificity errors in phenotypic assays. Herein, the conjugation scheme for oligo attachment and the conditions necessary for genetic detection are laid forth while results of the present study demonstrate the sensor’s ability to distinguish L. monocytogenes DNA from L. innocua with a limit of detection of ~2 × 104 cells/mL, which agrees with prior studies. Total time for this assay can be constrained to <2.5 h because a timely culture enrichment period is not necessary. Furthermore, the electrochemical detection assay can be performed with hand-held electronics, allowing this platform to be adopted for near-line monitoring systems.
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10
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Shan J, Jia Y, Teulières L, Patel F, Clokie MRJ. Targeting Multicopy Prophage Genes for the Increased Detection of Borrelia burgdorferi Sensu Lato (s.l.), the Causative Agents of Lyme Disease, in Blood. Front Microbiol 2021; 12:651217. [PMID: 33790883 PMCID: PMC8005754 DOI: 10.3389/fmicb.2021.651217] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/16/2021] [Indexed: 11/20/2022] Open
Abstract
The successful treatment of Lyme disease (LD) is contingent on accurate diagnosis. However, current laboratory detection assays lack sensitivity in the early stages of the disease. Because delayed diagnosis of LD incurs high healthcare costs and great suffering, new highly sensitive tests are in need. To overcome these challenges, we developed an internally controlled quantitative PCR (Ter-qPCR) that targets the multicopy terminase large subunit (terL) gene encoded by prophages that are only found in LD-causing bacteria. The terL protein helps phages pack their DNA. Strikingly, the detection limit of the Ter-qPCR was analytically estimated to be 22 copies and one bacterial cell in bacteria spiked blood. Furthermore, significant quantitative differences was observed in terms of the amount of terL detected in healthy individuals and patients with either early or late disease. Together, the data suggests that the prophage-targeting PCR has significant power to improve success detection for LD. After rigorous clinical validation, this new test could deliver a step-change in the detection of LD. Prophage encoded markers are prevalent in many other pathogenic bacteria rendering this approach highly applicable to bacterial identification in general.
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Affiliation(s)
- Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ying Jia
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Louis Teulières
- PhelixRD Charity 230 Rue du Faubourg St Honoré, Paris, France
| | - Faizal Patel
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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11
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Akuoko Y, Hanson RL, Harris DH, Nielsen JB, Lazalde E, Woolley AT. Rapid and simple pressure-sensitive adhesive microdevice fabrication for sequence-specific capture and fluorescence detection of sepsis-related bacterial plasmid gene sequences. Anal Bioanal Chem 2021; 413:1017-1025. [PMID: 33247338 PMCID: PMC7855688 DOI: 10.1007/s00216-020-03060-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 10/22/2022]
Abstract
Microbial resistance to currently available antibiotics poses a great threat in the global fight against infections. An important step in determining bacterial antibiotic resistance can be selective DNA sequence capture and fluorescence labeling. In this paper, we demonstrate the fabrication of simple, robust, inexpensive microfluidic devices for DNA capture and fluorescence detection of a model antibiotic resistance gene sequence. We laser micromachined polymethyl methacrylate microchannels and enclosed them using pressure-sensitive adhesive tapes. We then formed porous polymer monoliths with DNA capture probes in these microchannels and used them for sequence-specific capture, fluorescent labeling, and laser-induced fluorescence detection of picomolar (pM) concentrations of synthetic and plasmid antibiotic resistance gene targets. The relative fluorescence for the elution peaks increased with loaded target DNA concentration. We observed higher fluorescence signal and percent recovery for synthetic target DNA compared to plasmid DNA at the same loaded target concentration. A non-target gene was used for control experiments and produced < 3% capture relative to the same concentration of target. The full analysis process including device fabrication was completed in less than 90 min with a limit of detection of 30 pM. The simplicity of device fabrication and good DNA capture selectivity demonstrated herein have potential for application with processes for bacterial plasmid DNA extraction and single-particle counting to facilitate determination of antibiotic susceptibility. Graphical abstract.
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Affiliation(s)
- Yesman Akuoko
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Robert L Hanson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - David H Harris
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Jacob B Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Elaine Lazalde
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
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12
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Anderson CM, Pitt WG. Effect of dilution on sedimentational separation of bacteria from blood. Biotechnol Prog 2020; 36:e3056. [PMID: 32715664 DOI: 10.1002/btpr.3056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/04/2020] [Indexed: 11/07/2022]
Abstract
Bacteria must be separated from septic whole blood in preparation for rapid antibiotic susceptibility tests. This work improves upon past work isolating bacteria from whole blood by exploring an important experimental factor: Whole blood dilution. Herein, we use the continuity equation to model red blood cell sedimentation and show that overall spinning time decreases as the blood is diluted. We found that the bacteria can also be captured more efficiently from diluted blood, up to approximately 68 ± 8% recovery (95% confidence interval). However, diluting blood both requires and creates extra fluid that end users must handle; an optimal dilution, which maximizes bacteria recovery and minimizes waste, was found to scale with the square root of the whole blood hematocrit. This work also explores a hypothesis that plasma backflow, which occurs as red cells move radially outward, causes bacterial enrichment in the supernatant plasma with an impact proportional to the plasma backflow velocity. Bacteria experiments carried out with diluted blood demonstrate such bacterial enrichment, but not in the hypothesized manner as enrichment occurred only in undiluted blood samples at physiological hematocrit.
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Affiliation(s)
- Clifton M Anderson
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - William G Pitt
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
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13
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Direct Blood Culturing of Candida spp. on Solid Medium by a Rapid Enrichment Method with Magnetic Beads Coated with Recombinant Human Mannan-Binding Lectin. J Clin Microbiol 2020; 58:JCM.00057-20. [PMID: 32051260 PMCID: PMC7098737 DOI: 10.1128/jcm.00057-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/02/2020] [Indexed: 12/23/2022] Open
Abstract
A rapid and accurate method to identify the species and antibiotic resistance of Candida spp. in blood is vital to increase the survival rates of patients with bloodstream infections. However, the extremely low levels of Candida spp. in blood make rapid diagnosis by standard blood culture difficult. In this study, we constructed a direct blood culturing method (i.e., the M1 method) by a rapid enrichment method with magnetic beads coated with a recombined human mannan-binding lectin (rhMBL; i. A rapid and accurate method to identify the species and antibiotic resistance of Candida spp. in blood is vital to increase the survival rates of patients with bloodstream infections. However, the extremely low levels of Candida spp. in blood make rapid diagnosis by standard blood culture difficult. In this study, we constructed a direct blood culturing method (i.e., the M1 method) by a rapid enrichment method with magnetic beads coated with a recombined human mannan-binding lectin (rhMBL; i.e., M1 protein), which demonstrated much higher Candida sp.-binding capacity than that of full-length MBL expressed in vitro (i.e., M2). With the M1 method, individual colonies were obtained before the standard blood culture method for each species of Candida spp. tested at <1 CFU/ml (an average of 29 h earlier). Additionally, the clinical sensitivity of the M1 method was 90.5% compared with that of the standard blood culture method when detecting frozen plasma from patients. More significantly, the turnaround time of the M1 method for blood culture could be reduced by approximately 37 to 43 h compared with that of the standard blood culture method in clinical sample identification.
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14
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Roux-Dalvai F, Gotti C, Leclercq M, Hélie MC, Boissinot M, Arrey TN, Dauly C, Fournier F, Kelly I, Marcoux J, Bestman-Smith J, Bergeron MG, Droit A. Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning. Mol Cell Proteomics 2019; 18:2492-2505. [PMID: 31585987 PMCID: PMC6885708 DOI: 10.1074/mcp.tir119.001559] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
Fast identification of microbial species in clinical samples is essential to provide an appropriate antibiotherapy to the patient and reduce the prescription of broad-spectrum antimicrobials leading to antibioresistances. MALDI-TOF-MS technology has become a tool of choice for microbial identification but has several drawbacks: it requires a long step of bacterial culture before analysis (≥24 h), has a low specificity and is not quantitative. We developed a new strategy for identifying bacterial species in urine using specific LC-MS/MS peptidic signatures. In the first training step, libraries of peptides are obtained on pure bacterial colonies in DDA mode, their detection in urine is then verified in DIA mode, followed by the use of machine learning classifiers (NaiveBayes, BayesNet and Hoeffding tree) to define a peptidic signature to distinguish each bacterial species from the others. Then, in the second step, this signature is monitored in unknown urine samples using targeted proteomics. This method, allowing bacterial identification in less than 4 h, has been applied to fifteen species representing 84% of all Urinary Tract Infections. More than 31,000 peptides in 190 samples were quantified by DIA and classified by machine learning to determine an 82 peptides signature and build a prediction model. This signature was validated for its use in routine using Parallel Reaction Monitoring on two different instruments. Linearity and reproducibility of the method were demonstrated as well as its accuracy on donor specimens. Within 4h and without bacterial culture, our method was able to predict the predominant bacteria infecting a sample in 97% of cases and 100% above the standard threshold. This work demonstrates the efficiency of our method for the rapid and specific identification of the bacterial species causing UTI and could be extended in the future to other biological specimens and to bacteria having specific virulence or resistance factors.
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Affiliation(s)
- Florence Roux-Dalvai
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Clarisse Gotti
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Marie-Claude Hélie
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | | | | | - Frédéric Fournier
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Isabelle Kelly
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Judith Marcoux
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Julie Bestman-Smith
- Laboratoire de microbiologie-infectiologie, CHU de Québec-Université Laval, pavillon Hôpital de l'Enfant-Jésus, Québec City, Québec, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City, Québec, Canada
| | - Arnaud Droit
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada; Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada; Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada.
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15
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Pitt WG, Alizadeh M, Blanco R, Hunter AK, Bledsoe CG, McClellan DS, Wood ME, Wood RL, Ravsten TV, Hickey CL, Cameron Beard W, Stepan JR, Carter A, Husseini GA, Robison RA, Welling E, Torgesen RN, Anderson CM. Factors affecting sedimentational separation of bacteria from blood. Biotechnol Prog 2019; 36:e2892. [PMID: 31425635 DOI: 10.1002/btpr.2892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/19/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022]
Abstract
Rapid diagnosis of blood infections requires fast and efficient separation of bacteria from blood. We have developed spinning hollow disks that separate bacteria from blood cells via the differences in sedimentation velocities of these particles. Factors affecting separation included the spinning speed and duration, and disk size. These factors were varied in dozens of experiments for which the volume of separated plasma, and the concentration of bacteria and red blood cells (RBCs) in separated plasma were measured. Data were correlated by a parameter of characteristic sedimentation length, which is the distance that an idealized RBC would travel during the entire spin. Results show that characteristic sedimentation length of 20 to 25 mm produces an optimal separation and collection of bacteria in plasma. This corresponds to spinning a 12-cm-diameter disk at 3,000 rpm for 13 s. Following the spin, a careful deceleration preserves the separation of cells from plasma and provides a bacterial recovery of about 61 ± 5%.
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Affiliation(s)
- William G Pitt
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | - Mahsa Alizadeh
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | - Rae Blanco
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | - Alex K Hunter
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | - Colin G Bledsoe
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | | | - Madison E Wood
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah
| | - Ryan L Wood
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | - Tanner V Ravsten
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | - Caroline L Hickey
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | | | - Jacob R Stepan
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Alexandra Carter
- Chemical Engineering Department, Brigham Young University, Provo, Utah
| | - Ghaleb A Husseini
- Chemical Engineering Department, American University of Sharjah, Sharjah, United Arab Emirates
| | - Richard A Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah
| | - Evelyn Welling
- Chemical Engineering Department, Brigham Young University, Provo, Utah
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16
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Pilecky M, Schildberger A, Orth-Höller D, Weber V. Pathogen enrichment from human whole blood for the diagnosis of bloodstream infection: Prospects and limitations. Diagn Microbiol Infect Dis 2018; 94:7-14. [PMID: 30579657 DOI: 10.1016/j.diagmicrobio.2018.11.015] [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: 09/26/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 02/07/2023]
Abstract
Blood culture represents the current reference method for the detection of bacteria or fungi in the circulation. To accelerate pathogen identification, molecular diagnostic methods, mainly based on polymerase chain reaction (PCR), have been introduced to ensure early and targeted antibiotic treatment of patients suffering from bloodstream infection. Still, these approaches suffer from a lack of sensitivity and from inhibition of PCR in a number of clinical samples, leading to false negative results. To overcome these limitations, various approaches aiming at the enrichment of pathogens from larger blood volumes prior to the extraction of pathogen DNA, thereby also depleting factors interfering with PCR, have been developed. Here, we provide an overview of current systems for diagnosing bloodstream infection, with a focus on approaches for pre-analytical pathogen enrichment, and highlight emerging applications of pathogen depletion for therapeutic purposes as a potential adjunctive treatment of sepsis patients.
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Affiliation(s)
- Matthias Pilecky
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
| | - Anita Schildberger
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
| | - Dorothea Orth-Höller
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, A-6020 Innsbruck, Austria.
| | - Viktoria Weber
- Center for Biomedical Technology, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria; Christian Doppler Laboratory for Innovative Therapy Approaches in Sepsis, Department for Biomedical Research, Danube University Krems, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems, Austria.
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17
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Pasitka L, van Noort D, Lim W, Park S, Mandenius CF. A Microbore Tubing Based Spiral for Multistep Cell Fractionation. Anal Chem 2018; 90:12909-12916. [DOI: 10.1021/acs.analchem.8b03532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Pasitka
- Division of Biotechnology, IFM, Linköping University, Linköping 58183, Sweden
| | - Danny van Noort
- Division of Biotechnology, IFM, Linköping University, Linköping 58183, Sweden
| | - Wanyoung Lim
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sungsu Park
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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18
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Knob R, Hanson RL, Tateoka OB, Wood RL, Guerrero-Arguero I, Robison RA, Pitt WG, Woolley AT. Sequence-specific sepsis-related DNA capture and fluorescent labeling in monoliths prepared by single-step photopolymerization in microfluidic devices. J Chromatogr A 2018; 1562:12-18. [PMID: 29859687 DOI: 10.1016/j.chroma.2018.05.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/16/2018] [Accepted: 05/20/2018] [Indexed: 02/08/2023]
Abstract
Fast determination of antibiotic resistance is crucial in selecting appropriate treatment for sepsis patients, but current methods based on culture are time consuming. We are developing a microfluidic platform with a monolithic column modified with oligonucleotides designed for sequence-specific capture of target DNA related to the Klebsiella pneumoniae carbapenemase (KPC) gene. We developed a novel single-step monolith fabrication method with an acrydite-modified capture oligonucleotide in the polymerization mixture, enabling fast monolith preparation in a microfluidic channel using UV photopolymerization. These prepared columns had a threefold higher capacity compared to monoliths prepared in a multistep process involving Schiff-base DNA attachment. Conditions for denaturing, capture and fluorescence labeling using hybridization probes were optimized with synthetic 90-mer oligonucleotides. These procedures were applied for extraction of a PCR amplicon from the KPC antibiotic resistance gene in bacterial lysate obtained from a blood sample spiked with E. coli. The results showed similar eluted peak areas for KPC amplicon extracted from either hybridization buffer or bacterial lysate. Selective extraction of the KPC DNA was verified by real time PCR on eluted fractions. These results show great promise for application in an integrated microfluidic diagnostic system that combines upstream blood sample preparation and downstream single-molecule counting detection.
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Affiliation(s)
- Radim Knob
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States
| | - Robert L Hanson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States
| | - Olivia B Tateoka
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, United States
| | - Ryan L Wood
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, United States
| | - Israel Guerrero-Arguero
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, United States
| | - Richard A Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, United States
| | - William G Pitt
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, United States
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States.
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