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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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Chu PY, Yang CM, Huang KL, Wu AY, Hsieh CH, Chao AC, Wu MH. Development of an Optically Induced Dielectrophoresis (ODEP) Microfluidic System for High-Performance Isolation and Purification of Bacteria. BIOSENSORS 2023; 13:952. [PMID: 37998128 PMCID: PMC10669672 DOI: 10.3390/bios13110952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023]
Abstract
For the rapid detection of bacteria in a blood sample, nucleic acid amplification-based assays are believed to be promising. Nevertheless, the nucleic acids released from the dead blood cells or bacteria could affect the assay performance. This highlights the importance of the isolation of live bacteria from blood samples. To address this issue, this study proposes a two-step process. First, a blood sample was treated with the immuno-magnetic microbeads-based separation to remove the majority of blood cells. Second, an optically induced dielectrophoresis (ODEP) microfluidic system with an integrated dynamic circular light image array was utilized to further isolate and purify the live bacteria from the remaining blood cells based on their size difference. In this work, the ODEP microfluidic system was developed. Its performance for the isolation and purification of bacteria was evaluated. The results revealed that the method was able to harvest the live bacteria in a high purity (90.5~99.2%) manner. Overall, the proposed method was proven to be capable of isolating and purifying high-purity live bacteria without causing damage to the co-existing cells. This technical feature was found to be valuable for the subsequent nucleic-acid-based bacteria detection, in which the interferences caused by the nontarget nucleic acids could be eliminated.
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Affiliation(s)
- Po-Yu Chu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
| | - Chia-Ming Yang
- Department of Electronic Engineering, Chang Gung University, Taoyuan City 33302, Taiwan;
- Institute of Electro-Optical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan
- Biosensor Group, Biomedical Engineering Research Center, Chang Gung University, Taoyuan City 33302, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City 243303, Taiwan
| | - Kai-Lin Huang
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
| | - Ai-Yun Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
| | - Chia-Hsun Hsieh
- Division of Hematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan;
- Division of Hematology/Oncology, Department of Internal Medicine, New Taipei Municipal TuCheng Hospital, New Taipei City 236017, Taiwan
| | - A-Ching Chao
- Department of Neurology, Kaohsiung Medical University Hospital, Kaohsiung City 80756, Taiwan
- Department of Neurology, College of Medicine, Kaohsiung Medical University, Kaohsiung City 80756, Taiwan
| | - Min-Hsien Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33302, Taiwan; (P.-Y.C.); (K.-L.H.); (A.-Y.W.)
- Division of Hematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33302, Taiwan;
- Division of Hematology/Oncology, Department of Internal Medicine, New Taipei Municipal TuCheng Hospital, New Taipei City 236017, Taiwan
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Zhu Y, Girault HH. Algorithms push forward the application of MALDI–TOF mass fingerprinting in rapid precise diagnosis. VIEW 2023. [DOI: 10.1002/viw.20220042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Yingdi Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences Hangzhou China
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne Lausanne Switzerland
| | - Hubert H. Girault
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne Lausanne Switzerland
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Rapid Pathogen Identification in Aqueous Humor Samples by Combining Fc-MBL@Fe 3O 4 Enrichment and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Profiling. Microbiol Spectr 2022; 10:e0176722. [PMID: 36346251 PMCID: PMC9769506 DOI: 10.1128/spectrum.01767-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Prompt clinical diagnosis and antimicrobial therapy are key to managing infective endophthalmitis. The small volume of aqueous humor, low bacterial counts, and empirical medication by physicians make existing diagnostic methods time-consuming and imprecise. Here, we investigated the feasibility of combining Fc-containing mannose-binding lectin-coated Fe3O4 (Fc-MBL@Fe3O4) enrichment with matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) profiling to identify pathogens in aqueous humor. Aqueous humor aspirated from freshly enucleated porcine eyes was treated with different inocula of Staphylococcus aureus, Staphylococcus epidermidis, and Klebsiella pneumoniae. We performed identification directly in aqueous humor samples and after short-term culture of micro-LB broth. Aqueous humor endophthalmitis samples were enriched with Fc-MBL@Fe3O4 and analyzed using MALDI-TOF MS. The identification time and minimum bacterial concentration required for identification were determined. The enrichment efficiency of Fc-MBL@Fe3O4 for different bacteria was greater than (87.5 ± 5.0)%. The objects of direct identification include live bacteria and bacteria treated with antibiotics, which can be completed within 1.5 h. The minimum number of bacteria needed for positive identification was 2.20 × 106 CFU. For micro-LB broth culture, the identification of bacteria can be completed within 6.5 to 9.5 h for aqueous humor samples with an initial bacterial count of tens to hundreds. IMPORTANCE Fc-MBL@Fe3O4 capture not only live bacteria in aqueous humor but also bacteria inactivated by antibiotics. Fc-MBL@Fe3O4 combined with micro-LB broth culture significantly reduced the turnaround time (TAT) by more than half a day by shortening the time required for bacterial identification. Our findings demonstrate that combining Fc-MBL@Fe3O4 enrichment with MALDI-TOF MS identification is a fast, sensitive, and efficient analytical method with great potential for identifying pathogens in aqueous humor samples.
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Fc-MBL-modified Fe 3O 4 magnetic bead enrichment and fixation in Gram stain for rapid detection of low-concentration bacteria. Mikrochim Acta 2022; 189:169. [PMID: 35364796 DOI: 10.1007/s00604-022-05277-7] [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: 12/25/2021] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
Abstract
Functional bacterial enrichment magnetic beads (Fe3O4@SiO2@Fc-MBL) and Gram staining were combined for the fast diagnosis of infecting bacteria in meningitis. Fe3O4@SiO2@Fc-MBL has excellent microbial binding ability and can be used for bacterial enrichment from cerebrospinal fluid (CSF). The enriched bacteria are recognized by Gram stain at very low concentrations (10 CFU·mL-1). The feasibility of this method was verified by five common bacteria in meningitis infection (Gram-positive: Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus capitis; Gram-negative: Klebsiella pneumoniae and Escherichia coli). The extraction efficiency of Fc-MBL-modified Fe3O4 magnetic beads was approximately 90% in artificial CSF for the selected bacteria, with the exception of E. coli (~ 60%). The bacteria were successfully recognized by Gram staining and microscopic observation. Fe3O4@SiO2@Fc-MBL acts by capturing and fixing the bacteria in a magnetic field throughout the experiment. Compared with traditional CSF Gram staining, this new method avoids interference by inflammatory cells and red blood cells during microscopic examination. Furthermore, the sensitivity of this method is much better than the centrifugation smear method. The whole process can be accomplished within 30 min. This novel method may have potential as a clinical tool for analysis of bacteria in the CSF.
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