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Zolotareva M, Cascalheira F, Caneiras C, Bárbara C, Caetano DM, Teixeira MC. In the flow of molecular miniaturized fungal diagnosis. Trends Biotechnol 2024:S0167-7799(24)00157-4. [PMID: 38987118 DOI: 10.1016/j.tibtech.2024.06.010] [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: 03/21/2024] [Revised: 06/03/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.
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Affiliation(s)
- Maria Zolotareva
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Francisco Cascalheira
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal
| | - Cátia Caneiras
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, 2829-511 Almada, Portugal; Institute of Preventive Medicine and Public Health, Universidade de Lisboa, 1649-026 Lisboa, Portugal
| | - Cristina Bárbara
- Environmental Health Institute (ISAMB), Faculdade de Medicina, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, 1649-026 Lisboa, Portugal; Centro Hospitalar Universitário Lisboa Norte, 1600-190, Lisboa, Portugal
| | - Diogo Miguel Caetano
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias, INESC-, MN, 1000-029 Lisboa, Portugal; Department of Electrical and Computer Engineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
| | - Miguel Cacho Teixeira
- iBB - Institute for Bioengineering and Biosciences, Associate Laboratory Institute for Health and Bioeconomy - i4HB, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, 1049-001 Lisboa, Portugal.
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Ongwae GM, Chordia MD, Cawley JL, Dalesandro BE, Wittenberg NJ, Pires MM. Targeting of Pseudomonas aeruginosa cell surface via GP12, an Escherichia coli specific bacteriophage protein. Sci Rep 2022; 12:721. [PMID: 35031652 PMCID: PMC8760310 DOI: 10.1038/s41598-021-04627-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/28/2021] [Indexed: 11/08/2022] Open
Abstract
Bacteriophages are highly abundant molecular machines that have evolved proteins to target the surface of host bacterial cells. Given the ubiquity of lipopolysaccharides (LPS) on the outer membrane of Gram-negative bacteria, we reasoned that targeting proteins from bacteriophages could be leveraged to target the surface of Gram-negative pathogens for biotechnological applications. To this end, a short tail fiber (GP12) from the T4 bacteriophage, which infects Escherichia coli (E. coli), was isolated and tested for the ability to adhere to whole bacterial cells. We found that, surprisingly, GP12 effectively bound the surface of Pseudomonas aeruginosa cells despite the established preferred host of T4 for E. coli. In efforts to elucidate why this binding pattern was observed, it was determined that the absence of the O-antigen region of LPS on E. coli improved cell surface tagging. This indicated that O-antigens play a significant role in controlling cell adhesion by T4. Probing GP12 and LPS interactions further using deletions of the enzymes involved in the biosynthetic pathway of LPS revealed the inner core oligosaccharide as a possible main target of GP12. Finally, we demonstrated the potential utility of GP12 for biomedical applications by showing that GP12-modified agarose beads resulted in the depletion of pathogenic bacteria from solution.
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Affiliation(s)
- George M Ongwae
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA
| | - Mahendra D Chordia
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jennie L Cawley
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA
| | - Brianna E Dalesandro
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.
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Sun A, Stanton JAL, Bergquist PL, Sunna A. Universal Enzyme-Based Field Workflow for Rapid and Sensitive Quantification of Water Pathogens. Microorganisms 2021; 9:2367. [PMID: 34835492 PMCID: PMC8618791 DOI: 10.3390/microorganisms9112367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022] Open
Abstract
A universal filtration and enzyme-based workflow has been established to allow for the rapid and sensitive quantification of leading pathogens Cryptosporidium parvum, Giardia gamblia, Campylobacter jejuni, and Escherichia coli from tap water samples with volumes up to 100 mL, and the potential to scale up to larger volumes. qPCR limits of quantification as low as four oocysts for Cryptosporidium, twelve cysts for Giardia, two cells for C. jejuni, and nineteen cells for E. coli per reaction were achieved. A polycarbonate filter-based sampling method coupled with the prepGEM enzyme-based DNA extraction system created a single-step transfer workflow that required as little as 20 min of incubation time and a 100 µL reaction mix. The quantification via qPCR was performed directly on the prepGEM extract, bypassing time-consuming, labour-intensive conventional culture-based methods. The tap water samples were shown to contain insoluble particles that inhibited detection by reducing the quantification efficiency of a representative pathogen (C. jejuni) to 30-60%. This sample inhibition was effectively removed by an on-filter treatment of 20% (v/v) phosphoric acid wash. Overall, the established workflow was able to achieve quantification efficiencies of 92% and higher for all four leading water pathogens, forming the basis of a rapid, portable, and low-cost solution to water monitoring.
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Affiliation(s)
- Angela Sun
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
| | - Jo-Ann L. Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Peter L. Bergquist
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
- Department of Molecular Medicine & Pathology, University of Auckland, Auckland 1142, New Zealand
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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Abstract
Silk fibroin produced from silkworms has been intensively utilized as a scaffold material for a variety of biotechnological applications owing to its remarkable mechanical strength, extensibility, biocompatibility, and ease of biofunctionalization. In this research, we engineered silk as a novel trap platform capable of capturing microorganisms. Specifically, we first fabricated the silk material into a silk sponge by lyophilization, yielding a 3D scaffold with porous microstructures. The sponge stability in water was significantly improved by ethanol treatment with elevated β-sheet content and crystallinity of silk. Next, we biofunctionalized the silk sponge with a poly-specific microbial targeting molecule, ApoH (apolipoprotein H), to enable a novel silk-based microbial trap. The recombinant ApoH engineered with an additional penta-tyrosine was assembled onto the silk sponge through the horseradish peroxidase (HRP) mediated dityrosine cross-linking. Last, the ApoH-decorated silk sponge was demonstrated to be functional in capturing our model microorganism targets, E. coli and norovirus-like particles. We envision that this biofabricated silk platform, capable of trapping a variety of microbial entities, could serve as a versatile scaffold for rapid isolation and enrichment of microbial samples toward future diagnostics and therapeutics. This strategy, in turn, can expedite advancing future biodevices with functionality and sustainability.
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Affiliation(s)
- Shan-Ru Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Jheng-Liang Chen
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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Hass K, Bao M, He Q, Liu L, He J, Park M, Qin P, Du K. Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection System for Viral DNA Sensing. ACS OMEGA 2020; 5:27433-27441. [PMID: 33134706 PMCID: PMC7594154 DOI: 10.1021/acsomega.0c03917] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/30/2020] [Indexed: 05/13/2023]
Abstract
A fully Integrated Micropillar Polydimethylsiloxane Accurate CRISPR deTection (IMPACT) system is developed for viral DNA detection. This powerful system is patterned with high-aspect-ratio micropillars to enhance reporter probe binding. After surface modification and probe immobilization, the CRISPR-Cas12a/crRNA complex is injected into the fully enclosed microchannel. With the presence of a double-stranded DNA target, the CRISPR enzyme is activated and denatures the single-stranded DNA reporters from the micropillars. This collateral cleavage releases fluorescence reporters into the assay, and the intensity is linearly proportional to the target DNA concentration ranging from 0.1 to 10 nM. Importantly, this system does not rely on the traditional dye-quencher-labeled probe, thus reducing the fluorescence background presented in the assay. Furthermore, our one-step detection protocol is performed on-chip at isothermal conditions (37 °C) without using complicated and time-consuming off-chip probe hybridization and denaturation. This miniaturized and fully packed IMPACT chip demonstrates sensitive and accurate DNA detection within 120 min and paves ways to the next-generation point-of-care diagnostics, responding to emerging and deadly pathogen outbreaks.
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Affiliation(s)
- Kenneth
N. Hass
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
| | - Mengdi Bao
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
| | - Qian He
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Li Liu
- Department
of Microsystems Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
| | - Jiacheng He
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
| | - Myeongkee Park
- Department
of Chemistry, Dong-A University, Busan 49315, Republic of Korea
| | - Peiwu Qin
- Center
of Precision Medicine and Healthcare, Tsinghua-Berkeley
Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Ke Du
- Department
of Mechanical Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
- Department
of Microsystems Engineering, Rochester Institute
of Technology, Rochester, New York 14623, United States
- School
of Chemistry and Materials Science, Rochester
Institute of Technology, Rochester, New York 14623, United States
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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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Kim G, Karbaschi M, Cooke M, Gaitas A. Light-based methods for whole blood bacterial inactivation enabled by a recirculating flow system. Photochem Photobiol 2018; 94:744-751. [PMID: 29418006 PMCID: PMC6136252 DOI: 10.1111/php.12899] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/03/2018] [Indexed: 12/25/2022]
Abstract
Light of certain wavelengths can be used to inactivate pathogens. Whole blood is opaque; thus, the penetration of light is reduced. Here, we overcame this limitation using a thin transparent tube that is illuminated from all angles. Three light-based techniques were evaluated: photodynamic therapy (PDT) using a 660-nm light and antibody-photosensitizer conjugates, ultraviolet, and violet light. We observed a reduction of 55-71% of Staphylococcus aureus after 5 h of exposure (starting concentration 107 CFU mL-1 ) and an 88-97% reduction in methicillin-resistant Staphylococcus aureus (MRSA) (starting 104 CFU mL-1 ). An 83-92% decrease for S. aureus and 98-99.9% decrease for MRSA were observed when combined with an immunocapture approach. Complete blood count with differential analysis did not reveal any significant changes in the blood cell numbers. Genotoxicity studies showed that violet and ultraviolet did not induce any significant level of single strand breaks and alkali labile sites in the peripheral blood mononuclear cells (PBMC). In contrast, ultraviolet did induce a very low level of cyclobutane pyrimidine dimers, a UV damage indicator. PDT generated a significant level of single strand breaks and 8-oxoGua in these cells. The approaches showed promise for whole blood pathogen inactivation with minimal collateral damage to PBMC.
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Affiliation(s)
- Gwangseong Kim
- Kytaro, Inc., Miami, FL 33199
- Department of Electrical Engineering, Florida International University, Miami, FL 33199
| | - Mahsa Karbaschi
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199
| | - Marcus Cooke
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199
| | - Angelo Gaitas
- Kytaro, Inc., Miami, FL 33199
- Department of Electrical Engineering, Florida International University, Miami, FL 33199
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