1
|
Sveiven M, Serrano AK, Rosenberg J, Conrad DJ, Hall DA, O’Donoghue AJ. A GMR enzymatic assay for quantifying nuclease and peptidase activity. Front Bioeng Biotechnol 2024; 12:1363186. [PMID: 38544982 PMCID: PMC10966768 DOI: 10.3389/fbioe.2024.1363186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/01/2024] [Indexed: 04/17/2024] Open
Abstract
Hydrolytic enzymes play crucial roles in cellular processes, and dysregulation of their activities is implicated in various physiological and pathological conditions. These enzymes cleave substrates such as peptide bonds, phosphodiester bonds, glycosidic bonds, and other esters. Detecting aberrant hydrolase activity is vital for understanding disease mechanisms and developing targeted therapeutic interventions. This study introduces a novel approach to measuring hydrolase activity using giant magnetoresistive (GMR) spin valve sensors. These sensors change resistance in response to magnetic fields, and here, they are functionalized with specific substrates for hydrolases conjugated to magnetic nanoparticles (MNPs). When a hydrolase cleaves its substrate, the tethered magnetic nanoparticle detaches, causing a measurable shift in the sensor's resistance. This design translates hydrolase activity into a real-time, activity-dependent signal. The assay is simple, rapid, and requires no washing steps, making it ideal for point-of-care settings. Unlike fluorescent methods, it avoids issues like autofluorescence and photobleaching, broadening its applicability to diverse biofluids. Furthermore, the sensor array contains 80 individually addressable sensors, allowing for the simultaneous measurement of multiple hydrolases in a single reaction. The versatility of this method is demonstrated with substrates for nucleases, Bcu I and DNase I, and the peptidase, human neutrophil elastase. To demonstrate a clinical application, we show that neutrophil elastase in sputum from cystic fibrosis patients hydrolyze the peptide-GMR substrate, and the cleavage rate strongly correlates with a traditional fluorogenic substrate. This innovative assay addresses challenges associated with traditional enzyme measurement techniques, providing a promising tool for real-time quantification of hydrolase activities in diverse biological contexts.
Collapse
Affiliation(s)
- Michael Sveiven
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Ana K. Serrano
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joshua Rosenberg
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Douglas J. Conrad
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Drew A. Hall
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| |
Collapse
|
2
|
Koterwa A, Pierpaoli M, Nejman-Faleńczyk B, Bloch S, Zieliński A, Adamus-Białek W, Jeleniewska Z, Trzaskowski B, Bogdanowicz R, Węgrzyn G, Niedziałkowski P, Ryl J. Discriminating macromolecular interactions based on an impedimetric fingerprint supported by multivariate data analysis for rapid and label-free Escherichia coli recognition in human urine. Biosens Bioelectron 2023; 238:115561. [PMID: 37549553 DOI: 10.1016/j.bios.2023.115561] [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: 05/12/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
This manuscript presents a novel approach to address the challenges of electrode fouling and highly complex electrode nanoarchitecture, which are primary concerns for biosensors operating in real environments. The proposed approach utilizes multiparametric impedance discriminant analysis (MIDA) to obtain a fingerprint of the macromolecular interactions on flat glassy carbon surfaces, achieved through self-organized, drop-cast, receptor-functionalized Au nanocube (AuNC) patterns. Real-time monitoring is combined with singular value decomposition and partial least squares discriminant analysis, which enables selective identification of the analyte from raw impedance data, without the use of electric equivalent circuits. As a proof-of-concept, the authors demonstrate the ability to detect Escherichia coli in real human urine using an aptamer-based biosensor that targets RNA polymerase. This is significant, as uropathogenic E. coli is a difficult-to-treat pathogen that is responsible for the majority of hospital-acquired urinary tract infection cases. The proposed approach offers a limit of detection of 11.3 CFU/mL for the uropathogenic E. coli strain No. 57, an analytical range in all studied concentrations (up to 105 CFU/mL), without the use of antifouling strategies, yet not being specific vs other E.coli strain studied (BL21(DE3)). The MIDA approach allowed to identify negative overpotentials (-0.35 to -0.10 V vs Ag/AgCl) as most suitable for the analysis, offering over 80% sensitivity and accuracy, and the measurement was carried out in just 2 min. Moreover, this approach is scalable and can be applied to other biosensor platforms.
Collapse
Affiliation(s)
- Adrian Koterwa
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Mattia Pierpaoli
- Department of Metrology and Optoelectronics, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - Bożena Nejman-Faleńczyk
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Poland.
| | - Sylwia Bloch
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Poland.
| | - Artur Zieliński
- Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - Wioletta Adamus-Białek
- Institute of Medical Sciences, Jan Kochanowski University of Kielce, IX Wieków Kielc 19A, 25-317, Kielce, Poland.
| | - Zofia Jeleniewska
- Division of Electrochemistry and Surface Physical Chemistry, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland.
| | - Bartosz Trzaskowski
- Centre of New Technologies, University of Warsaw, Banach 2c, 02-097, Warsaw, Poland.
| | - Robert Bogdanowicz
- Department of Metrology and Optoelectronics, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Poland.
| | - Paweł Niedziałkowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
| | - Jacek Ryl
- Division of Electrochemistry and Surface Physical Chemistry, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk, 80-233, Poland.
| |
Collapse
|
3
|
Smartphone-controlled biosensor for viral respiratory infectious diseases: Screening and response. Talanta 2023; 254:124167. [PMID: 36493567 PMCID: PMC9721129 DOI: 10.1016/j.talanta.2022.124167] [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] [Received: 09/04/2022] [Revised: 11/03/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Outbreaks of emerging viral respiratory infectious diseases (VRIDs) including coronavirus disease 2019 (COVID-19) seriously endanger people's health. However, the traditional nucleic acid detection required professionals and larger instruments and antigen-antibody detection suffered a long window period of target generation. To facilitate the VRIDs detection in time for common populations, a smartphone-controlled biosensor, which integrated sample preparation (electromembrane extraction), biomarker detection (red-green-blue model) and remote response technology (a built-in APP), was developed in this work. With the intelligent biosensor, VRIDs could be recognized in the early stage by using endogenous hydrogen sulfide as the biomarker. Importantly, it only took 15 min to accomplish the whole process of screening and response to VRIDs. Moreover, the experimental data showed that this smartphone-controlled biosensor was suitable for ordinary residents and could successfully differentiate non-communicable respiratory diseases from VRIDs. To the best of our knowledge, this is the first time that a smartphone-controlled biosensor for screening and response to VRIDs was reported. We believe that the present biosensor will help ordinary residents jointly deal with the challenges brought by COVID-19 or other VRIDs in the future.
Collapse
|
4
|
Bacterial Urinary Tract Infection and Early Asymptomatic Bacteriuria in Kidney Transplantation Still Negatively Affect Kidney Transplant Outcomes in the Era of Modern Immunosuppression and Cotrimoxazole Prophylaxis. Biomedicines 2022; 10:biomedicines10112984. [PMID: 36428552 PMCID: PMC9687497 DOI: 10.3390/biomedicines10112984] [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] [Received: 10/14/2022] [Revised: 11/04/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Risk factors and consequences of urinary tract infection (UTI) post-kidney transplant have been variously reported by studies that were heterogenous in immunosuppressants and prophylactic protocols. We aimed to clarify the risks and consequences of UTI in kidney transplant recipients with post-transplantation cotrimoxazole prophylaxis in the context of modern immunosuppression. This retrospective cohort included kidney transplant recipients receiving tacrolimus, mycophenolate, prednisolone, and cotrimoxazole for bacterial UTI prophylaxis. Recipients were categorized into non-UTI and UTI groups. Asymptomatic bacteriuria (ASB) was screened in the first 3 months and was evaluated for association with UTI. Of 348 kidney transplant recipients, 129 were in the UTI group and 219 in the non-UTI group. UTI risk factors were female sex, body mass index ≥ 25 kg/m2, human leukocyte antigen mismatch, and panel reactive antibody ≥ 50%. Recipients with recurrent UTI had inferior allograft function compared with non-UTI recipients. Patient survival was significantly lower in recipients with UTI in the first post-transplant month. Higher degree of immunosuppressions was associated with recurrent UTI and drug-resistant organisms. In conclusion, UTI continues to negatively affect graft function and survival of kidney transplant recipients. Treating ASB in the first 3 months did not reduce the UTI incidence in the first transplantation year.
Collapse
|
5
|
Zhang W, Sun H, He S, Chen X, Yao L, Zhou L, Wang Y, Wang P, Hong W. Compound Raman microscopy for rapid diagnosis and antimicrobial susceptibility testing of pathogenic bacteria in urine. Front Microbiol 2022; 13:874966. [PMID: 36090077 PMCID: PMC9449455 DOI: 10.3389/fmicb.2022.874966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Rapid identification and antimicrobial susceptibility testing (AST) of bacteria are key interventions to curb the spread and emergence of antimicrobial resistance. The current gold standard identification and AST methods provide comprehensive diagnostic information but often take 3 to 5 days. Here, a compound Raman microscopy (CRM), which integrates Raman spectroscopy and stimulated Raman scattering microscopy in one system, is presented and demonstrated for rapid identification and AST of pathogens in urine. We generated an extensive bacterial Raman spectral dataset and applied deep learning to identify common clinical bacterial pathogens. In addition, we employed stimulated Raman scattering microscopy to quantify bacterial metabolic activity to determine their antimicrobial susceptibility. For proof-of-concept, we demonstrated an integrated assay to diagnose urinary tract infection pathogens, S. aureus and E. coli. Notably, the CRM system has the unique ability to provide Gram-staining classification and AST results within ~3 h directly from urine samples and shows great potential for clinical applications.
Collapse
Affiliation(s)
- Weifeng Zhang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Hongyi Sun
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Shipei He
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Xun Chen
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- School of Engineering Medicine, Beihang University, Beijing, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, China
- Lin Yao,
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Yi Wang
- Department of Clinical Laboratory, China Rehabilitation Research Center, Capital Medical University, Beijing, China
| | - Pu Wang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- *Correspondence: Pu Wang,
| | - Weili Hong
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Weili Hong,
| |
Collapse
|
6
|
Serapinas S, Gineitytė J, Butkevičius M, Danilevičius R, Dagys M, Ratautas D. Biosensor prototype for rapid detection and quantification of DNase activity. Biosens Bioelectron 2022; 213:114475. [PMID: 35714494 DOI: 10.1016/j.bios.2022.114475] [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: 04/14/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/19/2022]
Abstract
DNases are enzymes that cleave phosphodiesteric bonds of deoxyribonucleic acid molecules and are found everywhere in nature, especially in bodily fluids, i.e., saliva, blood, or sweat. Rapid and sensitive detection of DNase activity is highly important for quality control in the pharmaceutical and biotechnology industries. For clinical diagnostics, recent reports indicate that increased DNase activity could be related to various diseases, such as cancers. In this paper, we report a new bioelectronic device for the determination of nuclease activity in various fluids. The system consists of a sensor electrode, a custom design DNA target to maximize the DNase cleavage rate, a signal analysis algorithm, and supporting electronics. The developed sensor enables the determination of DNase activity in the range of 3.4 × 10-4 - 3.0 × 10-2 U mL-1 with a limit of detection of up to 3.4 × 10-4 U mL-1. The sensor was tested by measuring nuclease activity in real human saliva samples and found to demonstrate high accuracy and reproducibility compared to the industry standard DNaseAlert™️. Finally, the entire detection system was implemented as a prototype device system utilizing single-use electrodes, custom-made cells, and electronics. The developed technology can improve nuclease quality control processes in the pharmaceutical/biotechnology industry and provide new insights into the importance of nucleases for medical applications.
Collapse
Affiliation(s)
- Skomantas Serapinas
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Laboratorija 1", Pamėnkalnio g. 36, LT-01114, Vilnius, Lithuania
| | - Justina Gineitytė
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Bioanalizės sistemos", Saulėtekio al. 15, LT-10224, Vilnius, Lithuania
| | - Marius Butkevičius
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Laboratorija 1", Pamėnkalnio g. 36, LT-01114, Vilnius, Lithuania
| | | | - Marius Dagys
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Bioanalizės sistemos", Saulėtekio al. 15, LT-10224, Vilnius, Lithuania
| | - Dalius Ratautas
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Bioanalizės sistemos", Saulėtekio al. 15, LT-10224, Vilnius, Lithuania.
| |
Collapse
|
7
|
Garcia Gonzalez J, Hernandez FJ. Nuclease activity: an exploitable biomarker in bacterial infections. Expert Rev Mol Diagn 2022; 22:265-294. [PMID: 35240900 DOI: 10.1080/14737159.2022.2049249] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications. AREAS COVERED This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected. EXPERT OPINION Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.
Collapse
Affiliation(s)
- Javier Garcia Gonzalez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| |
Collapse
|
8
|
Reyes S, Le N, Fuentes MD, Upegui J, Dikici E, Broyles D, Quinto E, Daunert S, Deo SK. An Intact Cell Bioluminescence-Based Assay for the Simple and Rapid Diagnosis of Urinary Tract Infection. Int J Mol Sci 2020; 21:E5015. [PMID: 32708609 PMCID: PMC7404122 DOI: 10.3390/ijms21145015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 11/16/2022] Open
Abstract
Urinary tract infection (UTI) is one of the most common infections, accounting for a substantial portion of outpatient hospital and clinic visits. Standard diagnosis of UTI by culture and sensitivity can take at least 48 h, and improper diagnosis can lead to an increase in antibiotic resistance following therapy. To address these shortcomings, rapid bioluminescence assays were developed and evaluated for the detection of UTI using intact, viable cells of Photobacterium mandapamensis USTCMS 1132 or previously lyophilized cells of Photobacterium leiognathi ATCC 33981™. Two platform technologies-tube bioluminescence extinction technology urine (TuBETUr) and cellphone-based UTI bioluminescence extinction technology (CUBET)-were developed and standardized using artificial urine to detect four commonly isolated UTI pathogens-namely, Escherichia coli, Proteus mirabilis, Staphylococcus aureus, and Candida albicans. Besides detection, these assays could also provide information regarding pathogen concentration/level, helping guide treatment decisions. These technologies were able to detect microbes associated with UTI at less than 105 CFU/mL, which is usually the lower cut-off limit for a positive UTI diagnosis. Among the 29 positive UTI samples yielding 105-106 CFU/mL pathogen concentrations, a total of 29 urine specimens were correctly detected by TuBETUr as UTI-positive based on an 1119 s detection window. Similarly, the rapid CUBET method was able to discriminate UTIs from normal samples with high confidence (p ≤ 0.0001), using single-pot conditions and cell phone-based monitoring. These technologies could potentially address the need for point-of-care UTI detection while reducing the possibility of antibiotic resistance associated with misdiagnosed cases of urinary tract infections, especially in low-resource environments.
Collapse
Affiliation(s)
- Sherwin Reyes
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (S.R.); (N.L.); (J.U.); (E.D.); (D.B.); (S.D.)
- The Dr. John T. McDonald Foundation Bionanotechnology Institute of University of Miami, Miami, FL 33136, USA
- FEU-Nicanor Reyes Medical Foundation, Institute of Medicine, West Fairview, Quezon City 1118, Philippines;
- The Graduate School, University of Santo Tomas, España Manila 1015, Philippines;
| | - Nga Le
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (S.R.); (N.L.); (J.U.); (E.D.); (D.B.); (S.D.)
| | - Mary Denneth Fuentes
- FEU-Nicanor Reyes Medical Foundation, Institute of Medicine, West Fairview, Quezon City 1118, Philippines;
- The Graduate School, University of Santo Tomas, España Manila 1015, Philippines;
| | - Jonathan Upegui
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (S.R.); (N.L.); (J.U.); (E.D.); (D.B.); (S.D.)
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (S.R.); (N.L.); (J.U.); (E.D.); (D.B.); (S.D.)
- The Dr. John T. McDonald Foundation Bionanotechnology Institute of University of Miami, Miami, FL 33136, USA
| | - David Broyles
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (S.R.); (N.L.); (J.U.); (E.D.); (D.B.); (S.D.)
- The Dr. John T. McDonald Foundation Bionanotechnology Institute of University of Miami, Miami, FL 33136, USA
| | - Edward Quinto
- The Graduate School, University of Santo Tomas, España Manila 1015, Philippines;
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (S.R.); (N.L.); (J.U.); (E.D.); (D.B.); (S.D.)
- The Dr. John T. McDonald Foundation Bionanotechnology Institute of University of Miami, Miami, FL 33136, USA
- Clinical and Translational Science Institute of University of Miami, Miami, FL 33136, USA
| | - Sapna K. Deo
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; (S.R.); (N.L.); (J.U.); (E.D.); (D.B.); (S.D.)
- The Dr. John T. McDonald Foundation Bionanotechnology Institute of University of Miami, Miami, FL 33136, USA
| |
Collapse
|
9
|
Haag E, Molitor A, Gregoriano C, Müller B, Schuetz P. The value of biomarker-guided antibiotic therapy. Expert Rev Mol Diagn 2020; 20:829-840. [PMID: 32529871 DOI: 10.1080/14737159.2020.1782193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION There is an increasing interest to individualize patient management and decisions regarding antibiotic treatment. Biomarkers may provide relevant information for this purpose. AREAS COVERED Despite a growing number of clinical trials investigating several biomarkers, there remain open questions regarding the best type of biomarker, timing or frequency of testing, and optimal cutoffs among others. The most promising results in regard to diagnosis of bacterial infection and therapy monitoring are found for procalcitonin (PCT), although some recent trials were not able to validate the promising earlier findings. Furthermore, less specific markers like C-reactive protein (CRP) and new prognostic biomarkers such as proadrenomedullin (MR-proADM) may improve the prognostic assessment of patients and proteomics may help shorten time to microbiological results. The aim of this review is to summarize the current concept of biomarker-guided management and provide an outlook of promising ongoing investigations. EXPERT OPINION 'Antibiotic stewardship' is complex and needs more than just the measurement of one single biomarker. However, when integrated into the context of a thorough clinical examination, standard blood parameters and a well done risk stratification by clinical scores such as the SOFA-score, biomarkers have great potential to improve the diagnostic and prognostic assessment of patients.
Collapse
Affiliation(s)
- Ellen Haag
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Alexandra Molitor
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Claudia Gregoriano
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Beat Müller
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| | - Philipp Schuetz
- University Department of Medicine, Kantonsspital Aarau , Aarau, Switzerland
| |
Collapse
|
10
|
Goetsch HE, Love NG, Wigginton KR. Fate of Extracellular DNA in the Production of Fertilizers from Source-Separated Urine. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1808-1815. [PMID: 31965791 DOI: 10.1021/acs.est.9b04263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The practice of urine source-separation for fertilizer production necessitates an understanding of the presence and impact of extracellular DNA in the urine. This study examines the fate of plasmid DNA carrying ampicillin and tetracycline resistance genes in aged urine, including its ability to be taken up and expressed by competent bacteria. Plasmid DNA incubated in aged urine resulted in a >2 log loss of bacterial transformation efficiency in Acinetobacter baylyi within 24 h. The concentration of ampicillin and tetracycline resistance genes, as measured with quantitative polymerase chain reaction, did not correspond with the observed transformation loss. When the plasmid DNA was incubated in aged urine that had been filtered (0.22 μm) or heated (75 °C), the transformation efficiencies were more stable than when the plasmids were incubated in unfiltered and unheated aged urine. Gel electrophoresis results indicated that plasmid linearization by materials larger than 100 kDa in the aged urine caused the observed transformation efficiency decreases. The results of this study suggest that extracellular DNA released into aged urine poses a low potential for the spread of antibiotic resistance genes to bacteria once it is released to the environment.
Collapse
Affiliation(s)
- Heather E Goetsch
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Nancy G Love
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Krista R Wigginton
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| |
Collapse
|
11
|
Sharma P, Garg N, Sharma A, Capalash N, Singh R. Nucleases of bacterial pathogens as virulence factors, therapeutic targets and diagnostic markers. Int J Med Microbiol 2019; 309:151354. [PMID: 31495663 DOI: 10.1016/j.ijmm.2019.151354] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/12/2019] [Accepted: 08/29/2019] [Indexed: 12/25/2022] Open
Abstract
New frontiers of therapy are being explored against the upcoming bacterial diseases rendered untreatable due to multiple, extreme and pan- antibiotic resistance. Nucleases are ubiquitous in bacterial pathogens performing various functions like acquiring nucleotide nutrients, allowing or preventing uptake of foreign DNA, controlling biofilm formation/dispersal/architecture, invading host by tissue damage, evading immune defence by degrading DNA matrix of neutrophil extracellular traps (NETs) and immunomodulating the host immune response. Secretory nucleases also provide means of survival to other bacteria like iron-reducing Shewanella and such functions help them adapt and survive proficiently. Other than their pro-pathogen roles in survival, nucleases can be used directly as therapeutics. One of the powerful armours of pathogens is the formation of biofilms, thus helping them resist and persist in the harshest of environments. As eDNA forms the structural and binding component of biofilm, nucleases can be used against the adhering component, thus increasing the permeability of antimicrobial agents. Nucleases have recently become a model system of intense study for their biological functions and medical applications in diagnosis, immunoprophylaxis and therapy. Rational implications of these enzymes can impact human medicine positively in future by opening new ways for therapeutics which have otherwise reached saturation due to multi drug resistance.
Collapse
Affiliation(s)
- Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, India.
| | - Nisha Garg
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Anshul Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Ravinder Singh
- Department of Microbiology, Panjab University, Chandigarh, India
| |
Collapse
|
12
|
Qing T, Long C, Wang X, Zhang K, Zhang P, Feng B. Detection of micrococcal nuclease for identifying Staphylococcus aureus based on DNA templated fluorescent copper nanoclusters. Mikrochim Acta 2019; 186:248. [DOI: 10.1007/s00604-019-3363-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/09/2019] [Indexed: 02/07/2023]
|
13
|
Rapid and specific detection of Salmonella infections using chemically modified nucleic acid probes. Anal Chim Acta 2018; 1054:157-166. [PMID: 30712586 DOI: 10.1016/j.aca.2018.12.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/07/2018] [Accepted: 12/10/2018] [Indexed: 12/17/2022]
Abstract
Salmonella is a leading source of bacterial foodborne illness in humans, causing gastroenteritis outbreaks with bacteraemia occurrences that can lead to clinical complications and death. Eggs, poultry and pig products are considered as the main carriers of the pathogenic Salmonella for humans. To prevent this relevant zoonosis, key changes in food safety regulations were undertaken to improve controls in the food production chain. Despite these measures, large outbreaks of salmonellosis were reported worldwide in the last decade. Thus, new strategies for Salmonella detection are a priority for both, food safety and public health authorities. Such detection systems should provide significant reduction in diagnostic time (hours) compared to the currently available methods (days). Herein, we report on the discovery and characterization of nucleic acid probes for the sensitive and specific detection of live Salmonella within less than 8 h of incubation. We are the first to postulate the nuclease activity derived from Salmonella as biomarker of infection and its utility to develop innovative detection strategies. Our results have shown the screening and identification of two oligonucleotide sequences (substrates) as the most promising probes for detecting Salmonella - Sal-3 and Sal-5. The detection limits for both probes were determined with the reference Salmonella Typhimurium (STM 1) and Salmonella Enteritidis (SE 1) cultures. Sal-3 has reported LOD values around 105 CFU mL-1 for STM 1 and 104 CFU mL-1 for SE 1, while Sal-5 proves to be a slightly better probe, with LODs of 104 CFU mL-1 for STM 1 and 104 CFU mL-1 for SE 1. Both selected probes have shown the capability to recognize 49 out of 51 different Salmonella serotypes tested in vitro and the most frequent serotypes in porcine mesenteric lymph nodes as a standard sample used in fattening-pig salmonellosis baseline studies. Notably, our results showed 100% correlation between nuclease detection and the PCR-InvA or ISO-6579 standard method, underlining the great potential of this innovative nucleic acids technology to be implemented as a rapid method for food safety testing.
Collapse
|