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Shan J, Jia Y, Hickenbotham P, Teulières L, Clokie MRJ. Combining citizen science and molecular diagnostic methods to investigate the prevalence of Borrelia burgdorferi s.l. and Borrelia miyamotoi in tick pools across Great Britain. Front Microbiol 2023; 14:1126498. [PMID: 37180256 PMCID: PMC10169747 DOI: 10.3389/fmicb.2023.1126498] [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: 12/17/2022] [Accepted: 03/31/2023] [Indexed: 05/16/2023] Open
Abstract
Lyme disease is the most common tick-borne disease and is caused by a group of bacteria known as Borrelia burgdorferi sensu lato (s.l.) complex. Sharing the same genus as B. burgdorferi, Borrelia miyamotoi is a distinct genotype that causes relapsing fever disease. This emerging tick-borne disease is increasingly becoming a concern in public health. To investigate the prevalence of B. burgdorferi s.l. and B. miyamotoi in ticks first, we developed a PCR (Bmer-qPCR) that targets the phage terminase large subunit (terL) gene carried by B. miyamotoi. A similar approach had been used successfully in developing Ter-qPCR for detecting B. burgdorferi s.l. The terL protein functions as an enzyme in packaging phage DNA. Analytical validation of the Bmer-qPCR confirmed its specificity, efficiency and sensitivity. Second, we designed a citizen science-based approach to detect 838 ticks collected from numerous sites across Great Britain. Finally, we applied Bmer-qPCR and Ter-qPCR to 153 tick pools and revealed that the prevalence of B. burgdorferi s.l. and B. miyamotoi was dependent on their geographical locations, i.e. Scotland showed a higher rate of B. burgdorferi s.l. and lower rate of B. miyamotoi carriage as compared to those of the England data. A pattern of diminishing rate of B. miyamotoi carriage from southern England to northern Scotland was visible. Together, the citizen science-based approach provided an estimation of the carriage rate of B. burgdorferi s.l. and B. miyamotoi in tick pools and a potential spreading pattern of B. miyamotoi from the south to the north of Great Britain. Our findings underscore the power of combining citizen science with the molecular diagnostic method to reveal hidden pattern of pathogen-host-environment interplay. Our approach can provide a powerful tool to elucidate the ecology of tick-borne diseases and may offer guidance for pathogen control initiatives. In an era of limited resources, monitoring pathogens requires both field and laboratory support. Citizen science approaches provide a method to empower the public for sample collection. Coupling citizen science approaches with laboratory diagnostic tests can make real-time monitoring of pathogen distribution and prevalence possible.
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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
| | - Peter Hickenbotham
- 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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Jiang K, Wu J, Kim JE, An S, Nam JM, Peng YK, Lee JH. Plasmonic Cross-Linking Colorimetric PCR for Simple and Sensitive Nucleic Acid Detection. NANO LETTERS 2023; 23:3897-3903. [PMID: 37083438 DOI: 10.1021/acs.nanolett.3c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Simple, low-cost, and accurate nucleic acid assay platforms hold great promise for point-of-care (POC) pathogen detection, disease surveillance, and control. Plasmonic photothermal polymerase chain reaction (PPT-PCR) is a powerful and efficient nucleic acid amplification technique, but it lacks a simple and convenient analysis method for POC applications. Herein, we propose a novel plasmonic cross-linking colorimetric PCR (PPT-ccPCR) assay by integrating plasmonic magnetic nanoparticle (PMN)-based PPT-PCR with gold nanoparticle (AuNP)-based cross-linking colorimetry. AuNPs form assembled structures with the PMNs in the presence of amplicons and collect in a magnetic field, resulting in color changes to the supernatant. Target DNA with concentrations as low as 5 copies/μL can be visually detected within 40 min. The achieved limit of detection was 1.8 copies/μL based on the absorption signals. This simple and sensitive strategy needs no expensive instrumentation and demonstrates high potential for POC detection while enabling further applications in clinical diagnostics.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ji-Eun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sujin An
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yung-Kang Peng
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
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Berger CS, Bougas B, Côté G, Dumont JF, Bernatchez L. A qPCR-based method to detect the eel parasitic nematode Anguillicola crassus in intermediate and final hosts. Parasitol Res 2023; 122:1435-1443. [PMID: 37071205 DOI: 10.1007/s00436-023-07843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Being able to systematically detect parasitic infection, even when no visual signs of infection are present, is crucial to the establishment of accurate conservation policies. The nematode Anguillicola crassus infects the swimbladder of anguillid species and is a potential threat for eel populations. In North America, naïve hosts such as the American eel Anguilla rostrata are affected by this infection. The accidental introduction of A. crassus following restocking programs may contribute to the actual decline of the American eel in Canada. We present a quantitative real time PCR-based method to detect A. crassus infection in final and intermediate hosts. We tested two protocols on samples from different geographical origins in Canada: 1) a general detection of A. crassus DNA in pools of young final hosts (glass eels) or crustacean intermediate hosts 2) a detection at the individual scale by analyzing swim bladders from elvers, or from adult yellow and silver eels. The DNA of A. crassus was detected in one pool of zooplankton (intermediate host) from the Richelieu River (Montérégie-Québec), as well as in individual swim bladders of 13 elvers from Grande and Petite Trinité rivers (Côte-Nord-Québec). We suggest that our qPCR approach could be used in a quantitative way to estimate the parasitic burden in individual swim bladders of elvers. Our method, which goes beyond most of previous developed protocols that restricted the diagnosis of A. crassus to the moment when it was fully established in its final host, should help to detect early A. crassus infection in nature.
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Affiliation(s)
- Chloé Suzanne Berger
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
| | - Bérénice Bougas
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Guillaume Côté
- Ministère de L'Environnement, de La Lutte Contre Les Changements Climatiques, de La Faune Et Des Parcs (MELCCFP), Québec, QC, Canada
| | - Jean-François Dumont
- Ministère de L'Environnement, de La Lutte Contre Les Changements Climatiques, de La Faune Et Des Parcs (MELCCFP), Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative Et Des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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54
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Pfuderer L, Stark WJ, Grass RN. Synthetic Microbial Surrogates Consisting of Lipid Nanoparticles Encapsulating DNA for the Validation of Surface Disinfection Procedures. ACS APPLIED BIO MATERIALS 2023; 6:1252-1259. [PMID: 36854082 PMCID: PMC10031560 DOI: 10.1021/acsabm.3c00004] [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] [Indexed: 03/02/2023]
Abstract
Effective cleaning and disinfection procedures are an integral part of good manufacturing practice and in maintaining hygiene standards in health-care facilities. In this study, a method to validate such cleaning and disinfection procedures of surfaces was established employing lipid nanoparticles (LNPs) encapsulating DNA. It was possible to determine and distinguish between the physical cleaning effect (dilution) and the chemical cleaning effect (disintegration) on the LNPs during the cleaning and disinfection procedure (wiping). After treatment with 70 v % ethanol as a disinfectant and SDS solution as a cleaning agent, LNPs showed log10 reductions of 4.5 and 4.0, respectively. These values are similar to the log10 reductions exhibited by common bacteria, such as Escherichia coli and Serratia marcescens. Therefore, LNPs pose as useful tools for cleaning validation with advantages over the already existing tools and enable a separate detection of dilution and chemical disinfectant action.
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Affiliation(s)
- Lara Pfuderer
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Wendelin J Stark
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Robert N Grass
- Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
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Yeh SC, Strilets T, Tan WL, Castillo D, Medkour H, Rey-Cadilhac F, Serrato-Pomar IM, Rachenne F, Chowdhury A, Chuo V, Azar SR, Singh MK, Hamel R, Missé D, Kini RM, Kenney LJ, Vasilakis N, Marti-Renom MA, Nir G, Pompon J, Garcia-Blanco MA. The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity. PLoS Pathog 2023; 19:e1011224. [PMID: 36996041 PMCID: PMC10062553 DOI: 10.1371/journal.ppat.1011224] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/20/2023] [Indexed: 03/31/2023] Open
Abstract
Mosquito transmission of dengue viruses to humans starts with infection of skin resident cells at the biting site. There is great interest in identifying transmission-enhancing factors in mosquito saliva in order to counteract them. Here we report the discovery of high levels of the anti-immune subgenomic flaviviral RNA (sfRNA) in dengue virus 2-infected mosquito saliva. We established that sfRNA is present in saliva using three different methods: northern blot, RT-qPCR and RNA sequencing. We next show that salivary sfRNA is protected in detergent-sensitive compartments, likely extracellular vesicles. In support of this hypothesis, we visualized viral RNAs in vesicles in mosquito saliva and noted a marked enrichment of signal from 3'UTR sequences, which is consistent with the presence of sfRNA. Furthermore, we show that incubation with mosquito saliva containing higher sfRNA levels results in higher virus infectivity in a human hepatoma cell line and human primary dermal fibroblasts. Transfection of 3'UTR RNA prior to DENV2 infection inhibited type I and III interferon induction and signaling, and enhanced viral replication. Therefore, we posit that sfRNA present in salivary extracellular vesicles is delivered to cells at the biting site to inhibit innate immunity and enhance dengue virus transmission.
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Affiliation(s)
- Shih-Chia Yeh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Tania Strilets
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Wei-Lian Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Hacène Medkour
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | | | | | | | - Avisha Chowdhury
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Vanessa Chuo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Sasha R. Azar
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Moirangthem Kiran Singh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rodolphe Hamel
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Dorothée Missé
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Biodefense and Emerging Infectious Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Tropical Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Preventive Medicine and Population Health, University of University of Texas Medical Branch, Galveston, Texas, United States of America
- World Reference Center for Emerging Viruses and Arboviruses, University of University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Guy Nir
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Julien Pompon
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- MIVEGEC, Univ. Montpellier, IRD, CNRS, Montpellier, France
| | - Mariano A. Garcia-Blanco
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, United States of America
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56
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Lindsay DL, Guan X, Harms NE, Cronin JT, Meyerson LA, Lance RF. DNA assays for genetic discrimination of three Phragmites australis subspecies in the United States. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11512. [PMID: 37051584 PMCID: PMC10083467 DOI: 10.1002/aps3.11512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Premise To genetically discriminate subspecies of the common reed (Phragmites australis), we developed real-time quantitative (qPCR) assays for identifying P. australis subsp. americanus, P. australis subsp. australis, and P. australis subsp. berlandieri. Methods and Results Utilizing study-generated chloroplast DNA sequences, we developed three novel qPCR assays. Assays were verified on individuals of each subspecies and against two non-target species, Arundo donax and Phalaris arundinacea. One assay amplifies only P. australis subsp. americanus, one amplifies P. australis subsp. australis and/or P. australis subsp. berlandieri, and one amplifies P. australis subsp. americanus and/or P. australis subsp. australis. This protocol enhances currently available rapid identification methods by providing genetic discrimination of all three subspecies. Conclusions The newly developed assays were validated using P. australis samples from across the United States. Application of these assays outside of this geographic range should be preceded by additional testing.
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Affiliation(s)
- Denise L. Lindsay
- United States Army Engineer Research and Development Center Environmental LaboratoryVicksburgMississippi39180USA
| | - Xin Guan
- Bennett AerospaceVicksburgMississippi39180USA
- Present address:
ModernaTX, Moderna Technology CenterNorwoodMarylandUSA
| | - Nathan E. Harms
- United States Army Engineer Research and Development Center Environmental LaboratoryVicksburgMississippi39180USA
| | | | | | - Richard F. Lance
- United States Army Engineer Research and Development Center Environmental LaboratoryVicksburgMississippi39180USA
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Anderson SD, Gleason CA. A molecular beacon real-time polymerase chain reaction assay for the identification of M. chitwoodi, M. fallax, and M. minor. FRONTIERS IN PLANT SCIENCE 2023; 14:1096239. [PMID: 36909438 PMCID: PMC9994647 DOI: 10.3389/fpls.2023.1096239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) are major pests of many important crops around the world. In the Northwestern region of the United States of America (USA), Meloidogyne chitwoodi causes economic losses in potatoes because the nematodes can infect the tubers, which leads to potato galling and reductions in marketable yield. Meloidogyne chitwoodi is a quarantine pathogen in certain potato export markets, and there is little industry tolerance for the presence of this nematode. Recently, two Meloidogyne species that are not known to be present in agricultural fields in the USA were detected on golf turfgrasses in California and Washington. These species, M. fallax and M. minor, are morphologically similar to M. chitwoodi and can infect potatoes and cause tuber damage. Their detection in the USA means that they could potentially infest potato fields and become a problem in potato production. Additionally, M. fallax is a regulated plant pest in the USA, which makes the correct identification of potato-infecting root-knot nematodes important. Previously, there was no single-tube assay that could determine whether M. chitwoodi, M. fallax, and/or M. minor were present in a sample. Thus, a molecular beacon real-time PCR assay which can reliably detect M. chitwoodi, M. fallax, or M. minor from crude nematode extracts was designed and characterized.
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Nauta M, McManus O, Træholt Franck K, Lindberg Marving E, Dam Rasmussen L, Raith Richter S, Ethelberg S. Early detection of local SARS-CoV-2 outbreaks by wastewater surveillance: a feasibility study. Epidemiol Infect 2023; 151:e28. [PMID: 36722251 PMCID: PMC9990400 DOI: 10.1017/s0950268823000146] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/01/2022] [Accepted: 01/26/2023] [Indexed: 02/02/2023] Open
Abstract
Wastewater surveillance and quantitative analysis of SARS-CoV-2 RNA are increasingly used to monitor the spread of COVID-19 in the community. We studied the feasibility of applying the surveillance data for early detection of local outbreaks. A Monte Carlo simulation model was constructed, applying data on reported variation in RNA gene copy concentration in faeces and faecal masses shed. It showed that, even with a constant number of SARS-CoV-2 RNA shedders, the variation in concentrations found in wastewater samples will be large, and that it will be challenging to translate viral concentrations into incidence estimates, especially when the number of shedders is low. Potential signals for early detection of hypothetical outbreaks were analysed for their performance in terms of sensitivity and specificity of the signals. The results suggest that a sudden increase in incidence is not easily identified on the basis of wastewater surveillance data, especially in small sampling areas and in low-incidence situations. However, with a high number of shedders and when combining data from multiple consecutive tests, the performance of wastewater sampling is expected to improve considerably. The developed modelling approach can increase our understanding of the results from wastewater surveillance of SARS-CoV-2.
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Affiliation(s)
- Maarten Nauta
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark
| | - Oliver McManus
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 16973 Solna, Sweden
| | - Kristina Træholt Franck
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark
| | - Ellinor Lindberg Marving
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark
| | - Lasse Dam Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark
| | - Stine Raith Richter
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology & Prevention, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen S, Denmark
- Department of Public Health, Global Health Section, University of Copenhagen, Øster Farimagsgade 5, 1014 København K, Denmark
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Kechin A, Oscorbin I, Cherednichenko A, Khrapov E, Schwartz Y, Stavitskaya N, Filipenko M. Selection of IS6110 conserved regions for the detection of Mycobacterium tuberculosis using qPCR and LAMP. Arch Microbiol 2023; 205:71. [PMID: 36688992 DOI: 10.1007/s00203-023-03410-5] [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: 08/24/2022] [Revised: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
IS6110 insertion sequence is a frequently used target for Mycobacterium tuberculosis detection. However, its sequence variability is studied insufficiently. We aimed to identify the most conservative and variable regions in IS6110 sequences and develop qPCR and LAMP oligonucleotide sets for the conservative regions. Using in-house Python scripts, 3609 M. tuberculosis genome sequences from the NCBI database were aligned; conservative regions were identified to design oligonucleotide sets. IS6110 fragments located within the 31-231 bp region were the most conservative and represented in genomes and were used to design qPCR and LAMP oligonucleotides. The in silico sensitivity of the qPCR oligonucleotides on the whole genome set was 99.1% and 98.4%. For the LAMP primers developed, the sensitivity was 96.9%. For qPCR, the limit of detection with 95% confidence (LoD95%) was four IS6110 copies per reaction, with LoD90% being 200 BCG cells per ml of artificial sputum. For LAMP, LoD95% was 16 copies per reaction, with LoD90% being 400 Mycobacterium bovis Bacille Calmette-Guerin (BCG) cells per ml of artificial sputum. We have demonstrated the IS6110 sequence variability and designed highly sensitive qPCR and LAMP oligonucleotides to detect M. tuberculosis.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation.
| | - Igor Oscorbin
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
| | - Andrey Cherednichenko
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
| | - Yakov Schwartz
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Nataliya Stavitskaya
- Federal State Budgetary Institution "Novosibirsk Tuberculosis Research Institute" (NTRI) of the Ministry of Health of the Russian Federation, Okhotskaya St. 81 A, 630040, Novosibirsk, Russian Federation
| | - Maksim Filipenko
- Institute of Chemical Biology and Fundamental Medicine Siberian Branch Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russian Federation
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Wang D, Liu E, Liu H, Jin X, Niu C, Gao Y, Su X. A droplet digital PCR assay for detection and quantification of Verticillium nonalfalfae and V. albo-atrum. Front Cell Infect Microbiol 2023; 12:1110684. [PMID: 36710974 PMCID: PMC9874294 DOI: 10.3389/fcimb.2022.1110684] [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: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Verticillium nonalfalfae and V. albo-atrum are notorious pathogenic fungi that cause a destructive vascular disease called Verticillium wilt worldwide. Thus, timely and quantitative monitoring of fungal progression is highly desirable for early diagnosis and risk assessment. In this study, we developed a droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify V. nonalfalfae and V. albo-atrum. The performance of this assay was validated in comparison with that of a quantitative real-time polymerase chain reaction (qPCR) assay. The standard curve analysis of the ddPCR assay showed good linearity. The ddPCR assay indicated similar detection sensitivity to that of qPCR on pure genomic DNA, while it enhanced the positive rate for low-abundance fungi, especially in alfalfa stems. Receiver operating characteristic analysis revealed that ddPCR provided superior diagnostic performance on field tissues compared to qPCR, and the area under curve values were 0.94 and 0.90 for alfalfa roots and stems, respectively. Additionally, the quantitative results of the two methods were highly concordant (roots: R2 = 0.91; stems: R2 = 0.76); however, the concentrations determined by ddPCR were generally higher than those determined by qPCR. This discrepancy was potentially caused by differing amplification efficiencies for qPCR between cultured and field samples. Furthermore, the ddPCR assays appreciably improved quantitative precision, as reflected by lower coefficients of variation. Overall, the ddPCR method enables sensitive detection and accurate quantification of V. nonalfalfae and V. albo-atrum, providing a valuable tool for evaluating disease progression and enacting effective disease control.
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Affiliation(s)
- Di Wang
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Enliang Liu
- 2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyang Liu
- 3Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xi Jin
- 4Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Chunyan Niu
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yunhua Gao
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
| | - Xiaofeng Su
- 5Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
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Schmidt PJ, Acosta N, Chik AHS, D’Aoust PM, Delatolla R, Dhiyebi HA, Glier MB, Hubert CRJ, Kopetzky J, Mangat CS, Pang XL, Peterson SW, Prystajecky N, Qiu Y, Servos MR, Emelko MB. Realizing the value in "non-standard" parts of the qPCR standard curve by integrating fundamentals of quantitative microbiology. Front Microbiol 2023; 14:1048661. [PMID: 36937263 PMCID: PMC10020645 DOI: 10.3389/fmicb.2023.1048661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
The real-time polymerase chain reaction (PCR), commonly known as quantitative PCR (qPCR), is increasingly common in environmental microbiology applications. During the COVID-19 pandemic, qPCR combined with reverse transcription (RT-qPCR) has been used to detect and quantify SARS-CoV-2 in clinical diagnoses and wastewater monitoring of local trends. Estimation of concentrations using qPCR often features a log-linear standard curve model calibrating quantification cycle (Cq) values obtained from underlying fluorescence measurements to standard concentrations. This process works well at high concentrations within a linear dynamic range but has diminishing reliability at low concentrations because it cannot explain "non-standard" data such as Cq values reflecting increasing variability at low concentrations or non-detects that do not yield Cq values at all. Here, fundamental probabilistic modeling concepts from classical quantitative microbiology were integrated into standard curve modeling approaches by reflecting well-understood mechanisms for random error in microbial data. This work showed that data diverging from the log-linear regression model at low concentrations as well as non-detects can be seamlessly integrated into enhanced standard curve analysis. The newly developed model provides improved representation of standard curve data at low concentrations while converging asymptotically upon conventional log-linear regression at high concentrations and adding no fitting parameters. Such modeling facilitates exploration of the effects of various random error mechanisms in experiments generating standard curve data, enables quantification of uncertainty in standard curve parameters, and is an important step toward quantifying uncertainty in qPCR-based concentration estimates. Improving understanding of the random error in qPCR data and standard curve modeling is especially important when low concentrations are of particular interest and inappropriate analysis can unduly affect interpretation, conclusions regarding lab performance, reported concentration estimates, and associated decision-making.
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Affiliation(s)
- Philip J. Schmidt
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, ON, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | | | - Patrick M. D’Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Hadi A. Dhiyebi
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Melissa B. Glier
- Public Health Laboratory, BC Centre for Disease Control, Vancouver, BC, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jennifer Kopetzky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chand S. Mangat
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Alberta Precision Laboratories, Public Health Laboratory, Alberta Health Services, Edmonton, AB, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | - Shelley W. Peterson
- Wastewater Surveillance Unit, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Natalie Prystajecky
- Public Health Laboratory, BC Centre for Disease Control, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Mark R. Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Monica B. Emelko
- Department of Civil and Environmental Engineering, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Monica B. Emelko,
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62
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Nafian F, Nafian S, Kamali Doust Azad B, Hashemi M. CRISPR-Based Diagnostics and Microfluidics for COVID-19 Point-of-Care Testing: A Review of Main Applications. Mol Biotechnol 2023; 65:497-508. [PMID: 36183037 PMCID: PMC9526387 DOI: 10.1007/s12033-022-00570-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 09/15/2022] [Indexed: 12/04/2022]
Abstract
An ongoing pandemic of coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). So far, there have been various approaches for SARS-CoV-2 detection, each having its pros and cons. The current gold-standard method for SARS-CoV-2 detection, which offers acceptable specificity and sensitivity, is the quantitative reverse transcription-PCR (qRT-PCR). However, this method requires considerable cost and time to transport samples to specialized laboratories and extract, amplify, and detect the viral genome. On the other hand, antigen and antibody testing approaches that bring rapidity and affordability into play have lower sensitivity and specificity during the early stages of COVID-19. Moreover, the immune response is variable depending on the individual. Methods based on clustered regularly interspaced short palindromic repeats (CRISPR) can be used as an alternative approach to controlling the spread of disease by a high-sensitive, specific, and low-cost molecular diagnostic system. CRISPR-based detection systems (CRISPR-Dx) target the desired sequences by specific CRISPR-RNA (crRNA)-pairing on a pre-amplified sample and a subsequent collateral cleavage. In the present article, we have reviewed different CRISPR-Dx methods and presented their benefits and drawbacks for point-of-care testing (POCT) of suspected SARS-CoV-2 infections at home or in small clinics.
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Affiliation(s)
- Fatemeh Nafian
- Department of Medical Laboratory Sciences, Faculty of Paramedics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Simin Nafian
- Department of Stem Cell and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran
| | | | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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63
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Gold Z, Shelton AO, Casendino HR, Duprey J, Gallego R, Van Cise A, Fisher M, Jensen AJ, D'Agnese E, Andruszkiewicz Allan E, Ramón-Laca A, Garber-Yonts M, Labare M, Parsons KM, Kelly RP. Signal and noise in metabarcoding data. PLoS One 2023; 18:e0285674. [PMID: 37167310 PMCID: PMC10174484 DOI: 10.1371/journal.pone.0285674] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from a single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates of underlying biological communities from metabarcoding is critical for enhancing the utility of such approaches for health and conservation. Recent work has demonstrated that correcting for amplification biases in genetic metabarcoding data can yield quantitative estimates of template DNA concentrations. However, a major source of uncertainty in metabarcoding data stems from non-detections across technical PCR replicates where one replicate fails to detect a species observed in other replicates. Such non-detections are a special case of variability among technical replicates in metabarcoding data. While many sampling and amplification processes underlie observed variation in metabarcoding data, understanding the causes of non-detections is an important step in distinguishing signal from noise in metabarcoding studies. Here, we use both simulated and empirical data to 1) suggest how non-detections may arise in metabarcoding data, 2) outline steps to recognize uninformative data in practice, and 3) identify the conditions under which amplicon sequence data can reliably detect underlying biological signals. We show with both simulations and empirical data that, for a given species, the rate of non-detections among technical replicates is a function of both the template DNA concentration and species-specific amplification efficiency. Consequently, we conclude metabarcoding datasets are strongly affected by (1) deterministic amplification biases during PCR and (2) stochastic sampling of amplicons during sequencing-both of which we can model-but also by (3) stochastic sampling of rare molecules prior to PCR, which remains a frontier for quantitative metabarcoding. Our results highlight the importance of estimating species-specific amplification efficiencies and critically evaluating patterns of non-detection in metabarcoding datasets to better distinguish environmental signal from the noise inherent in molecular detections of rare targets.
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Affiliation(s)
- Zachary Gold
- Cooperative Institute for Climate, Ocean, & Ecosystem Studies, UW, Seattle, Washington, United States of America
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Andrew Olaf Shelton
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Helen R Casendino
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Joe Duprey
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Ramón Gallego
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Amy Van Cise
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Mary Fisher
- School of Aquatic Fisheries Science, UW, Seattle, Washington, United States of America
| | - Alexander J Jensen
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Erin D'Agnese
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | | | - Ana Ramón-Laca
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Maya Garber-Yonts
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
| | - Michaela Labare
- Scripps Institution of Oceanography, UCSD, La Jolla, California, United States of America
| | - Kim M Parsons
- Northwest Fisheries Science Center, NMFS/NOAA, Seattle, Washington, United States of America
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, UW, Seattle, Washington, United States of America
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64
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Alves CPA, Prazeres DMF, Monteiro GA. Real-Time PCR Method for Assessment of ParA-Mediated Recombination Efficiency in Minicircle Production. Methods Mol Biol 2023; 2967:117-131. [PMID: 37608107 DOI: 10.1007/978-1-0716-3358-8_10] [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] [Indexed: 08/24/2023]
Abstract
The in vivo intramolecular recombination of a parental plasmid allows excising prokaryotic backbone from the eukaryotic cassette of interest, leading to the formation of, respectively, a miniplasmid and a minicircle. Here we describe a real-time PCR protocol suitable for the determination of recombination efficiency of parental plasmids with multimer resolution sites (MRS). The protocol was successfully applied to purified DNA samples obtained from E. coli cultures, allowing a more reproducible determination of recombination efficiency than densitometry analysis of agarose gels.
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Affiliation(s)
- Cláudia P A Alves
- iBB- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Duarte Miguel F Prazeres
- iBB- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Gabriel A Monteiro
- iBB- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
- Associate Laboratory i4HB - Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.
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65
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Qin X, Wang X, Xu K, Zhang Y, Tian H, Li Y, Qi B, Yang X. Quantitative analysis of miRNAs using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER)-qPCR. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:241-255. [PMID: 36700047 PMCID: PMC9842969 DOI: 10.1016/j.omtn.2022.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Here, a method using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER) for miRNAs quantification was established. The strategy has two steps: (1) ligation of two DNA probes specifically hybridize to target miRNA and (2) qPCR amplifying the ligated probe. The miRNA-binding regions of the probes are stem-looped, a motif significantly reduces nonspecific ligation at high ligation temperature (65°C). The ends of the probes are designed complementary to form a paired probe, facilitating the recognition of target miRNAs with low concentrations. RNase H proved to be able to stabilize the heteroduplex formed by the probe and target miRNA, contributing to enhanced sensitivity (limit of detection = 60 copies). High specificity (discriminating homology miRNAs differing only one nucleotide), wide dynamic range (seven orders of magnitude) and ability to accurately detect plant miRNAs (immune to hindrance of 2'-O-methyl moiety) enable SPLICER comparable with the commercially available TaqMan and miRCURY assays. SYBR green I, rather than expensive hydrolysis or locked nucleic acid probes indispensable to TaqMan and miRCURY assays, is adequate for SPLICER. The method was efficient (<1 h), economical ($7 per sample), and robust (able to detect xeno-miRNAs in mammalian bodies), making it a powerful tool for molecular diagnosis and corresponding therapy.
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Affiliation(s)
- Xinshu Qin
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Xingyu Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China,Corresponding author: Xingyu Wang, College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710054, Shaanxi, China.
| | - Ke Xu
- Department of Joint Surgery, Hong Hui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi, China
| | - Yi Zhang
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hongye Tian
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Yinglei Li
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Bangran Qi
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Xingbin Yang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China,Corresponding author: Xingbin Yang, College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710054, Shaanxi, China.
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66
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Identification and determination of (Z)-11-hexadecenal in sex pheromone of Helicoverpa armigera by GC–MS and bacterial bioluminescence methods. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02682-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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67
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Chung LTK, Vung ND, Uyen NT, Hanh BTM, Huong LT, Hien PT, Xuan LTT, Ha NT, Dat DX. A brief review on the validation of biology methods for COVID-19 detection. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.1013130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The COVID-19 global pandemic has been going on for more than two years, and the evolution of SARS-CoV-2 with many variants of concern still poses a risk to public health. Sufficient access to qualified and validated testing plays an important role in detecting and alerting trends of the pandemic and provides evidence for making decisions in preventive strategies and policies. Depending on the method of testing and laboratory conditions, validation parameters (i.e., analytical sensitivity, limit of detection, diagnostic sensitivity, analytical specificity, diagnostic specificity, repeatability, reproducibility, robustness, positive predictive value, negative predictive value, applicability, practicability, and time to results) can be very different. With three main types of COVID-19 detection kits available, comprising nucleic acid, serological, and antigen detection, the kind of validation parameters that should be used becomes a complicated consideration and takes time to assess. Our review provides valuable and comprehensive information for laboratories in the assessment and selection of the optimal parameters to validate new COVID-19 test kits.
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68
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Xie Y, Challis JK, Oloye FF, Asadi M, Cantin J, Brinkmann M, McPhedran KN, Hogan N, Sadowski M, Jones PD, Landgraff C, Mangat C, Servos MR, Giesy JP. RNA in Municipal Wastewater Reveals Magnitudes of COVID-19 Outbreaks across Four Waves Driven by SARS-CoV-2 Variants of Concern. ACS ES&T WATER 2022; 2:1852-1862. [PMID: 37552734 PMCID: PMC8887651 DOI: 10.1021/acsestwater.1c00349] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 05/07/2023]
Abstract
There are no standardized protocols for quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater to date, especially for population normalization. Here, a pipeline was developed, applied, and assessed to quantify SARS-CoV-2 and key variants of concern (VOCs) RNA in wastewater at Saskatoon, Canada. Normalization approaches using recovery ratio and extraction efficiency, wastewater parameters, or population indicators were assessed by comparing to daily numbers of new cases. Viral load was positively correlated with daily new cases reported in the sewershed. Wastewater surveillance (WS) had a lead time of approximately 7 days, which indicated surges in the number of new cases. WS revealed the variant α and δ driving the third and fourth wave, respectively. The adjustment with the recovery ratio and extraction efficiency improved the correlation between viral load and daily new cases. Normalization of viral concentration to concentrations of the artificial sweetener acesulfame K improved the trend of viral load during the Christmas and New Year holidays when populations were dynamic and variable. Acesulfame K performed better than pepper mild mottle virus, creatinine, and ammonia for population normalization. Hence, quality controls to characterize recovery ratios and extraction efficiencies and population normalization with acesulfame are promising for precise WS programs supporting decision-making in public health.
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Affiliation(s)
- Yuwei Xie
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Jonathan K. Challis
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Femi F. Oloye
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Mohsen Asadi
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
| | - Jenna Cantin
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Markus Brinkmann
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Kerry N. McPhedran
- Department of Civil, Geological and Environmental
Engineering, College of Engineering, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5A9,
Canada
- Global Institute for Water Security,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 3H5,
Canada
| | - Natacha Hogan
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- College of Agriculture and Bioresources, Department of
Animal and Poultry Sciences, University of Saskatchewan,
Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Mike Sadowski
- Wastewater Treatment Plant, Saskatoon Water Department,
City of Saskatoon, Saskatoon, Saskatchewan S7M 1X5,
Canada
| | - Paul D. Jones
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- School of Environment and Sustainability,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
| | - Chrystal Landgraff
- Division of Enteric Diseases, National Microbiology
Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba
R3E 3R2, Canada
- Food Science Department, University of
Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Chand Mangat
- Antimicrobial Resistance and Nosocomial Infections,
National Microbiology Laboratory, Public Health Agency of
Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Mark R. Servos
- Department of Biology, University of
Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - John P. Giesy
- Toxicology Centre, University of
Saskatchewan, Saskatoon, Saskatchewan S7N 5B3,
Canada
- Department of Veterinary Biomedical Sciences,
University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4,
Canada
- Department of Environmental Sciences,
Baylor University, Waco, Texas 76706, United
States
- Department of Zoology and Center for Integrative
Toxicology, Michigan State University, East Lansing, Michigan
48824, United States
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69
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Nguyen KH, Smith S, Roundtree A, Feistel DJ, Kirby AE, Levy K, Mattioli MC. Fecal indicators and antibiotic resistance genes exhibit diurnal trends in the Chattahoochee River: Implications for water quality monitoring. Front Microbiol 2022; 13:1029176. [PMID: 36439800 PMCID: PMC9684717 DOI: 10.3389/fmicb.2022.1029176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/19/2022] [Indexed: 11/12/2022] Open
Abstract
Water bodies that serve as sources of drinking or recreational water are routinely monitored for fecal indicator bacteria (FIB) by state and local agencies. Exceedances of monitoring thresholds set by those agencies signal likely elevated human health risk from exposure, but FIB give little information about the potential source of contamination. To improve our understanding of how within-day variation could impact monitoring data interpretation, we conducted a study at two sites along the Chattahoochee River that varied in their recreational usage and adjacent land-use (natural versus urban), collecting samples every 30 min over one 24-h period. We assayed for three types of microbial indicators: FIB (total coliforms and Escherichia coli); human fecal-associated microbial source tracking (MST) markers (crAssphage and HF183/BacR287); and a suite of clinically relevant antibiotic resistance genes (ARGs; blaCTX-M, blaCMY, MCR, KPC, VIM, NDM) and a gene associated with antibiotic resistance (intl1). Mean levels of FIB and clinically relevant ARGs (blaCMY and KPC) were similar across sites, while MST markers and intI1 occurred at higher mean levels at the natural site. The human-associated MST markers positively correlated with antibiotic resistant-associated genes at both sites, but no consistent associations were detected between culturable FIB and any molecular markers. For all microbial indicators, generalized additive mixed models were used to examine diurnal variability and whether this variability was associated with environmental factors (water temperature, turbidity, pH, and sunlight). We found that FIB peaked during morning and early afternoon hours and were not associated with environmental factors. With the exception of HF183/BacR287 at the urban site, molecular MST markers and intI1 exhibited diurnal variability, and water temperature, pH, and turbidity were significantly associated with this variability. For blaCMY and KPC, diurnal variability was present but was not correlated with environmental factors. These results suggest that differences in land use (natural or urban) both adjacent and upstream may impact overall levels of microbial contamination. Monitoring agencies should consider matching sample collection times with peak levels of target microbial indicators, which would be in the morning or early afternoon for the fecal associated indicators. Measuring multiple microbial indicators can lead to clearer interpretations of human health risk associated with exposure to contaminated water.
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Affiliation(s)
| | - Shanon Smith
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Alexis Roundtree
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Dorian J. Feistel
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Amy E. Kirby
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Karen Levy
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Mia Catharine Mattioli
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
- *Correspondence: Mia Catharine Mattioli,
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70
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Development and validation of methods that enable high-quality droplet digital PCR and hematological profiling data from microvolume blood samples. Bioanalysis 2022; 14:1197-1211. [PMID: 36331037 DOI: 10.4155/bio-2022-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aim: Mouse models have been crucial to preclinical studies in the increasingly relevant fields of cell and gene therapy. However, only small quantities of mouse blood can be collected without producing adverse physiological effects that compromise data integrity. Results: To address this limitation, two combined methods were developed to create detailed droplet digital PCR (ddPCR) and hematological profiles using only ∼20 μl of mouse blood. The validation of these methods, which can serve as a foundation for a standardized regulatory pipeline for ddPCR, is discussed. Even when using small amounts of input, this ddPCR protocol is accurate, precise, selective, specific, stable and robust. Conclusion: These techniques enable more frequent sample collection for higher-resolution pharmacokinetic data that meets or exceeds quality standards.
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71
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Korzun T, Moses AS, Kim J, Patel S, Schumann C, Levasseur PR, Diba P, Olson B, Rebola KGDO, Norgard M, Park Y, Demessie AA, Eygeris Y, Grigoriev V, Sundaram S, Pejovic T, Brody JR, Taratula OR, Zhu X, Sahay G, Marks DL, Taratula O. Nanoparticle-Based Follistatin Messenger RNA Therapy for Reprogramming Metastatic Ovarian Cancer and Ameliorating Cancer-Associated Cachexia. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204436. [PMID: 36098251 PMCID: PMC9633376 DOI: 10.1002/smll.202204436] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 06/15/2023]
Abstract
This study presents the first messenger RNA (mRNA) therapy for metastatic ovarian cancer and cachexia-induced muscle wasting based on lipid nanoparticles that deliver follistatin (FST) mRNA predominantly to cancer clusters following intraperitoneal administration. The secreted FST protein, endogenously synthesized from delivered mRNA, efficiently reduces elevated activin A levels associated with aggressive ovarian cancer and associated cachexia. By altering the cancer cell phenotype, mRNA treatment prevents malignant ascites, delays cancer progression, induces the formation of solid tumors, and preserves muscle mass in cancer-bearing mice by inhibiting negative regulators of muscle mass. Finally, mRNA therapy provides synergistic effects in combination with cisplatin, increasing the survival of mice and counteracting muscle atrophy induced by chemotherapy and cancer-associated cachexia. The treated mice develop few nonadherent tumors that are easily resected from the peritoneum. Clinically, this nanomedicine-based mRNA therapy can facilitate complete cytoreduction, target resistance, improve resilience during aggressive chemotherapy, and improve survival in advanced ovarian cancer.
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Affiliation(s)
- Tetiana Korzun
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR, 97239, USA
- Medical Scientist Training Program, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | - Abraham S Moses
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Siddharth Patel
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Canan Schumann
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Peter R Levasseur
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | - Parham Diba
- Medical Scientist Training Program, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | - Brennan Olson
- Medical Scientist Training Program, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | | | - Mason Norgard
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | - Youngrong Park
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Ananiya A Demessie
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Yulia Eygeris
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Vladislav Grigoriev
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | - Subisha Sundaram
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | - Tanja Pejovic
- Departments of Obstetrics and Gynecology and Pathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Jonathan R Brody
- Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Avenue, Portland, OR, 97201, USA
| | - Olena R Taratula
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Xinxia Zhu
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Daniel L Marks
- Papé Family Pediatric Research Institute, Oregon Health & Science University, SW Sam Jackson Park Rd, Mail Code L481, Portland, OR, 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Avenue, Portland, OR, 97201, USA
- Brenden-Colson Center for Pancreatic Care, Oregon Health & Science University, 2730 S Moody Avenue, Portland, OR, 97201, USA
| | - Oleh Taratula
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 2730 S Moody Avenue, Portland, OR, 97201, USA
- Department of Biomedical Engineering, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR, 97239, USA
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Quezada‐Rodriguez PR, Taylor RS, Downes J, Egan F, White S, Brenan A, Rigby M, Nowak BF, Ruane NM, Wynne JW. Prevalence of epitheliocystis in freshwater Atlantic salmon reared in flow-through and recirculation aquaculture systems. JOURNAL OF FISH DISEASES 2022; 45:1721-1731. [PMID: 36017570 PMCID: PMC9805179 DOI: 10.1111/jfd.13694] [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] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Epitheliocystis, an intracellular bacterial infection in the gills and skin epithelium, has been frequently reported in Atlantic salmon (Salmo salar) during freshwater production in a number of countries. This study describes the prevalence and intensity of a natural epitheliocystis infection present in the gills of two strains of Atlantic salmon reared in either a flow-through (FT) or a recirculation aquaculture system (RAS) in Ireland. Repeated sampling of gills prior to and throughout seawater transfer, histology and quantitative real-time PCR were used to determine infection prevalence and intensity. Despite no clinical gill disease, and minor histopathological changes, epitheliocystis lesions were identified in histology at all time points. Specific PCR confirmed the presence of Candidatus Clavichlamydia salmonicola in both strains and its number of copies was correlated with intensity of epitheliocystis lesions. A significant interaction between hatchery system and fish strain on the prevalence and intensity of gill epitheliocystis was found both using histological and molecular methods. Specifically, fish from FT had higher prevalence and intensity than RAS reared fish and within FT, the Irish cohort were more affected than Icelandic.
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Affiliation(s)
- Petra R. Quezada‐Rodriguez
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaLauncestonTasmaniaAustralia
| | - Richard S. Taylor
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
| | | | | | | | | | - Megan Rigby
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaLauncestonTasmaniaAustralia
| | | | - James W. Wynne
- Livestock and AquacultureCommonwealth Scientific and Industrial Research Organisation, Agriculture and FoodHobartTasmaniaAustralia
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Alič Š, Dermastia M, Burger J, Dickinson M, Pietersen G, Pietersen G, Dreo T. Genome-Informed Design of a LAMP Assay for the Specific Detection of the Strain of ' Candidatus Phytoplasma asteris' Phytoplasma Occurring in Grapevines in South Africa. PLANT DISEASE 2022; 106:2927-2939. [PMID: 35380469 DOI: 10.1094/pdis-10-21-2312-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine 'Candidatus Phytoplasma asteris' that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Špela Alič
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Marina Dermastia
- National Institute of Biology, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
| | - Johan Burger
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Matthew Dickinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Gerhard Pietersen
- Department of Microbiology and Plant Pathology, University of Pretoria, Hatfield 0028, South Africa
| | | | - Tanja Dreo
- National Institute of Biology, 1000 Ljubljana, Slovenia
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Zhang H, Gao J, Chen J, Peng Y, Han Z. RNA-dependent RNA polymerase could extend the lasting validity period of exogenous dsRNA. PEST MANAGEMENT SCIENCE 2022; 78:4569-4578. [PMID: 35831266 DOI: 10.1002/ps.7076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Previous studies have found that pesticide double-stranded (ds)RNA usually has a long-lasting validity period in plants. However, it is uncertain if any factors in plants could extend dsRNA duration. It has been reported that RNA-dependent RNA polymerases (RdRP) in plants and some other eukaryotes could catalyze RNA amplification and be involved in RNAi (interference). Thus, this study evaluated the effect of RdRP on the tissue content, activity, and duration of exogenous dsRNA. RESULTS We found that RdRP knockdown in Arabidopsis thaliana had no significant effect on tissue contents of reporter dsRNA parent molecules (8.91% reduction), but it caused significant decrease in the tissue contents of derived short fragments of 200, 120 and 59 bp tested (51.22%, 52.83% and 59.35%, respectively). Aphid inoculation tests showed that the same dose of insecticidal dsAgZFP exhibited a significantly lower lethal effect (mortality 58.8%) in the plants with RdRP knockdown than in the control plants with normal RdRP (86.0%). For Caenorhabditis elegans, the worms treated simultaneously with dsRdRP and reporter dsRNA had similar body contents to reporter dsRNA parent molecules and its long-fragment derivative (200 bp) as the control (1.28- and 1.07-fold greater, respectively). However, 120- and 59-bp short-fragment derivatives were significantly reduced by 28.78% and 59.84%, respectively, which also diminished faster in the descendants. CONCLUSIONS We conclude that RdRP could significantly enhance the tissue content of dsRNA derivatives by catalyzing amplification, thus improving dsRNA activity and extending its lasting validity period. Otherwise, RNAi by exogenous dsRNA was proven to be noninheritable in A. thaliana. This work confirmed the merit of dsRNA as a plant protectant. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Hainan Zhang
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jing Gao
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jiasheng Chen
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yue Peng
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhaojun Han
- The Key Laboratory of Monitoring and Management of Plant Diseases and Insects/Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Zhao SG, Sperger JM, Schehr JL, McKay RR, Emamekhoo H, Singh A, Schultz ZD, Bade RM, Stahlfeld CN, Gilsdorf CS, Hernandez CI, Wolfe SK, Mayberry RD, Krause HM, Bootsma M, Helzer KT, Rydzewski N, Bakhtiar H, Shi Y, Blitzer G, Kyriakopoulos CE, Kosoff D, Wei XX, Floberg J, Sethakorn N, Sharifi M, Harari PM, Huang W, Beltran H, Choueiri TK, Scher HI, Rathkopf DE, Halabi S, Armstrong AJ, Beebe DJ, Yu M, Sundling KE, Taplin ME, Lang JM. A clinical-grade liquid biomarker detects neuroendocrine differentiation in prostate cancer. J Clin Invest 2022; 132:e161858. [PMID: 36317634 PMCID: PMC9621140 DOI: 10.1172/jci161858] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/23/2022] [Indexed: 11/07/2022] Open
Abstract
BackgroundNeuroendocrine prostate cancer (NEPC) is an aggressive subtype, the presence of which changes the prognosis and management of metastatic prostate cancer.MethodsWe performed analytical validation of a Circulating Tumor Cell (CTC) multiplex RNA qPCR assay to identify the limit of quantification (LOQ) in cell lines, synthetic cDNA, and patient samples. We next profiled 116 longitudinal samples from a prospectively collected institutional cohort of 17 patients with metastatic prostate cancer (7 NEPC, 10 adenocarcinoma) as well as 265 samples from 139 patients enrolled in 3 adenocarcinoma phase II trials of androgen receptor signaling inhibitors (ARSIs). We assessed a NEPC liquid biomarker via the presence of neuroendocrine markers and the absence of androgen receptor (AR) target genes.ResultsUsing the analytical validation LOQ, liquid biomarker NEPC detection in the longitudinal cohort had a per-sample sensitivity of 51.35% and a specificity of 91.14%. However, when we incorporated the serial information from multiple liquid biopsies per patient, a unique aspect of this study, the per-patient predictions were 100% accurate, with a receiver-operating-curve (ROC) AUC of 1. In the adenocarcinoma ARSI trials, the presence of neuroendocrine markers, even while AR target gene expression was retained, was a strong negative prognostic factor.ConclusionOur analytically validated CTC biomarker can detect NEPC with high diagnostic accuracy when leveraging serial samples that are only feasible using liquid biopsies. Patients with expression of NE genes while retaining AR-target gene expression may indicate the transition to neuroendocrine differentiation, with clinical characteristics consistent with this phenotype.FundingNIH (DP2 OD030734, 1UH2CA260389, R01CA247479, and P30 CA014520), Department of Defense (PC190039 and PC200334), and Prostate Cancer Foundation (Movember Foundation - PCF Challenge Award).
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Affiliation(s)
- Shuang G. Zhao
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Jamie M. Sperger
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Jennifer L. Schehr
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Rana R. McKay
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Hamid Emamekhoo
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Anupama Singh
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Zachery D. Schultz
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Rory M. Bade
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Charlotte N. Stahlfeld
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Cole S. Gilsdorf
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Camila I. Hernandez
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Serena K. Wolfe
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | | | - Hannah M. Krause
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Matt Bootsma
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Kyle T. Helzer
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Nicholas Rydzewski
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Hamza Bakhtiar
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Yue Shi
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Grace Blitzer
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Christos E. Kyriakopoulos
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - David Kosoff
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Xiao X. Wei
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John Floberg
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Nan Sethakorn
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Marina Sharifi
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Paul M. Harari
- Department of Human Oncology and
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Wei Huang
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Himisha Beltran
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Toni K. Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Howard I. Scher
- Genitourinary Oncology Service, Department of Medicine and
- Biomarker Development Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Susan Halabi
- Department of Biostatistics and Bioinformatics and
| | - Andrew J. Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Department of Medicine, Duke University, Durham, North Carolina, USA
| | - David J. Beebe
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Biomedical Engineering and
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Kaitlin E. Sundling
- Wisconsin State Lab of Hygiene, Madison, Wisconsin, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Mary-Ellen Taplin
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joshua M. Lang
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin–Madison, Madison, Wisconsin, USA
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Xiang Z, Jiang Y, Cui C, Luo Y, Peng Z. Sensitive, Selective and Reliable Detection of Fe 3+ in Lake Water via Carbon Dots-Based Fluorescence Assay. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196749. [PMID: 36235283 PMCID: PMC9573028 DOI: 10.3390/molecules27196749] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022]
Abstract
In this study, C-dots were facilely synthesized via microwave irradiation using citric acid and ethylenediamine as carbon precursors. The fluorescence emissions of the C-dots could be selectively quenched by Fe3+, and the degree of quenching was linearly related to the concentrations of Fe3+ presented. This phenomenon was utilized to develop a sensitive fluorescence assay for Fe3+ detection with broad linear range (0–250, 250–1200 μmol/L) and low detection limit (1.68 μmol/L). Most importantly, the assay demonstrated high reliability towards samples in deionized water, tap water and lake water, which should find potential applications for Fe3+ monitoring in complicated environments.
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Affiliation(s)
- Zhuang Xiang
- School of Materials and Energy, Yunnan University, Kunming 650091, China
- Yunnan Key Laboratory for Micro/Nano Materials & Technology, Yunnan University, Kunming 650091, China
| | - Yuxiang Jiang
- School of Materials and Energy, Yunnan University, Kunming 650091, China
| | - Chen Cui
- School of Materials and Energy, Yunnan University, Kunming 650091, China
| | - Yuanping Luo
- School of Materials and Energy, Yunnan University, Kunming 650091, China
| | - Zhili Peng
- School of Materials and Energy, Yunnan University, Kunming 650091, China
- Correspondence: ; Tel.: +86-871-65037399
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Dzhembekova N, Moncheva S, Slabakova N, Zlateva I, Nagai S, Wietkamp S, Wellkamp M, Tillmann U, Krock B. New Knowledge on Distribution and Abundance of Toxic Microalgal Species and Related Toxins in the Northwestern Black Sea. Toxins (Basel) 2022; 14:685. [PMID: 36287954 PMCID: PMC9610735 DOI: 10.3390/toxins14100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/19/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023] Open
Abstract
Numerous potentially toxic plankton species commonly occur in the Black Sea, and phycotoxins have been reported. However, the taxonomy, phycotoxin profiles, and distribution of harmful microalgae in the basin are still understudied. An integrated microscopic (light microscopy) and molecular (18S rRNA gene metabarcoding and qPCR) approach complemented with toxin analysis was applied at 41 stations in the northwestern part of the Black Sea for better taxonomic coverage and toxin profiling in natural populations. The combined dataset included 20 potentially toxic species, some of which (Dinophysis acuminata, Dinophysis acuta, Gonyaulax spinifera, and Karlodinium veneficum) were detected in over 95% of the stations. In parallel, pectenotoxins (PTX-2 as a major toxin) were registered in all samples, and yessotoxins were present at most of the sampling points. PTX-1 and PTX-13, as well as some YTX variants, were recorded for the first time in the basin. A positive correlation was found between the cell abundance of Dinophysis acuta and pectenotoxins, and between Lingulodinium polyedra and Protoceratium reticulatum and yessotoxins. Toxic microalgae and toxin variant abundance and spatial distribution was associated with environmental parameters. Despite the low levels of the identified phycotoxins and their low oral toxicity, chronic toxic exposure could represent an ecosystem and human health hazard.
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Affiliation(s)
- Nina Dzhembekova
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Snejana Moncheva
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Nataliya Slabakova
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Ivelina Zlateva
- Institute of Oceanology “Fridtjof Nansen”—Bulgarian Academy of Sciences, 9000 Varna, Bulgaria
| | - Satoshi Nagai
- Fisheries Research and Education Agency, Fisheries Technology Institute, Yokohama 236-8648, Kanagawa, Japan
| | - Stephan Wietkamp
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
| | - Marvin Wellkamp
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
| | - Urban Tillmann
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
| | - Bernd Krock
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Ökologische Chemie, 0471 Bremerhaven, Germany
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Masri NZ, Card KG, Caws EA, Babcock A, Powell R, Lowe CJ, Donovan S, Norum S, Lyons S, De Pol S, Kostenchuk L, Dorea C, Lachowsky NJ, Willerth SM, Fyles TM, Buckley HL. Testing specificity and sensitivity of wastewater-based epidemiology for detecting SARS-CoV-2 in four communities on Vancouver Island, Canada. ENVIRONMENTAL ADVANCES 2022; 9:100310. [PMID: 36321068 PMCID: PMC9613784 DOI: 10.1016/j.envadv.2022.100310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/22/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
We report wastewater surveillance of the spread of SARS-CoV-2 based upon 24-h composite influent samples taken weekly from four wastewater treatment plants (WWTP) on Vancouver Island, BC, Canada between January 3, 2021 and July 10, 2021. Samples were analyzed by reverse transcription quantitative polymerase chain reaction targeting the N1 and N2 gene fragments of SARS-CoV-2 and a region of the replication associate protein of the pepper mottle mosaic virus (PMMoV) serving as endemic control. Only a small proportion of samples had quantifiable levels of N1 or N2. Overall case rates are weakly correlated with the concentration (gene copies/L) and with the flux of viral material influent to the WWTP (gene copies/day); the latter accounts for influent flow variations. Poisson multimodal rank correlation accounts for differences between the four WWTP and shows a significant correlation with a significant positive intercept. Receiver operator characteristics (ROC) analysis confirms a cut-off of cases based on amplified/not-amplified experimental data. At the optimal cut point of 19 (N1) or 17 (N2) cases/week/100,000 the sensitivity and specificity is about 75% for N1 and 67% for N2.
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Affiliation(s)
- Nadia Zeina Masri
- Division of Medical Sciences, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | | | - Emmanuelle A Caws
- Department of Civil Engineering and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
| | - Alana Babcock
- Division of Medical Sciences, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | | | | | - Shelley Donovan
- Environmental Monitoring Program, Capital Regional District, Canada
| | | | - Shirley Lyons
- Environmental Monitoring Program, Capital Regional District, Canada
| | | | | | - Caetano Dorea
- Department of Civil Engineering and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
| | - Nathan J Lachowsky
- School of Public Health and Social Policy, University of Victoria, Canada
| | - Stephanie M Willerth
- Department of Mechanical Engineering and Division of Medical Sciences, University of Victoria; Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
- School of Biomedical Engineering, University of British Columbia, Canada
| | | | - Heather L Buckley
- Department of Civil Engineering, Department of Chemistry, and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, Canada
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Jiménez-Montenegro L, Mendizabal JA, Alfonso L, Azparren L, Urrutia O. Development of a duplex qPCR assay with locked nucleic acid probes for A, B and E kappa-casein variants detection. Sci Rep 2022; 12:16387. [PMID: 36180500 PMCID: PMC9525573 DOI: 10.1038/s41598-022-20586-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
Milk proteins determine important milk technological characteristics. Among caseins, Ƙ-casein has been correlated with fat and protein content and cheese yield. Fourteen Ƙ-caseins variants have been described but the alleles A, B and E are the most important ones due to their frequency and/or influence on the technological aptitudes of milk. Therefore, in the present study two different duplex qPCR assays with locked nucleic acid probes (for positions 13104 and 13124 of the Ƙ-casein gene) were developed for the detection of A, B and E variants. Firstly, DNA isolation method from milk somatic cells and hair was optimised. The developed 13124-qPCR assay showed an increased sensitivity reaching up to 6.7 copies DNA copies/reaction at a 95% confidence level with A, B and E alleles reference samples. The 13104-qPCR assay reached up to 6.7 DNA copies/reaction for A allele reference sample and 67 DNA copies/reaction for B and E samples. Intra-assay variation results were below 6%. Applicability was determined using DNA samples from animals with known genotype for Ƙ-casein (AA, AB, BB, BE, AE, EE) and both assays were able to discriminate among the six genotypes with 100% accuracy. Thus, this qPCR method represents a sensitive and rapid option for the detection of Ƙ-casein alleles in both hair and milk samples.
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Affiliation(s)
- L Jiménez-Montenegro
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - J A Mendizabal
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - L Alfonso
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - L Azparren
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain
| | - O Urrutia
- IS-FOOD, School of Agricultural Engineering and Biosciences, Public University of Navarre (UPNA), Campus de Arrosadia, 31006, Pamplona, Spain.
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80
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Acer PT, Kelly LM, Lover AA, Butler CS. Quantifying the Relationship between SARS-CoV-2 Wastewater Concentrations and Building-Level COVID-19 Prevalence at an Isolation Residence: A Passive Sampling Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11245. [PMID: 36141515 PMCID: PMC9517461 DOI: 10.3390/ijerph191811245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 05/26/2023]
Abstract
SARS-CoV-2 RNA loads can be detected in the excreta of individuals with COVID-19 and have demonstrated positive correlations with clinical infection trends. Consequently, wastewater-based epidemiology (WBE) approaches have been implemented globally as a public health surveillance tool to monitor community-level prevalence of infections. The majority of wastewater specimens are gathered as either composite samples via automatic samplers (autosamplers) or grab samples. However, autosamplers are expensive and can be challenging to maintain in cold weather, while grab samples are particularly susceptible to temporal variation when sampling sewage directly from complex matrices outside residential buildings. Passive sampling can provide an affordable, practical, and scalable sampling system while maintaining a reproducible SARS-CoV-2 signal. In this regard, we deployed tampons as passive samplers outside of a COVID-19 isolation unit (a segregated residence hall) at a university campus from 1 February 2021-21 May 2021. Samples (n = 64) were collected 3-5 times weekly and remained within the sewer for a median duration of 24 h. SARS-CoV-2 RNA was quantified using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) targeting the N1 and N2 gene fragments. We quantified the mean viral load captured per individual and the association between the daily viral load and total persons, adjusting for covariates using multivariable models to provide a baseline estimate of viral shedding. Samples were processed through two distinct laboratory pipelines on campus, yielding highly correlated N2 concentrations. Data obtained here highlight the success of passive sampling utilizing tampons to capture SARS-CoV-2 in wastewater coming from a COVID-19 isolation residence, indicating that this method can help inform building-level public health responses.
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Affiliation(s)
- Patrick T. Acer
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Arnold House, 715 North Pleasant Street, Amherst, MA 01003, USA
| | - Lauren M. Kelly
- Department of Environmental and Water Resources Engineering, University of Massachusetts Amherst, Engineering Lab II, 101 N Service Rd, Amherst, MA 01003, USA
| | - Andrew A. Lover
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Arnold House, 715 North Pleasant Street, Amherst, MA 01003, USA
| | - Caitlyn S. Butler
- Department of Environmental and Water Resources Engineering, University of Massachusetts Amherst, Engineering Lab II, 101 N Service Rd, Amherst, MA 01003, USA
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Juanola-Falgarona M, Peñarrubia L, Jiménez-Guzmán S, Porco R, Congost-Teixidor C, Varo-Velázquez M, Rao SN, Pueyo G, Manissero D, Pareja J. Ct values as a diagnostic tool for monitoring SARS-CoV-2 viral load using the QIAstat-Dx® Respiratory SARS-CoV-2 Panel. Int J Infect Dis 2022; 122:930-935. [PMID: 35840097 PMCID: PMC9273520 DOI: 10.1016/j.ijid.2022.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/17/2022] [Accepted: 07/07/2022] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES Qualitative real-time polymerase chain reaction tests are not designed to provide quantitative or semiquantitative results because cycle threshold (Ct) values are not normalized to standardized controls of known concentration. The aim of this study was to characterize SARS-CoV-2 viral loads based on Ct values, using the QIAstat-Dx® Respiratory SARS-CoV-2 Panel. METHODS Different lineages of SARS-CoV-2 clinical samples and the World Health Organization international standard were used to assess the linearity of the QIAstat-Dx Respiratory SARS-CoV-2 Panel. Limit of detection for the different lineages was characterized. RESULTS Comparable efficiencies and linearity for all samples resulted in R2 ≥0.99, covering a dynamic range of 1,000,000-100 copies/mL for the SARS-CoV-2 assay, showing linear correlation between Ct values and viral load down to 300 copies/mL. CONCLUSION The SARS-CoV-2 Ct values provided by the QIAstat-Dx® Respiratory SARS-CoV-2 Panel could be used as a surrogate for viral load given the linear correlation between Ct values and viral concentration down to limit of detection. This panel allows to obtain reproducible Ct values for SARS-CoV-2 ribonucleic acid downstream of the sample collection, reducing the sample-to-Ct workflow variability. Ct values can help provide a reliable assessment and comparison of viral loads in patients when tested with the QIAstat-Dx Respiratory SARS-CoV-2 Panel.
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Affiliation(s)
- Martí Juanola-Falgarona
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain,Corresponding author
| | - Luis Peñarrubia
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Sara Jiménez-Guzmán
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Roberto Porco
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | | | - Marta Varo-Velázquez
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Sonia N Rao
- QIAGEN Inc., 19300 Germantown Road, Germantown, MD, 20874, USA
| | - Gemma Pueyo
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
| | - Davide Manissero
- QIAGEN Manchester Ltd, Citylabs 2.0. Hathersage Road, Manchester, M13 0BH, UK
| | - Josep Pareja
- STAT-Dx Life S.L. (A QIAGEN company), Carrer de Baldiri Reixac, 4–8, 08028 Barcelona, Spain
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82
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Douillet A, Laurent B, Beslay J, Massot M, Raynal M, Delmotte F. LAMP for in-field quantitative assessments of airborne grapevine downy mildew inoculum. J Appl Microbiol 2022; 133:3404-3412. [PMID: 35977551 DOI: 10.1111/jam.15762] [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: 05/13/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022]
Abstract
AIMS Cheap, rapid tools for measuring emissions of Plasmopara viticola sporangia directly in the field are required to protect grapevines efficiently and sustainably against downy mildew. To this end, we adapted an existing loop-mediated isothermal amplification (LAMP) protocol based on ITS2 sequences, coupled with a rotating-arm sampler and simple cell lysis, for the in-field measurement of airborne sporangia of P. viticola. METHODS AND RESULTS We estimated the sensitivity and specificity of the molecular reaction with an unpurified DNA template in controlled conditions, using the Droplet Digital PCR (ddPCR) as a reference. We show that the LAMP lower limit of quantification is 3.3 sporangia.m-3 air sampled. Cell lysis in KOH solution was less efficient than CTAB for DNA extraction, but the repeatability of the method was good. We tested this protocol directly in a plot at Chateau Dillon (Blanquefort, France) in which we monitored P. viticola sporangia concentrations from March to October 2020 (88 samples which revealed concentrations ranging from 0 to 243 sporangia.m-3 ). There was a significant quantitative correlation (R2 = 0.52) between ddPCR and LAMP results. CONCLUSION LAMP analysis of an unpurified DNA matrix is a simple and reliable method for in-field estimations of the concentration of airborne P. viticola sporangia. SIGNIFICANCE AND IMPACT OF STUDY This study constitutes a first step towards the development of a regional grapevine downy mildew monitoring network in the vineyards of Bordeaux.
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Affiliation(s)
- Antonin Douillet
- IFV, UMT SEVEN, Vinopôle, F-33290 Blanquefort, France.,INRAE, Bordeaux Sciences Agro, ISVV, SAVE, F-33140 Villenave d'Ornon, France
| | | | - Jessie Beslay
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, F-33140 Villenave d'Ornon, France
| | - Marie Massot
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Marc Raynal
- IFV, UMT SEVEN, Vinopôle, F-33290 Blanquefort, France
| | - François Delmotte
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, F-33140 Villenave d'Ornon, France
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83
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Sandwich Hybridization Assay for In Situ Real-Time Cyanobacterial Detection and Monitoring: A Review. BIOSENSORS 2022; 12:bios12080640. [PMID: 36005037 PMCID: PMC9405892 DOI: 10.3390/bios12080640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
As cyanobacterial harmful algal bloom (cHAB) events increase in scale, severity, frequency, and duration around the world, rapid and accurate monitoring and characterization tools have become critically essential for regulatory and management decision-making. The composition of cHAB-forming cyanobacteria community can change significantly over time and space and be altered by sample preservation and transportation, making in situ monitoring necessary to obtain real-time and localized information. Sandwich hybridization assay (SHA) utilizes capture oligonucleotide probes for sensitive detection of target-specific nucleic acid sequences. As an amplification-free molecular biology technology, SHA can be adapted for in-situ, real-time or near real-time detection and qualitatively or semi-quantitatively monitoring of cHAB-forming cyanobacteria, owing to its characteristics such as being rapid, portable, inexpensive, and amenable to automation, high sensitivity, specificity and robustness, and multiplexing (i.e., detecting multiple targets simultaneously). Despite its successful application in the monitoring of marine and freshwater phytoplankton, there is still room for improvement. The ability to identify a cHAB community rapidly would decrease delays in cyanotoxin analyses, reduce costs, and increase sample throughput, allowing for timely actions to improve environmental and human health and the understanding of short- and long-term bloom dynamics. Real-time detection and quantitation of HAB-forming cyanobacteria is essential for improving environmental and public health and reducing associated costs. We review and propose to apply SHA for in situ cHABs monitoring.
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84
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Udenze D, Trus I, Berube N, Karniychuk U. CpG content in the Zika virus genome affects infection phenotypes in the adult brain and fetal lymph nodes. Front Immunol 2022; 13:943481. [PMID: 35983032 PMCID: PMC9379343 DOI: 10.3389/fimmu.2022.943481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing the number of CpG dinucleotides in RNA viral genomes, while preserving the original amino acid composition, leads to impaired infection which does not cause disease. Beneficially, impaired infection evokes antiviral host immune responses providing a cutting-edge vaccine approach. For example, we previously showed that CpG-enriched Zika virus variants cause attenuated infection phenotypes and protect against lethal challenge in mice. While CpG recoding is an emerging and promising vaccine approach, little is known about infection phenotypes caused by recoded viruses in vivo, particularly in non-rodent species. Here, we used well-established mouse and porcine models to study infection phenotypes of the CpG-enriched neurotropic and congenital virus—Zika virus, directly in the target tissues—the brain and placenta. Specifically, we used the uttermost challenge and directly injected mice intracerebrally to compare infection phenotypes caused by wild-type and two CpG-recoded Zika variants and model the scenario where vaccine strains breach the blood-brain barrier. Also, we directly injected porcine fetuses to compare in utero infection phenotypes and model the scenario where recoded vaccine strains breach the placental barrier. While overall infection kinetics were comparable between wild-type and recoded virus variants, we found convergent phenotypical differences characterized by reduced pathology in the mouse brain and reduced replication of CpG-enriched variants in fetal lymph nodes. Next, using next-generation sequencing for the whole virus genome, we compared the stability of de novo introduced CpG dinucleotides during prolonged virus infection in the brain and placenta. Most de novo introduced CpG dinucleotides were preserved in sequences of recoded Zika viruses showing the stability of vaccine variants. Altogether, our study emphasized further directions to fine-tune the CpG recoding vaccine approach for better safety and can inform future immunization strategies.
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Affiliation(s)
- Daniel Udenze
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ivan Trus
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Uladzimir Karniychuk,
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85
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Nanoarchitectured nickel phosphate integrated with graphene oxide for the toxicant diphenylamine detection in food samples. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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86
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Nnachi RC, Sui N, Ke B, Luo Z, Bhalla N, He D, Yang Z. Biosensors for rapid detection of bacterial pathogens in water, food and environment. ENVIRONMENT INTERNATIONAL 2022; 166:107357. [PMID: 35777116 DOI: 10.1016/j.envint.2022.107357] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/10/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Conventional techniques (e.g., culture-based method) for bacterial detection typically require a central laboratory and well-trained technicians, which may take several hours or days. However, recent developments within various disciplines of science and engineering have led to a major paradigm shift in how microorganisms can be detected. The analytical sensors which are widely used for medical applications in the literature are being extended for rapid and on-site monitoring of the bacterial pathogens in food, water and the environment. Especially, within the low-resource settings such as low and middle-income countries, due to the advantages of low cost, rapidness and potential for field-testing, their use is indispensable for sustainable development of the regions. Within this context, this paper discusses analytical methods and biosensors which can be used to ensure food safety, water quality and environmental monitoring. In brief, most of our discussion is focused on various rapid sensors including biosensors and microfluidic chips. The analytical performances such as the sensitivity, specificity and usability of these sensors, as well as a brief comparison with the conventional techniques for bacteria detection, form the core part of the discussion. Furthermore, we provide a holistic viewpoint on how future research should focus on exploring the synergy of different sensing technologies by developing an integrated multiplexed, sensitive and accurate sensors that will enable rapid detection for food safety, water and environmental monitoring.
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Affiliation(s)
- Raphael Chukwuka Nnachi
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Ning Sui
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Bowen Ke
- Laboratory of Anesthesiology & Critical Care Medicine, Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan 61004, PR China
| | - Zhenhua Luo
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom
| | - Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern Ireland, United Kingdom; Healthcare Technology Hub, Ulster University, Jordanstown Shore Road, BT37 0QB, Northern Ireland, United Kingdom
| | - Daping He
- School of Science, Wuhan University of Technology, Wuhan 430070, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Milton Keynes MK43, 0AL, United Kingdom.
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87
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Polymer–Metal Composite Healthcare Materials: From Nano to Device Scale. JOURNAL OF COMPOSITES SCIENCE 2022. [DOI: 10.3390/jcs6080218] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Metals have been investigated as biomaterials for a wide range of medical applications. At nanoscale, some metals, such as gold nanoparticles, exhibit plasmonics, which have motivated researchers’ focus on biosensor development. At the device level, some metals, such as titanium, exhibit good physical properties, which could allow them to act as biomedical implants for physical support. Despite these attractive features, the non-specific delivery of metallic nanoparticles and poor tissue–device compatibility have greatly limited their performance. This review aims to illustrate the interplay between polymers and metals, and to highlight the pivotal role of polymer–metal composite/nanocomposite healthcare materials in different biomedical applications. Here, we revisit the recent plasmonic engineered platforms for biomolecules detection in cell-free samples and highlight updated nanocomposite design for (1) intracellular RNA detection, (2) photothermal therapy, and (3) nanomedicine for neurodegenerative diseases, as selected significant live cell–interactive biomedical applications. At the device scale, the rational design of polymer–metallic medical devices is of importance for dental and cardiovascular implantation to overcome the poor physical load transfer between tissues and devices, as well as implant compatibility under a dynamic fluidic environment, respectively. Finally, we conclude the treatment of these innovative polymer–metal biomedical composite designs and provide a future perspective on the aforementioned research areas.
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Prevalence and Risk Factors for Bartonella spp. and Haemoplasma Infections in Cats from Greece. Vet Sci 2022; 9:vetsci9070337. [PMID: 35878354 PMCID: PMC9315813 DOI: 10.3390/vetsci9070337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/19/2022] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Bartonellosis and haemoplasmosis are diseases with global impact on the health of domestic cats and of zoonotic importance. This is the first study investigating the risk factors for Bartonella spp. and haemoplasma species infections in cats from Greece. In addition, this study determined the serologic and molecular prevalence of Bartonella spp. and haemoplasma species infections in different populations of cats living in different regions of Greece. A total of 452 cats were enrolled into the study. Blood was collected from each cat for the serological detection of Bartonella henselae antibodies and the molecular detection of Bartonella spp. and haemoplasma species infections. Overall, the seroprevalence of B. henselae was 35.4%, while the molecular prevalence of Bartonella spp. and haemoplasma species was 2.9% and 19%, respectively. The results of this study indicate that cats with partial or exclusive outdoor access and cats with flea infestation are at the greatest risk for B. henselae seropositivity. Furthermore, cats living in warmer regions such as Attica and Crete are at the greatest risk. Lack of ectoparasiticide use was identified as a risk factor for haemoplasma species infection. This suggests that the use of ectoparasiticides in cats may be an effective means of preventing haemoplasma species infection in cats. Abstract Bartonellosis and haemoplasmosis are vector-borne diseases with global impact on the health of domestic cats and of zoonotic importance. The aim of this study was to describe the epidemiological aspects of various populations of cats infected with Bartonella spp. or haemoplasma species. The populations evaluated included client-owned cats, stray cats and cats that live in breeding catteries in Greece. A total of 452 cats were prospectively enrolled into the study. A commercially available indirect immunofluorescence antibody testkit was used for the detection of Bartonella henselae IgG antibodies in serum. PCRs for the detection of Bartonella spp. and haemoplasma species DNA in the blood were also performed in a subgroup of 242 of the 452 cats. Risk factors for B. henselae seropositivity and infection with the haemoplasma species were determined using multivariable analysis. Overall, 160 (35.4%) of the 452 cats were seropositive for B. henselae. Seven (2.9%) and 46 (19%) of the 242 cats were PCR-positive for Bartonella spp. and haemoplasma species, respectively. The factors associated with B. henselae seropositivity, based on multivariate analysis, included older age, outdoor access, living region and flea infestation. Non-administration of ectoparasiticides was associated with haemoplasma species infection. This study shows a high prevalence of seropositivity for B. henselae and a relatively high prevalence of infection with haemoplasma species. Therefore, it is necessary to establish optimal strategies for the prevention of Bartonella spp. and haemoplasma species infections, considering the high-risk groups of cats identified in this study.
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Lamien-Meda A, Köhsler M, Walochnik J. Real-Time PCR for the Diagnosis of Acanthamoeba Genotype T4. Microorganisms 2022; 10:microorganisms10071307. [PMID: 35889026 PMCID: PMC9325200 DOI: 10.3390/microorganisms10071307] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/14/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023] Open
Abstract
Acanthamoeba spp. are ubiquitous and opportunistic free-living amoebae (FLA) that can cause Acanthamoeba keratitis and other infections in the human host. A quick and efficient diagnosis is often challenging. Our study aimed to establish a qPCR assay to detect and, at the same time, quantify the predominant Acanthamoeba genotype T4. DNA from clinical corneal scrapings and Acanthamoeba reference strains, including genotypes T3, T4, T5, T6, T10, T11, and T12, were used to develop the new T4 assay and it was compared to published protocols and one commercial kit for evaluation. The T4 assay showed no amplification with Acanthamoeba genotypes T3, T5, T6, T10, T11, and T12. The efficiencies ranged from 92.01 to 97.59% (R2 of 0.9768 to 0.9951). The calculated LOD range was 3.63 to 33.27 cells/µL. The protocol published by Qvarnstrom and colleagues was more sensitive compared to the other assays, and an overall good agreement was observed between the new T4 and the Qvarnstrom assays. We successfully developed and validated a genotype T4 assay that could be run in duplex with the Qvarnstrom assay to reliably and simultaneously diagnose Acanthamoeba genotype T4 and other genotypes from clinical samples.
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90
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Fertig TE, Chitoiu L, Marta DS, Ionescu VS, Cismasiu VB, Radu E, Angheluta G, Dobre M, Serbanescu A, Hinescu ME, Gherghiceanu M. Vaccine mRNA Can Be Detected in Blood at 15 Days Post-Vaccination. Biomedicines 2022; 10:biomedicines10071538. [PMID: 35884842 PMCID: PMC9313234 DOI: 10.3390/biomedicines10071538] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
COVID-19 mRNA vaccines effectively reduce incidence of severe disease, hospitalisation and death. The biodistribution and pharmacokinetics of the mRNA-containing lipid nanoparticles (LNPs) in these vaccines are unknown in humans. In this study, we used qPCR to track circulating mRNA in blood at different time-points after BNT162b2 vaccination in a small cohort of healthy individuals. We found that vaccine-associated synthetic mRNA persists in systemic circulation for at least 2 weeks. Furthermore, we used transmission electron microscopy (TEM) to investigate SARS-CoV-2 spike protein expression in human leukemic cells and in primary mononuclear blood cells treated in vitro with the BNT162b2 vaccine. TEM revealed morphological changes suggestive of LNP uptake, but only a small fraction of K562 leukemic cells presented spike-like structures at the cell surface, suggesting reduced levels of expression for these specific phenotypes.
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Affiliation(s)
- Tudor Emanuel Fertig
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (E.R.); (G.A.)
- Correspondence:
| | - Leona Chitoiu
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
| | - Daciana Silvia Marta
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
- Faculty of Medicine, Titu Maiorescu University, 040441 Bucharest, Romania
| | - Victor-Stefan Ionescu
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
| | - Valeriu Bogdan Cismasiu
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
| | - Eugen Radu
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (E.R.); (G.A.)
- Laboratory of Molecular Biology and Pathology Research, Emergency University Hospital Bucharest, 050098 Bucharest, Romania
| | - Giulia Angheluta
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (E.R.); (G.A.)
| | - Maria Dobre
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
| | - Ana Serbanescu
- Cantacuzino NIRDMM-Research and Development Center, 050096 Bucharest, Romania;
| | - Mihail Eugen Hinescu
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (E.R.); (G.A.)
| | - Mihaela Gherghiceanu
- Victor Babeș National Institute of Pathology, 050096 Bucharest, Romania; (L.C.); (D.S.M.); (V.-S.I.); (V.B.C.); (M.D.); (M.E.H.); (M.G.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania; (E.R.); (G.A.)
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91
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Dąbek J, Piotrkowicz J, Głogowska-Ligus J, Domagalska-Szopa M, Szopa A, Schreiber L. Expression of the Endothelin-1 Gene and Its Type a Receptor including Physical Activity among Patients with Acute Myocardial Infarction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:7289. [PMID: 35742539 PMCID: PMC9224255 DOI: 10.3390/ijerph19127289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023]
Abstract
Cardiovascular diseases are the most common causes of death, in both Poland and the world. Their development and progression are largely influenced by the lifestyle with the presence/occurrence of classic, modifiable risk factors. Among them, low physical activity plays a significant role. The aim of the study was to evaluate the expression of the endothelin-1 gene and its type A receptor, taking into account physical activity (International Physical Activity Questionnaire-IPAQ) among patients with acute myocardial infarction. A total of 234 patients with acute myocardial infarction were examined, including 167 patients undergoing early post-hospital cardiac rehabilitation and 67 not participating in it. All of them were assessed with the IPAQ questionnaire and the quantitative real-time polymerase reaction method (QRT-PCR). Physical activity in the group of patients after early post-hospital cardiac rehabilitation increased after rehabilitation. Transcriptional activity of the endothelin-1 (ET-1) gene in both studied group of patients increased significantly, but in a group of patients not participating in early post-hospital cardiac rehabilitation more than in a group of patients participating in it. In our study, the expression of ET-1 was also significantly higher in the group of patients with acute myocardial infarction with ST-segment elevation, without diabetes, with lipid disorders, smoking, with normal body weight. Expression of the ENDRA (Endothelin receptor A) gene increased with age. These results prove the beneficial effect of rehabilitation and may indicate another pathomechanism of pro-atherogenic activity of above-mentioned factors.
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Affiliation(s)
- Józefa Dąbek
- Department of Cardiology, Faculty of Health Sciences in Katowice, Medical University of Silesia in Katowice, Ziołowa Street 45-47, 40-635 Katowice, Poland;
| | - Joanna Piotrkowicz
- Doctoral Studies, Faculty of Health Sciences in Katowice, Medical University of Silesia in Katowice, Medyków Street 12, 40-751 Katowice, Poland;
| | - Joanna Głogowska-Ligus
- Department of Epidemiology, Faculty of Health Science in Bytom, Medical University of Silesia in Katowice, Piekarska 18, 41-902 Bytom, Poland
| | - Małgorzata Domagalska-Szopa
- Department of Medical Rehabilitation, Faculty of Health Sciences in Katowice, Medical University of Silesia in Katowice, Zapolskiej Street 3, 41-218 Sosnowiec, Poland;
| | - Andrzej Szopa
- Department of Physiotherapy, Faculty of Health Sciences in Katowice, Medical University of Silesia in Katowice, Medyków Street 12, 40-751 Katowice, Poland;
| | - Lutz Schreiber
- Department of Neurosurgery Klinikum Vest, Academic Teaching Hospital, Ruhr University Bochum Germany, 44801 Bochum, Germany;
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92
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Considerations regarding Interpretation of Positive SARS-CoV-2 Molecular Results with Late Cycle Threshold Values. J Clin Microbiol 2022; 60:e0050122. [PMID: 35658526 PMCID: PMC9491168 DOI: 10.1128/jcm.00501-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
COVID-19 disease lies on a spectrum, ranging from completely asymptomatic to mild disease to severe and critical disease. Studies have shown that prolonged shedding or sporadic detection of SARS-CoV-2 RNA can occur long after symptom resolution. Adding to these clinical complexities is the demand for testing for SARS-CoV-2 at all stages of diseases, frequently driven by screening of asymptomatic persons, something that traditionally has not been performed for other viral respiratory diseases. This can lead to positive results from nucleic acid amplification tests (NAATs), such as RT-PCR, with late cycle threshold (CT) values near the test’s limit of detection. In this commentary, we review unique attributes of COVID-19 and causes of NAAT late CT values. We provide interpretation considerations as well as strategies to aid in test interpretation.
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93
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Kesavan G, Vinothkumar V, Chen SM, Thangadurai DT. Phosphorus-Doped Graphitic Carbon Nitride: A Metal-Free Electrocatalyst for Quercetin Sensing in Fruit samples. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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94
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Fast and Sensitive Multiplex Real-Time Quantitative PCR to Detect Cutibacterium Periprosthetic Joint Infections. J Mol Diagn 2022; 24:666-673. [PMID: 35364323 DOI: 10.1016/j.jmoldx.2022.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 03/04/2022] [Indexed: 12/26/2022] Open
Abstract
Diagnosis of Cutibacterium periprosthetic joint infections (PJIs) is challenging due to a long cultivation time of up to 14 days. Faster culture-independent diagnosis would improve patient care with early and accurate treatment. Specific primers and probes were designed for Cutibacterium acnes, Cutibacterium avidum, and Cutibacterium granulosum and evaluated in a multiplex TaqMan real-time quantitative PCR (qPCR) format on 57 skin swabs and 20 culture-negative cerebrospinal fluid samples. The multiplex qPCR was tested in a PJI cohort of 41 sonication fluid samples from removed implants infected with different pathogens. All five culture-positive Cutibacterium PJIs were detected with the corresponding Cutibacterium-specific probe (100% positive percent agreement). The multiplex qPCR additionally detected C. avidum in two PJI sonication fluid samples that were diagnosed as Staphylococcus species infections according to culture (95% negative percent agreement). The new multiplex qPCR can provide a Cutibacterium PJI diagnosis within 1 day, allowing early and accurate antibiotic treatment. A prospective diagnostic trial in PJI with a high number of Cutibacterium species infections (shoulder PJI) is needed for further evaluation.
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95
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Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
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Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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96
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2021 White Paper on Recent Issues in Bioanalysis: TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness ( Part 3 - Recommendations on Gene Therapy, Cell Therapy, Vaccine Assays; Immunogenicity of Biotherapeutics and Novel Modalities; Integrated Summary of Immunogenicity Harmonization). Bioanalysis 2022; 14:737-793. [PMID: 35578991 DOI: 10.4155/bio-2022-0081] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The 15th edition of the Workshop on Recent Issues in Bioanalysis (15th WRIB) was held on 27 September to 1 October 2021. Even with a last-minute move from in-person to virtual, an overwhelmingly high number of nearly 900 professionals representing pharma and biotech companies, contract research organizations (CROs), and multiple regulatory agencies still eagerly convened to actively discuss the most current topics of interest in bioanalysis. The 15th WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on biomarker assay development and validation (BAV) (focused on clarifying the confusion created by the increased use of the term "Context of Use - COU"); mass spectrometry of proteins (therapeutic, biomarker and transgene); state-of-the-art cytometry innovation and validation; and, critical reagent and positive control generation were the special features of the 15th edition. This 2021 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2021 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 3) covers the recommendations on TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness. Part 1A (Endogenous Compounds, Small Molecules, Complex Methods, Regulated Mass Spec of Large Molecules, Small Molecule, PoC), Part 1B (Regulatory Agencies' Inputs on Bioanalysis, Biomarkers, Immunogenicity, Gene & Cell Therapy and Vaccine) and Part 2 (ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry) are published in volume 14 of Bioanalysis, issues 9 and 10 (2022), respectively.
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97
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Pecson BM, Darby E, Danielson R, Dearborn Y, Giovanni GD, Jakubowski W, Leddy M, Lukasik G, Mull B, Nelson KL, Olivieri A, Rock C, Slifko T. Distributions of waterborne pathogens in raw wastewater based on a 14-month, multi-site monitoring campaign. WATER RESEARCH 2022; 213:118170. [PMID: 35183914 DOI: 10.1016/j.watres.2022.118170] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
The California State Water Resources Control Board is the first regulatory body in the United States to develop statewide regulations for direct potable reuse (DPR). To support this effort, a pathogen monitoring campaign was undertaken to develop and implement an optimized standard operating protocol to better characterize the concentration of human pathogens in raw wastewater. Methods to detect relevant viral and protozoan pathogens in raw wastewater were optimized and implemented during a 14-month monitoring campaign. Over 120 samples were collected from five wastewater treatment plants treating a quarter of California's population. Samples were analyzed for two protozoa (Cryptosporidium and Giardia) using microscopy methods, three enteric viruses (enterovirus, adenovirus, and norovirus) using culture and/or molecular methods, and male-specific coliphage using culture methods. The method recovery efficiency was measured in every protozoa sample and every other virus sample to confirm minimum recovery efficiencies were achieved and to correct the concentrations for pathogen losses during sample processing. The results from this study provide the industry with a large, high-quality dataset as demonstrated by the high degree of method sensitivity, method recovery, and QA/QC steps. Such high-quality data on pathogen concentrations in raw wastewater are critical for confirming the level of treatment needed to reduce pathogen concentrations down to acceptable levels for potable water in DPR projects.
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Affiliation(s)
| | | | | | | | - George Di Giovanni
- Metropolitan Water District of Southern California, Los Angeles, CA, USA
| | | | - Menu Leddy
- Essential Environmental & Engineering Systems, Huntington Beach, CA, USA
| | | | | | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | | | - Channah Rock
- Department of Environmental Science, University of Arizona, Maricopa, AZ, USA
| | - Theresa Slifko
- Metropolitan Water District of Southern California, Los Angeles, CA, USA
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98
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Ahmed W, Bivins A, Metcalfe S, Smith WJM, Verbyla ME, Symonds EM, Simpson SL. Evaluation of process limit of detection and quantification variation of SARS-CoV-2 RT-qPCR and RT-dPCR assays for wastewater surveillance. WATER RESEARCH 2022; 213:118132. [PMID: 35152136 PMCID: PMC8812148 DOI: 10.1016/j.watres.2022.118132] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/21/2022] [Accepted: 01/29/2022] [Indexed: 05/21/2023]
Abstract
Effective wastewater surveillance of SARS-CoV-2 RNA requires the rigorous characterization of the limit of detection resulting from the entire sampling process - the process limit of detection (PLOD). Yet to date, no studies have gone beyond quantifying the assay limit of detection (ALOD) for RT-qPCR or RT-dPCR assays. While the ALOD is the lowest number of gene copies (GC) associated with a 95% probability of detection in a single PCR reaction, the PLOD represents the sensitivity of the method after considering the efficiency of all processing steps (e.g., sample handling, concentration, nucleic acid extraction, and PCR assays) to determine the number of GC in the wastewater sample matrix with a specific probability of detection. The primary objective of this study was to estimate the PLOD resulting from the combination of primary concentration and extraction with six SARS-CoV-2 assays: five RT-qPCR assays (US CDC N1 and N2, China CDC N and ORF1ab (CCDC N and CCDC ORF1ab), and E_Sarbeco RT-qPCR, and one RT-dPCR assay (US CDC N1 RT-dPCR) using two models (exponential survival and cumulative Gaussian). An adsorption extraction (AE) concentration method (i.e., virus adsorption on membrane and the RNA extraction from the membrane) was used to concentrate gamma-irradiated SARS-CoV-2 seeded into 36 wastewater samples. Overall, the US CDC N1 RT-dPCR and RT-qPCR assays had the lowest ALODs (< 10 GC/reaction) and PLODs (<3,954 GC/50 mL; 95% probability of detection) regardless of the seeding level and model used. Nevertheless, consistent amplification and detection rates decreased when seeding levels were < 2.32 × 103 GC/50 mL even for US CDC N1 RT-qPCR and RT-dPCR assays. Consequently, when SARS-CoV-2 RNA concentrations are expected to be low, it may be necessary to improve the positive detection rates of wastewater surveillance by analyzing additional field and RT-PCR replicates. To the best of our knowledge, this is the first study to assess the SARS-CoV-2 PLOD for wastewater and provides important insights on the analytical limitations for trace detection of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Matthew E Verbyla
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, CA, USA
| | - Erin M Symonds
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
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99
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Oh C, Sashittal P, Zhou A, Wang L, El-Kebir M, Nguyen TH. Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Appl Environ Microbiol 2022; 88:e0228921. [PMID: 35285246 PMCID: PMC9004361 DOI: 10.1128/aem.02289-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monitoring the prevalence of SARS-CoV-2 variants is necessary to make informed public health decisions during the COVID-19 pandemic. PCR assays have received global attention, facilitating a rapid understanding of variant dynamics because they are more accessible and scalable than genome sequencing. However, as PCR assays target only a few mutations, their accuracy could be reduced when these mutations are not exclusive to the target variants. Here we introduce PRIMES, an algorithm that evaluates the sensitivity and specificity of SARS-CoV-2 variant-specific PCR assays across different geographical regions by incorporating sequences deposited in the GISAID database. Using PRIMES, we determined that the accuracy of several PCR assays decreased when applied beyond the geographic scope of the study in which the assays were developed. Subsequently, we used this tool to design Alpha and Delta variant-specific PCR assays for samples from Illinois, USA. In silico analysis using PRIMES determined the sensitivity/specificity to be 0.99/0.99 for the Alpha variant-specific PCR assay and 0.98/1.00 for the Delta variant-specific PCR assay in Illinois, respectively. We applied these two variant-specific PCR assays to six local sewage samples and determined the dominant SARS-CoV-2 variant of either the wild type, the Alpha variant, or the Delta variant. Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Δ156/157, S:L452R, S:T478K, S:P681R, and S:D950N). The consistency between the variant-specific PCR assays and the NGS results supports the applicability of PRIMES. IMPORTANCE Monitoring the introduction and prevalence of variants of concern (VOCs) and variants of interest (VOIs) in a community can help the local authorities make informed public health decisions. PCR assays can be designed to keep track of SARS-CoV-2 variants by measuring unique mutation markers that are exclusive to the target variants. However, the mutation markers may not be exclusive to the target variants because of regional and temporal differences in variant dynamics. We introduce PRIMES, an algorithm that enables the design of reliable PCR assays for variant detection. Because PCR is more accessible, scalable, and robust for sewage samples than sequencing technology, our findings will contribute to improving global SARS-CoV-2 variant surveillance.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Palash Sashittal
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Aijia Zhou
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
| | - Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
- Institute of Genomic Biology, University of Illinois at Urbana-Champaigngrid.35403.31, Urbana, Illinois, USA
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100
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Koventhan C, Vinothkumar V, Chen SM. Rational design of manganese oxide/tin oxide hybrid nanocomposite based electrochemical sensor for detection of prochlorperazine (Antipsychotic drug). Microchem J 2022. [DOI: 10.1016/j.microc.2021.107082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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