1
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Chang Y, Sung JH, Lee SW, Lee EH. Interference-resistant gold nanoparticle assay for detecting Enterococcus in fresh and marine waters. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135463. [PMID: 39173393 DOI: 10.1016/j.jhazmat.2024.135463] [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: 06/03/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
Enterococci are common indicators of fecal contamination and are used to assess the quality of fresh and marine water, sand, soil, and sediment. However, samples collected from these environments contain various cells and other factors that can interfere with the assays used to detect enterococci. We developed a novel assay for the sensitive and specific detection of enterococci that is resistant to interference from other cells and environmental factors. Our interference-resistant assay used 30-nm gold nanoparticles (AuNPs), streptavidin, and a biotinylated Enterococcus antibody. Enterococci inhibited the interaction between streptavidin and biotin and led to the disaggregation of AuNPs. The absence of enterococci led to the aggregation of AuNPs, and this difference was easily detected by spectrophotometry. This interference-resistant AuNP assay was able to detect whole cells of Enterococcus in the range of 10 to 107 CFU/mL within 3 h, had high specificity for enterococci, and was unaffected by the presence of other intestinal bacteria, such as Escherichia coli. Our examination of fresh and marine water samples demonstrated no interference from other cells or environmental factors. The interference-resistant AuNP assay described here has the potential to be used as a rapid, simple, and effective method for monitoring enterococci in diverse environmental samples.
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Affiliation(s)
- Yunsoo Chang
- Department of Microbiology, Pusan National University, 2 Busandaehak-ro 63 Beon-gil, Geumjeong-gu, Busan, Republic of Korea
| | - Ji-Hyeon Sung
- Department of Fine Chemistry, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul, Republic of Korea
| | - Seung-Woo Lee
- Department of Fine Chemistry, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul, Republic of Korea; Department of Nano Bio Engineering, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul, Republic of Korea; Center for Functional Biomaterials, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul, Republic of Korea
| | - Eun-Hee Lee
- Department of Microbiology, Pusan National University, 2 Busandaehak-ro 63 Beon-gil, Geumjeong-gu, Busan, Republic of Korea; Institute for Future Earth, Pusan National University, 2 Busandaehak-ro 63 Beon-gil, Geumjeong-gu, Busan, Republic of Korea.
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2
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Hayes EK, Gagnon GA. From capture to detection: A critical review of passive sampling techniques for pathogen surveillance in water and wastewater. WATER RESEARCH 2024; 261:122024. [PMID: 38986282 DOI: 10.1016/j.watres.2024.122024] [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: 03/21/2024] [Revised: 06/05/2024] [Accepted: 06/29/2024] [Indexed: 07/12/2024]
Abstract
Water quality, critical for human survival and well-being, necessitates rigorous control to mitigate contamination risks, particularly from pathogens amid expanding urbanization. Consequently, the necessity to maintain the microbiological safety of water supplies demands effective surveillance strategies, reliant on the collection of representative samples and precise measurement of contaminants. This review critically examines the advancements of passive sampling techniques for monitoring pathogens in various water systems, including wastewater, freshwater, and seawater. We explore the evolution from conventional materials to innovative adsorbents for pathogen capture and the shift from culture-based to molecular detection methods, underscoring the adaptation of this field to global health challenges. The comparison highlights passive sampling's efficacy over conventional techniques like grab sampling and its potential to overcome existing sampling challenges through the use of innovative materials such as granular activated carbon, thermoplastics, and polymer membranes. By critically evaluating the literature, this work identifies standardization gaps and proposes future research directions to augment passive sampling's efficiency, specificity, and utility in environmental and public health surveillance.
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Affiliation(s)
- Emalie K Hayes
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada
| | - Graham A Gagnon
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia B3H 4R2, Canada.
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3
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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4
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Vanin S, Tuccia F, Pradelli J, Carta G, Giordani G. Identification of Diptera Puparia in Forensic and Archeo-Funerary Contexts. INSECTS 2024; 15:599. [PMID: 39194804 DOI: 10.3390/insects15080599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/28/2024] [Accepted: 07/31/2024] [Indexed: 08/29/2024]
Abstract
Diptera identification is fundamental in forensic entomology as well as in funerary archeoentomology, where the challenge is exacerbated by the presence of immature stages such as larvae and puparia. In these two developmental stages, specimens possess a very limited number of diagnostic features, and for puparia, there is also a lack of identification tools such as descriptions and identification keys. Morphological analysis, DNA-based techniques, and cuticular chemical analyses all show good potential for species identification; however, they also have some limitations. DNA-based identification is primarily hindered by the incompleteness of genetic databases and the presence of PCR inhibitors often co-extracted from the puparial cuticle. Chemical analysis of the cuticle is showing promising results, but this approach is also limited by the insufficient profile database and requires specific, expensive equipment, as well as trained personnel. Additionally, to ensure the repeatability of the analysis-a critical aspect in forensic investigations-and to preserve precious and unique specimens from museum collections, non-invasive protocols and techniques must be prioritized for species identification.
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Affiliation(s)
- Stefano Vanin
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, 16132 Genoa, Italy
- National Research Council, Institute for the Study of Anthropic Impact and Sustainability in the Marine Environment (CNR-IAS), 16149 Genova, Italy
| | - Fabiola Tuccia
- School of applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Jennifer Pradelli
- School of applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Giuseppina Carta
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, 16132 Genoa, Italy
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5
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Dong C, Li F, Sun Y, Long D, Chen C, Li M, Wei T, Martins RP, Chen T, Mak PI. A syndromic diagnostic assay on a macrochannel-to-digital microfluidic platform for automatic identification of multiple respiratory pathogens. LAB ON A CHIP 2024; 24:3850-3862. [PMID: 37961846 DOI: 10.1039/d3lc00728f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The worldwide COVID-19 pandemic has changed people's lives and the diagnostic landscape. The nucleic acid amplification test (NAT) as the gold standard for SARS-CoV-2 detection has been applied in containing its transmission. However, there remains a lack of an affordable on-site detection system at resource-limited areas. In this study, a low cost "sample-in-answer-out" system incorporating nucleic acid extraction, purification, and amplification was developed on a single macrochannel-to-digital microfluidic chip. The macrochannel fluidic subsystem worked as a world-to-chip interface receiving 500-1000 μL raw samples, which then underwent bead-based extraction and purification processes before being delivered to DMF. Electrodes actuate an eluent dispensed to eight independent droplets for reverse transcription quantitative polymerase chain reaction (RT-qPCR). By reading with 4 florescence channels, the system can accommodate a maximum of 32 detection targets. To evaluate the proposed platform, a comprehensive assessment was conducted on the microfluidic chip as well as its functional components (i.e., extraction and amplification). The platform demonstrated a superior performance. In particular, using clinical specimens, the chip targeting SARS-CoV-2 and Flu A/B exhibited 100% agreement with off-chip diagnoses. Furthermore, the fabrication of chips is ready for scaled-up manufacturing and they are cost-effective for disposable use since they are assembled using a printed circuit board (PCB) and prefabricated blocks. Overall, the macrochannel-to-digital microfluidic platform coincides with the requirements of point-of-care testing (POCT) because of its advantages: low-cost, ease of use, comparable sensitivity and specificity, and availability for mass production.
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Affiliation(s)
- Cheng Dong
- School of Intelligent Systems Science and Engineering/JNU-Industry School of Artificial Intelligence, Jinan University, Zhuhai 519000, China
| | - Fei Li
- Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Yun Sun
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Dongling Long
- Zhuhai Center for Disease Control and Prevention, Zhuhai 519087, China
| | - Chunzhao Chen
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhu Hai 519087, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, 07102, USA
| | - Tao Wei
- Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, 510640, China
- Pan Asia (Jiangmen) Institute of Biological Engineering and Health, Jiangmen, 529080, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
| | | | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
- Faculty of Science and Technology, University of Macau, Taipa, Macau SAR, 999078, China
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6
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Sakatoku A, Suzuki T, Hatano K, Seki M, Tanaka D, Nakamura S, Suzuki N, Isshiki T. Inhibitors of LAMP used to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease in Akoya pearl oysters, and additives to reduce the effect of the inhibitors. J Microbiol Methods 2024; 223:106986. [PMID: 38969181 DOI: 10.1016/j.mimet.2024.106986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/30/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024]
Abstract
Black-spot shell disease is an unresolved disease that decreases pearl quality and threatens pearl oyster survival. In previous studies, the bacterium Tenacibaculum sp. strain Pbs-1 was isolated from diseased Akoya pearl oysters Pinctada fucata, and a rapid, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay for detecting this pathogen was established. This technology has considerable potential for routine diagnosis of strain Pbs-1 in oyster hatcheries and/or pearl farms; therefore, it is vital to identify substances in environmental samples that might inhibit LAMP and to find additives that can reduce the inhibition. In this study, we investigated the effects of six chemicals or proteins, otherwise known as conventional PCR inhibitors, on LAMP, using the DNA of strain Pbs-1 as template: humic acid, urea, iron (III) chloride hexahydrate, melanin, myoglobin, and Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA; pH 6.5). Next, to reduce the effects of identified inhibitors, we tested the addition of bovine serum albumin (BSA) or T4 gene 32 protein (gp32) to the LAMP assay. When 50 ng of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, and 10 mM of EDTA (pH 6.5) inhibited the LAMP reaction, whereas myoglobin, urea, and FeCl3 had no effect. When 50 pg of DNA template was used, 4 ng/μL of humic acid, 0.05% melanin, 4 μg/μL of myoglobin, 10 μg/μL of urea, and 10 mM of EDTA inhibited the LAMP reaction. Thus, it was shown that the gene-amplification inhibitory effect of melanin, humic acid, and urea could be reduced by adding BSA or gp32 to the LAMP reaction mixture. This technique could be applied as part of a protocol to prevent mass mortalities of pearl oysters; moreover, the results enhance our knowledge about substances that inhibit LAMP and methods to reduce the inhibition, which have rarely been reported.
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Affiliation(s)
- Akihiro Sakatoku
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan.
| | - Takaya Suzuki
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Kaito Hatano
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan
| | - Makoto Seki
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Daisuke Tanaka
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Shogo Nakamura
- School of Science, Academic Assembly, University of Toyama, Toyama 930-8555, Japan
| | - Nobuo Suzuki
- Noto Marine Laboratory, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa 927-0553, Japan
| | - Tadashi Isshiki
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan
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7
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Adedokun G, Alipanah M, Fan ZH. Sample preparation and detection methods in point-of-care devices towards future at-home testing. LAB ON A CHIP 2024; 24:3626-3650. [PMID: 38952234 PMCID: PMC11270053 DOI: 10.1039/d3lc00943b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Timely and accurate diagnosis is critical for effective healthcare, yet nearly half the global population lacks access to basic diagnostics. Point-of-care (POC) testing offers partial solutions by enabling low-cost, rapid diagnosis at the patient's location. At-home POC devices have the potential to advance preventive care and early disease detection. Nevertheless, effective sample preparation and detection methods are essential for accurate results. This review surveys recent advances in sample preparation and detection methods at POC. The goal is to provide an in-depth understanding of how these technologies can enhance at-home POC devices. Lateral flow assays, nucleic acid tests, and virus detection methods are at the forefront of POC diagnostic technology, offering rapid and sensitive tools for identifying and measuring pathogens, biomarkers, and viral infections. By illuminating cutting-edge research on assay development for POC diagnostics, this review aims to accelerate progress towards widely available, user-friendly, at-home health monitoring tools that empower individuals in personalized healthcare in the future.
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Affiliation(s)
- George Adedokun
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Morteza Alipanah
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, FL 32611, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, FL 32611, USA
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611, USA
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8
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De Silva S, Cagliero C, Gostel MR, Johnson G, Anderson JL. Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility. PLANT METHODS 2024; 20:91. [PMID: 38877523 PMCID: PMC11177442 DOI: 10.1186/s13007-024-01217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND There is a growing demand for fast and reliable plant biomolecular analyses. DNA extraction is the major bottleneck in plant nucleic acid-based applications especially due to the complexity of tissues in different plant species. Conventional methods for plant cell lysis and DNA extraction typically require extensive sample preparation processes and large quantities of sample and chemicals, elevated temperatures, and multiple sample transfer steps which pose challenges for high throughput applications. RESULTS In a prior investigation, an ionic liquid (IL)-based modified vortex-assisted matrix solid phase dispersion approach was developed using the model plant, Arabidopsis thaliana (L.) Heynh. Building upon this foundational study, the present study established a simple, rapid and efficient protocol for DNA extraction from milligram fragments of plant tissue representing a diverse range of taxa from the plant Tree of Life including 13 dicots and 4 monocots. Notably, the approach was successful in extracting DNA from a century old herbarium sample. The isolated DNA was of sufficient quality and quantity for sensitive molecular analyses such as qPCR. Two plant DNA barcoding markers, the plastid rbcL and nuclear ribosomal internal transcribed spacer (nrITS) regions were selected for DNA amplification and Sanger sequencing was conducted on PCR products of a representative dicot and monocot species. Successful qPCR amplification of the extracted DNA up to 3 weeks demonstrated that the DNA extracted using this approach remains stable at room temperature for an extended time period prior to downstream analysis. CONCLUSIONS The method presented here is a rapid and simple approach enabling cell lysis and DNA extraction from 1.5 mg of plant tissue across a broad range of plant taxa. Additional purification prior to DNA amplification is not required due to the compatibility of the extraction solvents with qPCR. The method has tremendous potential for applications in plant biology that require DNA, including barcoding methods for agriculture, conservation, ecology, evolution, and forensics.
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Affiliation(s)
- Shashini De Silva
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Turin, I-10125, Italy
| | - Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, TX, 76107-3400, USA
| | | | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA.
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9
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Ewalt MD, Hsiao SJ. Molecular Methods: Clinical Utilization and Designing a Test Menu. Clin Lab Med 2024; 44:123-135. [PMID: 38821636 DOI: 10.1016/j.cll.2023.08.008] [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: 06/02/2024]
Abstract
Pre-analytical factors in molecular oncology diagnostics are reviewed. Issues around sample collection, storage, and transport that might affect the stability of nucleic acids and the ability to perform molecular testing are addressed. In addition, molecular methods used commonly in clinical diagnostic laboratories, including newer technologies such as next-generation sequencing and digital droplet polymerase chain reaction, as well as their applications, are reviewed. Finally, we discuss considerations in designing a molecular test menu to deliver accurate and timely results in an efficient and cost-effective manner.
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Affiliation(s)
- Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, S-801C, New York, NY 10065, USA
| | - Susan J Hsiao
- Department of Pathology & Cell Biology, Columbia University Medical Center, 630 West 168th Street, P&S16-408CB, New York, NY 10032, USA.
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10
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Sivaganesan M, Willis JR, Diedrich A, Shanks OC. A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements. WATER RESEARCH 2024; 255:121482. [PMID: 38598887 DOI: 10.1016/j.watres.2024.121482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Adam Diedrich
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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11
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Johnson FE, Lerch RN, Motavalli PP, Veum KS, Scharf PC. Comparative analysis of three next-generation sequencing techniques to measure nosZ gene abundance in Missouri claypan soils. ENVIRONMENTAL RESEARCH 2024; 249:118346. [PMID: 38311204 DOI: 10.1016/j.envres.2024.118346] [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: 07/24/2023] [Revised: 01/16/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
Quantitative next-generation sequencing techniques have been critical in gaining a better understanding of microbial ecosystems. In soils, denitrifying microorganisms are responsible for dinitrogen (N2) production. The nosZ gene codes for nitrous oxide reductase, the enzyme facilitating the reduction of nitrous oxide (N2O) to N2. The objectives of this research were to: 1) understand how soil depth influences RNA concentration and nosZ gene abundance; 2) assess the spatial dependence of nosZ gene abundance in two claypan soil fields; and 3) compare and evaluate multiple RNA-based sequencing methods for quantifying nosZ gene abundance in soils in relation to dinitrogen (N2) production. Research sites consisted of two intensively studied claypan soil fields in Central Missouri, USA. Soil cores were collected from two landscape transects across both fields and analyzed for extractable soil RNA at two depths (0-15 cm and 15-30 cm). Measurements of nosZ gene abundance were obtained using real-time quantitative polymerase chain reaction (RT-qPCR), droplet digital polymerase chain reaction (ddPCR), and nanostring sequencing (NS). In both fields, soil RNA concentrations were significantly greater at 0-15 cm depth compared to 15-30 cm. These data indicated low overall soil microbial activity below 15 cm. Due to low quantities of extractable soil RNA in the subsoil, nosZ gene abundance was only determined in the 0-15 cm depth. Sequencing method comparisons of average nosZ gene abundance showed that NS results were constrained to a narrow range and were 10-20-fold lower than ddPCR and RT-qPCR at each landscape position within each field. Droplet digital PCR appears to be the most promising method, as it reflected changes in N2 production across landscape position.
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Affiliation(s)
- Frank E Johnson
- School of Natural Resources, University of Missouri, Columbia, MO, USA; Now at Water Quality and Ecology Research Unit, USDA-ARS, Oxford, MS, USA.
| | - Robert N Lerch
- Cropping Systems and Water Quality Research Unit, USDA-ARS, Columbia, MO, USA
| | - Peter P Motavalli
- School of Natural Resources, University of Missouri, Columbia, MO, USA
| | - Kristen S Veum
- Cropping Systems and Water Quality Research Unit, USDA-ARS, Columbia, MO, USA
| | - Peter C Scharf
- Division of Plant Sciences and Technology, University of Missouri, Columbia, MO, USA
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12
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Mouliou DS. John Cunningham Virus and Progressive Multifocal Leukoencephalopathy: A Falsely Played Diagnosis. Diseases 2024; 12:100. [PMID: 38785755 PMCID: PMC11120163 DOI: 10.3390/diseases12050100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Progressive Multifocal Leukoencephalopathy (PML) is a possibly fatal demyelinating disease and John Cunningham Polyomavirus (JCPyV) is believed to cause this condition. The so-called JCPyV was initially reported in lymphoma and Human Immunodeficiency Virus (HIV) cases, whereas nowadays, its incidence is increasing in Multiple Sclerosis (MS) cases treated with natalizumab (Tysabri). However, there are conflicting literature data on its pathology and diagnosis, whereas some misdiagnosed reports exist, giving rise to further questions towards the topic. In reality, the so-called PML and the supposed JCPyV are not what they seem to be. In addition, novel and more frequent PML-like conditions may be reported, especially after the Coronavirus Disease 2019 (COVID-19) pandemic.
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13
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Spurlock N, Gabella WE, Nelson DJ, Evans DT, Pask ME, Schmitz JE, Haselton FR. Implementing L-DNA analogs as mirrors of PCR reactant hybridization state: theoretical and practical guidelines for PCR cycle control. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2840-2849. [PMID: 38567817 PMCID: PMC11079981 DOI: 10.1039/d4ay00083h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/22/2024] [Indexed: 05/12/2024]
Abstract
In previous reports, we described a PCR cycle control approach in which the hybridization state of optically labeled L-DNA enantiomers of the D-DNA primers and targets determined when the thermal cycle was switched from cooling to heating and heating to cooling. A consequence of this approach is that it also "adapts" the cycling conditions to compensate for factors that affect the hybridization kinetics of primers and targets. It assumes, however, that the hybridization state of the labeled L-DNA analogs accurately reflects the hybridization state of the D-DNA primers and targets. In this report, the Van't Hoff equation is applied to determine the L-DNA concentration and ratio of L-DNA strands required by this assumption. Simultaneous fluorescence and temperature measurements were taken during L-DNA controlled cycling, and the optical and thermal switch points compared as a function of both total L-DNA concentration and ratio of strands. Based on the Van't Hoff relationship and these experimental results, L-DNA best mirrors the hybridization of PCR primers and targets when total L-DNA concentration is set equal to the initial concentration of the D-DNA primer of interest. In terms of strand ratios, L-DNA hybridization behavior most closely matches the behavior of their D-DNA counterparts throughout the reaction when one of the L-DNA strands is far in excess of the other. The L-DNA control algorithm was then applied to the practical case of the SARS-CoV-2 N2 reaction, which has been shown to fail or have a delayed Cq when PCR was performed without nucleic acid extraction. PCR Cq values for simulated "unextracted" PCR samples in a nasopharyngeal background and in an NaCl concentration similar to that of viral transport media were determined using either the L-DNA control algorithm (N = 6) or preset cycling conditions (N = 3) and compared to water background controls run in parallel. For preset cycling conditions, the presence of nasopharyngeal background or a high salt background concentration significantly increased Cq, but the L-DNA control algorithm had no significant delay. This suggests that a carefully designed L-DNA-based control algorithm "adapts" the cycling conditions to compensate for hybridization errors of the PCR D-DNA reactants that produce false negatives.
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Affiliation(s)
- Nicholas Spurlock
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - William E Gabella
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, USA
| | - Dalton J Nelson
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - David T Evans
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - Megan E Pask
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - Jonathan E Schmitz
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
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14
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Bonsu DNO, Higgins D, Simon C, Henry JM, Austin JJ. Metal-DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis. Electrophoresis 2024; 45:779-793. [PMID: 37638716 DOI: 10.1002/elps.202300070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 08/29/2023]
Abstract
Forensic DNA analysis continues to be hampered by the complex interactions between metals and DNA. Metal ions may cause direct DNA damage, inhibit DNA extraction and polymerase chain reaction (PCR) amplification or both. This study evaluated the impact of metal ions on DNA extraction, quantitation, and short tandem repeat profiling using cell-free and cellular (saliva) DNA. Of the 11 metals assessed, brass exhibited the strongest PCR inhibitory effects, for both custom and Quantifiler Trio quantitation assays. Metal ion inhibition varied across the two quantitative PCR assays and the amount of DNA template used. The Quantifiler Trio internal PCR control (IPC) only revealed evidence of PCR inhibition at higher metal ion concentrations, limiting the applicability of IPC as an indicator of the presence of metal inhibitor in a sample. Notably, ferrous ions were found to significantly decrease the extraction efficiency of the DNA-IQ DNA extraction system. The amount of DNA degradation and inhibition in saliva samples caused by metal ions increased with a dilution of the sample, suggesting that the saliva matrix provides protection from metal ion effects.
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Affiliation(s)
- Dan Nana Osei Bonsu
- Chemistry and Forensic Science, School of Environment and Science, Griffith University, Nathan, Queensland, Australia
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Denice Higgins
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- School of Dentistry, Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Claire Simon
- Forensic Science SA, Attorney-General's Department, Adelaide, South Australia, Australia
| | - Julianne M Henry
- Forensic Science SA, Attorney-General's Department, Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Forensic Research Group, Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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15
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Velloso Alvarez A, Jose-Cunilleras E, Dorrego-Rodriguez A, Santiago-Llorente I, de la Cuesta-Torrado M, Troya-Portillo L, Rivera B, Vitale V, de Juan L, Cruz-Lopez F. Detection of equine herpesvirus-1 (EHV-1) in urine samples during outbreaks of equine herpesvirus myeloencephalopathy. Equine Vet J 2024; 56:456-463. [PMID: 37699794 DOI: 10.1111/evj.14007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
BACKGROUND Real-time PCR is the diagnostic technique of choice for the diagnosis and control of equine herpesvirus-1 (EHV-1) in an outbreak setting. The presence of EHV-1 in nasal swabs (NS), whole blood, brain and spinal cord samples has been extensively described; however, there are no reports on the excretion of EHV-1 in urine, its DNA detection patterns, and the role of urine in viral spread during an outbreak. OBJECTIVES To determine the presence of EHV-1 DNA in urine during natural infection and to compare the DNA detection patterns of EHV-1 in urine, buffy coat (BC) and NS. STUDY DESIGN Descriptive study of natural infection. METHODS Urine and whole blood/NS samples were collected at different time points during the hospitalisation of 21 horses involved in two EHV-1 myeloencephalopathy outbreaks in 2021 and 2023 in Spain. Quantitative real-time PCR was performed to compare the viral DNA load between BC-urine samples in 2021 and NS-urine samples in 2023. Sex, age, breed, presence of neurological signs, EHV-1 vaccination status and treatment data were recorded for all horses. RESULTS A total of 18 hospitalised horses during the 2021 and 2023 outbreaks were positive for EHV-1, and viral DNA was detected in urine samples from a total of 11 horses in both outbreaks. Compared with BC samples, DNA presence was detected in urine samples for longer duration and with slightly higher concentration; however, compared with NS, detection of EHV-1 in urine was similar in duration with lower DNA concentrations. MAIN LIMITATIONS Limited sample size, different sampling times and protocols (BC vs. NS) in two natural infection outbreak settings. CONCLUSIONS EHV-1 was detected in the urine from naturally infected horses. Urine should be considered as complimentary to blood and NS in diagnosis of EHV-1 infection.
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Affiliation(s)
| | - E Jose-Cunilleras
- Unitat Equina, Fundació Hospital Clínic Veterinari, Cerdañola del Valles, Spain
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Cerdañola del Valles, Spain
| | | | | | | | - Lucas Troya-Portillo
- Unitat Equina, Fundació Hospital Clínic Veterinari, Cerdañola del Valles, Spain
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Cerdañola del Valles, Spain
| | - Belen Rivera
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain
| | | | - Lucia de Juan
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain
- Animal Health Department, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Fatima Cruz-Lopez
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain
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16
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Bachoon DS, Redhead ASZ, Mead AJ. Mitochondrial DNA marker: A PCR approach for tracking rat (Rattus rattus and Rattus norvegicus) fecal pollution in surface water systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171164. [PMID: 38402984 DOI: 10.1016/j.scitotenv.2024.171164] [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: 11/16/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
Rats act as reservoirs for a wide range of zoonotic pathogens and can negatively impact human health. In this study, we developed a novel dye base mitochondrial DNA (mtDNA) PCR-assay (RatMt) specifically targeting a 180 bp fragment of the NADH dehydrogenase subunit 2 gene for detecting fecal pollution from two species of rats (Rattus rattus and Rattus norvegicus) in environmental samples. Estimation of Escherichia coli concentrations in Rattus norvegicus fecal pellets suggested that there were approximately 2.24 × 10 4 ± 4.86 × 103 MPN/g of fecal pellet. The RatMt PCR assay was robust, had a detection limit of rat feces in water of 0.274 ± 0.14 mg/100 mL and was 100 % specific for detecting Rattus rattus and Rattus norvegicus fecal mtDNA. Fecal Indicator Bacteria (FIB) along an urbanized gradient in Pensacola-Bay was assessed by the IDEXX Colilert™ - 18 and indicated that the majority of the fifteen sampling sites in the Pensacola-Bay area had E. coli concentrations >410 MPN/100 mL. Rattus rattus and Rattus norvegicus mtDNA were detected in all the urban marine sites, three of the urban freshwater sampling areas, and three of the forested sampling sites. The RatMt PCR assay is a useful tool for rapidly detecting Rattus rattus and Rattus norvegicus fecal pollution in environmental samples.
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Affiliation(s)
- Dave S Bachoon
- Department of Biological and Environmental Sciences, Georgia College & State University, Campus Box 81, Milledgeville, GA 31061-0490, USA.
| | - Aaden S Z Redhead
- Department of Biological and Environmental Sciences, Georgia College & State University, Campus Box 81, Milledgeville, GA 31061-0490, USA
| | - Alfred J Mead
- Department of Biological and Environmental Sciences, Georgia College & State University, Campus Box 81, Milledgeville, GA 31061-0490, USA
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17
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Kelly LA, Yost CK, Cooke SJ. Opportunities and challenges with transitioning to non-lethal sampling of wild fish for microbiome research. JOURNAL OF FISH BIOLOGY 2024; 104:912-919. [PMID: 38226503 DOI: 10.1111/jfb.15650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The microbial communities of fish are considered an integral part of maintaining the overall health and fitness of their host. Research has shown that resident microbes reside on various mucosal surfaces, such as the gills, skin, and gastrointestinal tract, and play a key role in various host functions, including digestion, immunity, and disease resistance. A second, more transient group of microbes reside in the digesta, or feces, and are primarily influenced by environmental factors such as the host diet. The vast majority of fish microbiome research currently uses lethal sampling to analyse any one of these mucosal and/or digesta microbial communities. The present paper discusses the various opportunities that non-lethal microbiome sampling offers, as well as some inherent challenges, with the ultimate goal of creating a sound argument for future researchers to transition to non-lethal sampling of wild fish in microbiome research. Doing so will reduce animal welfare and population impacts on fish while creating novel opportunities to link host microbial communities to an individual's behavior and survival across space and time (e.g., life-stages, seasons). Current lethal sampling efforts constrain our ability to understand the mechanistic ecological consequences of variation in microbiome communities in the wild. Transitioning to non-lethal sampling will open new frontiers in ecological and microbial research.
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Affiliation(s)
- Lisa A Kelly
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Christopher K Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, Saskatchewan, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
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18
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Chen Q, Wu J, Tang C, Wang Y. CRISPR-based platforms for the specific and dual detection of defoliating/nondefoliating strains of Verticillium dahliae. PEST MANAGEMENT SCIENCE 2024; 80:2042-2052. [PMID: 38117128 DOI: 10.1002/ps.7940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Verticillium dahliae is a soil-borne pathogenic fungus that causes Verticillium wilt disease on more than 400 plant species worldwide. Because of its broad host range and its ability to survive long term in the soil, there are few effective control measures for V. dahliae once it has become established. Accurate, sensitive, and rapid detection of V. dahliae is crucial for limiting pathogen entry into new regional environments and early management of Verticillium wilt. RESULTS In this study, we developed a method to detect V. dahliae based on recombinase polymerase amplification (RPA) and CRISPR/Cas technology and used fluorescence and lateral flow test strips to monitor the outcomes. Through the establishment and optimization of RPA-CRISPR/Cas13a detection, the sensitivity of the fluorescence method was 1 am for genomic DNA (gDNA) within 20 min, whereas the sensitivity of the lateral flow strip method was 100 am for gDNA in 30 min. The field applicability of RPA-CRISPR/Cas13a was also validated by the detection of V. dahliae on smoke trees (Cotinus coggygria) in Xiangshan Park, Beijing, China. Finally, diplex detection for defoliating and nondefoliating pathotypes of V. dahliae was established by combining CRISPR-Cas12a/Cas13a with specific target genes. CONCLUSION Taken together, this study achieved rapid, sensitive, and accurate detection of V. dahliae and the differentiation of defoliating and nondefoliating pathotypes and provides potential for field-deployable diagnostic tools for rapid and ultrasensitive detection. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Qi Chen
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Jin Wu
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Chen Tang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Yonglin Wang
- State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, Beijing, China
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19
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Zhang Y, Tian G, Sun X, Yang X, Zhang Y, Tan W, Duan L, Gao S, Yu J. Ultrasensitive colorimetric detection of Staphylococcus aureus using wheat germ agglutinin and IgY as a dual-recognition strategy. Mikrochim Acta 2024; 191:209. [PMID: 38499840 DOI: 10.1007/s00604-024-06288-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
A novel colorimetric platform was designed for the determination of S. aureus by utilizing a dual-recognition strategy, where wheat germ agglutinin (WGA)-functionalized magnetic beads were served as separation elements to capture and enrich S. aureus efficiently from the matrix. Horseradish peroxidase (HRP) labeled chicken anti-protein A IgY (HRP-IgY) was used to label the captured S. aureus. A chicken IgY was introduced as a signal tracer to bind with staphylococcal protein A (SPA) on the surface of S. aureus, which can circumvent the interference from protein G-producing Streptococcus. Subsequently, the colorimetric signal was achieved by an HRP-catalyzed reaction, which was amplified by HRP-IgY bound by approximately 80,000 SPA molecules on one S. aureus. The entire detection process could be accomplished within 90 min. Under optimal conditions, the linear response of different S. aureus concentrations ranged from 7.8 × 102 to 2.0 × 105 CFU/mL and the limit of detection reached down to 3.9 × 102 CFU/mL. Some common non-target bacteria yielded negative results, indicating the excellent specificity of the method. The developed strategy was successfully applied to the determination of S. aureus in various types of samples with satisfactory recoveries. Therefore, the novel dual-recognition strategy possessed the advantages of high sensitivity, specificity, and low cost and exhibited considerable potential as a promising tool to defend public health.
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Affiliation(s)
- Yun Zhang
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Ge Tian
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Xueni Sun
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Xiaoli Yang
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Yi Zhang
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Wenqing Tan
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China
| | - Liangwei Duan
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China.
| | - Shunxiang Gao
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, People's Republic of China.
| | - Junping Yu
- Laboratory of Infection and Immunology, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, People's Republic of China.
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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20
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Zhang Z, Chen B, Luo Y. A Deep Ensemble Dynamic Learning Network for Corona Virus Disease 2019 Diagnosis. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2024; 35:3912-3926. [PMID: 36054386 DOI: 10.1109/tnnls.2022.3201198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Corona virus disease 2019 is an extremely fatal pandemic around the world. Intelligently recognizing X-ray chest radiography images for automatically identifying corona virus disease 2019 from other types of pneumonia and normal cases provides clinicians with tremendous conveniences in diagnosis process. In this article, a deep ensemble dynamic learning network is proposed. After a chain of image preprocessing steps and the division of image dataset, convolution blocks and the final average pooling layer are pretrained as a feature extractor. For classifying the extracted feature samples, two-stage bagging dynamic learning network is trained based on neural dynamic learning and bagging algorithms, which diagnoses the presence and types of pneumonia successively. Experimental results manifest that using the proposed deep ensemble dynamic learning network obtains 98.7179% diagnosis accuracy, which indicates more excellent diagnosis effect than existing state-of-the-art models on the open image dataset. Such accurate diagnosis effects provide convincing evidences for further detections and treatments.
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21
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Armstrong CM, Capobianco JA, Lee J. Magnetic capture device for large volume sample analysis. PLoS One 2024; 19:e0297806. [PMID: 38335195 PMCID: PMC10857679 DOI: 10.1371/journal.pone.0297806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
Immunomagnetic separation (IMS) techniques employing superparamagnetic particles can successfully isolate various components from mixtures. However, their utility can be limited for large-volume samples, viscous samples, or those containing a high density of particulate matter because of the need to generate high field gradients for particle recovery. Therefore, a new class of immunomagnetic particles was devised utilizing a single, macroscopic Pyrex spinbar conjugated with biorecognition elements to address these limitations. Advantages include an inherent capacity for effective mixing, an almost instantaneous recovery of the spinbar that can be performed without expensive equipment and with no loss of magnetic particles during processing, and reduced transfer of sample matrix. As a result, spinbars can provide an effective means for IMS with large-volume assays composed of complex matrices.
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Affiliation(s)
- Cheryl M. Armstrong
- United States Department of Agriculture, Agriculture Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Joseph A. Capobianco
- United States Department of Agriculture, Agriculture Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Joe Lee
- United States Department of Agriculture, Agriculture Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
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22
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Foysal MJ, Salgar-Chaparro SJ. Improving the efficiency of DNA extraction from iron incrustations and oilfield-produced water. Sci Rep 2024; 14:2954. [PMID: 38316948 PMCID: PMC10844625 DOI: 10.1038/s41598-024-53134-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024] Open
Abstract
The quantity and quality of DNA isolated from environmental samples are crucial for getting robust high-throughput sequencing data commonly used for microbial community analysis. The differences in the nature and physicochemical properties of environmental samples impact DNA yields, and therefore, an optimisation of the protocols is always recommended. For instance, samples collected from corroded areas contain high concentrations of metals, salts, and hydrocarbons that can interfere with several steps of the DNA extraction protocols, thereby reducing yield and quality. In this study, we compared the efficiency of commercially available DNA extraction kits and laboratory-adopted methods for microbial community analysis of iron incrustations and oilfield-produced water samples. Modifications to the kits manufacturers' protocols were included to maximise the yield and quality. For iron incrustations, the modified protocol for FastDNA Spin Kit for Soil yielded higher DNA and resulted in higher diversity, including the recovery of low-abundant and rare taxa in the samples, compared to DNeasy PowerSoil Pro Kit. The DNA extracted with modified phenol-chloroform methods yielded higher DNA but failed to pass quality control PCR for 16S sequencing with and without purification. The protocols mentioned here can be used to maximise DNA recovery from iron incrustations and oilfield-produced water samples.
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Affiliation(s)
- Md Javed Foysal
- Curtin Corrosion Centre, Western Australian School of Mines, Minerals and Energy, Curtin University, Bentley, WA, Australia
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Silvia J Salgar-Chaparro
- Curtin Corrosion Centre, Western Australian School of Mines, Minerals and Energy, Curtin University, Bentley, WA, Australia.
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23
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Chauhan G, Arya M, Kumar V, Verma D, Sharma M. An improved protocol for metagenomic DNA isolation from low microbial biomass alkaline hot-spring sediments and soil samples. 3 Biotech 2024; 14:34. [PMID: 38188309 PMCID: PMC10769977 DOI: 10.1007/s13205-023-03824-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/25/2023] [Indexed: 01/09/2024] Open
Abstract
High-quality, humic-acid-free pure DNA is a prerequisite for functional and sequence-based approaches of metagenomics. In the present investigation, an improved extraction buffer was developed by making a combination of powdered activated charcoal (2%; w/v), polyvinyl poly pyrrolidone (2%; w/v), and CaCl2 (2%; w/v). This trio significantly improved the purity and yield of the metagenomic DNA from the hot spring's hot and alkaline soil. The quality of extracted metagenomic DNA was successfully validated by PCR amplification and restriction enzymes. Besides, the thermophilic amylase encoding genes were also retrieved from these soil DNA samples. Extreme habitats I harbour low microbial biomass and, therefore, demand in-situ lysis of the microbial cells to access their genomes. The protocol can potentially extract DNA from geothermal spring habitats where the count of microbial cells is low.
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Affiliation(s)
- Garima Chauhan
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
| | - Meghna Arya
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
| | - Vikas Kumar
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
| | - Monica Sharma
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
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24
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Lau M, King BJ, Keegan A, Drigo B, Donner E, Monis P. Comparison of kits for SARS-CoV-2 extraction in liquid and passive samples. Lett Appl Microbiol 2023; 76:ovad136. [PMID: 38066699 DOI: 10.1093/lambio/ovad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/19/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Effective extraction and detection of viral nucleic acids from sewage are fundamental components of a successful SARS-CoV-2 sewage surveillance programme. As there is no standard method employed in sewage surveillance, understanding the performance of different extraction kits in the recovery of SARS-CoV-2 and the impact that PCR inhibitors have on quantification is essential to minimize data discrepancies caused by sample extraction. Three commercial nucleic acid extraction kits: the RNeasy PowerSoil Total RNA Kit (PS), the RNeasy PowerMicrobiome Kit (PMB), and the MagMAX™ Microbiome Ultra Nucleic Acid Isolation Kit (MM), with minor modifications, were evaluated. Their efficacy in recovering viral ribonucleic acid and removal of PCR inhibitors was assessed using two South Australian wastewater matrices-one from a major metropolitan site and one from a regional centre. Both had SARS-CoV-2 present due to active COVID-19 cases in these communities. Overall, the MM kit had a higher recovery of SARS-CoV-2 from the samples tested, followed by PMB and PS. The PMB kit performance was strongly influenced by the sample matrix when compared to the MM kit. It is recommended to assess the performance of extraction kits using different local wastewater matrices to ensure the accuracy and reliability of monitoring results to avoid false reporting.
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Affiliation(s)
- Melody Lau
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
| | - Brendon J King
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
| | - Alexandra Keegan
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
- UniSA STEM, University of South Australia, Adelaide, SA 5001, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
- Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, SA 5001, Australia
| | - Paul Monis
- SA Water Utility, 250 Victoria Square, Adelaide SA 5000, Australia
- Future Industries Institute, University of South Australia, Adelaide, SA, 5001, Australia
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25
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Park SM, Choi C, Rhee MS. Cultivation-free sample preparation and DNA purification for direct real-time qPCR of intracellular or spore-like Coxiella burnetii in beef, goat, and lamb meat. Food Res Int 2023; 173:113312. [PMID: 37803623 DOI: 10.1016/j.foodres.2023.113312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 10/08/2023]
Abstract
Coxiella burnetii is a zoonotic pathogen that has been associated with foodborne outbreaks in products with ruminant origins. However, a method to detect C. burnetii in meat has been merely studied, and commercial kits cannot efficiently fulfill this purpose. In this study, an in-house preparation method for direct real-time qPCR of C. burnetii in beef, goat, and lamb meat was designed. In the sample preparation step (step 1), trypsin digestion and cell disruption techniques were introduced to target C. burnetii in an obligate intracellular or spore-like form. Afterward, 16 DNA purification protocols involving the following steps (steps 2-3) were assessed: the precipitation of meat proteins (step 2; using 2.5, 5.0 M NaCl or 1:1, 2:1 ethanol as the precipitant) and binding of DNA to silicon dioxide particles with chaotropic salts (step 3; using 2.5, 5.0 M NaCl or 2.5, 5.0 M guanidine thiocyanate as the salt). The protocols with superior performance in high-spiked loins (estimated 4-5 log cells/g) were verified in low-spiked (1-2 log cells/g) or Bacillus thuringiensis spore-inoculated (1-2 log CFU/g) loins, ribs, and hind legs. During the protein precipitation, 5.0 M NaCl induced significantly lower protein level as demonstrated by A280, when compared to 2.5 M NaCl or ethanol (P < 0.05). For the DNA binding step, Ct values were lowered in high-spiked goat or lamb loins (3.5-6.0▾; P < 0.05) when the concentration of NaCl was doubled or guanidine thiocyanate was introduced instead of NaCl as a chaotropic salt. Based on these results, two protocols using 5.0 M NaCl as the protein precipitant and 5.0 M NaCl (N2 + N2) or guanidine thiocyanate (N2 + G2) as the chaotropic salt were selected, which demonstrated successful detection in low-spiked (Ct values of N2 + N2, 32.9-35.6; N2 + G2, 32.3-36.4) or spore-inoculated meat (N2 + N2, 30.9-37.5; N2 + G2, 29.7-32.7). Verification in low-spiked meat showed that meat type/part significantly impacted the Ct values of N2 + G2 but not those of N2 + N2. To our knowledge, this is the first study that developed a highly accessible method for detecting C. burnetii in meat which could reveal the possibility of meat-borne Q fever in humans.
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Affiliation(s)
- Sun Min Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Changsun Choi
- Department of Food and Nutrition, School of Food Science and Technology, Chung-Ang University, Gyeonggi Province 17546, Republic of Korea
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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26
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Alex-Sanders N, Woodhall N, Farkas K, Scott G, Jones DL, Walker DI. Development and validation of a duplex RT-qPCR assay for norovirus quantification in wastewater samples. J Virol Methods 2023; 321:114804. [PMID: 37643662 DOI: 10.1016/j.jviromet.2023.114804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 08/31/2023]
Abstract
Norovirus (NoV) is a highly contagious enteric virus that causes widespread outbreaks and a substantial number of deaths across communities. As clinical surveillance is often insufficient, wastewater-based epidemiology (WBE) may provide novel pathways of tracking outbreaks. To utilise WBE, it is important to use accurate and sensitive methods for viral quantification. In this study, we developed a one-step duplex RT-qPCR assay to simultaneously test the two main human pathogenic NoV genogroups, GI and GII, in wastewater samples. The assay had low limits of detection (LOD), namely 0.52 genome copies (gc)/µl for NoVGI and 1.37 gc/µl for NoVGII. No significant concentration-dependent interactions were noted for both NoVGI and for NoVGII when the two targets were mixed at different concentrations in the samples. When tested on wastewater-derived RNA eluents, no significant difference between duplex and singleplex concentrations were found for either target. Low levels of inhibition (up to 32 %) were noted due to organic matter present in the wastewater extracts. From these results we argue that the duplex RT-qPCR assay developed enables the sensitive detection of both NoVGI and NoVGII in wastewater-derived RNA eluents, in a time and cost-effective way and may be used for surveillance to monitor public and environmental health.
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Affiliation(s)
| | - Nick Woodhall
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - George Scott
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
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27
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Li J, Li Y, Li Y, Ma Y, Xu W, Wang J. An enhanced activity and thermostability of chimeric Bst DNA polymerase for isothermal amplification applications. Appl Microbiol Biotechnol 2023; 107:6527-6540. [PMID: 37672070 DOI: 10.1007/s00253-023-12751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a widely used method for clinical diagnosis, customs quarantine, and disease prevention. However, the low catalytic activity of Bst DNA polymerase has made it challenging to develop rapid and reliable point-of-care testing. Herein, we developed a series of Bst DNA polymerase mutants with enhanced activity by predicting and analyzing the activity sites. Among these mutants, single mutants K431D and K431E showed a 1.93- and 2.03-fold increase in catalytic efficiency, respectively. We also created a chimeric protein by fusing the DNA-binding domain of DNA ligase from Pyrococcus abyssi (DBD), namely DBD-K431E, which enabled real-time LAMP at high temperatures up to 73 ℃ and remained active after heating at 70 ℃ for 8 h. The chimeric DBD-K431E remained active in the presence of 50 U/mL heparin, 10% ethanol, and up to 100 mM NaCl, and showed higher activity in 110 mM (NH4)2SO4, 110 mM KCl, and 12 mM MgSO4. Notably, it generated a fluorescence signal during the detection of Salmonella typhimurium at 2 × 102 ag/μL of genomic DNA and 1.24 CFU/mL of bacterial colony, outperforming the wild type and the commercial counterpart Bst 2.0. Our results suggest that the DBD-K431E variant could be a promising tool for general molecular biology research and clinical diagnostics. KEY POINTS: • Residue K431 is probably a key site of Bst DNA polymerase activity • The chimeric DBD-K431E is more inhibitor tolerant and thermostable than Bst-LF • The DBD-K431E variant can detect Salmonella typhimurium at 102 ag/μL or 100 CFU/mL.
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Affiliation(s)
- Jiaxuan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yanmei Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Wei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, China.
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28
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Sharma N, Neill T, Yang HC, Oliver CL, Mahaffee WF, Naegele R, Moyer MM, Miles TD. Development of a PNA-LNA-LAMP Assay to Detect an SNP Associated with QoI Resistance in Erysiphe necator. PLANT DISEASE 2023; 107:3238-3247. [PMID: 37005502 DOI: 10.1094/pdis-09-22-2027-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The repetitive use of quinone outside inhibitor fungicides (QoIs, strobilurins; Fungicide Resistance Action Committee [FRAC] 11) to manage grape powdery mildew has led to development of resistance in Erysiphe necator. While several point mutations in the mitochondrial cytochrome b gene are associated with resistance to QoI fungicides, the substitution of glycine to alanine at codon 143 (G143A) has been the only mutation observed in QoI-resistant field populations. Allele-specific detection methods such as digital droplet PCR and TaqMan probe-based assays can be used to detect the G143A mutation. In this study, a peptide nucleic acid-locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA-LAMP) assay consisting of an A-143 reaction and a G-143 reaction, was designed for rapidly detecting QoI resistance in E. necator. The A-143 reaction amplifies the mutant A-143 allele faster than the wild-type G-143 allele, while the G-143 reaction amplifies the G-143 allele faster than the A-143 allele. Identification of resistant or sensitive E. necator samples was determined by which reaction had the shorter time to amplification. Sixteen single-spore QoI-resistant and -sensitive E. necator isolates were tested using both assays. Assay specificity in distinguishing the single nucleotide polymorphism (SNP) approached 100% when tested using purified DNA of QoI-sensitive and -resistant E. necator isolates. This diagnostic tool was sensitive to one-conidium equivalent of extracted DNA with an R2 value of 0.82 and 0.87 for the G-143 and A-143 reactions, respectively. This diagnostic approach was also evaluated against a TaqMan probe-based assay using 92 E. necator samples collected from vineyards. The PNA-LNA-LAMP assay detected QoI resistance in ≤30 min and showed 100% agreement with the TaqMan probe-based assay (≤1.5 h) for the QoI-sensitive and -resistant isolates. There was 73.3% agreement with the TaqMan probe-based assay when samples had mixed populations with both G-143 and A-143 alleles present. Validation of the PNA-LNA-LAMP assay was conducted in three different laboratories with different equipment. The results showed 94.4% accuracy in one laboratory and 100% accuracy in two other laboratories. The PNA-LNA-LAMP diagnostic tool was faster and required less expensive equipment relative to the previously developed TaqMan probe-based assay, making it accessible to a broader range of diagnostic laboratories for detection of QoI resistance in E. necator. This research demonstrates the utility of the PNA-LANA-LAMP for discriminating SNPs from field samples and its utility for point-of-care monitoring of plant pathogen genotypes.
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Affiliation(s)
- Nancy Sharma
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI
| | - Tara Neill
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR
| | - Hui-Ching Yang
- USDA-ARS Crop Diseases, Pests and Genetics Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA
| | - Charlotte L Oliver
- Department of Horticulture, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA
| | - Walter F Mahaffee
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR
| | - Rachel Naegele
- USDA-ARS Crop Diseases, Pests and Genetics Unit, San Joaquin Valley Agricultural Sciences Center, Parlier, CA
| | - Michelle M Moyer
- Department of Horticulture, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA
| | - Timothy D Miles
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI
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Hess J, Kreitlow A, Rohn K, Hennig-Pauka I, Abdulmawjood A. Rapid Diagnostic of Streptococcus suis in Necropsy Samples of Pigs by thrA-Based Loop-Mediated Isothermal Amplification Assay. Microorganisms 2023; 11:2447. [PMID: 37894105 PMCID: PMC10608932 DOI: 10.3390/microorganisms11102447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Streptococcus (S.) suis presents a serious threat to the pig industry as well as food safety and public health. Although several LAMP assays have been developed for the identification of S. suis, no universal assay is so far available for the field-suitable examination of clinical pig specimens. Based on the thrA housekeeping gene, a new loop-mediated isothermal amplification (LAMP) assay was developed and validated for the detection of S. suis in the brain and joints of pigs. For this LAMP assay, two different methods for the extraction of DNA from brain and joint swabs were compared. Using the LPTV boiling method, the detection limit of LAMP was 1.08 CFU/reaction, while the detection limit was 53.8 CFU/reaction using a commercial DNA extraction kit. The detection limits of thrA-LAMP in combination with the LPTV boiling method were 104-105 CFU/swab in the presence of brain tissue and 103-104 CFU/swab in the presence of joint tissue. The diagnostic quality criteria of LAMP were determined by the examination of 49 brain swabs and 34 joint swabs obtained during routine diagnostic necropsies. Applying the LPTV boiling method to brain swabs, the sensitivity, specificity, and positive and negative predictive values of thrA-LAMP were 88.0, 95.8, 95.7, and 88.5% using cultural investigation as a reference method, and 76.7, 100, 100, and 73.1% using real-time PCR as a reference method. Based on these results, the thrA-LAMP assay combined with the LPTV boiling method is suitable for rapid detection of S. suis from brain swabs.
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Affiliation(s)
- Julian Hess
- Field Station for Epidemiology (Bakum), University of Veterinary Medicine Hannover, Foundation, 49456 Bakum, Germany;
| | - Antonia Kreitlow
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany;
| | - Karl Rohn
- Institute for Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany;
| | - Isabel Hennig-Pauka
- Field Station for Epidemiology (Bakum), University of Veterinary Medicine Hannover, Foundation, 49456 Bakum, Germany;
| | - Amir Abdulmawjood
- Institute for Food Quality and Food Safety, University of Veterinary Medicine Hannover, Foundation, 30173 Hannover, Germany;
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30
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Deng K, Wang SS, Kiener S, Smith E, Chen KS, Pamboukian R, Laasri A, Pelaez C, Ulaszek J, Kmet M, De Jesus A, Hammack T, Reddy R, Wang H. Multi-laboratory validation study of a real-time PCR method for detection of Salmonella in baby spinach. Food Microbiol 2023; 114:104299. [PMID: 37290875 DOI: 10.1016/j.fm.2023.104299] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 06/10/2023]
Abstract
The FDA Bacteriological Analytical Manual (BAM) Salmonella culture method takes at least 3 days for a presumptive positive result. The FDA developed a quantitative PCR (qPCR) method to detect Salmonella from 24-h preenriched cultures, using ABI 7500 PCR system. The qPCR method has been evaluated as a rapid screening method for a broad range of foods by single laboratory validation (SLV) studies. The present multi-laboratory validation (MLV) study was aimed to measure the reproducibility of this qPCR method and compare its performance with the culture method. Sixteen laboratories participated in two rounds of MLV study to analyze twenty-four blind-coded baby spinach test portions each. The first round yielded ∼84% and ∼82% positive rates across laboratories for the qPCR and culture methods, respectively, which were both outside the fractional range (25%-75%) required for fractionally inoculated test portions by the FDA's Microbiological Method Validation Guidelines. The second round yielded ∼68% and ∼67% positive rates. The relative level of detection (RLOD) for the second-round study was 0.969, suggesting that qPCR and culture methods had similar sensitivity (p > 0.05). The study demonstrated that the qPCR yields reproducible results and is sufficiently sensitive and specific for the detection of Salmonella in food.
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Affiliation(s)
- Kaiping Deng
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 6502 S. Archer Rd, Bedford Park, IL, 60501, USA
| | - Shizhen Steven Wang
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Dr, College Park, MD 20740, USA
| | - Shannon Kiener
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 6502 S. Archer Rd, Bedford Park, IL, 60501, USA
| | - Emily Smith
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 6502 S. Archer Rd, Bedford Park, IL, 60501, USA
| | - Kai-Shun Chen
- FDA-Office of Regulatory Affairs (ORA), 109 Holton Street, Winchester, MA, 01890, USA
| | - Ruiqing Pamboukian
- FDA-Office of Regulatory Affairs (ORA), 12420 Parklawn Dr, Rockville, MD, 20857, USA
| | - Anna Laasri
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Dr, College Park, MD 20740, USA
| | - Catalina Pelaez
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 6502 S. Archer Rd, Bedford Park, IL, 60501, USA
| | - Jodie Ulaszek
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 6502 S. Archer Rd, Bedford Park, IL, 60501, USA
| | - Matthew Kmet
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 6502 S. Archer Rd, Bedford Park, IL, 60501, USA
| | - Antonio De Jesus
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Dr, College Park, MD 20740, USA
| | - Thomas Hammack
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Dr, College Park, MD 20740, USA
| | - Ravinder Reddy
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 6502 S. Archer Rd, Bedford Park, IL, 60501, USA
| | - Hua Wang
- FDA-Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Dr, College Park, MD 20740, USA.
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31
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Keenum I, Player R, Kralj J, Servetas S, Sussman MD, Russell JA, Stone J, Chandrapati S, Sozhamannan S. Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications. J AOAC Int 2023; 106:1424-1430. [PMID: 37067472 PMCID: PMC10472743 DOI: 10.1093/jaoacint/qsad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND Accurate, high-confidence data is critical for assessing potential biothreat incidents. In a biothreat event, false-negative and -positive results have serious consequences. Worst case scenarios can result in unnecessary shutdowns or fatalities at an exorbitant monetary and psychological cost, respectively. Quantitative PCR assays for agents of interest have been successfully used for routine biosurveillance. Recently, there has been increased impetus for adoption of amplicon sequencing (AS) for biosurveillance because it enables discrimination of true positives from near-neighbor false positives, as well as broad, simultaneous detection of many targets in many pathogens in a high-throughput scheme. However, the high sensitivity of AS can lead to false positives. Appropriate controls and workflow reporting can help address these challenges. OBJECTIVES Data reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection. METHODS We present a set of standards, Amplicon Sequencing Minimal Information (ASqMI), developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program on Agent Detection Assays for making actionable calls in biosurveillance applications. In addition to the first minimum information guidelines for AS, we provide a controls checklist and scoring scheme to assure AS run quality and assess potential sample contamination. RESULTS Adoption of the ASqMI guidelines will improve data quality, help track workflow performance, and ultimately provide decision makers confidence to trust the results of this new and powerful technology. CONCLUSION AS workflows can provide robust, confident calls for biodetection; however, due diligence in reporting and controls are needed. The ASqMI guideline is the first AS minimum reporting guidance document that also provides the means for end users to evaluate their workflows to improve confidence. HIGHLIGHTS Standardized reporting guidance for actionable calls is critical to ensuring trustworthy data.
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Affiliation(s)
- Ishi Keenum
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Robert Player
- The Johns Hopkins University, Applied Physics Laboratory, Laurel, MD 20723, USA
- Datirium, LLC, Cincinnati, OH 45526, USA
| | - Jason Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Stephanie Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Michael D Sussman
- US Department of Agriculture, Agricultural Analytics Division, Livestock and Poultry Programs, Agricultural Marketing Service, Washington, DC 20250 USA
| | | | | | | | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD 21702, USA
- Joint Research and Development, Inc., Stafford, VA 22556, USA
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32
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Lin TY, Liu WT. Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor. WATER RESEARCH 2023; 243:120358. [PMID: 37481999 DOI: 10.1016/j.watres.2023.120358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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33
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Bott T, Shaw G, Gregory S. A simple method for testing and controlling inhibition in soil and sediment samples for qPCR. J Microbiol Methods 2023; 212:106795. [PMID: 37541445 DOI: 10.1016/j.mimet.2023.106795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
The presence of polymerase-chain-reaction (PCR) inhibitors in many environmental samples can make reliable and repeatable quantitative-polymerase-chain-reaction (qPCR) analysis difficult without sample dilution. To estimate an optimal sample dilution for qPCR and reduce effects of inhibition, a simple test based on multiple dilution series of samples is presented that avoids the use of internal controls and standards reducing complexity and cost.
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Affiliation(s)
- Tom Bott
- British Geological Survey, Keyworth, Nottingham NG12 5GG, UK; School of Biosciences, Sutton Bonington, University of Nottingham, Loughborough LE12 5RD, UK.
| | - George Shaw
- School of Biosciences, Sutton Bonington, University of Nottingham, Loughborough LE12 5RD, UK
| | - Simon Gregory
- British Geological Survey, Keyworth, Nottingham NG12 5GG, UK.
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34
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Wu M, Huang Y, Huang Y, Wang H, Li M, Zhou Y, Zhao H, Lan Y, Wu Z, Jia C, Feng S, Zhao J. Droplet magnetic-controlled microfluidic chip integrated nucleic acid extraction and amplification for the detection of pathogens and tumor mutation sites. Anal Chim Acta 2023; 1271:341469. [PMID: 37328249 DOI: 10.1016/j.aca.2023.341469] [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: 02/06/2023] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/18/2023]
Abstract
Traditional nucleic acid extraction and detection is based on open operation, which may cause cross-contamination and aerosol formation. This study developed a droplet magnetic-controlled microfluidic chip integrated nucleic acid extraction, purification and amplification. The reagent is sealed in oil to form a droplet, and the nucleic acid is extracted and purified by controlling the movement of the magnetic beads (MBs) through a permanent magnet, ensuring a closed environment. This chip can automatically extract nucleic acid from multiple samples within 20 min, and can be directly placed in the in situ amplification instrument for amplification without further transfer of nucleic acid, characterized by simple, fast, time-saving and labor-saving. The results showed that the chip was able to detect <10 copies/test SARS-CoV-2 RNA, and EGFR exon 21 L858R mutations were detected in H1975 cells as low as 4 cells. In addition, on the basis of the droplet magnetic-controlled microfluidic chip, we further developed a multi-target detection chip, which used MBs to divide the nucleic acid of the sample into three parts. And the macrolides resistance mutations A2063G and A2064G, and the P1 gene of mycoplasma pneumoniae (MP) were successfully detected in clinical samples by the multi-target detection chip, providing the possibility for future application in the detection of multiple pathogens.
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Affiliation(s)
- Man Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhang Huang
- Shanghai Normal University, Shanghai, 200030, China
| | - Yaru Huang
- Shanghai Normal University, Shanghai, 200030, China
| | - Hua Wang
- Renji Hospital Affiliated to Shanghai Jiao Tong University, 200127, China
| | - Min Li
- Renji Hospital Affiliated to Shanghai Jiao Tong University, 200127, China
| | - Yang Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuwei Lan
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenhua Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shilun Feng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Liu Q, Sun T, Wen X, Zeng M, Chen J. Detecting the Minimum Limit on Wheat Stripe Rust in the Latent Period Using Proximal Remote Sensing Coupled with Duplex Real-Time PCR and Machine Learning. PLANTS (BASEL, SWITZERLAND) 2023; 12:2814. [PMID: 37570968 PMCID: PMC10420842 DOI: 10.3390/plants12152814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Wheat stripe rust (WSR) is an airborne disease that causes severe damage to wheat. The rapid and early detection of WSR is essential for the prevention and control of this disease. The minimum detection limit (MDL) is one of the most important characteristics of quantitative methods that can be used to determine the scope and applicability of a measurement technique. Three wheat cultivars were inoculated with Puccinia striiformis f.sp. tritici (Pst), and a spectrometer was used to collect the canopy hyperspectral data, and the Pst content was obtained via a duplex real-time polymerase chain reaction (PCR) during the latent period, respectively. The disease index (DI) and molecular disease index (MDI) were calculated. The regression tree algorithm was used to determine the MDL of the Pst based on hyperspectral feature parameters. The logistic, IBK, and random committee algorithms were used to construct the classification model based on the MDL. The results showed that when the MDL was 0.7, IBK had the best recognition accuracy. The optimal model, which used the spectral feature R_2nd.dv ((the second derivative of the original hyperspectral value)) and the modeling ratio 2:1, had an accuracy of 91.67% on the testing set and 90.67% on the 10-fold cross-validation. Thus, during the latent period, the MDL of Pst was determined using hyperspectral technology as 0.7.
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Affiliation(s)
- Qi Liu
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (T.S.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
| | - Tingting Sun
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (T.S.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
| | - Xiaojie Wen
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (T.S.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
| | - Minghao Zeng
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (T.S.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
| | - Jing Chen
- Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region, College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China; (T.S.)
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture & Forestry of the North-Western Desert Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830052, China
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Wang J, Wei B, Chen Z, Chen Y, Liu S, Zhang B, Zhu B, Ye D. A rapid and reliable method for the determination of Lactiplantibacillus plantarum during wine fermentation based on PMA-CELL-qPCR. Front Microbiol 2023; 14:1154768. [PMID: 37529324 PMCID: PMC10389660 DOI: 10.3389/fmicb.2023.1154768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Real-time monitoring of microbial dynamics during fermentation is essential for wine quality control. This study developed a method that combines the fluorescent dye propidium monoazide (PMA) with CELL-qPCR, which can distinguish between dead and live microbes for Lactiplantibacillus plantarum. This method could detect the quantity of microbes efficiently and rapidly without DNA extraction during wine fermentation. The results showed that (1) the PMA-CELL-qPCR enumeration method developed for L. plantarum was optimized for PMA treatment concentration, PMA detection sensitivity and multiple conditions of sample pretreatment in wine environment, and the optimized method can accurately quantify 104-108 CFU/mL of the target strain (L. plantarum) in multiple matrices; (2) when the concentration of dead bacteria in the system is 104 times higher than the concentration of live bacteria, there is an error of 0.5-1 lg CFU/mL in the detection results. The optimized sample pretreatment method in wine can effectively reduce the inhibitory components in the qPCR reaction system; (3) the optimized PMA-CELL-qPCR method was used to monitor the dynamic changes of L. plantarum during the fermentation of Cabernet Sauvignon wine, and the results were consistent with the plate counting method. In conclusion, the live bacteria quantification method developed in this study for PMA-CELL-qPCR in L. plantarum wines is accurate in quantification and simple in operation, and can be used as a means to accurately monitor microbial dynamics in wine and other fruit wines.
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Affiliation(s)
- Jie Wang
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Bo Wei
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Zhuojun Chen
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Yixin Chen
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Songyu Liu
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Bolin Zhang
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Baoqing Zhu
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Dongqing Ye
- Guangxi Key Laboratory of Fruits and Vegetables Storage-Processing Technology, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
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Zhao Y, De Coninck B, Ribeiro B, Nicolaï B, Hertog M. Early detection of Botrytis cinerea in strawberry fruit during quiescent infection using selected ion flow tube mass spectrometry (SIFT-MS). Int J Food Microbiol 2023; 402:110313. [PMID: 37421873 DOI: 10.1016/j.ijfoodmicro.2023.110313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/11/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
Botrytis cinerea is a devastating pathogen that can cause huge postharvest losses of strawberry. Although this fungus usually infects strawberries through their flowers, symptoms mainly appear when fruit are fully mature. A fast and sensitive method to detect and quantify the fungal infection, prior to symptom development, is, therefore, needed. In this study, we explore the possibility of using the strawberry volatilome to identify biomarkers for B. cinerea infection. Strawberry flowers were inoculated with B. cinerea to mimic the natural infection. First, quantitative polymerase chain reaction (qPCR) was used to quantify B. cinerea in the strawberry fruit. The detection limit of qPCR for B. cinerea DNA extracted from strawberries was 0.01 ng. Subsequently, changes in the fruit volatilome at different fruit developmental stages were characterized using gas chromatography - mass spectrometry (GC-MS) and selected ion flow tube mass spectrometry (SIFT-MS). Based on GC-MS data, 1-octen-3-ol produced by B. cinerea was confirmed as a potential biomarker of B. cinerea infection. Moreover, the product ion NO+ 127, obtained by SIFT-MS measurements, was proposed as a potential biomarker for B. cinerea infection by comparing its relative level with that of 1-octen-3-ol (obtained by GC-MS) and B. cinerea (obtained by qPCR). Separate PLS regressions were carried out for each developmental stages, and 11 product ions were significantly altered at all developmental stages. Finally, PLS regressions using these 11 ions as variables allowed the discrimination between samples containing different amount of B. cinerea. This work showed that profiling the fruit's volatilome using SIFT-MS can be used as a potential alternative to detect B. cinerea during the quiescent stage of B. cinerea infection prior to symptom development. Moreover, the corresponding compounds of potential biomarkers suggest that the volatile changes caused by B. cinerea infection may contribute to strawberry defense.
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Affiliation(s)
- Yijie Zhao
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; KU Leuven Plant Institute, 3001 Heverlee, Belgium
| | - Barbara De Coninck
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; KU Leuven Plant Institute, 3001 Heverlee, Belgium
| | - Bianca Ribeiro
- Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; KU Leuven Plant Institute, 3001 Heverlee, Belgium
| | - Bart Nicolaï
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; Flanders Centre of Postharvest Technology, Willem de Croylaan 42, 3001 Leuven, Belgium; KU Leuven Plant Institute, 3001 Heverlee, Belgium
| | - Maarten Hertog
- Division of Mechatronics, Biostatistics and Sensors, Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium; KU Leuven Plant Institute, 3001 Heverlee, Belgium.
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Vassallo A, Modi A, Quagliariello A, Bacci G, Faddetta T, Gallo M, Provenzano A, La Barbera A, Lombardo G, Maggini V, Firenzuoli F, Zaccaroni M, Gallo G, Caramelli D, Aleo Nero C, Baldi F, Fani R, Palumbo Piccionello A, Pucciarelli S, Puglia AM, Sineo L. Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy). Microbiol Spectr 2023; 11:e0437422. [PMID: 37071008 PMCID: PMC10269861 DOI: 10.1128/spectrum.04374-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/26/2023] [Indexed: 04/19/2023] Open
Abstract
The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.
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Affiliation(s)
- Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Michele Gallo
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Aldesia Provenzano
- Department of Clinical and Experimental Biomedical Sciences “Mario Serio,” University of Florence, Florence (FI), Italy
| | - Andrea La Barbera
- Unit of Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genoa (GE), Italy
| | - Giovanna Lombardo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Valentina Maggini
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Fabio Firenzuoli
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Carla Aleo Nero
- Soprintendenza ai Beni culturali e ambientali di Palermo, Palermo (PA), Italy
| | - Franco Baldi
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Luca Sineo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
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Haveman NJ, Schuerger AC, Yu PL, Brown M, Doebler R, Paul AL, Ferl RJ. Advancing the automation of plant nucleic acid extraction for rapid diagnosis of plant diseases in space. FRONTIERS IN PLANT SCIENCE 2023; 14:1194753. [PMID: 37389293 PMCID: PMC10304293 DOI: 10.3389/fpls.2023.1194753] [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: 03/27/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023]
Abstract
Human space exploration missions will continue the development of sustainable plant cultivation in what are obviously novel habitat settings. Effective pathology mitigation strategies are needed to cope with plant disease outbreaks in any space-based plant growth system. However, few technologies currently exist for space-based diagnosis of plant pathogens. Therefore, we developed a method of extracting plant nucleic acid that will facilitate the rapid diagnosis of plant diseases for future spaceflight applications. The microHomogenizer™ from Claremont BioSolutions, originally designed for bacterial and animal tissue samples, was evaluated for plant-microbial nucleic acid extractions. The microHomogenizer™ is an appealing device in that it provides automation and containment capabilities that would be required in spaceflight applications. Three different plant pathosystems were used to assess the versatility of the extraction process. Tomato, lettuce, and pepper plants were respectively inoculated with a fungal plant pathogen, an oomycete pathogen, and a plant viral pathogen. The microHomogenizer™, along with the developed protocols, proved to be an effective mechanism for producing DNA from all three pathosystems, in that PCR and sequencing of the resulting samples demonstrated clear DNA-based diagnoses. Thus, this investigation advances the efforts to automate nucleic acid extraction for future plant disease diagnosis in space.
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Affiliation(s)
- Natasha J. Haveman
- NASA Utilization & Life Sciences Office (UB-A), Kennedy Space Center, Merritt Island, FL, United States
| | - Andrew C. Schuerger
- Department of Plant Pathology, University of Florida, Space Life Science Lab, Merritt Island, FL, United States
| | - Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Mark Brown
- Claremont BioSolutions Limited Liability Company (LLC), Upland, CA, United States
| | - Robert Doebler
- Claremont BioSolutions Limited Liability Company (LLC), Upland, CA, United States
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Robert J. Ferl
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- University of Florida Office of Research, University of Florida, Gainesville, FL, United States
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Drummond MR, Dos Santos LS, de Almeida AR, Lins KDA, Barjas-Castro ML, Diniz PPVDP, Velho PENF. Comparison of molecular methods for Bartonella henselae detection in blood donors. PLoS Negl Trop Dis 2023; 17:e0011336. [PMID: 37262044 DOI: 10.1371/journal.pntd.0011336] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
The Bartonella genus consists of neglected pathogens associated with potentially transfusional-transmitted and fatal human diseases. We aimed to evaluate Bartonella sp. prevalence in 500 blood donors and compare the results with the data already published about these samples. We used molecular diagnostic methods to detect Bartonella sp.-DNA from blood and liquid culture samples: (A) conventional PCR for two gene regions, the ITS targeting the genus Bartonella and the specific gltA Bartonella henselae; (B) nested PCR for the ftsZ gene and (C) qualitative real-time PCR for the gltA gene, both B. henselae specific. We obtained 30/500 (6%) DNA detections from the blood samples; 77/500 (15.4%) DNA detections from liquid culture samples and five (1%) samples had DNA detection from both. In total, we detected B. henselae DNA from 102/500 (20.4%) donors. The samples used in this study had already been submitted for Bartonella sp.-DNA detection using only a conventional PCR in liquid culture. Sixteen samples (3.2%) were positive previously, and from these 16 samples, 13 were negative in the new investigation. We concluded that the use of liquid culture combined with different molecular tests increases the possibility of detecting Bartonella sp.-DNA, but the tests do not avoid false-negative results. More than a fifth of blood donors had at least one PCR that detected Bartonella sp.-DNA among the eight molecular reactions performed now (four reactions in whole blood and four in liquid culture). Seven percent had B. henselae-DNA detection for two or more distinct regions. Considering the results obtained previously, the DNA of Bartonella spp. was detected or the agent isolated in 23% of analyzed blood donors. The results establish that the low bacteremia and the fastidious characteristics of the bacterium are challenges to laboratory diagnosis and can make it difficult to confirm the infection in patients with bartonelloses.
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Affiliation(s)
- Marina Rovani Drummond
- Applied Research in Dermatology and Bartonella Infection Laboratory, University of Campinas-UNICAMP; Campinas, Sao Paulo, Brazil
| | - Luciene Silva Dos Santos
- Applied Research in Dermatology and Bartonella Infection Laboratory, University of Campinas-UNICAMP; Campinas, Sao Paulo, Brazil
| | - Amanda Roberta de Almeida
- Applied Research in Dermatology and Bartonella Infection Laboratory, University of Campinas-UNICAMP; Campinas, Sao Paulo, Brazil
| | - Karina de Almeida Lins
- Applied Research in Dermatology and Bartonella Infection Laboratory, University of Campinas-UNICAMP; Campinas, Sao Paulo, Brazil
| | | | | | - Paulo Eduardo Neves Ferreira Velho
- Applied Research in Dermatology and Bartonella Infection Laboratory, University of Campinas-UNICAMP; Campinas, Sao Paulo, Brazil
- Division of Dermatology, Department of Medicine, UNICAMP, Campinas, Sao Paulo, Brazil
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Jo TS. Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis. Proc Biol Sci 2023; 290:20230979. [PMID: 37253423 PMCID: PMC10229230 DOI: 10.1098/rspb.2023.0979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.
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Affiliation(s)
- Toshiaki S. Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
- Ryukoku Center for Biodiversity Science, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
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Schenk JJ, Becklund LE, Carey SJ, Fabre PP. What is the "modified" CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11517. [PMID: 37342162 PMCID: PMC10278931 DOI: 10.1002/aps3.11517] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/22/2023]
Abstract
Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how the protocol had been altered, creating non-reproducible studies. Furthermore, the various modifications that have been applied to the CTAB protocol have not been rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed the literature for modified CTAB protocols used for the isolation of plant DNA. We found that every stage of the CTAB protocol has been modified, and we summarized those modifications to provide recommendations for extraction optimization. Future genomic studies will rely on optimized CTAB protocols. Our review of the modifications that have been used, as well as the protocols we provide here, could better standardize DNA extractions, allowing for repeatable and transparent studies.
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Affiliation(s)
- John J. Schenk
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
| | - L. Ellie Becklund
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
| | - S. James Carey
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
| | - Paige P. Fabre
- Department of Environmental and Plant BiologyOhio UniversityAthensOhio45701–2979USA
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Zheng J, Liu L, Li X, Xu Z, Gai Z, Zhang X, Lei H, Shen X. Rapid and Simple Detection of Burkholderia gladioli in Food Matrices Using RPA-CRISPR/Cas12a Method. Foods 2023; 12:foods12091760. [PMID: 37174300 PMCID: PMC10178126 DOI: 10.3390/foods12091760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
Pathogenic variants of Burkholderia gladioli pose a serious threat to human health and food safety, but there is a lack of rapid and sensitive field detection methods for Burkholderia gladioli. In this study, the CRISPR/Cas12a system combined with recombinant enzyme polymerase amplification (RPA) was used to detect Burkholderia gladioli in food. The optimized RPA-CRISPR/Cas12a assay was able to specifically and stably detect Burkholderia gladioli at a constant 37 °C without the assistance of large equipment. The detection limit of the method was evaluated at two aspects, the genomic DNA (gDNA) level and bacterial quantity, of which there were 10-3 ng/μL and 101 CFU/mL, respectively. Three kinds of real food samples were tested. The detection limit for rice noodles, fresh white noodles, and glutinous rice flour samples was 101 CFU/mL, 102 CFU/mL, and 102 CFU/mL, respectively, without any enrichment steps. The whole detection process, including sample pretreatment and DNA extraction, did not exceed one hour. Compared with the qPCR method, the established RPA-CRISPR /Cas12a method was simpler and even more sensitive. Using this method, a visual detection of Burkholderia gladioli that is suitable for field detection can be achieved quickly and easily.
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Affiliation(s)
- Jiale Zheng
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Li Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Xiangmei Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Zuoqi Gai
- Guangzhou Editgene Co., Ltd., Guangzhou 510630, China
| | - Xu Zhang
- Guangzhou Editgene Co., Ltd., Guangzhou 510630, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xing Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
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Tang M, Liao N, Tian P, Shen K, Liu C, Ruan L, Wu G. Use of bentonite-coated activated carbon for improving the sensitivity of RT-qPCR detection of norovirus from vegetables and fruits: The ISO 15216-1:2017 standard method extension. Food Microbiol 2023; 110:104165. [PMID: 36462822 DOI: 10.1016/j.fm.2022.104165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
Abstract
Produce-related foodborne outbreaks are becoming increasingly prevalent worldwide. In plant tissues, various compounds, including polysaccharides, phenolic compounds, and chlorophyll, can inhibit RT-PCR detection of viruses. In this study, we developed a highly sensitive RT-qPCR in combination with the bentonite-coated activated carbon (BCAC) assay for detection of norovirus from fruits and vegetables, which could be completed within 7 h and was about 10-100 fold more sensitive than the standard procedures (ISO 15216-1:2017). The extraction efficiencies of three surrogate viruses (MS2, MNV-1, and TV) from five fresh produce (lettuce, cherry tomato, blueberry, strawberry, and spinach) were higher with BCAC treatment than those of control groups, ranging from 17.82% to 98.60%. The average detection limit of these viruses using the BCAC-RT-qPCR method was stable at an average of 102 PFU/g or GC/g. Finally, this BCAC-RT-qPCR method was applied for detection of human norovirus GII.4 spiked onto lettuce and cherry tomato. The viral extraction efficiencies were up to 53.43% and 95.56%, respectively, which is almost four and seven times better than those without BCAC. Therefore, the BCAC-RT-qPCR method can be used to detect low levels of foodborne viruses from produce.
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Affiliation(s)
- Mengxuan Tang
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ningbo Liao
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, China; Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Nanchang, Jiangxi, China.
| | - Peng Tian
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA, United States
| | - Kaisheng Shen
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chengwei Liu
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Nanchang, Jiangxi, China; Jiangxi Province Center for Disease Control and Prevention, Nanchang, Jiangxi, China
| | - Lu Ruan
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Guoping Wu
- School of Food Science & Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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45
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Schurig S, Kobialka R, Wende A, Ashfaq Khan MA, Lübcke P, Eger E, Schaufler K, Daugschies A, Truyen U, Abd El Wahed A. Rapid Reverse Purification DNA Extraction Approaches to Identify Microbial Pathogens in Wastewater. Microorganisms 2023; 11:microorganisms11030813. [PMID: 36985386 PMCID: PMC10056086 DOI: 10.3390/microorganisms11030813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/06/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Wastewater monitoring became a promising solution in the early detection of outbreaks. Despite the achievements in the identification of pathogens in wastewater using real-time PCR, there is still a lack of reliable rapid nucleic acid extraction protocols. Therefore, in this study, samples were subjected to alkali, proteinase K and/or bead-beating followed by reverse purification magnetic beads-based separation. Wastewater samples spiked with S. aureus, E. coli and C. parvum were used as examples for Gram-positive and -negative bacteria and protozoa, respectively. All results were compared with a spin column technology as a reference method. Proteinase K with bead beating (vortexing with 0.1 mm glass beads for three minutes) was particularly successful for bacterial DNA extraction (three- to five-fold increase). The most useful extraction protocol for protozoa was pre-treatment with proteinase K (eight-fold increase). The selected methods were sensitive as far as detecting one bacterial cell per reaction for S. aureus, ten bacterial cells for E. coli and two oocysts for C. parvum. The extraction reagents are cold chain independent and no centrifuge or other large laboratory equipment is required to perform DNA extraction. A controlled validation trial is needed to test the effectiveness at field levels.
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Affiliation(s)
- Sarah Schurig
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
- Xpedite Diagnostics GmbH, 80687 Munich, Germany
| | - Rea Kobialka
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
| | - Andy Wende
- Xpedite Diagnostics GmbH, 80687 Munich, Germany
| | - Md Anik Ashfaq Khan
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
| | - Phillip Lübcke
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Elias Eger
- Institute of Infection Medicine, Christian-Albrecht University Kiel, 24105 Kiel, Germany
- University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Katharina Schaufler
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel, 24105 Kiel, Germany
- University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Arwid Daugschies
- Institute of Parasitology, Centre for Infectious Disease, Leipzig University, 04103 Leipzig, Germany
| | - Uwe Truyen
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, 04103 Leipzig, Germany
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46
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Houston G, Blomme A, Harrison O, Bai J, Woodworth J, Jones C, Poulsen-Porter E, Paulk C, Gebhardt J. Evaluating the impact of organic matter and sample processing techniques on RNA detection using environmental samples. JOURNAL OF SWINE HEALTH AND PRODUCTION 2023. [DOI: 10.54846/jshap/1311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
This study evaluated sample processing methods and the presence of organic matter on detection of porcine epidemic diarrhea virus (PEDV) from environmental samples using real-time reverse transcriptase-polymerase chain reaction (qRT-PCR). Steel coupons were inoculated with PEDV and different types of organic material contamination. Surface samples were collected and processed in one of four ways: none, centrifugation, syringe filtration, or combination of centrifugation and syringe filtration, then submitted for PEDV qRT-PCR. There was a surface inoculation type by processing method interaction (P < .001) that impacted the sample cycle threshold value. Centrifugation resulted in the most consistent detection of PEDV RNA.
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47
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Andrade Zampieri R, Ide Aoki J, Müller KE, Jon Shaw J, Maria Floeter-Winter L. Comparison of Sampling Procedures for the Molecular Diagnosis of Leishmaniases. Am J Trop Med Hyg 2023; 108:548-554. [PMID: 36689945 PMCID: PMC9978564 DOI: 10.4269/ajtmh.21-1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/03/2022] [Indexed: 01/24/2023] Open
Abstract
The present work evaluates sampling protocols, storage procedures, and DNA purification methods for Leishmania spp. detection and quantification in different biological samples. The efficiency of three preservation solutions, a phosphate buffer solution, an ethylenediaminetetraacetic acid (EDTA) buffer solution, and 70% ethanol, was compared in combination with three DNA extraction protocols: a commercial silica column kit, salting-out protein precipitation, and organic extraction with phenol-chloroform. Tissue samples from BALB/c mice experimentally infected with Leishmania (Leishmania) amazonensis, Leishmania (Viannia) braziliensis, or Leishmania (Leishmania) infantum were stored in the three preservation solutions and subsequently subjected to the three different DNA extraction methods. The extracted DNA was then used in real-time polymerase chain reaction (PCR) assays for the detection and quantification of parasite ribosomal small subunit DNA targets as well as mammalian glyceraldehyde-3-phosphate dehydrogenase (gapdh) targets. The results of the optimized protocols showed that the DNA extraction method did not influence test quality, but DNA from samples preserved with the EDTA buffer solution produced higher amounts of target amplicons. Based on these results, we concluded that samples from suspected cases of leishmaniasis for submission to molecular diagnostic procedures should be preferentially preserved in EDTA, followed by any one of the DNA purification methods evaluated.
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Affiliation(s)
| | - Juliana Ide Aoki
- Department of Physiology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Karl Erik Müller
- Department of Internal Medicine, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Jeffrey Jon Shaw
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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48
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Chakrabarti S, Loyd AL, Dhillon B. Multilocus, Multiplex Detection of Ganoderma zonatum from Environmental Samples. PLANT DISEASE 2023; 107:682-687. [PMID: 35869585 DOI: 10.1094/pdis-12-21-2837-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Ganoderma butt rot of palms is caused by a white rot basidiomycete fungus, Ganoderma zonatum. Typical symptoms include wilting of fronds that starts in the lower canopy and moves to the top. As wilting symptoms are also associated with other diseases and disorders, appearance of basidiomata on the trunks is necessary to confirm this disease. Basidiomata develop late in the disease cycle, making early diagnostics challenging. Here, we describe a DNA-based molecular diagnostic assay that could be used to confirm the presence of G. zonatum in palm trunks before conks are observed. Primers tailored to end on single-nucleotide polymorphisms (SNPs), that differentiate G. zonatum from 14 other Ganoderma taxa, were designed from multiple regions in four genes: internal transcribed spacer (ITS), RNA polymerase 1 (rpb1), rpb2, and translation elongation factor 1-α (tef1-α). A set of three primer pairs could successfully determine the incidence of G. zonatum with high specificity and sensitivity in different environmental samples such as sawdust collected from naturally infected palm trunks and soil samples containing G. zonatum basidiospores. This rapid PCR-based assay could potentially be used to detect inoculum sources of the fungus and track its movement and survival in different palm tissues and environments. Early detection of G. zonatum is a crucial step toward building and implementing better disease management strategies and mitigating potential risks from palm failures due to decay.
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Affiliation(s)
- Seemanti Chakrabarti
- Department of Plant Pathology, University of Florida, Fort Lauderdale Research and Education Center, Davie, FL 33314
| | - Andrew L Loyd
- The F.A. Bartlett Tree Experts Company, Charlotte, NC 28278
| | - Braham Dhillon
- Department of Plant Pathology, University of Florida, Fort Lauderdale Research and Education Center, Davie, FL 33314
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49
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Poethe SS, Holtel J, Biermann JP, Riemer T, Grabmüller M, Madea B, Thiele R, Jäger R. Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples. Int J Mol Sci 2023; 24:ijms24043382. [PMID: 36834791 PMCID: PMC9960623 DOI: 10.3390/ijms24043382] [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: 12/13/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Forensic DNA profiles are established by multiplex PCR amplification of a set of highly variable short tandem repeat (STR) loci followed by capillary electrophoresis (CE) as a means to assign alleles to PCR products of differential length. Recently, CE analysis of STR amplicons has been supplemented by high-throughput next generation sequencing (NGS) techniques that are able to detect isoalleles bearing sequence polymorphisms and allow for an improved analysis of degraded DNA. Several such assays have been commercialised and validated for forensic applications. However, these systems are cost-effective only when applied to high numbers of samples. We report here an alternative, cost-efficient shallow-sequence output NGS assay called maSTR assay that, in conjunction with a dedicated bioinformatics pipeline called SNiPSTR, can be implemented with standard NGS instrumentation. In a back-to-back comparison with a CE-based, commercial forensic STR kit, we find that for samples with low DNA content, with mixed DNA from different individuals, or containing PCR inhibitors, the maSTR assay performs equally well, and with degraded DNA is superior to CE-based analysis. Thus, the maSTR assay is a simple, robust and cost-efficient NGS-based STR typing method applicable for human identification in forensic and biomedical contexts.
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Affiliation(s)
- Sara-Sophie Poethe
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Julia Holtel
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Jan-Philip Biermann
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Trine Riemer
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - Melanie Grabmüller
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Burkhard Madea
- Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
| | - Ralf Thiele
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Computer Science Department, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
| | - Richard Jäger
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
- Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Correspondence:
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50
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Hodgson LM, Cox BA, Lopez-Ruiz FJ, Gibberd MR, Thomas GJ, Zerihun A. Optimized Sample Processing Pipeline for PCR-Based Fungicide Resistance Quantification of Stubble-Borne Fungal Pathogens. PHYTOPATHOLOGY 2023; 113:321-333. [PMID: 36075052 DOI: 10.1094/phyto-07-22-0239-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Globally, yield losses associated with failed crop protection due to fungicide-resistant pathogens present an increasing problem. For stubble-borne pathogens, assessment of crop residues during the off-season could provide early fungicide resistance quantification for informed management decisions to mitigate yield losses. However, stubble assessment is hampered by assay inhibitors that are derived from decaying organic matter. To overcome assay inhibition from weathered stubble samples, we used a systems approach to quantify the frequency of resistance to demethylase inhibitor fungicides of the barley pathogen Pyrenophora teres f. teres. The system canvassed (i) 10 ball-milling conditions; (ii) four DNA extraction methodologies; and (iii) three column purification techniques for the provision of sufficient yield, quality, and purity of fungal DNA for a PCR-based fungicide resistance assay. Results show that DNA quantity and purity differed within each of the above three categories, with the optimized pipeline being (i) ball-milling samples in a 50-ml stainless steel canister for 5 min using a 20-mm ball at 30 revolutions s-1; (ii) a modified Brandfass method (extracted 64% more DNA than other methods assessed); and (iii) use of silica resin columns for the highest DNA concentration with optimal DNA purity. The chip-digital PCR assay, which quantified fungicide resistance from field samples, was unaffected by the DNA extraction method or purification technique, provided that thresholds of template quantity and purity were satisfied. In summary, this study has developed molecular pipeline options for pathogen fungicide resistance quantification from cereal stubbles, which can guide management for improved crop protection outcomes.
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Affiliation(s)
- Leon M Hodgson
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Belinda A Cox
- School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mark R Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Geoff J Thomas
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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