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Lee J, Jeong H, Kang HG, Park J, Choi EY, Lee CS, Byeon SH, Kim M. Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study. Ocul Immunol Inflamm 2024; 32:463-469. [PMID: 36758246 DOI: 10.1080/09273948.2023.2173243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 12/09/2022] [Accepted: 01/22/2023] [Indexed: 02/11/2023]
Abstract
PURPOSE We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS). METHODS In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS. RESULTS All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal. CONCLUSION Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.
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Affiliation(s)
- Junwon Lee
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Han Jeong
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Goo Kang
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jinkyu Park
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Choi
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Christopher Seungkyu Lee
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Suk Ho Byeon
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Min Kim
- Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Grünwald NJ, Bock CH, Chang JH, De Souza AA, Ponte EMD, du Toit LJ, Dorrance AE, Dung J, Gent D, Goss EM, Lowe-Power TM, Madden LV, Martin FN, McDowell J, Naegele RP, Potnis N, Quesada-Ocampo LM, Sundin GW, Thiessen L, Vinatzer BA, Zeng Q. Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices. Phytopathology 2024:PHYTO12230483IA. [PMID: 38330057 DOI: 10.1094/phyto-12-23-0483-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.
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Affiliation(s)
- Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97331, U.S.A
| | - Clive H Bock
- U.S. Department of Agriculture-Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31008, U.S.A
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | | | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Lindsey J du Toit
- Department of Plant Pathology, Washington State University, Mount Vernon, WA 98273, U.S.A
| | - Anne E Dorrance
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Jeremiah Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR 97741, U.S.A
| | - David Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A
| | - Tiffany M Lowe-Power
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A
| | - Laurence V Madden
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Frank N Martin
- U.S. Department of Agriculture-Agricultural Research Service, Crop Protection and Improvement Research Center, Salinas, CA 93905, U.S.A
| | - John McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Rachel P Naegele
- U.S. Department of Agriculture-Agricultural Research Service, Sugarbeet and Bean Research Unit, East Lansing, MI 48824, U.S.A
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Lindsey Thiessen
- Domestic and Emergency Scientific Support, U.S. Department of Agriculture-Animal & Plant Health Inspection Service-Plant Protection and Quarantine, Raleigh, NC 27606, U.S.A
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A
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3
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Zhao X, He Y, Shao S, Ci Q, Chen L, Lu X, Liu Q, Chen J. CRISPR/Cas14 and G-Quadruplex DNAzyme-Driven Biosensor for Paper-Based Colorimetric Detection of African Swine Fever Virus. ACS Sens 2024. [PMID: 38635911 DOI: 10.1021/acssensors.4c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The highly contagious nature and 100% fatality rate contribute to the ongoing and expanding impact of the African swine fever virus (ASFV), causing significant economic losses worldwide. Herein, we developed a cascaded colorimetric detection using the combination of a CRISPR/Cas14a system, G-quadruplex DNAzyme, and microfluidic paper-based analytical device. This CRISPR/Cas14a-G4 biosensor could detect ASFV as low as 5 copies/μL and differentiate the wild-type and mutated ASFV DNA with 2-nt difference. Moreover, this approach was employed to detect ASFV in porcine plasma. A broad linear detection range was observed, and the limit of detection in spiked porcine plasma was calculated to be as low as 42-85 copies/μL. Our results indicate that the developed paper platform exhibits the advantages of high sensitivity, excellent specificity, and low cost, making it promising for clinical applications in the field of DNA disease detection and suitable for popularization in low-resourced areas.
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Affiliation(s)
- Xue Zhao
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Shengjie Shao
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Qiaoqiao Ci
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lin Chen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
| | - Xiaonan Lu
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Qian Liu
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Bioengineering, University of California, Riverside, California 92521, United States
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Minutolo M, Nicoloso V, Cinque M, Chiumenti M, Simeone GDR, Serio FD, Alioto D, Navarro B. A Polyvalent Tool for Detecting Coguviruses in Multiple Hosts Allowed the Identification of a Novel Seed-Transmitted Coguvirus Infecting Brassicaceae. Phytopathology 2024:PHYTO10230362R. [PMID: 38079350 DOI: 10.1094/phyto-10-23-0362-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The genus Coguvirus, a recently established genus in the family Phenuiviridae, includes several species whose members infect both woody and herbaceous hosts, suggesting a broader host range and wider distribution than previously. To gain insights into the epidemiology and biology of coguviruses, a polyvalent reverse transcription-PCR assay using degenerate primers was developed. The specificity of the assay for coguviruses was confirmed by testing citrus and apple plants infected by previously reported coguviruses and/or several unrelated viruses. The expected 236-bp amplicon was obtained from citrus, apple, pear, watermelon, and several species of the family Brassicaceae. Sequencing of the PCR amplicons allowed the identification, for the first time in Italy and/or Europe, of several coguviruses in multiple hosts, confirming the effectiveness of the assay. Moreover, a new virus, tentatively named Brassica oleracea Torzella virus 1 (BoTV1), was detected in several plants of Torzella cabbage. The complete +genome of BoTV1, determined by high-throughput sequencing and 5' rapid amplification of cDNA ends, revealed that it has the typical molecular features of coguviruses and fulfils the current criteria to be classified as a member of a new species, for which the tentative name Coguvirus torzellae is proposed. The same polyvalent assay was also used to investigate and confirm that BoTV1 is transmitted through seeds in black cabbage, thus providing the first evidence on the relevance of this natural transmission mode in the epidemiology of coguviruses. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Italy
| | - Vittorio Nicoloso
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | - Maria Cinque
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Italy
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | | | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055, Portici, Italy
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
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Marin MV, Ratti MF, Peres NA, Goss EM. New Genotypes of Phytophthora nicotianae Found on Strawberry in Florida. Phytopathology 2024:PHYTO05230175R. [PMID: 37942874 DOI: 10.1094/phyto-05-23-0175-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Phytophthora cactorum is the most common causal agent of Phytophthora crown rot and leather rot of strawberry, but P. nicotianae is also responsible for the disease in Florida. Studies of P. nicotianae populations have suggested that different groups of genotypes are associated with different hosts; however, it is not yet clear how many lineages exist globally and how they are related to different production systems. The aim of this study was to determine the genetic relationships of P. nicotianae isolates from Florida strawberry with genotypes reported from other hosts, quantify the genetic variation on strawberry, and test for an association with nursery source. A total of 49 isolates of P. nicotianae were collected from strawberry plants originating from multiple nursery sources during six seasons of commercial fruit production in Florida. Microsatellite genotyping identified 28 multilocus genotypes on strawberry that were distinct among 208 isolates originating from various hosts and locations. Based on STRUCTURE analysis, two genetic groups were identified: one consisting of isolates from strawberry, and the other comprising samples from different hosts. Multilocus genotypes were shared among nursery sources, and populations defined by nursery were not differentiated. Both mating types were found among the isolates from North Carolina- and California-origin plants and in most strawberry seasons; however, a predominance of A1 was observed, and regular sexual reproduction was not supported by the data. This study reveals a unique genetic population of P. nicotianae associated with strawberry and emphasizes the vital role of nursery monitoring in mitigating disease spread.
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Affiliation(s)
- Marcus V Marin
- Department of Plant Pathology, University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598, U.S.A
| | - Maria F Ratti
- Escuela Superior Politecnica del Litoral, Guayaquil, Guayas, República del Ecuador
| | - Natalia A Peres
- Department of Plant Pathology, University of Florida, Gulf Coast Research and Education Center, Wimauma, FL 33598, U.S.A
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A
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Bustamante MI, Elfar K, Kuzmenko J, Zaninovich T, Arreguin M, Carachure C, Zhuang G, Michailides TJ, Eskalen A. Reassessing the Etiology of Aspergillus Vine Canker and Summer Bunch Rot of Table Grapes in California. Plant Dis 2024:PDIS06231137RE. [PMID: 37845185 DOI: 10.1094/pdis-06-23-1137-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Fungal taxonomy is in constant flux, and the advent of reliable DNA barcodes has enabled the enhancement of plant pathogen identification accuracy. In California, Aspergillus vine canker (AVC) and summer bunch rot (SBR) are economically important diseases that affect the wood and fruit of grapevines, respectively, and their causal agents are primarily species of black aspergilli (Aspergillus section Nigri). During the last decade, the taxonomy of this fungal group has been rearranged several times using morphological, physiological, and genetic analyses, which resulted in the incorporation of multiple cryptic species that are difficult to distinguish. Therefore, in this study, we aimed to reassess the etiology of AVC and SBR using a combination of morphological observations with phylogenetic reconstructions based on nucleotide sequences of the calmodulin (CaM) gene. Results revealed that the isolates causing AVC from recent isolations corresponded to A. tubingensis, whereas the isolates obtained from initial surveys when the disease was discovered were confirmed as A. niger and A. carbonarius. Similarly, the isolates obtained from table grapes with SBR symptoms and from spore traps placed in those vineyards were identified primarily as A. tubingensis, followed by A. niger and A. carbonarius. Notably, the A. niger isolates formed a subclade with strains previously known as A. welwitschiae, which is a species that was recently synonymized with A. niger. Overall, the most prevalent species was A. tubingensis, which was associated with both AVC and SBR, and representative isolates recovered from AVC-symptomatic wood, berries SBR symptoms, and spore traps were equally pathogenic in healthy wood and berries of 'Red Globe' grapevines. This study also constitutes the first report of A. tubingensis causing AVC and SBR of grapes in California and in the United States.
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Affiliation(s)
| | - Karina Elfar
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Janet Kuzmenko
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Thomas Zaninovich
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Molly Arreguin
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Carlos Carachure
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - George Zhuang
- University of California Cooperative Extension, Fresno, CA 93710
| | - Themis J Michailides
- Department of Plant Pathology, University of California, Davis, CA 95616
- Kearney Agricultural Research and Extension Center, Parlier, CA 93648
| | - Akif Eskalen
- Department of Plant Pathology, University of California, Davis, CA 95616
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7
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Lim J, Han W, Thang LTH, Lee YW, Shin JH. Customizable Nichrome Wire Heaters for Molecular Diagnostic Applications. Biosensors (Basel) 2024; 14:152. [PMID: 38534259 DOI: 10.3390/bios14030152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Accurate sample heating is vital for nucleic acid extraction and amplification, requiring a sophisticated thermal cycling process in nucleic acid detection. Traditional molecular detection systems with heating capability are bulky, expensive, and primarily designed for lab settings. Consequently, their use is limited where lab systems are unavailable. This study introduces a technique for performing the heating process required in molecular diagnostics applicable for point-of-care testing (POCT), by presenting a method for crafting customized heaters using freely patterned nichrome (NiCr) wire. This technique, fabricating heaters by arranging protrusions on a carbon black-polydimethylsiloxane (PDMS) cast and patterning NiCr wire, utilizes cost-effective materials and is not constrained by shape, thereby enabling customized fabrication in both two-dimensional (2D) and three-dimensional (3D). To illustrate its versatility and practicality, a 2D heater with three temperature zones was developed for a portable device capable of automatic thermocycling for polymerase chain reaction (PCR) to detect Escherichia coli (E. coli) O157:H7 pathogen DNA. Furthermore, the detection of the same pathogen was demonstrated using a customized 3D heater surrounding a microtube for loop-mediated isothermal amplification (LAMP). Successful DNA amplification using the proposed heater suggests that the heating technique introduced in this study can be effectively applied to POCT.
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Affiliation(s)
- Juhee Lim
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Won Han
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Le Tran Huy Thang
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Yong Wook Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
- School of Electrical Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Joong Ho Shin
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea
- Major of Biomedical Engineering, Division of Smart Healthcare, College of Information Technology and Convergence, Pukyong National University, Busan 48513, Republic of Korea
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Avivi MY, Touitou N, Rohana H, Lerrer B, Shav-Tal Y, Peretz A, Cohen HY. Nucleic acid hybridization-based detection of pathogenic RNA using microscale thermophoresis. J Biol Chem 2024; 300:105676. [PMID: 38278326 PMCID: PMC10881438 DOI: 10.1016/j.jbc.2024.105676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
Infectious diseases are one of the world's leading causes of morbidity. Their rapid spread emphasizes the need for accurate and fast diagnostic methods for large-scale screening. Here, we describe a robust method for the detection of pathogens based on microscale thermophoresis (MST). The method involves the hybridization of a fluorescently labeled DNA probe to a target RNA and the assessment of thermophoretic migration of the resulting complex in solution within a 2 to 30-time window. We found that the thermophoretic migration of the nucleic acid-based probes is primarily determined by the fluorescent molecule used, rather than the nucleic acid sequence of the probe. Furthermore, a panel of uniformly labeled probes that bind to the same target RNA yields a more responsive detection pattern than a single probe, and moreover, can be used for the detection of specific pathogen variants. In addition, intercalating agents (ICA) can be used to alter migration directionality to improve detection sensitivity and resolving power by several orders of magnitude. We show that this approach can rapidly diagnose viral SARS-CoV2, influenza H1N1, artificial pathogen targets, and bacterial infections. Furthermore, it can be used for anti-microbial resistance testing within 2 h, demonstrating its diagnostic potential for early pathogen detection.
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Affiliation(s)
- Matan Yosef Avivi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Noga Touitou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hanan Rohana
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Tiberias, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Batia Lerrer
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Tiberias, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Haim Yosef Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
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9
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Lin BW, Hong JC, Jiang ZJ, Zhang WQ, Fan QC, Yao XP. Performance of metagenomic next-generation sequencing in cerebrospinal fluid for diagnosis of tuberculous meningitis. J Med Microbiol 2024; 73. [PMID: 38506717 DOI: 10.1099/jmm.0.001818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Purpose. Metagenomic next-generation sequencing (mNGS) has been widely used in the diagnosis of infectious diseases, while its performance in diagnosis of tuberculous meningitis (TBM) is incompletely characterized. The aim of this study was to assess the performance of mNGS in the diagnosis of TBM, and illustrate the sensitivity and specificity of different methods.Methods. We retrospectively recruited TBM patients between January 2021 and March 2023 to evaluate the performance of mNGS on cerebrospinal fluid (CSF) samples, in comparison with conventional microbiological testing, including culturing of Mycobacterium tuberculosis (MTB), acid-fast bacillus (AFB) stain, reverse transcription PCR and Xpert MTB/RIF.Results. Of the 40 enrolled, 34 participants were diagnosed with TBM, including 15(44.12 %) definite and 19(55.88 %) clinical diagnosis based upon clinical manifestations, CSF parameters, brain imaging, pathogen evidence and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MTBC) in 11 CSF samples. In patients with definite TBM, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of mNGS were 78.57, 100, 100, 66.67 and 85 %, respectively. Compared to conventional diagnostic methods, the sensitivity of mNGS (78.57 %) was higher than AFB (0 %), culturing (0 %), RT-PCR (60 %) and Xpert MTB/RIF (14.29 %).Conclusions. Our study indicates that mNGS of CSF exhibited an overall improved sensitivity over conventional diagnostic methods for TBM and can be considered a front-line CSF test.
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Affiliation(s)
- Bi-Wei Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
| | - Jian-Chen Hong
- Department of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Zai-Jie Jiang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
| | - Wei-Qing Zhang
- Department of Laboratory Medicine, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Qi-Chao Fan
- Department of Infectious Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, PR China
| | - Xiang-Ping Yao
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, PR China
- Department of Neurology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, PR China
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10
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Mahfouz M. Revolutionizing Point-of-Care Diagnostics via CRISPR Systems. ACS Synth Biol 2024; 13:411-412. [PMID: 38197893 DOI: 10.1021/acssynbio.3c00763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Affiliation(s)
- Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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11
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Zeng D, Jiao J, Mo T. Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection. Front Microbiol 2024; 15:1355234. [PMID: 38380103 PMCID: PMC10877009 DOI: 10.3389/fmicb.2024.1355234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.
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Affiliation(s)
| | | | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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12
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Veerakone S, W Waite D, Delmiglio C, Kanchiraopally D, Kelly M, Khan S, Liefting L, T Lilly S, Perez-Egusquiza Z, Tang J, Yan J, Tomiczek L, Thompson JR. Detection, Characterization, and Distribution of the First Case of Pepino Mosaic Virus in Aotearoa New Zealand. Plant Dis 2024; 108:291-295. [PMID: 37755419 DOI: 10.1094/pdis-02-23-0381-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
Tomato (Solanum lycopersicum L., family Solanaceae) represents one of the most economically valuable horticultural crops worldwide. Tomato production is affected by numerous emerging plant viruses. We identified, for the first time in New Zealand (NZ), Pepino mosaic virus (PepMV) in greenhouse grown tomato crops using a combination of methods from electron microscopy and herbaceous indexing to RT-qPCR and high-throughput sequencing. Phylogenetic and genomic analysis of a near-complete PepMV genome determined that the detected strain belonged to the mild form of the CH2 lineage of the virus. Subsequently, a delimiting survey of PepMV was conducted, and PepMV was detected at four additional locations. PCR-derived sequences obtained from samples collected from different greenhouses and from herbaceous indicator plants were identical to the original sequence. Since PepMV has never been reported in NZ before, seed pathways are speculated to be the most likely source of entry into the country.
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Affiliation(s)
- Stella Veerakone
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - David W Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Catia Delmiglio
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Deepika Kanchiraopally
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Michelle Kelly
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Subuhi Khan
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Lia Liefting
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Sonia T Lilly
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Zoila Perez-Egusquiza
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Joe Tang
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Juncong Yan
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
| | - Laura Tomiczek
- Biosecurity Surveillance and Incursion Investigation, MPI, Auckland 1140, New Zealand
| | - Jeremy R Thompson
- Plant Health and Environment Laboratory, Ministry for Primary Industries (MPI), Auckland 1140, New Zealand
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13
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Xie N, Lin Y, Li P, Zhao J, Li J, Wang K, Yang L, Jia L, Wang Q, Li P, Song H. Simultaneous identification of DNA and RNA pathogens using metagenomic sequencing in cases of severe acute respiratory infection. J Med Virol 2024; 96:e29406. [PMID: 38373115 DOI: 10.1002/jmv.29406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/21/2024]
Abstract
Metagenomic next-generation sequencing (mNGS) is a valuable technique for identifying pathogens. However, conventional mNGS requires the separate processing of DNA and RNA genomes, which can be resource- and time-intensive. To mitigate these impediments, we propose a novel method called DNA/RNA cosequencing that aims to enhance the efficiency of pathogen detection. DNA/RNA cosequencing uses reverse transcription of total nucleic acids extracted from samples by using random primers, without removing DNA, and then employs mNGS. We applied this method to 85 cases of severe acute respiratory infections (SARI). Influenza virus was identified in 13 cases (H1N1: seven cases, H3N2: three cases, unclassified influenza type: three cases) and was not detected in the remaining 72 samples. Bacteria were present in all samples. Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii were detected in four influenza-positive samples, suggesting coinfections. The sensitivity and specificity for detecting influenza A virus were 73.33% and 95.92%, respectively. A κ value of 0.726 indicated a high level of concordance between the results of DNA/RNA cosequencing and SARI influenza virus monitoring. DNA/RNA cosequencing enhanced the efficiency of pathogen detection, providing a novel capability to strengthen surveillance and thereby prevent and control infectious disease outbreaks.
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Affiliation(s)
- Nana Xie
- AnHui Medical University, Hefei, China
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
| | - Yanfeng Lin
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
| | - Jiachen Zhao
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Jinhui Li
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
| | - Kaiying Wang
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Peng Li
- AnHui Medical University, Hefei, China
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
| | - Hongbin Song
- AnHui Medical University, Hefei, China
- Chinese PLA Center for Disease Control and Prevention of PLA, Beijing, China
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14
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Kandukuri TR, Prattis I, Oluwasanya P, Occhipinti LG. Pathogen Detection via Impedance Spectroscopy-Based Biosensor. Sensors (Basel) 2024; 24:856. [PMID: 38339574 PMCID: PMC10857222 DOI: 10.3390/s24030856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
This paper presents the development of a miniaturized sensor device for selective detection of pathogens, specifically Influenza A Influenza virus, as an enveloped virus is relatively vulnerable to damaging environmental impacts. In consideration of environmental factors such as humidity and temperature, this particular pathogen proves to be an ideal choice for our study. It falls into the category of pathogens that pose greater challenges due to their susceptibility. An impedance biosensor was integrated into an existing platform and effectively separated and detected high concentrations of airborne pathogens. Bio-functionalized hydrogel-based detectors were utilized to analyze virus-containing particles. The sensor device demonstrated high sensitivity and specificity when exposed to varying concentrations of Influenza A virus ranging from 0.5 to 50 μg/mL. The sensitivity of the device for a 0.5 μg/mL analyte concentration was measured to be 695 Ω· mL/μg. Integration of this pathogen detector into a compact-design air quality monitoring device could foster the advancement of personal exposure monitoring applications. The proposed sensor device offers a promising approach for real-time pathogen detection in complex environmental settings.
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Affiliation(s)
| | | | - Pelumi Oluwasanya
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge CB3 0FA, UK; (T.R.K.); (I.P.)
| | - Luigi G. Occhipinti
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge CB3 0FA, UK; (T.R.K.); (I.P.)
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15
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Liu Y, Wang Z, Wang Z, Zhou J, Han J, Lu C, Liu B, Yu R, Sun X, Zhang Z, Wang R, Su X. Rapid and simultaneous multiepitope antigen-based detection of Enterococcus by microscale thermophoresis and immunomagnetic separation. Front Microbiol 2024; 15:1341451. [PMID: 38322321 PMCID: PMC10844561 DOI: 10.3389/fmicb.2024.1341451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024] Open
Abstract
Background Generally, enterococci bacteria cause nosocomial infections and are major indicators of bacterial contamination in marine bathing beach. However, a method for the rapid and simultaneous detection of multiple pathogenic enterococci has not been developed on account of the wide variety of pathogenic enterococci and their existence in complex matrices. Methods Immunoinformatics tools were used to design a multi-epitope antigen for the detection of various pathogenic enterococci by using the sequence of dltD gene on enterococci lipoteichoic acid (LTA) surface, which is associated with toxicological effects. The multi-epitopes included enterococci such as Enterococcus faecalis, E. gallinarum, E. raffinosus, E. durans, E. faecium, E. hirae, E. thailandicus, E. casseliflavus, E. avium, E. mundtii, E. lactis, E. solitarius, E. pseudoavium, and E. malodoratum. Microscale thermophoresis (MST) and western blot were carried out to detect the affinity between multi-epitope antigens and antibodies and between multi-epitope antibodies and bacteria. Furthermore, the detection of pathogenic enterococci was carried out by using immunomagnetic beads (IMBs) and immune chromatographic test strip (ICTS). Results The multi-epitope antibody had a satisfactory affinity to the antigen and enterococci. IMBs and ICTS were detected with a minimum of 101 CFU/mL and showed incompatibility for Vibrio parahemolyticus, V. vulnifcus, V. harveyi, V. anguillarum, and Edwardsiella tarda. Implication The present study demonstrated that the multi-epitope antigens exhibited excellent specificity and sensitivity, making them highly suitable for efficient on-site screening of enterococci bacteria in marine bathing beaches.
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Affiliation(s)
- Yan Liu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Ziyan Wang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Ze Wang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jiaojiao Han
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Chenyang Lu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Bing Liu
- Vigor Health Products Co., Ltd., Shenzhen, China
| | - Rongxian Yu
- Vigor Health Products Co., Ltd., Shenzhen, China
| | - Xiaoling Sun
- Vigor Health Products Co., Ltd., Shenzhen, China
| | - Zhen Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Rixin Wang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Xiurong Su
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
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16
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Xie M, Chen T, Cai Z, Lei B, Dong C. An All-in-One Platform for On-Site Multiplex Foodborne Pathogen Detection Based on Channel-Digital Hybrid Microfluidics. Biosensors (Basel) 2024; 14:50. [PMID: 38248427 PMCID: PMC10813315 DOI: 10.3390/bios14010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Recently, significant progress has been made in the development of microdevices for point-of-care infectious disease detection. However, most microdevices only allow limited steps, such as DNA amplification on the chip, while sample preparation, such as lysis and DNA extraction, is conducted off the chip using the traditional method. In this study, an all-in-one platform was developed, which incorporated all necessary procedures for nucleic acid detection. Our on-chip DNA extraction method utilized the magnetic bead-based technology on a hybrid channel-digital microfluidics (C-DMF) microdevice. It yielded high recovery rates, varying from 88.43% to 95.83%, with pathogen concentrations of 103-106 CFU/mL. In particular, the on-chip method exhibited significantly higher efficacy compared to the traditional off-chip manual method, for the DNA extraction of E. coli and S. aureus, representing Gram-negative and Gram-positive bacteria, respectively, at a sample concentration of 103 CFU/mL. To address the need for rapid and accessible diagnostics, colorimetric LAMP amplification was integrated into the proposed microdevice. The results were visually detectable with the naked eye, making it user-friendly for non-specialists. In addition, this platform demonstrated impressive sensitivity in simultaneously detecting common foodborne pathogens in spiked meat samples, achieving the LOD of 102-103 CFU/mL. The entire process, from sampling to result, was fully automated and only required approximately 60 min, offering promising applicability in resource-limited and on-site testing scenarios.
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Affiliation(s)
- Mei Xie
- Department of Life Sciences, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519000, China;
- Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | | | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Bo Lei
- Department of Life Sciences, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519000, China;
| | - Cheng Dong
- School of Intelligent Systems Science and Engineering, Jinan University, Zhuhai 519000, China
- Department of Biomedical Engineering, Jinan University, Guangzhou 510632, China
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17
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Hao L, Bian W, Qing Z, Ma T, Li H, Xu P, Wen P. Will previous antimicrobial therapy reduce the positivity rate of metagenomic next-generation sequencing in periprosthetic joint infections? A clinical study. Front Cell Infect Microbiol 2024; 13:1295962. [PMID: 38274732 PMCID: PMC10808557 DOI: 10.3389/fcimb.2023.1295962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a culture-independent massively parallel DNA sequencing technology and it has been widely used for rapid etiological diagnosis with significantly high positivity rate. Currently, clinical studies on evaluating the influence of previous antimicrobial therapy on positivity rate of mNGS in PJIs are rarely reported. The present study aimed to investigate whether the positivity rate of mNGS is susceptible to previous antimicrobial therapy. Methods We performed a prospective trial among patients who undergone hip or knee surgery due to periprosthetic joint infection (PJI) to compare the positivity rate of culture and mNGS between cases with and without previous antimicrobial therapy, and the positivity rates between cases with different antimicrobial-free intervals were also analysed. Results Among 131 included PJIs, 91 (69.5%) had positive cultures and 115 (87.8%) had positive mNGS results. There was no significant difference in the positivity rate of deep-tissue culture and synovial fluid mNGS between cases with and without previous antimicrobial therapy. The positivity rate of synovial fluid culture was higher in cases with previous antimicrobial therapy. The positivity rates of mNGS in synovial fluid decreased as the antimicrobial-free interval ranged from 4 to 14 days to 0 to 3 days. Conclusion mNGS is more advantageous than culture with a higher pathogen detection rate. However, our data suggested that antimicrobial agents may need to be discontinued more than 3 days before sampling to further increase the positivity rate of mNGS for PJIs.
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Affiliation(s)
- Linjie Hao
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Weiguo Bian
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zhong Qing
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Tao Ma
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Hui Li
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Peng Xu
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Pengfei Wen
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
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18
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Zhang H, Zhao H, Cao L, Yu B, Wei J, Pan G, Bao J, Zhou Z. Harnessing multiplex crRNA enables an amplification-free/CRISPR-Cas12a-based diagnostic methodology for Nosema bombycis. Microbiol Spectr 2024; 12:e0301423. [PMID: 38014967 PMCID: PMC10783057 DOI: 10.1128/spectrum.03014-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE The multiplex-crRNA CRISPR/Cas12a detection method saves hands-on time, reduces the risk of aerosol pollution, and can be directly applied to detecting silkworms infected with Nosema bombycis. This study provides a new approach for the inspection and quarantine of silkworm pébrine disease in sericulture and provides a new method for the detection of other pathogens.
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Affiliation(s)
- Huarui Zhang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Huijuan Zhao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Lu Cao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Bin Yu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Junhong Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Jialing Bao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
- College of Life Science, Chongqing Normal University, Chongqing, China
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Borowik P, Dyshko V, Tkaczyk M, Okorski A, Polak-Śliwińska M, Tarakowski R, Stocki M, Stocka N, Oszako T. Analysis of Wheat Grain Infection by Fusarium Mycotoxin-Producing Fungi Using an Electronic Nose, GC-MS, and qPCR. Sensors (Basel) 2024; 24:326. [PMID: 38257418 PMCID: PMC10820217 DOI: 10.3390/s24020326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024]
Abstract
Fusarium graminearum and F. culmorum are considered some of the most dangerous pathogens of plant diseases. They are also considerably dangerous to humans as they contaminate stored grain, causing a reduction in yield and deterioration in grain quality by producing mycotoxins. Detecting Fusarium fungi is possible using various diagnostic methods. In the manuscript, qPCR tests were used to determine the level of wheat grain spoilage by estimating the amount of DNA present. High-performance liquid chromatography was performed to determine the concentration of DON and ZEA mycotoxins produced by the fungi. GC-MS analysis was used to identify volatile organic components produced by two studied species of Fusarium. A custom-made, low-cost, electronic nose was used for measurements of three categories of samples, and Random Forests machine learning models were trained for classification between healthy and infected samples. A detection performance with recall in the range of 88-94%, precision in the range of 90-96%, and accuracy in the range of 85-93% was achieved for various models. Two methods of data collection during electronic nose measurements were tested and compared: sensor response to immersion in the odor and response to sensor temperature modulation. An improvement in the detection performance was achieved when the temperature modulation profile with short rectangular steps of heater voltage change was applied.
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Affiliation(s)
- Piotr Borowik
- Faculty of Physics, Warsaw University of Technology, ul. Koszykowa 75, 00-662 Warszawa, Poland;
| | - Valentyna Dyshko
- Ukrainian Research Institute of Forestry and Forest Melioration Named after G. M. Vysotsky, 61024 Kharkiv, Ukraine;
| | - Miłosz Tkaczyk
- Forest Protection Department, Forest Research Institute, ul. Braci Leśnej 3, 05-090 Sękocin Stary, Poland; (M.T.); (T.O.)
| | - Adam Okorski
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 5, 10-727 Olsztyn, Poland;
| | - Magdalena Polak-Śliwińska
- Department of Commodity Science and Food Analysis, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Heweliusza 6, 10-719 Olsztyn, Poland
| | - Rafał Tarakowski
- Faculty of Physics, Warsaw University of Technology, ul. Koszykowa 75, 00-662 Warszawa, Poland;
| | - Marcin Stocki
- Institute of Forest Sciences, Faculty of Civil Engineering and Environmental Sciences, Białystok University of Technology, ul. Wiejska 45E, 15-351 Białystok, Poland; (M.S.); (N.S.)
| | - Natalia Stocka
- Institute of Forest Sciences, Faculty of Civil Engineering and Environmental Sciences, Białystok University of Technology, ul. Wiejska 45E, 15-351 Białystok, Poland; (M.S.); (N.S.)
| | - Tomasz Oszako
- Forest Protection Department, Forest Research Institute, ul. Braci Leśnej 3, 05-090 Sękocin Stary, Poland; (M.T.); (T.O.)
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20
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Overbeek R, Leitl CJ, Stoll SE, Wetsch WA, Kammerer T, Mathes A, Böttiger BW, Seifert H, Hart D, Dusse F. The Value of Next-Generation Sequencing in Diagnosis and Therapy of Critically Ill Patients with Suspected Bloodstream Infections: A Retrospective Cohort Study. J Clin Med 2024; 13:306. [PMID: 38256440 PMCID: PMC10816005 DOI: 10.3390/jcm13020306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Bloodstream infection (BSI), a frequent cause of severe sepsis, is a life-threatening complication in critically ill patients and still associated with a high mortality rate. Rapid pathogen identification from blood is crucial for an early diagnosis and the treatment of patients with suspected BSI. For this purpose, novel diagnostic tools on the base of genetic analysis have emerged for clinical application. The aim of this study was to assess the diagnostic value of additional next-generation sequencing (NGS) pathogen test for patients with suspected BSI in a surgical ICU and its potential impact on antimicrobial therapy. In this retrospective single-centre study, clinical data and results from blood culture (BC) and NGS pathogen diagnostics were analysed for ICU patients with suspected BSI. Consecutive changes in antimicrobial therapy and diagnostic procedures were evaluated. Results: 41 cases with simultaneous NGS and BC sampling were assessed. NGS showed a statistically non-significant higher positivity rate than BC (NGS: 58.5% (24/41 samples) vs. BC: 21.9% (9/41); p = 0.056). NGS detected eight different potentially relevant bacterial species, one fungus and six different viruses, whereas BC detected four different bacterial species and one fungus. NGS results affected antimicrobial treatment in 7.3% of cases. Conclusions: NGS-based diagnostics have the potential to offer a higher positivity rate than conventional culture-based methods in patients with suspected BSI. Regarding the high cost, their impact on anti-infective therapy is currently limited. Larger randomized prospective clinical multicentre studies are required to assess the clinical benefit of this novel diagnostic technology.
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Affiliation(s)
- Remco Overbeek
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Christoph J. Leitl
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Sandra E. Stoll
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Wolfgang A. Wetsch
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Tobias Kammerer
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Alexander Mathes
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Bernd W. Böttiger
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
| | - Dominique Hart
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Fabian Dusse
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
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21
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Khan S, Monteiro JK, Prasad A, Filipe CDM, Li Y, Didar TF. Material Breakthroughs in Smart Food Monitoring: Intelligent Packaging and On-Site Testing Technologies for Spoilage and Contamination Detection. Adv Mater 2024; 36:e2300875. [PMID: 37085965 DOI: 10.1002/adma.202300875] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/26/2023] [Indexed: 05/03/2023]
Abstract
Despite extensive commercial and regulatory interventions, food spoilage and contamination continue to impose massive ramifications on human health and the global economy. Recognizing that such issues will be significantly eliminated by the accurate and timely monitoring of food quality markers, smart food sensors have garnered significant interest as platforms for both real-time, in-package food monitoring and on-site commercial testing. In both cases, the sensitivity, stability, and efficiency of the developed sensors are largely informed by underlying material design, driving focus toward the creation of advanced materials optimized for such applications. Herein, a comprehensive review of emerging intelligent materials and sensors developed in this space is provided, through the lens of three key food quality markers - biogenic amines, pH, and pathogenic microbes. Each sensing platform is presented with targeted consideration toward the contributions of the underlying metallic or polymeric substrate to the sensing mechanism and detection performance. Further, the real-world applicability of presented works is considered with respect to their capabilities, regulatory adherence, and commercial potential. Finally, a situational assessment of the current state of intelligent food monitoring technologies is provided, discussing material-centric strategies to address their existing limitations, regulatory concerns, and commercial considerations.
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Affiliation(s)
- Shadman Khan
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Jonathan K Monteiro
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8N 3Z5, Canada
| | - Akansha Prasad
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L7, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Mechanical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
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22
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Abdelrazek S, Bush E, Oliver C, Liu H, Sharma P, Johnson MA, Donegan MA, Almeida RPP, Nita M, Vinatzer BA. A Survey of Xylella fastidiosa in the U.S. State of Virginia Reveals Wide Distribution of Both Subspecies fastidiosa and multiplex in Grapevine. Phytopathology 2024; 114:35-46. [PMID: 37530473 DOI: 10.1094/phyto-06-23-0212-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Global travel and trade in combination with climate change are expanding the geographic distribution of plant pathogens. The bacterium Xylella fastidiosa is a prime example. Native to the Americas, it has spread to Europe, Asia, and the Middle East. To assess the risk that pathogen introductions pose to crops in newly invaded areas, it is key to survey their diversity, host range, and disease incidence in relation to climatic conditions where they are already present. We performed a survey of X. fastidiosa in grapevine in Virginia using a combination of quantitative PCR, multilocus sequencing, and metagenomics. We also analyzed samples from deciduous trees with leaf scorch symptoms. X. fastidiosa subspecies fastidiosa was identified in grapevines in all regions of the state, even in Northern Virginia, where the temperature was below -9°C for 10 days per year on average in the years preceding sampling. Unexpectedly, we also found for the first time grapevine samples infected with X. fastidiosa subspecies multiplex (Xfm). The Xfm lineage found in grapevines had been previously isolated from blueberries in the Southeastern United States and was distinct from that found in deciduous trees in Virginia. The obtained results will be important for risk assessment of X. fastidiosa introductions in other parts of the world.
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Affiliation(s)
- Sahar Abdelrazek
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
| | - Elizabeth Bush
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
| | - Charlotte Oliver
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Tech, Winchester, VA 22602
| | - Haijie Liu
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
| | - Parul Sharma
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061
| | - Marcela A Johnson
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061
| | - Monica A Donegan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720
| | - Mizuho Nita
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Tech, Winchester, VA 22602
| | - Boris A Vinatzer
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA 24061
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23
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Lin M, Dan H. Design of a novel affinity probe using the cell wall-binding domain of a Listeria monocytogenes autolysin for pathogen detection. Microbiol Spectr 2023; 11:e0535622. [PMID: 37795989 PMCID: PMC10714868 DOI: 10.1128/spectrum.05356-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/18/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Human listeriosis is caused by consuming foods contaminated with the bacterial pathogen Listeria monocytogenes, leading to the development of a severe and life-threatening foodborne illness. Detection of L. monocytogenes present in food and food processing environments is crucial for preventing Listeria infection. The L. monocytogenes peptidoglycan hydrolase IspC anchors non-covalently to the bacterial surface through its C-terminal cell wall-binding domain (CWBD), CWBDIspC. This study explored the surface binding property of CWBDIspC to design, construct, characterize, and assess an affinity molecular probe for detecting L. monocytogenes. CWBDIspC recognized a cell wall ligand lipoteichoic acid that remains evenly displayed and mostly unoccupied on the bacterial surface for interaction with the exogenously added CWBDIspC. CWBDIspC, when fused to the enhanced green fluorescent protein reporter or covalently conjugated onto magnetic beads, exhibited the functionality as an antibody alternative for rapid detection and efficient separation of the pathogen.
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Affiliation(s)
- Min Lin
- Ottawa Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
- Department of Biochemistry Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hanhong Dan
- Ottawa Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, Ontario, Canada
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24
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Rao G, Capone D, Zhu K, Knoble A, Linden Y, Clark R, Lai A, Kim J, Huang CH, Bivins A, Brown J. Simultaneous detection and quantification of multiple pathogen targets in wastewater. medRxiv 2023:2023.06.23.23291792. [PMID: 37425908 PMCID: PMC10327253 DOI: 10.1101/2023.06.23.23291792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Wastewater-based epidemiology has emerged as a critical tool for public health surveillance, building on decades of environmental surveillance work for pathogens such as poliovirus. Work to date has been limited to monitoring a single pathogen or small numbers of pathogens in targeted studies; however, few studies consider simultaneous quantitative analysis of a wide variety of pathogens, which could greatly increase the utility of wastewater surveillance. We developed a novel quantitative multi-pathogen surveillance approach (35 pathogen targets including bacteria, viruses, protozoa, and helminths) using TaqMan Array Cards (TAC) and applied the method on concentrated wastewater samples collected at four wastewater treatment plants in Atlanta, GA from February to October of 2020. From sewersheds serving approximately 2 million people, we detected a wide range of targets including many we expected to find in wastewater (e.g., enterotoxigenic E. coli and Giardia in 97% of 29 samples at stable concentrations) as well as unexpected targets including Strongyloides stercoralis (a human threadworm rarely observed in the USA). Other notable detections included SARS-CoV-2, but also several pathogen targets that are not commonly included in wastewater surveillance like Acanthamoeba spp., Balantidium coli, Entamoeba histolytica, astrovirus, norovirus, and sapovirus. Our data suggest broad utility in expanding the scope of enteric pathogen surveillance in wastewaters, with potential for application in a variety of settings where pathogen quantification in fecal waste streams can inform public health surveillance and selection of control measures to limit infections.
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Affiliation(s)
- Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Drew Capone
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Kevin Zhu
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abigail Knoble
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yarrow Linden
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ryan Clark
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Lai
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhee Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ching-Hua Huang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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25
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Liu Y, Wang X, Xu J, Yang Q, Zhu H, Yang J. Diagnostic value of metagenomic next-generation sequencing of lower respiratory tract specimen for the diagnosis of suspected Pneumocystis jirovecii pneumonia. Ann Med 2023; 55:2232358. [PMID: 37403381 DOI: 10.1080/07853890.2023.2232358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/06/2023] Open
Abstract
AIM To evaluate diagnostic performance of metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PCP), in comparison with polymerase chain reaction (PCR), Gomori methenamine silver (GMS) staining and serum 1,3-β-d-Glucan (BG) assay. METHODS 52 PCP patients and 103 patients with non-pneumocystic jirovecii pneumonia (non-PCP) were enrolled, and comparative analysis was conducted of different diagnostic tests. Clinical features and co-pathogen characteristics were reviewed. RESULTS The diagnostic sensitivity (92.3%) and specificity (87.4%) of mNGS did not show significant differences compared with that of PCR while mNGS had the advantage over PCR in the detection of co-pathogens. Despite its excellent specificity, the sensitivity of GMS staining (9.3%) was inferior to that of mNGS (p < .001). The combination of mNGS with serum BG statistically outperformed mNGS or serum BG alone in the areas under the receiver operating characteristic curves (AUCs, p = .0013 and p = .0015, respectively). Notably, all the blood samples showing positive mNGS for Pneumocystis jirovecii came from PCP patients. The leading co-pathogens among patients with PCP were cytomegalovirus, Epstein-Barr virus and Torque teno virus. CONCLUSIONS mNGS shows superiority over several common clinical methods in the diagnosis of suspected PCP. Serum BG in conjunction with mNGS further improved the diagnostic efficacy of mNGS.
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Affiliation(s)
- Yang Liu
- Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaoning Wang
- Emergency Department, Zhengzhou Central Hospital, Zhengzhou, China
| | - Jun Xu
- Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Huadong Zhu
- Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jing Yang
- Emergency Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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26
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Stein A, Soukup D, Rath PM, Felderhoff-Müser U. Diagnostic Accuracy of Multiplex Polymerase Chain Reaction in Early Onset Neonatal Sepsis. Children (Basel) 2023; 10:1809. [PMID: 38002900 PMCID: PMC10670518 DOI: 10.3390/children10111809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Early onset neonatal sepsis is a significant contributor to neonatal morbidity and mortality. Although blood cultures remain the diagnostic gold standard, they detect pathogens in only a minority of suspected cases. This study compared the accuracy of blood cultures with a rapid multiplex PCR test. Newborns at risk of neonatal sepsis were prospectively screened as recommended per national guidelines. Evaluations included laboratory parameters (CrP, IL6, differential blood count), blood culture, and a molecular multiplex PCR test (ROCHE LightCycler SeptiFast®) identifying 20 common microbial agents. Blood samples were taken simultaneously from umbilical cord or venous sources on the first day of life. Of 229 infants included, 69% were born preterm. Blood culture and multiplex PCR sensitivity were 7.4% and 14.8%, respectively. Specificity, negative and positive predictive values between methods showed no significant variance, although multiplex PCR had more false positives due to contamination. The limited sensitivity of blood cultures for early onset neonatal sepsis is concerning. Despite quicker results, multiplex PCR does not enhance diagnostic accuracy or antibiotic therapy guidance, thus it cannot be recommended for this indication.
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Affiliation(s)
- Anja Stein
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
| | - Daniel Soukup
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
- Service de Réanimation Pédiatrique, Centre Hospitalier Universitaire de Bordeaux, Place Amélie Raba Léon, 33000 Bordeaux, France
| | - Peter-Michael Rath
- Institute for Medical Microbiology, University Hospital Essen, Hufelandstraße 55, 45147 Essen, Germany;
| | - Ursula Felderhoff-Müser
- Department of Pediatrics I, Neonatology and Experimental Perinatal Neurosciences, Center for Translational and Behavioral Neuroscience, CTNBS, University Hospital Essen, Faculty of Medicine, University Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany; (D.S.); (U.F.-M.)
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27
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Huang X, Li L, Chen Z, Yu H, You X, Kong N, Tao W, Zhou X, Huang J. Nanomedicine for the Detection and Treatment of Ocular Bacterial Infections. Adv Mater 2023; 35:e2302431. [PMID: 37231939 DOI: 10.1002/adma.202302431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Ocular bacterial infection is a prevalent cause of blindness worldwide, with substantial consequences for normal human life. Traditional treatments for ocular bacterial infections areless effective, necessitating the development of novel techniques to enable accurate diagnosis, precise drug delivery, and effective treatment alternatives. With the rapid advancement of nanoscience and biomedicine, increasing emphasis has been placed on multifunctional nanosystems to overcome the challenges posed by ocular bacterial infections. Given the advantages of nanotechnology in the biomedical industry, it can be utilized to diagnose ocular bacterial infections, administer medications, and treat them. In this review, the recent advancements in nanosystems for the detection and treatment of ocular bacterial infections are discussed; this includes the latest application scenarios of nanomaterials for ocular bacterial infections, in addition to the impact of their essential characteristics on bioavailability, tissue permeability, and inflammatory microenvironment. Through an in-depth investigation into the effect of sophisticated ocular barriers, antibacterial drug formulations, and ocular metabolism on drug delivery systems, this review highlights the challenges faced by ophthalmic medicine and encourages basic research and future clinical transformation based on ophthalmic antibacterial nanomedicine.
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Affiliation(s)
- Xiaomin Huang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200030, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China
- Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Luoyuan Li
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200030, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China
- The Eighth Affiliated Hospital Sun Yat-sen University, Shenzhen, Guangdong, 518033, P. R. China
| | - Zhongxing Chen
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200030, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China
| | - Haoyu Yu
- The Eighth Affiliated Hospital Sun Yat-sen University, Shenzhen, Guangdong, 518033, P. R. China
| | - Xinru You
- Center for Nanomedicine and Department of Anesthesiology Brigham and Women's Hospital Harvard Medical School, Boston, MA, 02115, USA
| | - Na Kong
- Center for Nanomedicine and Department of Anesthesiology Brigham and Women's Hospital Harvard Medical School, Boston, MA, 02115, USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology Brigham and Women's Hospital Harvard Medical School, Boston, MA, 02115, USA
| | - Xingtao Zhou
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200030, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China
| | - Jinhai Huang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University; Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, 200030, China
- Shanghai Research Center of Ophthalmology and Optometry, Shanghai, 200030, China
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Otabi H, Miura H, Uryu H, Kobayashi-Harada R, Abe K, Nakano K, Umeyama K, Hasegawa K, Tsukahara T, Nagashima H, Inoue R. Development of a panel for detection of pathogens in xenotransplantation donor pigs. Xenotransplantation 2023; 30:e12825. [PMID: 37771249 DOI: 10.1111/xen.12825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
There have been high expectations in recent years of using xenotransplantation and regenerative medicine to treat humans, and pigs have been utilized as the donor model. Pigs used for these clinical applications must be microbiologically safe, that is, free of infectious pathogens, to prevent infections not only in livestock, but also in humans. Currently, however, the full spectrum of pathogens that can infect to the human host or cause disease in transplanted porcine organs/cells has not been fully defined. In the present study, we thus aimed to develop a larger panel for the detection of pathogens that could potentially infect xenotransplantation donor pigs. Our newly developed panel, which consisted of 76 highly sensitive PCR detection assays, was able to detect 41 viruses, 1 protozoa, and a broad range of bacteria (by use of universal 16S rRNA primers). The applicability of this panel was validated using blood samples from uterectomy-born piglets, and pathogens suspected to be vertically transmitted from sows to piglets were successfully detected. We estimate that, at least for viruses and bacteria, the number of target pathogens detected by the developed screening panel should suffice to meet the microbiological safety levels required worldwide for xenotransplantation and/or regenerative therapy. This panel provides greater diagnosis options to produce donor pigs so that it would render unnecessary to screen for all pathogens listed. Instead, the new panel could be utilized to detect only required pathogens within a given geographic range where the donor pigs for xenotransplantation have been and/or are being developed.
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Affiliation(s)
- Hikari Otabi
- Laboratory of Animal Science, Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Osaka, Japan
| | - Hiroto Miura
- Laboratory of Animal Science, Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Osaka, Japan
| | - Haruka Uryu
- Laboratory of Animal Science, Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Osaka, Japan
- Laboratory of Animal Science, Kyoto Prefectural University, Kyoto, Japan
| | | | - Kanako Abe
- Laboratory of Animal Science, Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Osaka, Japan
| | - Kazuaki Nakano
- Meiji University International Institute for Bio-Resource Research, Kawasaki, Japan
| | - Kazuhiro Umeyama
- Meiji University International Institute for Bio-Resource Research, Kawasaki, Japan
| | - Koki Hasegawa
- Laboratory of Medical Bioengineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | | | - Hiroshi Nagashima
- Meiji University International Institute for Bio-Resource Research, Kawasaki, Japan
- Laboratory of Medical Bioengineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Osaka, Japan
- Laboratory of Animal Science, Kyoto Prefectural University, Kyoto, Japan
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29
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Román-Reyna V, Curland RD, Velez-Negron Y, Ledman KE, Gutierrez-Castillo DE, Beutler J, Butchacas J, Brar GS, Roberts R, Dill-Macky R, Jacobs JM. Development of Genome-Driven, Lifestyle-Informed Markers for Identification of the Cereal-Infecting Pathogens Xanthomonas translucens Pathovars undulosa and translucens. Phytopathology 2023; 113:2110-2118. [PMID: 36224751 DOI: 10.1094/phyto-07-22-0262-sa] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacterial leaf streak, bacterial blight, and black chaff caused by Xanthomonas translucens pathovars are major diseases affecting small grains. Xanthomonas translucens pv. translucens and X. translucens pv. undulosa are seedborne pathogens that cause similar symptoms on barley, but only X. translucens pv. undulosa causes bacterial leaf streak of wheat. Recent outbreaks of X. translucens have been a concern for wheat and barley growers in the Northern Great Plains; however, there are limited diagnostic tools for pathovar differentiation. We developed a multiplex PCR based on whole-genome differences to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. We validated the primers across different Xanthomonas and non-Xanthomonas strains. To our knowledge, this is the first multiplex PCR to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. These molecular tools will support disease management strategies enabling detection and pathovar incidence analysis of X. translucens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Verónica Román-Reyna
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Yesenia Velez-Negron
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | | | - Jonathan Beutler
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Jules Butchacas
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Gurcharn Singh Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Robyn Roberts
- Agricultural Biology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Jonathan M Jacobs
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
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30
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Su CC, Fung JA, Chang RJ, Chang CJ, Jan FJ, Shih HT, Chen J. TaqMan Quantitative PCR Detection of Xylella taiwanensis in Taiwan. Plant Dis 2023; 107:3051-3056. [PMID: 36890125 DOI: 10.1094/pdis-01-23-0064-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Xylella taiwanensis (Xt) is a nutritionally fastidious bacterial pathogen causing pear leaf scorch disease (PLSD) in Taiwan. The disease causes early defoliation, loss of tree vigor, and reduction in fruit yield and quality. No cure for PLSD is available. The only option for growers to control the disease is to use pathogen-free propagation material, which requires early and accurate detection of Xt. Currently, only one simplex PCR method is available for the diagnosis of PLSD. We developed five Xt-specific TaqMan quantitative PCR (TaqMan qPCR) systems (primers-probe sets) for the detection of Xt. The PCR systems target three conserved genomic loci commonly used in bacterial pathogen detection: the 16S rRNA gene (rrs), the 16S-23S rRNA intergenic transcribed sequence (16S-23S rRNA ITS), and the DNA gyrase gene (gyrB). BLAST analysis using the GenBank nr sequence database, including whole genome sequences of 88 Xanthomonas campestris pv. campestris (Xcc) strains, 147 X. fastidiosa (Xf) strains, and 32 Xt strains, showed that all primer and probe sequences were specific only to Xt. Single nucleotide polymorphisms (SNPs) provided the primer/probe specificity to Xt. The PCR systems were evaluated by using DNA samples from pure cultures of two Xt strains, one Xf strain, one Xcc strain, and 140 plant samples collected from 23 pear orchards in four counties in Taiwan. The two-copy rrs and 16S-23S rRNA ITS-based PCR systems (Xt803-F/R, Xt731-F/R, and Xt16S-F/R) showed higher detection sensitivity than the two single-copy gyrB-based systems (XtgB1-F/R and XtgB2-F/R). A metagenomic analysis of a representative PLSD leaf sample detected the presence of non-Xt proteobacteria and fungal pathogens that should be taken into consideration in PLSD, as they might interfere with diagnosis.
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Affiliation(s)
- Chiou-Chu Su
- Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Wufeng, Taichung 41358, Taiwan
| | - Jie-An Fung
- Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Wufeng, Taichung 41358, Taiwan
| | - Ruey-Jang Chang
- Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Wufeng, Taichung 41358, Taiwan
| | - Chung-Jan Chang
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223, U.S.A
| | - Fuh-Jyh Jan
- Department of Plant Pathology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Hsien-Tzung Shih
- Applied Zoology Division, Taiwan Agricultural Research Institute, Council of Agriculture, Wufeng, Taichung 41362, Taiwan
| | - Jianchi Chen
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, U.S.A
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Prasad A, Khan S, Monteiro JK, Li J, Arshad F, Ladouceur L, Tian L, Shakeri A, Filipe CDM, Li Y, Didar TF. Advancing In Situ Food Monitoring through a Smart Lab-in-a-Package System Demonstrated by the Detection of Salmonella in Whole Chicken. Adv Mater 2023; 35:e2302641. [PMID: 37358057 DOI: 10.1002/adma.202302641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/16/2023] [Indexed: 06/27/2023]
Abstract
With food production shifting away from traditional farm-to-table approaches to efficient multistep supply chains, the incidence of food contamination has increased. Consequently, pathogen testing via inefficient culture-based methods has increased, despite its lack of real-time capabilities and need for centralized facilities. While in situ pathogen detection would address these limitations and enable individual product monitoring, accurate detection within unprocessed, packaged food products without user manipulation has proven elusive. Herein, "Lab-in-a-Package" is presented, a platform capable of sampling, concentrating, and detecting target pathogens within closed food packaging, without intervention. This system consists of a newly designed packaging tray and reagent-infused membrane that can be paired universally with diverse pathogen sensors. The inclined food packaging tray maximizes fluid localization onto the sensing interface, while the membrane acts as a reagent-immobilizing matrix and an antifouling barrier for the sensor. The platform is substantiated using a newly discovered Salmonella-responsive nucleic acid probe, which enables hands-free detection of 103 colony forming units (CFU) g-1 target pathogen in a packaged whole chicken. The platform remains effective when contamination is introduced with toolsand surfaces, ensuring widespread efficacy. Its real-world use for in situ detection is simulated using a handheld fluorescence scanner with smartphone connectivity.
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Affiliation(s)
- Akansha Prasad
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada
| | - Shadman Khan
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada
| | - Jonathan K Monteiro
- Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada
| | - Fatima Arshad
- School of Interdisciplinary Science, McMaster University, Hamilton, Ontario, L8S 4L7, Canada
| | - Liane Ladouceur
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario, L8S 4L7, Canada
| | - Lei Tian
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, L8S 4L7, Canada
| | - Amid Shakeri
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario, L8S 4L7, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, L8S 4L7, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4L8, Canada
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario, L8S 4L7, Canada
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Sirakov I, Velichkova K, Dinev T, Slavcheva-Sirakova D, Valkova E, Yorgov D, Veleva P, Atanasov V, Atanassova S. Detection of Fungal Diseases in Lettuce by VIR-NIR Spectroscopy in Aquaponics. Microorganisms 2023; 11:2348. [PMID: 37764192 PMCID: PMC10537723 DOI: 10.3390/microorganisms11092348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
One of the main challenges facing the development of aquaponics is disease control, due on one hand to the fact that plants cannot be treated with chemicals because they can lead to mortality in cultured fish. The aim of this study was to apply the visible-near-infrared spectroscopy and vegetation index approach to test aquaponically cultivated lettuce (Lactuca sativa L.) infected with different fungal pathogens (Aspergillus niger, Fusarium oxysporum, and Alternaria alternata). The lettuces on the third leaf formation were placed in tanks (with dimensions 1 m/0.50 m/0.35 m) filled up with water from the aquaponics system every second day. In this study, we included reference fungal strains Aspergillus niger NBIMCC 3252, Fusarium oxysporum NBIMCC 125, and Alternaria alternata NBIMCC 109. Diffuse reflectance spectra of the leaves of lettuce were measured directly on the plants using a USB4000 spectrometer in the 450-1100 nm wavelength range. In near-infrared spectral range, the reflectance values of infected leaves are lower than those of the control, which indicates that some changes in cell structures occurred as a result of the fungal infection. All three investigated pathogens had a statistically significant effect on leaf water content and water band index. Vegetative indices such as Chlorophyll Absorption in Reflectance Index (CARI), Modified chlorophyll absorption in reflectance index (MCARI), Plant Senescence Reflectance Index (PSRI), Red Edge Index (REI2), Red Edge Index (REI3), and Water band index (WBI) were found to be effective in distinguishing infected plants from healthy ones, with WBI demonstrating the greatest reliability.
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Affiliation(s)
- Ivaylo Sirakov
- Department of Animal Husbandry-Non-Ruminants and Other Animals, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Katya Velichkova
- Department of Biological Sciences, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Toncho Dinev
- Department of Biological Sciences, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Desislava Slavcheva-Sirakova
- Department of Botany and Agrometeorology, Faculty of Agronomy, Agricultural University, 12 Mendeleev blvd, 4000 Plovdiv, Bulgaria
| | - Elica Valkova
- Department of Biological Sciences, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Dimitar Yorgov
- Department of Agricultural Engineering, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Petya Veleva
- Department of Agricultural Engineering, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Vasil Atanasov
- Department of Biological Sciences, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
| | - Stefka Atanassova
- Department of Agricultural Engineering, Faculty of Agriculture, Students Campus, Trakia University, 6000 Stara Zagora, Bulgaria
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Borowik P, Dyshko V, Tarakowski R, Tkaczyk M, Okorski A, Oszako T. Analysis of the Response Signals of an Electronic Nose Sensor for Differentiation between Fusarium Species. Sensors (Basel) 2023; 23:7907. [PMID: 37765964 PMCID: PMC10535949 DOI: 10.3390/s23187907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
Fusarium is a genus of fungi found throughout the world. It includes many pathogenic species that produce toxins of agricultural importance. These fungi are also found in buildings and the toxins they spread can be harmful to humans. Distinguishing Fusarium species can be important for selecting effective preventive measures against their spread. A low-cost electronic nose applying six commercially available TGS-series gas sensors from Figaro Inc. was used in our research. Different modes of operation of the electronic nose were applied and compared, namely, gas adsorption and desorption, as well as modulation of the sensor's heating voltage. Classification models using the random forest technique were applied to differentiate between measured sample categories of four species: F. avenaceum, F. culmorum, F. greaminarum, and F. oxysporum. In our research, it was found that the mode of operation with modulation of the heating voltage had the advantage of collecting data from which features can be extracted, leading to the training of machine learning classification models with better performance compared to cases where the sensor's response to the change in composition of the measured gas was exploited. The optimization of the data collection time was investigated and led to the conclusion that the response of the sensor at the beginning of the heating voltage modulation provides the most useful information. For sensor operation in the mode of gas desorption/absorption (i.e., modulation of the gas composition), the optimal time of data collection was found to be longer.
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Affiliation(s)
- Piotr Borowik
- Faculty of Physics, Warsaw University of Technology, ul. Koszykowa 75, 00-662 Warszawa, Poland;
| | - Valentyna Dyshko
- Ukrainian Research Institute of Forestry and Forest Melioration Named after G. M. Vysotsky, 61024 Kharkiv, Ukraine;
| | - Rafał Tarakowski
- Faculty of Physics, Warsaw University of Technology, ul. Koszykowa 75, 00-662 Warszawa, Poland;
| | - Miłosz Tkaczyk
- Forest Protection Department, Forest Research Institute, ul. Braci Leśnej 3, 05-090 Sękocin Stary, Poland (T.O.)
| | - Adam Okorski
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Agriculture and Forestry, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 5, 10-727 Olsztyn, Poland;
| | - Tomasz Oszako
- Forest Protection Department, Forest Research Institute, ul. Braci Leśnej 3, 05-090 Sękocin Stary, Poland (T.O.)
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Spangler JR, Cooper DN, Malanoski AP, Walper SA. Promoter Identification and Optimization for the Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Molecule N-3-Oxododecanoyl Homoserine Lactone. ACS Biomater Sci Eng 2023; 9:5111-5122. [PMID: 35708239 DOI: 10.1021/acsbiomaterials.1c01191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quorum sensing (QS) in bacteria has been well studied as a cellular communication phenomenon for decades. In recent years, such systems have been repurposed for the use of biosensors in both cellular and cell-free contexts as well as for inducible protein expression in nontraditional chassis organisms. Such biosensors are particularly intriguing when considering the association between the pathogenesis of some bacteria and their signaling intermediates. Considering this relationship and considering the recent demonstration of the species Lactobacillus plantarum WCFS1 as both a synthetic biology chassis and an organism capable of detecting a pathogen-associated QS molecule, we wanted to develop this organism as a QS sentinel. We used an approach combining techniques from both systems and synthetic biology to identify a number of native QS-response genes and to alter associated promoter activity to tune the output of L. plantarum cultures exposed to N-3-oxododecanoyl homoserine lactone. The resulting engineered QS sentinel reinforces the potential of modified lactic acid bacteria (LAB) for use in human-health-promoting applications and also demonstrates a simple rational workflow to engineer sentinel organisms to respond to any environmental or chemical stimuli.
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Affiliation(s)
- Joseph R Spangler
- United States Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington, D.C. 20375, United States
| | - Denver N Cooper
- Spelman College, 350 Spelman Ln SW, Atlanta, Georgia 30314, United States
| | - Anthony P Malanoski
- United States Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington, D.C. 20375, United States
| | - Scott A Walper
- United States Naval Research Laboratory, Center for Biomolecular Science and Engineering, 4555 Overlook Ave SW, Washington, D.C. 20375, United States
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35
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Li Y, Lei J, Ren Z, Ma X. Case Report: Metagenomic next-generation sequencing assists in dynamic pathogen monitoring: powerful tool for progressing severe pneumonia. Front Cell Infect Microbiol 2023; 13:1230813. [PMID: 37743869 PMCID: PMC10512180 DOI: 10.3389/fcimb.2023.1230813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/16/2023] [Indexed: 09/26/2023] Open
Abstract
Background Severe community-acquired pneumonia (sCAP) is life-threatening and characterized by intensive care unit (ICU) admission and high mortality. And they are vulnerable to hospital-acquired infection. In such a severe condition, metagenomic next-generation sequencing (mNGS) outperforms for short turnaround time and broad detection spectrum. Case presentation A 15-year-old male with severe influenza and methicillin-resistant Staphylococcus aureus (MRSA) pneumonia progressed rapidly, initially misdiagnosed as influenza co-infected with Aspergillus for misleading bronchoscopy manifestations. The turnaround time of mNGS is 13 h, which has the potential to expedite the clinical medication process. With the powerful support of mNGS and extracorporeal membrane oxygenation (ECMO), anti-infective therapy was adjusted accordingly, and vital signs gradually stabilized. After tortuous treatment and unremitting efforts, the patient recovered well. Conclusions Rapid mNGS applications, timely medication adjustments, strong ECMO support and active family compliance contribute to this miracle of life. False-negative or false-positive results are alarming, anti-infective medications should be adjusted after a comprehensive review of physical status and other indicators.
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Affiliation(s)
- Yaoguang Li
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Lei
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoxu Ma
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Testen AL, Shaw RS, Rotondo F, Moodispaw MR, Miller SA. A Quantitative PCR Method to Detect the Tomato Corky Root Rot Pathogens, Pseudopyrenochaeta lycopersici and P. terrestris. Plant Dis 2023; 107:2673-2678. [PMID: 36774576 DOI: 10.1094/pdis-08-22-2009-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Corky root rot is an important disease in tomato production systems and is caused by Pseudopyrenochaeta terrestris and P. lycopersici (formerly Pyrenochaeta lycopersici Types 1 and 2, respectively). The corky root rot pathogens are slow growing and difficult to isolate and quantify in soil and plant tissue. A multiplex hydrolysis probe-based qPCR assay was designed to allow for simultaneous detection and quantification of P. lycopersici and P. terrestris with a competitive internal control to indicate if qPCR inhibitors are present. Single species and multiplex assays for Pseudopyrenochaeta spp. detected DNA levels above 0.013 pg of DNA per reaction. These highly specific assays had no nontarget amplification of other fungal and oomycete pathogens or rhizosphere-associated fungi of tomatoes that were tested. This assay can be used to quantify Pseudopyrenochaeta populations in roots and soils in tomato production systems to better determine the impacts of disease management strategies on Pseudopyrenochaeta spp. and provides a tool to study the biology of Pseudopyrenochaeta spp.
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Affiliation(s)
- Anna L Testen
- USDA-ARS Application Technology Research Unit, Wooster, OH
| | - R Scott Shaw
- USDA-ARS Application Technology Research Unit, Wooster, OH
| | - Francesca Rotondo
- The Ohio State University Department of Plant Pathology, Wooster, OH
| | | | - Sally A Miller
- The Ohio State University Department of Plant Pathology, Wooster, OH
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Davodabadi F, Mirinejad S, Fathi-Karkan S, Majidpour M, Ajalli N, Sheervalilou R, Sargazi S, Rozmus D, Rahdar A, Diez-Pascual AM. Aptamer-functionalized quantum dots as theranostic nanotools against cancer and bacterial infections: A comprehensive overview of recent trends. Biotechnol Prog 2023; 39:e3366. [PMID: 37222166 DOI: 10.1002/btpr.3366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
Aptamers (Apts) are synthetic nucleic acid ligands that can be engineered to target various molecules, including amino acids, proteins, and pharmaceuticals. Through a series of adsorption, recovery, and amplification steps, Apts are extracted from combinatorial libraries of synthesized nucleic acids. Using aptasensors in bioanalysis and biomedicine can be improved by combining them with nanomaterials. Moreover, Apt-associated nanomaterials, including liposomes, polymeric, dendrimers, carbon nanomaterials, silica, nanorods, magnetic NPs, and quantum dots (QDs), have been widely used as promising nanotools in biomedicine. Following surface modifications and conjugation with appropriate functional groups, these nanomaterials can be successfully used in aptasensing. Advanced biological assays can use Apts immobilized on QD surfaces through physical interaction and chemical bonding. Accordingly, modern QD aptasensing platforms rely on interactions between QDs, Apts, and targets to detect them. QD-Apt conjugates can be used to directly detect prostate, ovarian, colorectal, and lung cancers or simultaneously detect biomarkers associated with these malignancies. Tenascin-C, mucin 1, prostate-specific antigen, prostate-specific membrane antigen, nucleolin, growth factors, and exosomes are among the cancer biomarkers that can be sensitively detected using such bioconjugates. Furthermore, Apt-conjugated QDs have shown great potential for controlling bacterial infections such as Bacillus thuringiensis, Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Campylobacter jejuni, Staphylococcus aureus, and Salmonella typhimurium. This comprehensive review discusses recent advancements in the design of QD-Apt bioconjugates and their applications in cancer and bacterial theranostics.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sonia Fathi-Karkan
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mahdi Majidpour
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Narges Ajalli
- Department of Chemical Engineering, Faculty of Engineering, University of Tehran, Tehran, Iran
| | | | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Dominika Rozmus
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, Iran
| | - Ana M Diez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Quimica Analitica, Quimica Fisica e Ingenieria Quimica, Madrid, Spain
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38
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Fearer CJ, Conrad AO. Walnut Witches'-Broom Disease Threatens Butternut Restoration Efforts in Indiana. Plant Dis 2023; 107:2624-2627. [PMID: 36774570 DOI: 10.1094/pdis-11-22-2739-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Due to the devastating effects of butternut canker disease, efforts to protect the endangered butternut (Juglans cinerea) tree through resistance breeding have been a primary focus of forest restoration efforts. Walnut witches'-broom (WWB) disease poses a serious threat to these restoration efforts. This study sought to confirm the presence of the WWB disease phytoplasma, 'Candidatus Phytoplasma pruni', in butternut research plantings in Indiana using molecular methods and Sanger sequencing and to identify butternut families affected by the disease. We also sought to better understand the incidence of the WWB phytoplasma in asymptomatic trees and asymptomatic branches of symptomatic trees to better direct management decisions. Sanger sequencing confirmed the presence of the WWB phytoplasma in the butternut restoration plantings, the first confirmation in Indiana based on sequencing to our knowledge, in both symptomatic and some asymptomatic trees. In addition, the WWB phytoplasma was detected in asymptomatic branches of symptomatic trees, indicating that phytoplasma infection is not necessarily localized to symptomatic tissues in a tree. Trees with positive molecular confirmation of the WWB phytoplasma consisted of 23 different butternut families and one family of Japanese walnut (J. ailantifolia), which is considered to be one of the most susceptible species to WWB disease. Based on these findings, future studies should prioritize identifying the hybridity and pedigrees of families and their susceptibility to WWB disease to aid in butternut restoration efforts.
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Affiliation(s)
- Carrie J Fearer
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907
| | - Anna O Conrad
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, West Lafayette, IN 47907
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39
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Batson AM, Woodhall JW, du Toit LJ. Real-Time PCR Assays for Races of the Spinach Fusarium Wilt Pathogen, Fusarium oxysporum f. sp. spinaciae. Plant Dis 2023; 107:2633-2642. [PMID: 36734942 DOI: 10.1094/pdis-11-22-2658-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is a significant limitation for producers of vegetative spinach and spinach seed crops during warm temperatures and/or on acid soils. Identification of isolates of F. oxysporum f. sp. spinaciae, and distinction of isolates of the two known races, entails time-intensive pathogenicity tests. In this study, two real-time PCR assays were developed: one for a candidate effector gene common to both races of F. oxysporum f. sp. spinaciae, and another for a candidate effector gene unique to isolates of race 2. The assays were specific to isolates of F. oxysporum f. sp. spinaciae (n = 44) and isolates of race 2 (n = 23), respectively. Neither assay amplified DNA from 10 avirulent isolates of F. oxysporum associated with spinach, 57 isolates of other formae speciales and Fusarium spp., or 7 isolates of other spinach pathogens. When the assays were used to detect DNA extracted from spinach plants infected with an isolate of race 1, race 2, or a 1:1 mixture of both races, the amount of target DNA detected increased with increasing severity of wilt. Plants infected with one or both isolates could be distinguished based on the ratio in copy number for each target locus. The real-time PCR assays enable rapid diagnosis of Fusarium wilt of spinach and will facilitate research on the epidemiology and management of this disease, as well as surveys on the prevalence of this understudied pathogen in regions of spinach and/or spinach seed production.
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Affiliation(s)
- Alex M Batson
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273
| | - James W Woodhall
- University of Idaho Parma Research and Extension Center, Parma, ID 83360
| | - Lindsey J du Toit
- Washington State University Mount Vernon Northwestern Washington Research and Extension Center, Mount Vernon, WA 98273
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40
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Hu S, Yan C, Yu H, Zhang Y, Zhang CQ. Establishment of the Recombinase Polymerase Amplification-Lateral Flow Dipstick Detection Technique for Fusarium oxysporum. Plant Dis 2023; 107:2665-2672. [PMID: 36774580 DOI: 10.1094/pdis-12-22-2841-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium oxysporum causes crown rot, wilt, root rot, and many other major plant diseases worldwide. During the progression of strawberry crown rot disease, the pathogen is transmitted from the mother plant to the seedling through the stolon, with obvious characteristics of latent infection. Therefore, rapid and timely detection of F. oxysporum is important for efficient disease management. In this study, a recombinase polymerase amplification-lateral flow dipstick (RPA-LFD) detection technique was developed for the rapid detection of F. oxysporum on strawberry plants by targeting the CYP51C gene, which is unique to Fusarium spp. Because this RPA-LFD detection technique was highly specific to F. oxysporum, other Fusarium and non-Fusarium fungi were not detected. The optimal reaction temperature and time for this technique were 39°C and 8 min, respectively. The detection limit was 1 pg of F. oxysporum genomic DNA in a 50-μl reaction system. A total of 46 strawberry plants with or without crown rot symptoms collected from Jiande, Changxing, and Haining in Zhejiang Province were further assessed for F. oxysporum infection using both RPA-LFD and traditional tissue isolation techniques. The RPA-LFD test showed that 32 of the 46 strawberry plants tested were positive for F. oxysporum, while in the traditional isolation technique, F. oxysporum was isolated from 30 of the 46 strawberry plants. These results suggest that our established RPA-LFD method is rapid, sensitive, and highly specific in detecting F. oxysporum infection in strawberry plants.
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Affiliation(s)
- Shuodan Hu
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Chenyi Yan
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Hong Yu
- Research Institute for the Agriculture Science of Hangzhou, Hangzhou 310013, China
| | - Yu Zhang
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
| | - Chuan-Qing Zhang
- Department of Plant Pathology, Zhejiang Agriculture and Forest University, Hangzhou 311300, China
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Tserevelakis GJ, Theocharis A, Spyropoulou S, Trantas E, Goumas D, Ververidis F, Zacharakis G. Hybrid Autofluorescence and Optoacoustic Microscopy for the Label-Free, Early and Rapid Detection of Pathogenic Infections in Vegetative Tissues. J Imaging 2023; 9:176. [PMID: 37754940 PMCID: PMC10532063 DOI: 10.3390/jimaging9090176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Agriculture plays a pivotal role in food security and food security is challenged by pests and pathogens. Due to these challenges, the yields and quality of agricultural production are reduced and, in response, restrictions in the trade of plant products are applied. Governments have collaborated to establish robust phytosanitary measures, promote disease surveillance, and invest in research and development to mitigate the impact on food security. Classic as well as modernized tools for disease diagnosis and pathogen surveillance do exist, but most of these are time-consuming, laborious, or are less sensitive. To that end, we propose the innovative application of a hybrid imaging approach through the combination of confocal fluorescence and optoacoustic imaging microscopy. This has allowed us to non-destructively detect the physiological changes that occur in plant tissues as a result of a pathogen-induced interaction well before visual symptoms occur. When broccoli leaves were artificially infected with Xanthomonas campestris pv. campestris (Xcc), eventually causing an economically important bacterial disease, the induced optical absorption alterations could be detected at very early stages of infection. Therefore, this innovative microscopy approach was positively utilized to detect the disease caused by a plant pathogen, showing that it can also be employed to detect quarantine pathogens such as Xylella fastidiosa.
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Affiliation(s)
- George J. Tserevelakis
- Foundation for Research and Technology Hellas, Institute of Electronic Structure and Laser, N. Plastira 100, GR-70013 Heraklion, Crete, Greece; (G.J.T.); (S.S.)
| | - Andreas Theocharis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Estavromenos, GR-71410 Heraklion, Crete, Greece; (A.T.); (E.T.); (D.G.)
| | - Stavroula Spyropoulou
- Foundation for Research and Technology Hellas, Institute of Electronic Structure and Laser, N. Plastira 100, GR-70013 Heraklion, Crete, Greece; (G.J.T.); (S.S.)
| | - Emmanouil Trantas
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Estavromenos, GR-71410 Heraklion, Crete, Greece; (A.T.); (E.T.); (D.G.)
- Institute of Agri-Food and Life Sciences, University Research Centre, Hellenic Mediterranean University, GR-71410 Heraklion, Crete, Greece
| | - Dimitrios Goumas
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Estavromenos, GR-71410 Heraklion, Crete, Greece; (A.T.); (E.T.); (D.G.)
- Institute of Agri-Food and Life Sciences, University Research Centre, Hellenic Mediterranean University, GR-71410 Heraklion, Crete, Greece
| | - Filippos Ververidis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Estavromenos, GR-71410 Heraklion, Crete, Greece; (A.T.); (E.T.); (D.G.)
- Institute of Agri-Food and Life Sciences, University Research Centre, Hellenic Mediterranean University, GR-71410 Heraklion, Crete, Greece
| | - Giannis Zacharakis
- Foundation for Research and Technology Hellas, Institute of Electronic Structure and Laser, N. Plastira 100, GR-70013 Heraklion, Crete, Greece; (G.J.T.); (S.S.)
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Lin T, Tu X, Zhao J, Huang L, Dai X, Chen X, Xu Y, Li W, Wang Y, Lou J, Wu S, Zhang H. Corrigendum: Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia. Front Cell Infect Microbiol 2023; 13:1205802. [PMID: 37645381 PMCID: PMC10461624 DOI: 10.3389/fcimb.2023.1205802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/07/2023] [Indexed: 08/31/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fcimb.2023.1136588.].
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Affiliation(s)
- Tianlai Lin
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xueliang Tu
- Department of Clinical Laboratory, Huanghe Sanmenxia Hospital Affiliated to Henan University of Science and Technology, Sanmenxia, China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Ling Huang
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xiaodong Dai
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xiaoling Chen
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yue Xu
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Wushuang Li
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Yaoyao Wang
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Jingwei Lou
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Shouxin Wu
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Hongling Zhang
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
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Braley LE, Jewell JB, Figueroa J, Humann JL, Main D, Mora-Romero GA, Moroz N, Woodhall JW, White RA, Tanaka K. Nanopore Sequencing with GraphMap for Comprehensive Pathogen Detection in Potato Field Soil. Plant Dis 2023; 107:2288-2295. [PMID: 36724099 DOI: 10.1094/pdis-01-23-0052-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Early detection of causal pathogens is important to prevent crop loss from diseases. However, some diseases, such as soilborne diseases, are difficult to diagnose due to the absence of visible or characteristic symptoms. In the present study, the use of the Oxford Nanopore MinION sequencer as a molecular diagnostic tool was assessed due to its long-read sequencing capabilities and portability. Nucleotide samples (DNA or RNA) from potato field soils were sequenced and analyzed using a locally curated pathogen database, followed by identification via sequence mapping. We performed computational speed tests of three commonly used mapping/annotation tools (BLAST, BWA-BLAST, and BWA-GraphMap) and found BWA-GraphMap to be the fastest tool for local searching against our curated pathogen database. The data collected demonstrate the high potential of Nanopore sequencing as a minimally biased diagnostic tool for comprehensive pathogen detection in soil from potato fields. Our GraphMap-based MinION sequencing method could be useful as a predictive approach for disease management by identifying pathogens present in field soil prior to planting. Although this method still needs further experimentation with a larger sample size for practical use, the data analysis pipeline presented can be applied to other cropping systems and diagnostics for detecting multiple pathogens.
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Affiliation(s)
- Lauren E Braley
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Jeremy B Jewell
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Jose Figueroa
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, U.S.A
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, U.S.A
| | - Jodi L Humann
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, U.S.A
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, U.S.A
| | - Guadalupe A Mora-Romero
- Unidad de Investigación en Ambiente y Salud, Universidad Autónoma de Occidente, Los Mochis, Sinaloa 81223, México
| | - Natalia Moroz
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - James W Woodhall
- Parma Research and Extension Center, University of Idaho, Parma, ID 83660-6699, U.S.A
| | - Richard Allen White
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, U.S.A
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, U.S.A
| | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
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Nguyen A, Chen J, Isaza E, Panchal N, Deiter F, Hoover J, Trinh B, Hays SR, Golden JA, Singer JP, Brzezinski M, Greenland JR, Kukreja J. Biofire pneumonia panel in lung donors: faster detection but limited pathogens. Transpl Infect Dis 2023; 25:e14091. [PMID: 37428868 DOI: 10.1111/tid.14091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/24/2023] [Accepted: 06/15/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Culture of bronchoalveolar lavage (BAL) specimens takes time to report. We tested whether a molecular diagnostic test could accelerate donor lung assessment and treatment. METHODS We compared BioFire Film Array Pneumonia Panel (BFPP) with standard of care (SOC) tests on lung allograft samples at three time points: (1) donor BAL at organ recovery, (2) donor bronchial tissue and airway swab at implantation, and (3) first recipient BAL following lung implantation. Primary outcomes were the difference in time to result (Wilcoxon signed-ranked tests) and the agreement in results between BFPP and SOC assays (Gwet's agreement coefficient). RESULTS We enrolled 50 subjects. In donor lung BAL specimens, BFPP detected 52 infections (14 out of 26 pathogens in the panel). Viral and bacterial BFPP results were reported 2.4 h (interquartile range, IQR 2.0-6.4) following BAL versus 4.6 h (IQR 1.9-6.0, p = 0.625) for OPO BAL viral SOC results and 66 h (IQR 47-87, p < .0001) for OPO BAL bacterial SOC results. Although there was high overall agreement of results between BAL-BFPP versus OPO BAL-SOC tests (Gwet's AC p < .001 for all), the level of agreement differed among 26 pathogens designed in BFPP and differed by types of specimens. BFPP could not detect many infections identified by SOC assays. CONCLUSIONS BFPP decreased time to detection of lung pathogens among donated lungs, but it cannot replace SOC tests due to the limited number of pathogens in the panel.
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Affiliation(s)
- Anh Nguyen
- Department of Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Joy Chen
- Department of Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Erin Isaza
- Department of Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Niel Panchal
- Department of Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Fred Deiter
- Department of Medicine, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jonathan Hoover
- Department of Medicine, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Binh Trinh
- Department of Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Steve R Hays
- Department of Medicine, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey A Golden
- Department of Medicine, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jonathan P Singer
- Department of Medicine, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Marek Brzezinski
- Department of Anesthesia and Perioperative Care, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - John R Greenland
- Department of Medicine, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jasleen Kukreja
- Department of Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
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Zhao Z, Chen X, Wang Y, Feng J. Comparison of quality/quantity mNGS and usual mNGS for pathogen detection in suspected pulmonary infections. Front Cell Infect Microbiol 2023; 13:1184245. [PMID: 37588054 PMCID: PMC10425550 DOI: 10.3389/fcimb.2023.1184245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023] Open
Abstract
Improved metagenomic next-generation sequencing (mNGS), for example, quality/quantity mNGS (QmNGS), is being used in the diagnosis of pulmonary pathogens. There are differences between QmNGS and the usual mNGS (UmNGS), but reports that compare their detection performances are rare. In this prospective study of patients enrolled between December 2021 and March 2022, the bronchoalveolar lavage fluid of thirty-six patients with suspected pulmonary infection was assessed using UmNGS and QmNGS. The sensitivity of QmNGS was similar to that of UmNGS. The specificity of QmNGS was higher than that of UmNGS; however, the difference was not statistically significant. The positive likelihood ratios (+LR) of QmNGS and UmNGS were 3.956 and 1.394, respectively, and the negative likelihood ratios (-LR) were 0.342 and 0.527, respectively. For the co-detection of pathogens, the depth and coverage of the QmNGS sequencing were lower than those of UmNGS, while for the detection of pathogens isolated from patients with pulmonary infection, the concordance rate was 77.2%. In the eleven patients with nonpulmonary infection, only viruses were detected using QmNGS, while UmNGS detected not only viruses but also bacteria and fungi. This study provides a basis for the selection of mNGS for the diagnosis of suspected pulmonary infection.
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Affiliation(s)
- Zhan Zhao
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuefen Chen
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
- Department of Respiratory Medicine, Characteristic Medical Center of the Chinese People’s Armed Police Force, Tianjin, China
| | - Yubao Wang
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
| | - Jing Feng
- Respiratory Department, Tianjin Medical University General Hospital, Tianjin, China
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46
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Shukla S, Singh P, Shukla S, Ali S, Didwania N. Scope of Onsite, Portable Prevention Diagnostic Strategies for Alternaria Infections in Medicinal Plants. Biosensors (Basel) 2023; 13:701. [PMID: 37504100 PMCID: PMC10377195 DOI: 10.3390/bios13070701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/18/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
Medicinal plants are constantly challenged by different biotic inconveniences, which not only cause yield and economic losses but also affect the quality of products derived from them. Among them, Alternaria pathogens are one of the harmful fungal pathogens in medicinal plants across the globe. Therefore, a fast and accurate detection method in the early stage is needed to avoid significant economic losses. Although traditional methods are available to detect Alternaria, they are more time-consuming and costly and need good expertise. Nevertheless, numerous biochemical- and molecular-based techniques are available for the detection of plant diseases, but their efficacy is constrained by differences in their accuracy, specificity, sensitivity, dependability, and speed in addition to being unsuitable for direct on-field studies. Considering the effect of Alternaria on medicinal plants, the development of novel and early detection measures is required to detect causal Alternaria species accurately, sensitively, and rapidly that can be further applied in fields to speed up the advancement process in detection strategies. In this regard, nanotechnology can be employed to develop portable biosensors suitable for early and correct pathogenic disease detection on the field. It also provides an efficient future scope to convert innovative nanoparticle-derived fabricated biomolecules and biosensor approaches in the diagnostics of disease-causing pathogens in important medicinal plants. In this review, we summarize the traditional methods, including immunological and molecular methods, utilized in plant-disease diagnostics. We also brief advanced automobile and efficient sensing technologies for diagnostics. Here we are proposing an idea with a focus on the development of electrochemical and/or colorimetric properties-based nano-biosensors that could be useful in the early detection of Alternaria and other plant pathogens in important medicinal plants. In addition, we discuss challenges faced during the fabrication of biosensors and new capabilities of the technology that provide information regarding disease management strategies.
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Affiliation(s)
- Sadhana Shukla
- Manav Rachna Centre for Medicinal Plant Pathology, Manav Rachna International Institute of Research and Studies, Faridabad 121004, India
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurgaon 122003, India
| | - Pushplata Singh
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurgaon 122003, India
| | - Shruti Shukla
- TERI-Deakin Nanobiotechnology Centre, The Energy and Resources Institute, Gurgaon 122003, India
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Nidhi Didwania
- Manav Rachna Centre for Medicinal Plant Pathology, Manav Rachna International Institute of Research and Studies, Faridabad 121004, India
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Mao S, Zhao J, Ding X, Vuong VA, Song J, Que L. Integrated Sensing Chip for Ultrasensitive Label-Free Detection of the Products of Loop-Mediated Isothermal Amplification. ACS Sens 2023; 8:2255-2262. [PMID: 37276452 DOI: 10.1021/acssensors.3c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that has been widely used for the detection of pathogens in many organisms. Current LAMP-based sensors usually require the LAMP products to be labeled in order for them to be detected. Here, we present a novel label-free LAMP chip, which consists of a nanopore thin-film sensor embedded inside a LAMP reaction chamber. A fraction of LAMP primers is immobilized on the sensor surface, allowing the LAMP products to be synthesized and bound to the sensor surface via immobilized primers. After the LAMP reaction components are removed from the reaction chamber, the amplified LAMP products bound to the sensor surface give rise to significantly increased transducing signals, which can be measured by a portable optical spectrometer through an optical fiber probe. As a demonstration, we used the LAMP chip to detect the causal agent of late blight, Phytophthora infestans, which is one of the most devastating plant pathogens and poses a major threat to sustainable crop production worldwide. We show that this chip can detect as low as 1 fg/μL of P. infestans DNA in 30 min, which corresponds to an attomolar level of 1.6 × 10-6 attomole/μL and is at least 10 times more sensitive than the currently available methods. This label-free sensing technology holds great promise to open up a new avenue for ultrasensitive, highly specific, rapid, and cost-effective point-of-care diagnostics of plant, animal, human, and foodborne pathogens.
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Affiliation(s)
- Subin Mao
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
| | - Jinping Zhao
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
| | - Xiaoke Ding
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
| | - Van Anh Vuong
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, Texas 75252, United States
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas 77843, United States
| | - Long Que
- Electrical and Computer Engineering Department, Iowa State University, Ames, Iowa 50011, United States
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Lee J, Nguyen NT, Tran LM, Kim YH, Min J. Targeted Killing of Staphylococcus aureus Using Specific Peptides Displayed on Yeast Vacuoles. Microbiol Spectr 2023; 11:e0092023. [PMID: 37098917 PMCID: PMC10269669 DOI: 10.1128/spectrum.00920-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/04/2023] [Indexed: 04/27/2023] Open
Abstract
Staphylococcus aureus is a common pathogen that causes health care-related and community-associated infections. In this study, we provide a novel system that can recognize and kill S. aureus bacteria. The system is specifically based on a combination of the phage display library technique and yeast vacuoles. A phage clone displaying a peptide capable of specific binding to a whole S. aureus cell was selected from a 12-mer phage peptide library. The peptide sequence was SVPLNSWSIFPR. The selected phage's ability to bind specifically with S. aureus was confirmed using an enzyme-linked immunosorbent assay, and the chosen peptide was then synthesized. The results showed that the synthesized peptides displayed high affinity with S. aureus but low binding ability with other strains, including Gram-negative and Gram-positive bacteria such as Salmonella sp., Shigella spp., Escherichia coli, and Corynebacterium glutamicum. In addition, yeast vacuoles were used as a drug carrier by encapsulating daptomycin, a lipopeptide antibiotic used to treat Gram-positive bacterial infections. The expression of specific peptides at the encapsulated vacuole membrane created an efficient system that can specifically recognize and kill S. aureus bacteria. IMPORTANCE The phage display method was used to select peptides with high affinity and specificity for S. aureus, and these peptides were then induced to be expressed on the surface of yeast vacuoles. These surface-modified vacuoles can act as drug carriers, with drugs such as the lipopeptide antibiotic daptomycin loaded inside. An advantage of using yeast vacuoles as a drug carrier is that they can be easily produced through yeast culture, making the approach cost-effective and suitable for large-scale production and potential implementation in clinical settings. This novel approach offers a promising way to specifically target and eliminate S. aureus that could ultimately lead to improved treatment of bacterial infections and reduced risk of antibiotic resistance.
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Affiliation(s)
- Jaewoong Lee
- School of Chemical Engineering, Jeonbuk National University, Deokjin-Gu Jeonju, Jeonbuk, South Korea
- Center for Ecology and Environmental Toxicology (CEET), Chungbuk National University, Seowon-Gu, Cheongju, South Korea
| | - Ngoc-Tu Nguyen
- School of Chemical Engineering, Jeonbuk National University, Deokjin-Gu Jeonju, Jeonbuk, South Korea
- Center for Ecology and Environmental Toxicology (CEET), Chungbuk National University, Seowon-Gu, Cheongju, South Korea
| | - Le-Minh Tran
- School of Chemical Engineering, Jeonbuk National University, Deokjin-Gu Jeonju, Jeonbuk, South Korea
| | - Yang-Hoon Kim
- Center for Ecology and Environmental Toxicology (CEET), Chungbuk National University, Seowon-Gu, Cheongju, South Korea
- School of Biological Sciences, Chungbuk National University, Seowon-Gu, Cheongju, South Korea
| | - Jiho Min
- School of Chemical Engineering, Jeonbuk National University, Deokjin-Gu Jeonju, Jeonbuk, South Korea
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Erratum: Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia. Front Cell Infect Microbiol 2023; 13:1233180. [PMID: 37389218 PMCID: PMC10304277 DOI: 10.3389/fcimb.2023.1233180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fcimb.2023.1136588.].
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Jiang J, Feindel W, Swisher Grimm K, Harding M, Feindel D, Bajema S, Feng J. Development of a Loop-Mediated Isothermal Amplification (LAMP) Method to Detect the Potato Zebra Chip Pathogen ' Candidatus Liberibacter solanacearum' (Lso) and Differentiate Haplotypes A and B. Plant Dis 2023:PDIS09222258SR. [PMID: 36480736 DOI: 10.1094/pdis-09-22-2258-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
'Candidatus Liberibacter solanacearum' (Lso) is the causal agent of zebra chip of potato (Solanum tuberosum), which can significantly reduce potato yield. In this study, a loop-mediated isothermal amplification (LAMP) method for the detection of Lso haplotypes A and B was developed and evaluated. Two sets of LAMP primers named LAMP-A and LAMP-B were designed and tested for specificity and sensitivity. Both LAMP-A and LAMP-B were specific to Lso in in silico analysis using the Primer-Blast tool. The LAMP-A and LAMP-B could only produce positive signals from DNA mixtures of Lso-infected tomato but not from the genomic DNA of 37 nontarget plant pathogens. The sensitivity of LAMP-A and LAMP-B on Lso haplotypes A and B were tested on gBlocks and genomic DNA from Lso-infected tomato. On the genomic DNA for LAMP-A, the lowest amount of template DNA for a positive LAMP reaction was 2 to 20 ng on four haplotype A strains and 20 to 80 ng on four haplotype B strains; for LAMP-B, the lowest amount of template DNA for a positive LAMP reaction was 0.02 to 2 ng on four haplotype B strains and 20 ng to no amplification on four haplotype A strains. On gBlocks for LAMP-A, the lowest number of copies for a positive LAMP reaction was 60 on haplotype A and 600 on haplotype B; for LAMP-B, the lowest number of copies for a positive LAMP reaction was 60 on haplotype B and 600 on haplotype A. Therefore, considering the convenience of the LAMP technique, as well as the high specificity and sensitivity, the LAMP-A and LAMP-B primers can be used together to test the probable Lso-infected plant or psyllid samples to rapidly, accurately, and directly differentiate haplotypes A and B. We highly recommend this LAMP system to plant pathology practitioners and diagnostic labs for routine detection of Lso and confirmation of zebra chip disease on potato or tomato.
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Affiliation(s)
- Junye Jiang
- Potato Growers of Alberta, Edmonton, AB T5Y 6H3, Canada
- Alberta Plant Health Lab, Alberta Agriculture, Forestry, and Rural Economic Development (AAFRED), Edmonton, AB T5Y 6H3, Canada
| | - Will Feindel
- Potato Growers of Alberta, Edmonton, AB T5Y 6H3, Canada
- Alberta Plant Health Lab, Alberta Agriculture, Forestry, and Rural Economic Development (AAFRED), Edmonton, AB T5Y 6H3, Canada
| | - Kylie Swisher Grimm
- USDA-ARS Temperate Tree Fruit and Vegetable Research Unit, Prosser, WA 99350, U.S.A
| | - Michael Harding
- Crop Diversification Centre South, AAFRED, Brooks, AB T1R 1E6, Canada
| | - David Feindel
- Alberta Plant Health Lab, Alberta Agriculture, Forestry, and Rural Economic Development (AAFRED), Edmonton, AB T5Y 6H3, Canada
| | - Stacey Bajema
- Potato Growers of Alberta, Edmonton, AB T5Y 6H3, Canada
| | - Jie Feng
- Alberta Plant Health Lab, Alberta Agriculture, Forestry, and Rural Economic Development (AAFRED), Edmonton, AB T5Y 6H3, Canada
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