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Grouzdev D, Farhat S, Guo X, Espinosa EP, Reece K, McDowell J, Yang H, Rivara G, Reitsma J, Clemetson A, Tanguy A, Allam B. Development and validation of a 66K SNP array for the hard clam (Mercenaria mercenaria). BMC Genomics 2024; 25:847. [PMID: 39251920 PMCID: PMC11385495 DOI: 10.1186/s12864-024-10756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/02/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND The hard clam (Mercenaria mercenaria), a marine bivalve distributed along the U.S. eastern seaboard, supports a significant shellfish industry. Overharvest in the 1970s and 1980s led to a reduction in landings. While the transition of industry from wild harvest to aquaculture since that time has enhanced production, it has also exacerbated challenges such as disease outbreaks. In this study, we developed and validated a 66K SNP array designed to advance genetic studies and improve breeding programs in the hard clam, focusing particularly on the development of markers that could be useful in understanding disease resistance and environmental adaptability. RESULTS Whole-genome resequencing of 84 individual clam samples and 277 pooled clam libraries yielded over 305 million SNPs, which were filtered down to a set of 370,456 SNPs that were used as input for the design of a 66K SNP array. This medium-density array features 66,543 probes targeting coding and non-coding regions, including 70 mitochondrial SNPs, to capture the extensive genetic diversity within the species. The SNPs were distributed evenly throughout the clam genome, with an average interval of 25,641 bp between SNPs. The array incorporates markers for detecting the clam pathogen Mucochytrium quahogii (formerly QPX), enhancing its utility in disease management. Performance evaluation on 1,904 samples demonstrated a 72.7% pass rate with stringent quality control. Concordance testing affirmed the array's repeatability, with an average agreement of allele calls of 99.64% across multiple tissue types, highlighting its reliability. The tissue-specific analysis demonstrated that some tissue types yield better genotyping results than others. Importantly, the array, including its embedded mitochondrial markers, effectively elucidated complex genetic relationships across different clam groups, both wild populations and aquacultured stocks, showcasing its utility for detailed population genetics studies. CONCLUSIONS The 66K SNP array is a powerful and robust genotyping tool that offers unprecedented insights into the species' genomic architecture and population dynamics and that can greatly facilitate hard clam selective breeding. It represents an important resource that has the potential to transform clam aquaculture, thereby promoting industry sustainability and ecological and economic resilience.
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Affiliation(s)
- Denis Grouzdev
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
| | - Sarah Farhat
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, 75005, Paris, France
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | | | - Kimberly Reece
- Virginia Institute of Marine Science, P.O. Box 1346, Gloucester Point, VA, 23062, USA
| | - Jan McDowell
- Virginia Institute of Marine Science, P.O. Box 1346, Gloucester Point, VA, 23062, USA
| | - Huiping Yang
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, 7922 NW 71 Street, Gainesville, FL, 32653, USA
| | - Gregg Rivara
- Cornell University Cooperative Extension, 3690 Cedar Beach Road, Southold, NY, 11971, USA
| | - Joshua Reitsma
- Cape Cod Cooperative Extension, 3195 Main Street, Barnstable, MA, 02630, USA
| | - Antoinette Clemetson
- New York Sea Grant, Stony Brook University, 146 Suffolk Hall, Stony Brook, NY, 11794-5002, USA
| | - Arnaud Tanguy
- Sorbonne Université, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA.
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Aggregation-Based Bacterial Separation with Gram-Positive Selectivity by Using a Benzoxaborole-Modified Dendrimer. Molecules 2023; 28:molecules28041704. [PMID: 36838690 PMCID: PMC9958924 DOI: 10.3390/molecules28041704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Antimicrobial-resistant (AMR) bacteria have become a critical global issue in recent years. The inefficacy of antimicrobial agents against AMR bacteria has led to increased difficulty in treating many infectious diseases. Analyses of the environmental distribution of bacteria are important for monitoring the AMR problem, and a rapid as well as viable pH- and temperature-independent bacterial separation method is required for collecting and concentrating bacteria from environmental samples. Thus, we aimed to develop a useful and selective bacterial separation method using a chemically synthesized nanoprobe. The metal-free benzoxaborole-based dendrimer probe BenzoB-PAMAM(+), which was synthesized from carboxy-benzoxaborole and a poly(amidoamine) (PAMAM) dendrimer, could help achieve Gram-positive bacterial separation by recognizing Gram-positive bacterial surfaces over a wide pH range, leading to the formation of large aggregations. The recognition site of benzoxaborole has a desirable high acidity and may therefore be responsible for the improved Gram-positive selectivity. The Gram-positive bacterial aggregation was then successfully collected by using a 10 μm membrane filter, with Gram-negative bacteria remaining in the filtrate solution. BenzoB-PAMAM(+) will thus be useful for application in biological analyses and could contribute to further investigations of bacterial distributions in environmental soil or water.
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Huang T, Zhang R, Li J. CRISPR-Cas-based techniques for pathogen detection: Retrospect, recent advances, and future perspectives. J Adv Res 2022:S2090-1232(22)00240-5. [PMID: 36367481 PMCID: PMC10403697 DOI: 10.1016/j.jare.2022.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Early detection of pathogen-associated diseases are critical for effective treatment. Rapid, specific, sensitive, and cost-effective diagnostic technologies continue to be challenging to develop. The current gold standard for pathogen detection, polymerase chain reaction technology, has limitations such as long operational cycles, high cost, and high technician and instrumentation requirements. AIM OF REVIEW This review examines and highlights the technical advancements of CRISPR-Cas in pathogen detection and provides an outlook for future development, multi-application scenarios, and clinical translation. KEY SCIENTIFIC CONCEPTS OF REVIEW Approaches enabling clinical detection of pathogen nucleic acids that are highly sensitive, specific, cheap, and portable are necessary. CRISPR-Cas9 specificity in targeting nucleic acids and "collateral cleavage" activity of CRISPR-Cas12/Cas13/Cas14 show significant promise in nucleic acid detection technology. These methods have a high specificity, versatility, and rapid detection cycle. In this paper, CRISPR-Cas-based detection methods are discussed in depth. Although CRISPR-Cas-mediated pathogen diagnostic solutions face challenges, their powerful capabilities will pave the way for ideal diagnostic tools.
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4
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Bernard E, Peyret T, Plinet M, Contie Y, Cazaudarré T, Rouquet Y, Bernier M, Pesant S, Fabre R, Anton A, Maugis-Rabusseau C, François JM. The DendrisCHIP ® Technology as a New, Rapid and Reliable Molecular Method for the Diagnosis of Osteoarticular Infections. Diagnostics (Basel) 2022; 12:1353. [PMID: 35741163 PMCID: PMC9222036 DOI: 10.3390/diagnostics12061353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Osteoarticular infections are major disabling diseases that can occur after orthopedic implant surgery in patients. The management of these infections is very complex and painful, requiring surgical intervention in combination with long-term antibiotic treatment. Therefore, early and accurate diagnosis of the causal pathogens is essential before formulating chemotherapeutic regimens. Although culture-based microbiology remains the most common diagnosis of osteoarticular infections, its regular failure to identify the causative pathogen as well as its long-term modus operandi motivates the development of rapid, accurate, and sufficiently comprehensive bacterial species-specific diagnostics that must be easy to use by routine clinical laboratories. Based on these criteria, we reported on the feasibility of our DendrisCHIP® technology using DendrisCHIP®OA as an innovative molecular diagnostic method to diagnose pathogen bacteria implicated in osteoarticular infections. This technology is based on the principle of microarrays in which the hybridization signals between oligoprobes and complementary labeled DNA fragments from isolates queries a database of hybridization signatures corresponding to a list of pre-established bacteria implicated in osteoarticular infections by a decision algorithm based on machine learning methods. In this way, this technology combines the advantages of a PCR-based method and next-generation sequencing (NGS) while reducing the limitations and constraints of the two latter technologies. On the one hand, DendrisCHIP®OA is more comprehensive than multiplex PCR tests as it is able to detect many more germs on a single sample. On the other hand, this method is not affected by the large number of nonclinically relevant bacteria or false positives that characterize NGS, as our DendrisCHIP®OA has been designed to date to target only a subset of 20 bacteria potentially responsible for osteoarticular infections. DendrisCHIP®OA has been compared with microbial culture on more than 300 isolates and a 40% discrepancy between the two methods was found, which could be due in part but not solely to the absence or poor identification of germs detected by microbial culture. We also demonstrated the reliability of our technology in correctly identifying bacteria in isolates by showing a convergence (i.e., same bacteria identified) with NGS superior to 55% while this convergence was only 32% between NGS and microbial culture data. Finally, we showed that our technology can provide a diagnostic result in less than one day (technically, 5 h), which is comparatively faster and less labor intensive than microbial cultures and NGS.
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Affiliation(s)
- Elodie Bernard
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Thomas Peyret
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Mathilde Plinet
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Yohan Contie
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Thomas Cazaudarré
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Yannick Rouquet
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Matthieu Bernier
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Stéphanie Pesant
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Richard Fabre
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Aurore Anton
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Cathy Maugis-Rabusseau
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, INSA, F-31077 Toulouse, France;
| | - Jean Marie François
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, F-31077 Toulouse, France
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5
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Adegbenro A, Coleman S, Nesterova IV. Stoichiometric approach to quantitative analysis of biomolecules: the case of nucleic acids. Anal Bioanal Chem 2022; 414:1587-1594. [PMID: 34800148 PMCID: PMC8766926 DOI: 10.1007/s00216-021-03781-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
Majority of protocols for quantitative analysis of biomarkers (including nucleic acids) require calibrations and target standards. In this work, we developed a principle for quantitative analysis that eliminates the need for a standard of a target molecule. The approach is based on stoichiometric reporting. While stoichiometry is a simple and robust analytical platform, its utility toward the analysis of biomolecules is very limited due to the lack of general methodologies for detecting the equivalence point. In this work, we engineer a new target/probe-binding model that enables detecting the equivalence point while maintaining an appropriate level of specificity. We establish the probe design principles through theoretical simulations and experimental confirmation. Further, we demonstrate the utility of the stoichiometric analysis via a proof-of-concept system based on oligonucleotide hybridization. Overall, the approach that requires neither standard nor calibration yields quantitative results with an adequate accuracy (> 90-110%) and a high specificity. The principles established in our work are very general and can extend beyond oligonucleotide targets toward quantitative analysis of many other biomolecules such as antibodies and proteins.
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Affiliation(s)
- Adeyinka Adegbenro
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Seth Coleman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, 60115, USA.
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6
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Zhang L, Chen F, Zeng Z, Xu M, Sun F, Yang L, Bi X, Lin Y, Gao Y, Hao H, Yi W, Li M, Xie Y. Advances in Metagenomics and Its Application in Environmental Microorganisms. Front Microbiol 2022; 12:766364. [PMID: 34975791 PMCID: PMC8719654 DOI: 10.3389/fmicb.2021.766364] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/18/2021] [Indexed: 01/04/2023] Open
Abstract
Metagenomics is a new approach to study microorganisms obtained from a specific environment by functional gene screening or sequencing analysis. Metagenomics studies focus on microbial diversity, community constitute, genetic and evolutionary relationships, functional activities, and interactions and relationships with the environment. Sequencing technologies have evolved from shotgun sequencing to high-throughput, next-generation sequencing (NGS), and third-generation sequencing (TGS). NGS and TGS have shown the advantage of rapid detection of pathogenic microorganisms. With the help of new algorithms, we can better perform the taxonomic profiling and gene prediction of microbial species. Functional metagenomics is helpful to screen new bioactive substances and new functional genes from microorganisms and microbial metabolites. In this article, basic steps, classification, and applications of metagenomics are reviewed.
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Affiliation(s)
- Lu Zhang
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - FengXin Chen
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhan Zeng
- Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Mengjiao Xu
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fangfang Sun
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Liu Yang
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaoyue Bi
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yanjie Lin
- Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - YuanJiao Gao
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - HongXiao Hao
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Wei Yi
- Department of Gynecology and Obstetrics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Minghui Li
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Yao Xie
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
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7
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Mikagi A, Manita K, Yoyasu A, Tsuchido Y, Kanzawa N, Hashimoto T, Hayashita T. Rapid Bacterial Recognition over a Wide pH Range by Boronic Acid-Based Ditopic Dendrimer Probes for Gram-Positive Bacteria. Molecules 2021; 27:molecules27010256. [PMID: 35011488 PMCID: PMC8746651 DOI: 10.3390/molecules27010256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
We have developed a convenient and selective method for the detection of Gram-positive bacteria using a ditopic poly(amidoamine) (PAMAM) dendrimer probe. The dendrimer that was modified with dipicolylamine (dpa) and phenylboronic acid groups showed selectivity toward Staphylococcus aureus. The ditopic dendrimer system had higher sensitivity and better pH tolerance than the monotopic PAMAM dendrimer probe. We also investigated the mechanisms of various ditopic PAMAM dendrimer probes and found that the selectivity toward Gram-positive bacteria was dependent on a variety of interactions. Supramolecular interactions, such as electrostatic interaction and hydrophobic interaction, per se, did not contribute to the bacterial recognition ability, nor did they improve the selectivity of the ditopic dendrimer system. In contrast, the ditopic PAMAM dendrimer probe that had a phosphate-sensing dpa group and formed a chelate with metal ions showed improved selectivity toward S. aureus. The results suggested that the targeted ditopic PAMAM dendrimer probe showed selectivity toward Gram-positive bacteria. This study is expected to contribute to the elucidation of the interaction between synthetic molecules and bacterial surface. Moreover, our novel method showed potential for the rapid and species-specific recognition of various bacteria.
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Affiliation(s)
- Ayame Mikagi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan; (A.M.); (K.M.); (A.Y.); (Y.T.); (N.K.); (T.H.)
| | - Koichi Manita
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan; (A.M.); (K.M.); (A.Y.); (Y.T.); (N.K.); (T.H.)
| | - Asuka Yoyasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan; (A.M.); (K.M.); (A.Y.); (Y.T.); (N.K.); (T.H.)
| | - Yuji Tsuchido
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan; (A.M.); (K.M.); (A.Y.); (Y.T.); (N.K.); (T.H.)
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Nobuyuki Kanzawa
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan; (A.M.); (K.M.); (A.Y.); (Y.T.); (N.K.); (T.H.)
| | - Takeshi Hashimoto
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan; (A.M.); (K.M.); (A.Y.); (Y.T.); (N.K.); (T.H.)
| | - Takashi Hayashita
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan; (A.M.); (K.M.); (A.Y.); (Y.T.); (N.K.); (T.H.)
- Correspondence: ; Tel.: +81-3-3238-3372
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Fast and Sensitive Bacteria Detection by Boronic Acid Modified Fluorescent Dendrimer. SENSORS 2021; 21:s21093115. [PMID: 33946193 PMCID: PMC8124657 DOI: 10.3390/s21093115] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022]
Abstract
This study reports a novel, fast, easy, and sensitive detection method for bacteria which is urgently needed to diagnose infections in their early stages. Our work presents a complex of poly(amidoamine) dendrimer modified by phenylboronic acid and labeled by a fluorescent dansyl group (Dan-B8.5-PAMAM). Our system detects bacteria in 20 min with a sensitivity of approximately 104 colony-forming units (CFU)·mL−1. Moreover, it does not require any peculiar technical skills or expensive materials. The driving force for bacteria recognition is the binding between terminal phenylboronic acids on the probe and bacteria’s surface glycolipids, rather than electrostatic interactions. The aggregation caused by such binding reduces fluorescence. Even though our recognition method does not distinguish between live or dead bacteria, it shows selective antibacterial activity towards Gram-negative bacteria. This study may potentially contribute a new method for the convenient detection and killing of bacteria.
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Full pathogen characterisation: species identification including the detection of virulence factors and antibiotic resistance genes via multiplex DNA-assays. Sci Rep 2021; 11:6001. [PMID: 33727586 PMCID: PMC7966752 DOI: 10.1038/s41598-021-85438-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/19/2021] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistances progressively cause treatment failures, and their spreading dynamics reached an alarming level. Some strains have already been classified as highly critical, e.g. the ones summarised by the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.). To restrain this trend and enable effective medication, as much information as possible must be obtained in the least possible time. Here, we present a DNA microarray-based assay that screens for the most important sepsis-relevant 44 pathogenic species, 360 virulence factors (mediate pathogenicity in otherwise non-pathogenic strains), and 409 antibiotic resistance genes in parallel. The assay was evaluated with 14 multidrug resistant strains, including all ESKAPE pathogens, mainly obtained from clinical isolates. We used a cost-efficient ligation-based detection platform designed to emulate the highly specific multiplex detection of padlock probes. Results could be obtained within one day, requiring approximately 4 h for amplification, application to the microarray, and detection.
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10
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Development of a Low-Density DNA Microarray for Detecting Tick-Borne Bacterial and Piroplasmid Pathogens in African Cattle. Trop Med Infect Dis 2019; 4:tropicalmed4020064. [PMID: 31013749 PMCID: PMC6630218 DOI: 10.3390/tropicalmed4020064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/05/2019] [Accepted: 04/09/2019] [Indexed: 11/17/2022] Open
Abstract
In Africa, pathogens transmitted by ticks are of major concern in livestock production and human health. Despite noticeable improvements particularly of molecular screening methods, their widespread availability and the detection of multiple infections remain challenging. Hence, we developed a universally accessible and robust tool for the detection of bacterial pathogens and piroplasmid parasites of cattle. A low-cost and low-density chip DNA microarray kit (LCD-Array) was designed and tested towards its specificity and sensitivity for five genera causing tick-borne diseases. The blood samples used for this study were collected from cattle in Northern Cameroon. Altogether, 12 species of the genera Anaplasma, Ehrlichia, Rickettsia and Theileria, and their corresponding genus-wide probes including Babesia were tested on a single LCD-Array. The detection limit of plasmid controls by PCR ranged from 1 to 75 copies per µL depending on the species. All sequenced species hybridized on the LCD-Array. As expected, PCR, agarose gel electrophoresis and Sanger sequencing found significantly less pathogens than the LCD-Array (p < 0.001). Theileria and Rickettsia had lower detection limits than Anaplasma and Ehrlichia. The parallel identification of some of the most detrimental tick-borne pathogens of livestock, and the possible implementation in small molecular-diagnostic laboratories with limited capacities makes the LCD-Array an appealing asset.
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11
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Bera T, Xu J, Alusta P, Fong A, Linder SW, Torosian SD. Estimating Bacterial Concentrations in Fibrous Substrates Through a Combination of Scanning Electron Microscopy and ImageJ. Anal Chem 2019; 91:4405-4412. [PMID: 30835114 DOI: 10.1021/acs.analchem.8b04862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conventional signal-based microanalytical techniques for estimating bacterial concentrations are often susceptible to false signals. A visual quantification, therefore, may compliment such techniques by providing additional information and support better management decisions in the event of outbreaks. Herein, we explore a method that combines electron microscopy (EM) and image-analysis techniques and allows both visualization and quantification of pathogenic bacteria adherent even to complex nonuniform substrates. Both the estimation and imaging parameters were optimized to reduce the estimation error ( E, %) to close to ±5%. The method was validated against conventional microbiological techniques such as the use of optical density, flow cytometry, and quantitative real-time PCR (qPCR). It could easily be tailored to estimate different species of pathogens, such as Escherichia coli O157, Listeria innocua, Staphylococcus aureus, Enterococcus faecalis, and Bacillus anthracis, on samples similar to those in real-time contamination scenarios. The present method is sensitive enough to detect ∼100 bacterial CFU/mL but has the potential to estimate even lower concentrations with increased imaging and computation times. Overall, this imaging-based method may greatly complement any signal-based pathogen-detection technique, especially in negating false signals, and therefore may significantly contribute to the field of analytical microbiology and biochemistry.
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Affiliation(s)
- Tanmay Bera
- Arkansas Laboratory-Nanotechnology Core Facility (ARKL-NanoCore), Office of Regulatory Sciences, Office of Regulatory Affairs (ORS, ORA) , U.S. FDA , Jefferson , Arkansas 72079 , United States.,Division of Bioinformatics and Biostatistics , National Center for Toxicological Research (NCTR), U.S. FDA , Jefferson , Arkansas 72079 , United States
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics , National Center for Toxicological Research (NCTR), U.S. FDA , Jefferson , Arkansas 72079 , United States
| | - Pierre Alusta
- Division of Systems Biology , NCTR, U.S. FDA , Jefferson , Arkansas 72079 , United States
| | - Andrew Fong
- Arkansas Laboratory-Nanotechnology Core Facility (ARKL-NanoCore), Office of Regulatory Sciences, Office of Regulatory Affairs (ORS, ORA) , U.S. FDA , Jefferson , Arkansas 72079 , United States
| | - Sean W Linder
- ORS, ORA , U.S. FDA , Jefferson , Arkansas 72079 , United States
| | - Stephen D Torosian
- Winchester Engineering and Analytical Center (WEAC), ORS, ORA , U.S. FDA , Winchester , Massachusetts 01890 , United States
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12
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Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA. Sci Rep 2019; 9:4516. [PMID: 30872641 PMCID: PMC6418090 DOI: 10.1038/s41598-019-40792-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/18/2019] [Indexed: 01/05/2023] Open
Abstract
Rapid bacterial identification remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single, simple assay, exploiting the conservation, abundance, and rich phylogenetic content of ribosomal RNA in a rapid fluorescent hybridization assay that requires no amplification or enzymology. Of 117 isolates from 64 species across 4 phyla, this assay identified bacteria with >89% accuracy at the species level and 100% accuracy at the family level, enabling all critical clinical distinctions. In pilot studies on primary clinical specimens, including sputum, blood cultures, and pus, bacteria from 5 different phyla were identified.
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Mach KE, Kaushik AM, Hsieh K, Wong PK, Wang TH, Liao JC. Optimizing peptide nucleic acid probes for hybridization-based detection and identification of bacterial pathogens. Analyst 2019; 144:1565-1574. [PMID: 30656297 PMCID: PMC7039532 DOI: 10.1039/c8an02194e] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Point-of-care (POC) diagnostics for infectious diseases have the potential to improve patient care and antibiotic stewardship. Nucleic acid hybridization is at the core of many amplification-free molecular diagnostics and detection probe configuration is key to diagnostic performance. Modified nucleic acids such as peptide nucleic acid (PNA) offer advantages compared to conventional DNA probes allowing for faster hybridization, better stability and minimal sample preparation for direct detection of pathogens. Probes with tethered fluorophore and quencher allow for solution-based assays and eliminate the need for washing steps thereby facilitating integration into microfluidic devices. Here, we compared the sensitivity and specificity of double stranded PNA probes (dsPNA) and PNA molecular beacons targeting E. coli and P. aeruginosa for direct detection of bacterial pathogens. In bulk fluid assays, the dsPNAs had an overall higher fluorescent signal and better sensitivity and specificity than the PNA beacons for pathogen detection. We further designed and tested an expanded panel of dsPNA probes for detection of a wide variety of pathogenic bacteria including probes for universal detection of eubacteria, Enterobacteriaceae family, and P. mirablis. To confirm that the advantage translated to other assay types we compared the PNA beacon and dsPNA in a prototype droplet microfluidic device. Beyond the bulk fluid assay and droplet devices, use of dsPNA probes may be advantageous in a wide variety of assays that employ homogenous nucleic acid hybridization.
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Affiliation(s)
- Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Tsuchido Y, Horiuchi R, Hashimoto T, Ishihara K, Kanzawa N, Hayashita T. Rapid and Selective Discrimination of Gram-Positive and Gram-Negative Bacteria by Boronic Acid-Modified Poly(amidoamine) Dendrimer. Anal Chem 2019; 91:3929-3935. [PMID: 30652471 DOI: 10.1021/acs.analchem.8b04870] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is an urgent need to develop a rapid and selective method for the detection of bacteria because delayed diagnosis and the overuse of antibiotics have triggered drug resistance in bacteria. To this end, we prepared boronic acid-modified poly(amidoamine) generation 4 (B-PAMAM(G4)) dendrimer as cross-linking molecules that form aggregates with bacteria. Within 5 min of adding B-PAMAM(G4) dendrimer solution to a bacterial suspension, large aggregates were observed. Interestingly, the aggregate formation with various bacteria was pH-dependent. In basic pH, both Gram-positive and Gram-negative bacteria formed aggregates, but in neutral pH, only Gram-positive bacteria formed aggregates. We revealed that this bacteria-selective aggregation involved the bacterial surface recognition of the phenylboronic acid moiety of B-PAMAM(G4) dendrimer. In addition, we demonstrated that the spherical structure of B-PAMAM(G4) was one of the important factors for the formation of large aggregates. The aggregation was also observed in the presence of ≤10 mM fructose. B-PAMAM(G4) dendrimer is expected to be a powerful tool for the rapid and selective discrimination between Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Yuji Tsuchido
- Department of Materials and Life Sciences, Faculty of Science and Technology , Sophia University , 7-1 Kioi-cho , Chiyoda-ku , Tokyo 102-8554 , Japan
| | - Ryosuke Horiuchi
- Department of Materials and Life Sciences, Faculty of Science and Technology , Sophia University , 7-1 Kioi-cho , Chiyoda-ku , Tokyo 102-8554 , Japan
| | - Takeshi Hashimoto
- Department of Materials and Life Sciences, Faculty of Science and Technology , Sophia University , 7-1 Kioi-cho , Chiyoda-ku , Tokyo 102-8554 , Japan
| | - Kanako Ishihara
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture , Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho , Fuchu-shi , Tokyo 183-8509 , Japan
| | - Nobuyuki Kanzawa
- Department of Materials and Life Sciences, Faculty of Science and Technology , Sophia University , 7-1 Kioi-cho , Chiyoda-ku , Tokyo 102-8554 , Japan
| | - Takashi Hayashita
- Department of Materials and Life Sciences, Faculty of Science and Technology , Sophia University , 7-1 Kioi-cho , Chiyoda-ku , Tokyo 102-8554 , Japan
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15
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Ricke SC, Kim SA, Shi Z, Park SH. Molecular-based identification and detection of Salmonella in food production systems: current perspectives. J Appl Microbiol 2018; 125:313-327. [PMID: 29675864 DOI: 10.1111/jam.13888] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/25/2022]
Abstract
Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.
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Affiliation(s)
- S C Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S A Kim
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Z Shi
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S H Park
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
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16
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Quiñones B, Lee BG, Martinsky TJ, Yambao JC, Haje PK, Schena M. Sensitive Genotyping of Foodborne-Associated Human Noroviruses and Hepatitis A Virus Using an Array-Based Platform. SENSORS (BASEL, SWITZERLAND) 2017; 17:E2157. [PMID: 28930175 PMCID: PMC5621023 DOI: 10.3390/s17092157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 11/16/2022]
Abstract
Human noroviruses (NoV) are the leading cause of human gastroenteritis in populations of all ages and are linked to most of the foodborne outbreaks worldwide. Hepatitis A virus (HAV) is another important foodborne enteric virus and is considered the most common agent causing acute liver disease worldwide. In the present study, a focused, low-density DNA microarray was developed and validated for the simultaneous identification of foodborne-associated genotypes of NoV and HAV. By employing a novel algorithm, capture probes were designed to target variable genomic regions commonly used for typing these foodborne viruses. Validation results showed that probe signals, specific for the tested NoV or HAV genotypes, were on average 200-times or 38-times higher than those detected for non-targeted genotypes, respectively. To improve the analytical sensitivity of this method, a 12-mer oligonucleotide spacer sequence was added to the capture probes and resulted in a detection threshold of less than 10 cRNA transcripts. These findings have indicated that this array-based typing sensor has the accuracy and sensitivity for identifying NoV and HAV genotypic profiles predominantly linked to food poisoning. The implementation of this typing sensor would thus provide highly relevant and valuable information for use in surveillance and outbreak attribution.
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Affiliation(s)
- Beatriz Quiñones
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Unit, Albany, CA 94710, USA.
| | - Bertram G Lee
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Unit, Albany, CA 94710, USA.
| | | | - Jaszemyn C Yambao
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Unit, Albany, CA 94710, USA.
| | - Paul K Haje
- Arrayit Corporation, Sunnyvale, CA 94085, USA.
| | - Mark Schena
- Arrayit Corporation, Sunnyvale, CA 94085, USA.
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17
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Suaifan GARY, Alhogail S, Zourob M. Paper-based magnetic nanoparticle-peptide probe for rapid and quantitative colorimetric detection of Escherichia coli O157:H7. Biosens Bioelectron 2017; 92:702-708. [PMID: 27839734 DOI: 10.1016/j.bios.2016.10.023] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/30/2016] [Accepted: 10/08/2016] [Indexed: 12/31/2022]
Abstract
There is a critical and urgent demand for a simple, rapid and specific qualitative and quantitative colorimetric biosensor for the detection of the food contaminant Escherichia coli O157:H7 (E. coli O157:H7) in complex food products due to the recent outbreaks of food-borne diseases. Traditional detection techniques are time-consuming, require expensive instrumentation and are labour-intensive. To overcome these limitations, a novel, ultra-rapid visual biosensor was developed based on the ability of E. coli O157:H7 proteases to change the optical response of a surface-modified, magnetic nanoparticle-specific (MNP-specific) peptide probe. Upon proteolysis, a gradual increase in the golden color of the sensor surface was visually observed. The intensification of color was correlated with the E. coli O157:H7 concentration. The color change resulting from the dissociation of the self-assembled monolayer (SAM) was detected by the naked eye and analysed using an image analysis software (ImageJ) for the purpose of quantitative detection. This biosensor demonstrated high sensitivity and applicability, with lower limits of detection of 12CFUmL-1 in broth samples and 30-300CFUmL-1 in spiked complex food matrices. In conclusion, this approach permits the use of a disposable biosensor chip that can be mass-produced at low cost and can be used not only by food manufacturers but also by regulatory agencies for better control of potential health risks associated with the consumption of contaminated foods.
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Affiliation(s)
- Ghadeer A R Y Suaifan
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Sahar Alhogail
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia; King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 12713, Saudi Arabia.
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18
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Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA. Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. J Microbiol Methods 2017; 139:15-21. [PMID: 28438642 DOI: 10.1016/j.mimet.2017.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 02/06/2023]
Abstract
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology. Target VMG amplicons were obtained using multiplex polymerase chain reaction (PCR), labeled with biotin, and hybridized to the microarray. The signals generated after gold deposition and silver enhancement, were quantified using a flatbed scanner having 2-μm resolution. Data analysis indicated that reliable presence/absence calls could be made, if: i) over four probes were used per gene, ii) the signal-to-noise ratio (SNR) cutoff was greater than or equal to two, and iii) the positive fraction (PF), i.e., number of probes with SNR≥2 for a given VMG was greater than 0.75. Hybridization of the array with blind samples resulted in 100% correct calls, and no false positive. Because amplicons were obtained by multiplex PCR, sensitivity of this method is similar to PCR. This assay is an inexpensive and reliable technique for high throughput screening of multiple pathogens.
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Affiliation(s)
- Vidya Srinivasan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Dieter M Tourlousse
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Samuel W Baushke
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Yu Xin
- Department of Environmental Engineering, Nanjing University, China
| | - Sarah M Miller
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Trinh Pham
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jean-Marie Rouillard
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Erdogan Gulari
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - James M Tiedje
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States.
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19
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Holden MT, Carter MCD, Wu CH, Wolfer J, Codner E, Sussman MR, Lynn DM, Smith LM. Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates. Anal Chem 2015; 87:11420-8. [PMID: 26494264 PMCID: PMC4945104 DOI: 10.1021/acs.analchem.5b02893] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.
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Affiliation(s)
- Matthew T. Holden
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
| | | | - Cheng-Hsien Wu
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
| | - Jamison Wolfer
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
| | - Eric Codner
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, WI, 53706, USA
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Department of Biochemistry, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
| | - David M. Lynn
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, WI, 53706, USA
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin - Madison, WI, 53706, USA
- Biotechnology Center, University of Wisconsin - Madison, WI, 53706, USA
- Genome Center of Wisconsin, University of Wisconsin - Madison, WI, 53706, USA
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20
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Gomes M, Vieira H, Vale FF. Characterization, validation and application of a DNA microarray for the detection of mandatory and other waterborne pathogens. J Biochem 2015; 158:393-401. [PMID: 25998249 DOI: 10.1093/jb/mvv052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/13/2015] [Indexed: 11/15/2022] Open
Abstract
Culture methods for the detection of indicator bacteria are currently used for detection of waterborne bacteria. The need for an increased range of analyzed bacteria coupled with the obtainment of rapid and early results justify the development of a DNA microarray for the identification of waterborne pathogens. This DNA microarray has 16 implanted probes with a median size of 147 bases, targeting 12 different parameters, including all mandatory indicator microorganisms, such as Escherichia coli, Clostridium perfringens, Pseudomonas aeruginosa, Staphylococcus aureus, total and fecal coliforms and enterococci. The validation performed with DNA extracted from pure microbial cultures showed the suitability of the probes for detection of the target microorganism. To overcome the high dilution of water samples it was included either a prior culture step of bacterial contaminants retained after filtering 100 ml of water, or a 10-fold increase in the volume of filtered water, that resulted in the increase of the detected bacteria. The analysis of complex environmental water samples using culture methods and the DNA microarray revealed that the latter detected the same parameters plus other bacteria tested only in the DNA microarray. The results show that this DNA microarray may be a useful tool for water microbiological surveillance.
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Affiliation(s)
- Maria Gomes
- Faculdade de Engenharia, Universidade Católica Portuguesa, 2635-631 Rio de Mouro, Portugal
| | - Helena Vieira
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, 1749-106 Lisboa, Portugal
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Instituto de Medicina Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal
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21
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Madiyar FR, Bhana S, Swisher LZ, Culbertson CT, Huang X, Li J. Integration of a nanostructured dielectrophoretic device and a surface-enhanced Raman probe for highly sensitive rapid bacteria detection. NANOSCALE 2015; 7:3726-36. [PMID: 25641315 DOI: 10.1039/c4nr07183b] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This work reports a synergistic approach to the concentration, detection and kinetic monitoring of pathogens through the integration of nanostructured dielectrophoresis (DEP) with nanotag-labelled Surface Enhanced Raman Spectroscopy (SERS). A nanoelectrode array made of embedded Vertically Aligned Carbon Nanofibers (VACNFs) at the bottom of a microfluidic chip was used to effectively capture and concentrate nanotag-labelled E. coli DHα5 cells into a 200 μm × 200 μm area on which a Raman laser probe was focused. The SERS nanotags were based on iron oxide-gold (IO-Au) core-shell nanoovals (NOVs) of ∼50 nm size, which were coated with a QSY21 Raman reporter and attached to E. coli through specific immunochemistry. The combination of the greatly enhanced Raman signal by the SERS nanotags and the effective DEP concentration significantly improved the detection limit and speed. The SERS signal was measured with both a confocal Raman microscope and a portable Raman probe during DEP capture, and was fully validated with fluorescence microscopy measurements under all DEP conditions. The SERS measurements were sensitive enough to detect a single bacterium. A concentration detection limit as low as 210 cfu ml(-1) using a portable Raman system was obtained with a DEP capture time of only ∼50 s. These results demonstrate the potential to develop a compact portable system for rapid and highly sensitive detection of specific pathogens. This system is reusable, requires minimum sample preparation, and is amenable to field applications.
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22
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Mirmajlessi SM, Destefanis M, Gottsberger RA, Mänd M, Loit E. PCR-based specific techniques used for detecting the most important pathogens on strawberry: a systematic review. Syst Rev 2015; 4:9. [PMID: 25588564 PMCID: PMC4320524 DOI: 10.1186/2046-4053-4-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/02/2015] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Strawberry diseases are a major limiting factor that severely impact plant agronomic performance. Regarding limitations of traditional techniques for detection of pathogens, researchers have developed specific DNA-based tests as sensitive and specific techniques. The aim of this review is to provide an overview of polymerase chain reaction (PCR)-based methods used for detection or quantification of the most widespread strawberry pathogens, such as Fusarium oxysporum f.sp. fragariae, Phytophthora fragariae, Colletotrichum acutatum, Verticillium dahliae, Botrytis cinerea, Macrophomina phaseolina, and Xanthomonas fragariae. An updated and detailed list of published PCR protocols is presented and discussed, aimed at facilitating access to information that could be particularly useful for diagnostic laboratories in order to develop a rapid, cost-effective, and reliable monitoring technique. METHODS The study design was a systematic review of PCR-based techniques used for detection and quantification of strawberry pathogens. Using appropriate subject headings, AGRICOLA, AGRIS, BASE, Biological Abstracts, CAB Abstracts, Google Scholar, Scopus, Web of Knowledge, and SpringerLink databases were searched from their inception up to April 2014. Two assessors independently reviewed the titles, abstracts, and full articles of all identified citations. Selected articles were included if one of the mentioned strawberry pathogens was investigated based on PCR methods, and a summary of pre-analytical requirements for PCR was provided. RESULTS A total of 259 titles and abstracts were reviewed, of which 22 full texts met all the inclusion criteria. Our systematic review identified ten different protocols for X. fragariae, eight for P. fragariae, four for B. cinerea, six for C. acutatum, three for V. dahlia, and only one for F. oxysporum. The accuracy and sensitivity of PCR diagnostic methods is the focus of most studies included in this review. However, a large proportion of errors in laboratories occur in the pre-analytical phase of the testing process. Due to heterogeneity, results could not be meta-analyzed. CONCLUSIONS From a systematic review of the currently available published literature, effective detection assays to detect the major strawberry pathogens have been developed. These assays can function as a basis for clinical labs, regulatory personnel, and other diagnosticians to adapt or implement for detection of these six important strawberry pathogens.
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Affiliation(s)
- Seyed Mahyar Mirmajlessi
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Marialaura Destefanis
- />Pesticides, Plant Health and Seed Testing Laboratories, Department of Agriculture, Food and the Marine, Backweston Campus, Celbridge, Co. Kildare Ireland
| | - Richard Alexander Gottsberger
- />Department for Molecular Diagnostics of Plant Diseases, Institute for Sustainable Plant Production, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Marika Mänd
- />Department of Plant Protection, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Evelin Loit
- />Department of Field Crops and Grassland Husbandry, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
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Handley JA, Shi Z, Park SH, Dawoud TM, Kwon YM, Ricke SC. Salmonella and the Potential Role for Methods to Develop Microbial Process Indicators on Chicken Carcasses. Food Saf (Tokyo) 2015. [DOI: 10.1016/b978-0-12-800245-2.00006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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24
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Alizadeh-Hesar M, Bakhshi B, Najar-peerayeh S. Molecular Diagnosis of Salmonella enterica and Shigella spp. in Stool Sample of Children With Diarrhea in Tehran. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2014. [DOI: 10.17795/ijep17002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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25
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Venter M, Zaayman D, van Niekerk S, Stivaktas V, Goolab S, Weyer J, Paweska JT, Swanepoel R. Macroarray assay for differential diagnosis of meningoencephalitis in southern Africa. J Clin Virol 2014; 60:50-6. [DOI: 10.1016/j.jcv.2014.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 01/30/2014] [Accepted: 02/01/2014] [Indexed: 11/26/2022]
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26
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Park SH, Aydin M, Khatiwara A, Dolan MC, Gilmore DF, Bouldin JL, Ahn S, Ricke SC. Current and emerging technologies for rapid detection and characterization of Salmonella in poultry and poultry products. Food Microbiol 2014; 38:250-62. [DOI: 10.1016/j.fm.2013.10.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 07/28/2013] [Accepted: 10/04/2013] [Indexed: 12/19/2022]
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27
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Josephson R. Molecular cytogenetics: making it safe for human embryonic stem cells to enter the clinic. Expert Rev Mol Diagn 2014; 7:395-406. [PMID: 17620047 DOI: 10.1586/14737159.7.4.395] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Regenerative therapies based on transplantation of cells derived from human embryonic stem cells (hESC) are currently being prepared for clinical trials. Unfortunately, recent evidence indicates that many kinds of changes can occur to hESC during expansion in culture, and alterations to the growth control mechanisms may be required to establish hESC lines at all. Changes in the genome and epigenome can affect the validity of in vitro and animal studies, and put transplant recipients at increased risk of cancer. New molecular cytogenetic technologies enable us to examine the whole human genome with ever-finer resolution. This review describes several techniques for whole-genome analysis and the information they can provide about hESC lines. Adoption of high-resolution genotyping into routine characterization may prevent highly discouraging clinical outcomes.
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Bissonnette L, Bergeron MG. Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine. Expert Rev Mol Diagn 2014; 6:433-50. [PMID: 16706745 DOI: 10.1586/14737159.6.3.433] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.
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Affiliation(s)
- Luc Bissonnette
- Département de Biologie Médicale (Microbiologie), Faculté de Médecine, Université Laval, Québec City, Canada.
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29
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Ahmed FE. Microarray RNA transcriptional profiling: Part I. Platforms, experimental design and standardization. Expert Rev Mol Diagn 2014; 6:535-50. [PMID: 16824028 DOI: 10.1586/14737159.6.4.535] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review summarizes, in a balanced and comprehensive manner, the various components of microarrays and their types, substrate architecture, platforms for microarray probe implementation, standardizations and confounders. The review is intended to familiarize the beginner with the principles of experimental design and the selection of an appropriate microarray platform. This parallel technology has revolutionized transcriptomic approaches to data profiling and has a major role in the identification of expressed genes, classification and diagnosis studies. The technology is still evolving and guidelines for standardization and reporting have been developed and are being improved.
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Affiliation(s)
- Farid E Ahmed
- Leo W Jenkins Cancer Center, Department of Radiation Oncology, LSB 014, The Brody School of Medicine at East Carolina University, Greenville, NC 27858, USA.
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30
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Ince J, McNally A. Development of rapid, automated diagnostics for infectious disease: advances and challenges. Expert Rev Med Devices 2014; 6:641-51. [DOI: 10.1586/erd.09.46] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Liu T, Sin MLY, Pyne JD, Gau V, Liao JC, Wong PK. Electrokinetic stringency control in self-assembled monolayer-based biosensors for multiplex urinary tract infection diagnosis. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2014; 10:159-66. [PMID: 23891989 PMCID: PMC3858494 DOI: 10.1016/j.nano.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/24/2013] [Accepted: 07/05/2013] [Indexed: 11/30/2022]
Abstract
Rapid detection of bacterial pathogens is critical toward judicious management of infectious diseases. Herein, we demonstrate an in situ electrokinetic stringency control approach for a self-assembled monolayer-based electrochemical biosensor toward urinary tract infection diagnosis. The in situ electrokinetic stringency control technique generates Joule heating induced temperature rise and electrothermal fluid motion directly on the sensor to improve its performance for detecting bacterial 16S rRNA, a phylogenetic biomarker. The dependence of the hybridization efficiency reveals that in situ electrokinetic stringency control is capable of discriminating single-base mismatches. With electrokinetic stringency control, the background noise due to the matrix effects of clinical urine samples can be reduced by 60%. The applicability of the system is demonstrated by multiplex detection of three uropathogenic clinical isolates with similar 16S rRNA sequences. The results demonstrate that electrokinetic stringency control can significantly improve the signal-to-noise ratio of the biosensor for multiplex urinary tract infection diagnosis. FROM THE CLINICAL EDITOR Urinary tract infections remain a significant cause of mortality and morbidity as secondary conditions often related to chronic diseases or to immunosuppression. Rapid and sensitive identification of the causative organisms is critical in the appropriate management of this condition. These investigators demonstrate an in situ electrokinetic stringency control approach for a self-assembled monolayer-based electrochemical biosensor toward urinary tract infection diagnosis, establishing that such an approach significantly improves the biosensor's signal-to-noise ratio.
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Affiliation(s)
- Tingting Liu
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA
| | - Mandy L Y Sin
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA; Department of Urology, Stanford University, Stanford, CA, USA
| | - Jeff D Pyne
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA
| | | | - Joseph C Liao
- Department of Urology, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Pak Kin Wong
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, USA.
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32
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Specific discrimination of three pathogenic Salmonella enterica subsp. enterica serotypes by carB-based oligonucleotide microarray. Appl Environ Microbiol 2013; 80:366-73. [PMID: 24185846 DOI: 10.1128/aem.02978-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
It is important to rapidly and selectively detect and analyze pathogenic Salmonella enterica subsp. enterica in contaminated food to reduce the morbidity and mortality of Salmonella infection and to guarantee food safety. In the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the carB gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficiently detect and discriminate three S. enterica subsp. enterica serotypes: Choleraesuis, Enteritidis, and Typhimurium. Using the developed microarray system, three serotype targets were successfully analyzed in a range as low as 1.6 to 3.1 nM and were specifically discriminated from each other without nonspecific signals. In addition, the constructed microarray did not have cross-reactivity with other common pathogenic bacteria and even enabled the clear discrimination of the target Salmonella serotype from a bacterial mixture. Therefore, these results demonstrated that our novel carB-based oligonucleotide microarray can be used as an effective and specific detection system for S. enterica subsp. enterica serotypes.
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33
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Russell AJ, Del Bonis-O'Donnell JT, Wynne TM, Napoli MT, Pennathur S. Separation behavior of short single- and double-stranded DNA in 1 micron and 100 nm glass channels. Electrophoresis 2013; 35:412-8. [DOI: 10.1002/elps.201300177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/10/2013] [Accepted: 07/02/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander J. Russell
- Department of Mechanical Engineering; University of California; Santa Barbara CA USA
| | | | - Thomas M. Wynne
- Department of Mechanical Engineering; University of California; Santa Barbara CA USA
| | - Maria T. Napoli
- Department of Mechanical Engineering; University of California; Santa Barbara CA USA
| | - Sumita Pennathur
- Department of Mechanical Engineering; University of California; Santa Barbara CA USA
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Abstract
Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, U. S. Naval Research Laboratory, 4555 Overlook Avenue, S. W., Code 6900, Washington, DC, 20375, USA
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35
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Aguirre SD, Ali MM, Salena BJ, Li Y. A sensitive DNA enzyme-based fluorescent assay for bacterial detection. Biomolecules 2013; 3:563-77. [PMID: 24970181 PMCID: PMC4030956 DOI: 10.3390/biom3030563] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/09/2013] [Accepted: 08/11/2013] [Indexed: 12/27/2022] Open
Abstract
Bacterial detection plays an important role in protecting public health and safety, and thus, substantial research efforts have been directed at developing bacterial sensing methods that are sensitive, specific, inexpensive, and easy to use. We have recently reported a novel “mix-and-read” assay where a fluorogenic DNAzyme probe was used to detect model bacterium E. coli. In this work, we carried out a series of optimization experiments in order to improve the performance of this assay. The optimized assay can achieve a detection limit of 1000 colony-forming units (CFU) without a culturing step and is able to detect 1 CFU following as short as 4 h of bacterial culturing in a growth medium. Overall, our effort has led to the development of a highly sensitive and easy-to-use fluorescent bacterial detection assay that employs a catalytic DNA.
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Affiliation(s)
- Sergio D Aguirre
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada.
| | - M Monsur Ali
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada.
| | - Bruno J Salena
- Dvision of Gastroenterology, Department of Medicine, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada.
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4K1, Canada.
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36
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A pentaplex PCR assay for the detection and differentiation of Shigella species. BIOMED RESEARCH INTERNATIONAL 2013; 2013:412370. [PMID: 23509722 PMCID: PMC3586438 DOI: 10.1155/2013/412370] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/06/2013] [Accepted: 01/11/2013] [Indexed: 12/17/2022]
Abstract
The magnitude of shigellosis in developing countries is largely unknown because an affordable detection method is not available. Current laboratory diagnosis of Shigella spp. is laborious and time consuming and has low sensitivity. Hence, in the present study, a molecular-based diagnostic assay which amplifies simultaneously four specific genes to identify invC for Shigella genus, rfc for S. flexneri, wbgZ for S. sonnei, and rfpB for S. dysenteriae, as well as one internal control (ompA) gene, was developed in a single reaction to detect and differentiate Shigella spp. Validation with 120 Shigella strains and 37 non-Shigella strains yielded 100% specificity. The sensitivity of the PCR was 100 pg of genomic DNA, 5.4 × 104 CFU/ml, or approximately 120 CFU per reaction mixture of bacteria. The sensitivity of the pentaplex PCR assay was further improved following preincubation of the stool samples in Gram-negative broth. A preliminary study with 30 diarrhoeal specimens resulted in no cross-reaction with other non-Shigella strains tested. We conclude that the developed pentaplex PCR assay is robust and can provide information about the four target genes that are essential for the identification of the Shigella genus and the three Shigella species responsible for the majority of shigellosis cases.
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37
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Dong Y, Sheng H, Zeng X, Yan J, Li H, Xiao H, Li X, Yang S. Investigation of Genetic Diversity of theblaSHVGene and Development of an Oligonucleotide Microarray to Detect Mutations in theblaSHVGene. Microb Drug Resist 2012; 18:539-45. [DOI: 10.1089/mdr.2012.0057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yuanyuan Dong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Haihui Sheng
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Xainting Zeng
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Jufen Yan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Haiyan Li
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, China
| | - Huasheng Xiao
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Xiaokun Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
- Ministry of Education Engineering Research Center of Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, China
| | - Shulin Yang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
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38
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A New Generation Microarray for the Simultaneous Detection and Identification of Yersinia pestis and Bacillus anthracis in Food. J Pathog 2012; 2012:627036. [PMID: 23125935 PMCID: PMC3483683 DOI: 10.1155/2012/627036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 08/02/2012] [Accepted: 08/05/2012] [Indexed: 11/17/2022] Open
Abstract
The use of microarrays as a multiple analytic system has generated increased interest and provided a powerful analytical tool for the simultaneous detection of pathogens in a single experiment. A wide array of applications for this technology has been reported. A low density oligonucleotide microarray was generated from the genetic sequences of Y. pestis and B. anthracis and used to fabricate a microarray chip. The new generation chip, consisting of 2,240 spots in 4 quadrants with the capability of stripping/rehybridization, was designated as “Y-PESTIS/B-ANTHRACIS 4x2K Array.” The chip was tested for specificity using DNA from a panel of bacteria that may be potentially present in food. In all, 37 unique Y. pestis-specific and 83 B. anthracis-specific probes were identified. The microarray assay distinguished Y. pestis and B. anthracis from the other bacterial species tested and correctly identified the Y. pestis-specific oligonucleotide probes using DNA extracted from experimentally inoculated milk samples. Using a whole genome amplification method, the assay was able to detect as low as 1 ng genomic DNA as the start sample. The results suggest that oligonucleotide microarray can specifically detect and identify Y. pestis and B. anthracis and may be a potentially useful diagnostic tool for detecting and confirming the organisms in food during a bioterrorism event.
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39
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Zhang Z, Li P, Hu X, Zhang Q, Ding X, Zhang W. Microarray technology for major chemical contaminants analysis in food: current status and prospects. SENSORS (BASEL, SWITZERLAND) 2012; 12:9234-52. [PMID: 23012541 PMCID: PMC3444099 DOI: 10.3390/s120709234] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 06/14/2012] [Accepted: 06/15/2012] [Indexed: 01/11/2023]
Abstract
Chemical contaminants in food have caused serious health issues in both humans and animals. Microarray technology is an advanced technique suitable for the analysis of chemical contaminates. In particular, immuno-microarray approach is one of the most promising methods for chemical contaminants analysis. The use of microarrays for the analysis of chemical contaminants is the subject of this review. Fabrication strategies and detection methods for chemical contaminants are discussed in detail. Application to the analysis of mycotoxins, biotoxins, pesticide residues, and pharmaceutical residues is also described. Finally, future challenges and opportunities are discussed.
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Affiliation(s)
- Zhaowei Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; E-Mails: (Z.Z.); (X.H.); (Q.Z.); (X.D.); (W.Z.)
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture, Wuhan 430062, China
- Laboratory of Risk Assessment for Oilseeds Products, Ministry of Agriculture, Wuhan 430062, China
| | - Peiwu Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; E-Mails: (Z.Z.); (X.H.); (Q.Z.); (X.D.); (W.Z.)
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture, Wuhan 430062, China
- Laboratory of Risk Assessment for Oilseeds Products, Ministry of Agriculture, Wuhan 430062, China
| | - Xiaofeng Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; E-Mails: (Z.Z.); (X.H.); (Q.Z.); (X.D.); (W.Z.)
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Qi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; E-Mails: (Z.Z.); (X.H.); (Q.Z.); (X.D.); (W.Z.)
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture, Wuhan 430062, China
| | - Xiaoxia Ding
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; E-Mails: (Z.Z.); (X.H.); (Q.Z.); (X.D.); (W.Z.)
- Laboratory of Risk Assessment for Oilseeds Products, Ministry of Agriculture, Wuhan 430062, China
| | - Wen Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China; E-Mails: (Z.Z.); (X.H.); (Q.Z.); (X.D.); (W.Z.)
- Quality Inspection and Test Center for Oilseeds Products, Ministry of Agriculture, Wuhan 430062, China
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40
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Lu CH, Wang F, Willner I. Zn2+-Ligation DNAzyme-Driven Enzymatic and Nonenzymatic Cascades for the Amplified Detection of DNA. J Am Chem Soc 2012; 134:10651-8. [DOI: 10.1021/ja3037838] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Chun-Hua Lu
- Institute of Chemistry
and The Minerva Center for Complex
Biohybrid Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fuan Wang
- Institute of Chemistry
and The Minerva Center for Complex
Biohybrid Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry
and The Minerva Center for Complex
Biohybrid Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Abstract
Outbreaks linked to food-borne and hospital-acquired pathogens account for millions of deaths and hospitalizations as well as colossal economic losses each and every year. Prevention of such outbreaks and minimization of the impact of an ongoing epidemic place an ever-increasing demand for analytical methods that can accurately identify culprit pathogens at the earliest stage. Although there is a large array of effective methods for pathogen detection, none of them can satisfy all the following five premier requirements embodied for an ideal detection method: high specificity (detecting only the bacterium of interest), high sensitivity (capable of detecting as low as a single live bacterial cell), short time-to-results (minutes to hours), great operational simplicity (no need for lengthy sampling procedures and the use of specialized equipment), and cost effectiveness. For example, classical microbiological methods are highly specific but require a long time (days to weeks) to acquire a definitive result.(1) PCR- and antibody-based techniques offer shorter waiting times (hours to days), but they require the use of expensive reagents and/or sophisticated equipment.(2-4) Consequently, there is still a great demand for scientific research towards developing innovative bacterial detection methods that offer improved characteristics in one or more of the aforementioned requirements. Our laboratory is interested in examining the potential of DNAzymes as a novel class of molecular probes for biosensing applications including bacterial detection.(5) DNAzymes (also known as deoxyribozymes or DNA enzymes) are man-made single-stranded DNA molecules with the capability of catalyzing chemical reactions.(6-8) These molecules can be isolated from a vast random-sequence DNA pool (which contains as many as 10(16) individual sequences) by a process known as "in vitro selection" or "SELEX" (systematic evolution of ligands by exponential enrichment).(9-16) These special DNA molecules have been widely examined in recent years as molecular tools for biosensing applications.(6-8) Our laboratory has established in vitro selection procedures for isolating RNA-cleaving fluorescent DNAzymes (RFDs; Fig. 1) and investigated the use of RFDs as analytical tools.(17-29) RFDs catalyze the cleavage of a DNA-RNA chimeric substrate at a single ribonucleotide junction (R) that is flanked by a fluorophore (F) and a quencher (Q). The close proximity of F and Q renders the uncleaved substrate minimal fluorescence. However, the cleavage event leads to the separation of F and Q, which is accompanied by significant increase of fluorescence intensity. More recently, we developed a method of isolating RFDs for bacterial detection.(5) These special RFDs were isolated to "light up" in the presence of the crude extracellular mixture (CEM) left behind by a specific type of bacteria in their environment or in the media they are cultured (Fig. 1). The use of crude mixture circumvents the tedious process of purifying and identifying a suitable target from the microbe of interest for biosensor development (which could take months or years to complete). The use of extracellular targets means the assaying procedure is simple because there is no need for steps to obtain intracellular targets. Using the above approach, we derived an RFD that cleaves its substrate (FS1; Fig. 2A) only in the presence of the CEM produced by E. coli (CEM-EC).(5) This E. coli-sensing RFD, named RFD-EC1 (Fig. 2A), was found to be strictly responsive to CEM-EC but nonresponsive to CEMs from a host of other bacteria (Fig. 3). Here we present the key experimental procedures for setting up E. coli detection assays using RFD-EC1 and representative results.
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Affiliation(s)
- Sergio D Aguirre
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
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42
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De Boer SH, López MM. New grower-friendly methods for plant pathogen monitoring. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:197-218. [PMID: 22607454 DOI: 10.1146/annurev-phyto-081211-172942] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Accurate plant disease diagnoses and rapid detection and identification of plant pathogens are of utmost importance for controlling plant diseases and mitigating the economic losses they incur. Technological advances have increasingly simplified the tools available for the identification of pathogens to the extent that, in some cases, this can be done directly by growers and producers themselves. Commercially available immunoprinting kits and lateral flow devices (LFDs) for detection of selected plant pathogens are among the first tools of what can be considered grower-friendly pathogen monitoring methods. Research efforts, spurned on by point-of-care needs in the medical field, are paving the way for the further development of on-the-spot diagnostics and multiplex technologies in plant pathology. Grower-friendly methods need to be practical, robust, readily available, and cost-effective. Such methods are not restricted to on-the-spot testing but extend to laboratory services, which are sometimes more practicable for growers, extension agents, regulators, and other users of diagnostic tests.
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Affiliation(s)
- Solke H De Boer
- Charlottetown Laboratory, Canadian Food Inspection Agency, Charlottetown, PE, C1A 5T1 Canada.
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43
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Quiñones B, Swimley MS, Narm KE, Patel RN, Cooley MB, Mandrell RE. O-antigen and virulence profiling of shiga toxin-producing Escherichia coli by a rapid and cost-effective DNA microarray colorimetric method. Front Cell Infect Microbiol 2012; 2:61. [PMID: 22919652 PMCID: PMC3417394 DOI: 10.3389/fcimb.2012.00061] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 04/18/2012] [Indexed: 12/23/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a leading cause of foodborne illness worldwide. The present study developed the use of DNA microarrays with the ampliPHOX colorimetric method to rapidly detect and genotype STEC strains. A low-density 30-mer oligonucleotide DNA microarray was designed to target O-antigen gene clusters of 11 E. coli serogroups (O26, O45, O91, O103, O104, O111, O113, O121, O128, O145, and O157) that have been associated with the majority of STEC infections. In addition, the DNA microarray targeted 11 virulence genes, encoding adhesins, cytotoxins, proteases, and receptor proteins, which have been implicated in conferring increased ability to cause disease for STEC. Results from the validation experiments demonstrated that this microarray-based colorimetric method allowed for a rapid and accurate genotyping of STEC reference strains from environmental and clinical sources and from distinct geographical locations. Positive hybridization signals were detected only for probes targeting serotype and virulence genes known to be present in the STEC reference strains. Quantification analysis indicated that the mean pixel intensities of the signal for probes targeting O-antigen or virulence genes were at least three times higher when compared to the background. Furthermore, this microarray-based colorimetric method was then employed to genotype a group of E. coli isolates from watershed sediment and animal fecal samples that were collected from an important region for leafy-vegetable production in the central coast of California. The results indicated an accurate identification of O-type and virulence genes in the tested isolates and confirmed that the ampliPHOX colorimetric method with low-density DNA microarrays enabled a fast assessment of the virulence potential of STEC using low-cost reagents and instrumentation.
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Affiliation(s)
- Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, U.S. Department of Agriculture/Agricultural Research Service Albany, CA, USA.
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44
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A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomed Microdevices 2012; 14:769-78. [DOI: 10.1007/s10544-012-9658-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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45
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Label-free detection of bacterial RNA using polydiacetylene-based biochip. Biosens Bioelectron 2012; 35:44-49. [DOI: 10.1016/j.bios.2012.01.043] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/27/2012] [Accepted: 01/30/2012] [Indexed: 11/15/2022]
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46
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Simultaneous detection of multiple fish pathogens using a naked-eye readable DNA microarray. SENSORS 2012; 12:2710-28. [PMID: 22736973 PMCID: PMC3376613 DOI: 10.3390/s120302710] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 02/20/2012] [Accepted: 02/27/2012] [Indexed: 11/21/2022]
Abstract
We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum) commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer) complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3′-indolylphosphate, p-toluidine salt (NBT/BCIP), resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 103 CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens.
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47
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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48
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Detection and characterization of pathogenic vibrios in shellfish by a Ligation Detection Reaction-Universal Array approach. Int J Food Microbiol 2012; 153:474-82. [DOI: 10.1016/j.ijfoodmicro.2011.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 09/23/2011] [Accepted: 11/11/2011] [Indexed: 11/23/2022]
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49
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Patowary A, Chauhan RK, Singh M, Kv S, Periwal V, Kp K, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S, Scaria V. De novo identification of viral pathogens from cell culture hologenomes. BMC Res Notes 2012; 5:11. [PMID: 22226071 PMCID: PMC3284880 DOI: 10.1186/1756-0500-5-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 01/06/2012] [Indexed: 11/12/2022] Open
Abstract
Background Fast, specific identification and surveillance of pathogens is the cornerstone of any outbreak response system, especially in the case of emerging infectious diseases and viral epidemics. This process is generally tedious and time-consuming thus making it ineffective in traditional settings. The added complexity in these situations is the non-availability of pure isolates of pathogens as they are present as mixed genomes or hologenomes. Next-generation sequencing approaches offer an attractive solution in this scenario as it provides adequate depth of sequencing at fast and affordable costs, apart from making it possible to decipher complex interactions between genomes at a scale that was not possible before. The widespread application of next-generation sequencing in this field has been limited by the non-availability of an efficient computational pipeline to systematically analyze data to delineate pathogen genomes from mixed population of genomes or hologenomes. Findings We applied next-generation sequencing on a sample containing mixed population of genomes from an epidemic with appropriate processing and enrichment. The data was analyzed using an extensive computational pipeline involving mapping to reference genome sets and de-novo assembly. In depth analysis of the data generated revealed the presence of sequences corresponding to Japanese encephalitis virus. The genome of the virus was also independently de-novo assembled. The presence of the virus was in addition, verified using standard molecular biology techniques. Conclusions Our approach can accurately identify causative pathogens from cell culture hologenome samples containing mixed population of genomes and in principle can be applied to patient hologenome samples without any background information. This methodology could be widely applied to identify and isolate pathogen genomes and understand their genomic variability during outbreaks.
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Affiliation(s)
- Ashok Patowary
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India.
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50
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Rödiger S, Schierack P, Böhm A, Nitschke J, Berger I, Frömmel U, Schmidt C, Ruhland M, Schimke I, Roggenbuck D, Lehmann W, Schröder C. A highly versatile microscope imaging technology platform for the multiplex real-time detection of biomolecules and autoimmune antibodies. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 133:35-74. [PMID: 22437246 DOI: 10.1007/10_2011_132] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The analysis of different biomolecules is of prime importance for life science research and medical diagnostics. Due to the discovery of new molecules and new emerging bioanalytical problems, there is an ongoing demand for a technology platform that provides a broad range of assays with a user-friendly flexibility and rapid adaptability to new applications. Here we describe a highly versatile microscopy platform, VideoScan, for the rapid and simultaneous analysis of various assay formats based on fluorescence microscopic detection. The technological design is equally suitable for assays in solution, microbead-based assays and cell pattern recognition. The multiplex real-time capability for tracking of changes under dynamic heating conditions makes it a useful tool for PCR applications and nucleic acid hybridization, enabling kinetic data acquisition impossible to obtain by other technologies using endpoint detection. The paper discusses the technological principle of the platform regarding data acquisition and processing. Microbead-based and solution applications for the detection of diverse biomolecules, including antigens, antibodies, peptides, oligonucleotides and amplicons in small reaction volumes, are presented together with a high-content detection of autoimmune antibodies using a HEp-2 cell assay. Its adaptiveness and versatility gives VideoScan a competitive edge over other bioanalytical technologies.
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Affiliation(s)
- Stefan Rödiger
- Lausitz University of Applied Sciences, Senftenberg, Germany
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