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Yin HB, Chen CH, Katchman B, Newland C, May M, Patel J. Rapid detection of Salmonella enterica in leafy greens by a novel DNA microarray-based PathogenDx system. Food Microbiol 2022; 107:104086. [PMID: 35953180 DOI: 10.1016/j.fm.2022.104086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/17/2022] [Accepted: 06/26/2022] [Indexed: 11/04/2022]
Abstract
The diverse matrices pose great challenges for rapid detection of low Salmonella level (<10 CFU) in fresh produce. The applicability of microarray-based PathogenDx system for detecting low contamination of Salmonella Newport from leafy greens was evaluated. A pre-PCR preparation protocol including enrichment in universal pre-enrichment broth for 3 h followed by sample concentration using an InnovaPrep bio-concentrator or 6 h enrichment without a concentration step was used for detecting S. Newport from leafy greens with initial inoculum level at ∼6 CFU/25 g. Among 205 samples tested, 98%, 93%, 76%, and 60% of Romaine lettuce, Iceberg lettuce, kale, and spinach samples were tested positive after 3 h of enrichment with sample concentration. After 6 h of enrichment, 100%, 98%, 90%, and 82% of Romaine lettuce, Iceberg lettuce, kale, and spinach samples were positive. The samples were parallelly tested by the FDA bacterial analytical manual (BAM) method and 100% of spiked produce samples were tested positive. The overall analysis time of this methodology was between 8 and 11 h, including all pre-enrichment and concentration steps, in contrast to 4-5 days required for BAM method. The system correctly differentiated all 108 Salmonella strains and 35 non-Salmonella strains used in the study. This novel microarray approach provides a rapid method for detecting Salmonella in leafy greens.
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Affiliation(s)
- Hsin-Bai Yin
- U.S.Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Chi-Hung Chen
- U.S.Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA; Oak Ridge Institute for Science and Education (ORISE), Research Participation Program, USA
| | | | | | | | - Jitendra Patel
- U.S.Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA.
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Nehra M, Kumar V, Kumar R, Dilbaghi N, Kumar S. Current Scenario of Pathogen Detection Techniques in Agro-Food Sector. BIOSENSORS 2022; 12:489. [PMID: 35884292 PMCID: PMC9313409 DOI: 10.3390/bios12070489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 05/05/2023]
Abstract
Over the past-decade, agricultural products (such as vegetables and fruits) have been reported as the major vehicles for foodborne diseases, which are limiting food resources. The spread of infectious diseases due to foodborne pathogens poses a global threat to human health and the economy. The accurate and timely detection of infectious disease and of causative pathogens is crucial in the prevention and treatment of disease. Negligence in the detection of pathogenic substances can be catastrophic and lead to a pandemic. Despite the revolution in health diagnostics, much attention has been paid to the agro-food sector regarding the detection of food contaminants (such as pathogens). The conventional analytical techniques for pathogen detection are reliable and still in operation. However, laborious procedures and time-consuming detection via these approaches emphasize the need for simple, easy-to-use, and affordable detection techniques. The rapid detection of pathogens from food is essential to avoid the morbidity and mortality originating from the suboptimal nature of empiric pathogen treatment. This review critically discusses both the conventional and emerging bio-molecular approaches for pathogen detection in agro-food.
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Affiliation(s)
- Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Virendra Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Rajesh Kumar
- Department of Mechanical Engineering, University Institute of Engineering and Technology, Panjab University, Chandigarh 160014, India;
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
| | - Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar 125001, Haryana, India; (M.N.); (V.K.); (N.D.)
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3
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Hormsombut T, Rijiravanich P, Surareungchai W, Kalasin S. Highly sensitive and selective antibody microarrays based on a Cy5-antibody complexes coupling ES-biochip for E. coli and Salmonella detection. RSC Adv 2022; 12:24760-24768. [PMID: 36128368 PMCID: PMC9429895 DOI: 10.1039/d2ra03391g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/19/2022] [Indexed: 12/03/2022] Open
Abstract
Foodborne pathogens are threats in food and a cause of major health issues globally. Microbial safety has become a key concern to eliminate disease-causing pathogens from the food supply. For this purpose, the Cy5 dye conjugated with a double-biotin DNA linkage and a detection antibody (Cy5-Ab complexes) was developed to amplify a foodborne detection signal on a microarray. Additionally, the ES-biochip was designed to attain a visual screening of an antibody microarray for the simultaneous threat detection of Salmonella and Escherichia coli (E. coli). Quantification was also performed by fluorescence. After optimizing the Cy5-Ab complex appendage and enhancing the detection signal from a sandwich immunoassay, high sensitivity and selectivity were observed. The limits of detection for both pathogens in buffer and food samples were 103 CFU mL−1 and less than 9 CFU mL−1 by visual screening and fluorescent intensity quantification, respectively. Mono and duplex responses were not significantly different which means that no cross-reactivity occurred. Uniquely, the assays hold great potential to be used in several fields, such as clinical diagnosis of foodborne microbes, food hygiene screening, and pathogen detection. A visual ES-biochip was highly sensitive and selective as well as enabled simultaneous detection. An optimized amount of Cy5 dye was attached to a Cy5-Ab complex label using a double-biotin DNA linkage.![]()
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Affiliation(s)
- Timpika Hormsombut
- Faculty of Science and Nanoscience & Nanotechnology Graduate Program, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Patsamon Rijiravanich
- BioSciences and Systems Biology Research Team, National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Werasak Surareungchai
- Faculty of Science and Nanoscience & Nanotechnology Graduate Program, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Surachate Kalasin
- Faculty of Science and Nanoscience & Nanotechnology Graduate Program, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
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An Aptamer-Array-Based Sample-to-Answer Biosensor for Ochratoxin A Detection via Fluorescence Resonance Energy Transfer. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9110309] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Food toxins are a hidden threat that can cause cancer and tremendously impact human health. Therefore, the detection of food toxins in a timely manner with high sensitivity is of paramount importance for public health and food safety. However, the current detection methods are relatively time-consuming and not practical for field tests. In the present work, we developed a novel aptamer-chip-based sample-to-answer biosensor (ACSB) for ochratoxin A (OTA) detection via fluorescence resonance energy transfer (FRET). In this system, a cyanine 3 (Cy3)-labeled OTA-specific biotinylated aptamer was immobilized on an epoxy-coated chip via streptavidin-biotin binding. A complementary DNA strand to OTA aptamer at the 3′-end was labeled with a black hole quencher 2 (BHQ2) to quench Cy3 fluorescence when in proximity. In the presence of OTA, the Cy3-labeled OTA aptamer bound specifically to OTA and led to the physical separation of Cy3 and BHQ2, which resulted in an increase of fluorescence signal. The limit of detection (LOD) of this ACSB for OTA was 0.005 ng/mL with a linearity range of 0.01–10 ng/mL. The cross-reactivity of ACSB against other mycotoxins, ochratoxin B (OTB), aflatoxin B1 (AFB1), zearalenone (ZEA), or deoxynilvalenol (DON), was less than 0.01%. In addition, this system could accurately detect OTA in rice samples spiked with OTA, and the mean recovery rate of the spiked-in OTA reached 91%, with a coefficient of variation (CV) of 8.57–9.89%. Collectively, the ACSB may represent a rapid, accurate, and easy-to-use platform for OTA detection with high sensitivity and specificity.
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Barman SR, Khan I, Chatterjee S, Saha S, Choi D, Lee S, Lin ZH. Electrowetting-on-dielectric (EWOD): Current perspectives and applications in ensuring food safety. J Food Drug Anal 2020; 28:595-621. [PMID: 35696148 PMCID: PMC9261810 DOI: 10.38212/2224-6614.1239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/08/2020] [Accepted: 07/03/2020] [Indexed: 11/18/2022] Open
Abstract
Digital microfluidic (DMF) platforms have contributed immensely to the development of multifunctional lab-on-chip systems for performing complete sets of biological and analytical assays. Electrowetting-on-dielectric (EWOD) technology, due to its outstanding flexibility and integrability, has emerged as a promising candidate for such lab-on-chip applications. Triggered by an electrical stimulus, EWOD devices allow precise manipulation of single droplets along the designed electrode arrays without employing external pumps and valves, thereby enhancing the miniaturization and portability of the system towards transcending important laboratory assays in resource-limited settings. In recent years, the simple fabrication process and reprogrammable architecture of EWOD chips have led to their widespread applications in food safety analysis. Various EWOD devices have been developed for the quantitative monitoring of analytes such as food-borne pathogens, heavy metal ions, vitamins, and antioxidants, which are significant in food samples. In this paper, we reviewed the advances and developments in the design of EWOD systems for performing versatile functions starting from sample preparation to sample detection, enabling rapid and high-throughput food analysis.
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Affiliation(s)
- Snigdha Roy Barman
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013,
Taiwan
| | - Imran Khan
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013,
Taiwan
| | - Subhodeep Chatterjee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013,
Taiwan
| | - Subhajit Saha
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013,
Taiwan
| | - Dukhyun Choi
- Department of Mechanical Engineering, Kyung Hee University, Yongin, 17104,
South Korea
| | - Sangmin Lee
- School of Mechanical Engineering, Chung-Ang University, Seoul 06974,
South Korea
| | - Zong-Hong Lin
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013,
Taiwan
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013,
Taiwan
- Department of Mechanical Engineering, Kyung Hee University, Yongin, 17104,
South Korea
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6
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Satpathy G, Chandra GK, Manikandan E, Mahapatra DR, Umapathy S. Pathogenic Escherichia coli (E. coli) detection through tuned nanoparticles enhancement study. Biotechnol Lett 2020; 42:853-863. [PMID: 32040672 DOI: 10.1007/s10529-020-02835-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/04/2020] [Indexed: 01/25/2023]
Abstract
OBJECTIVE This study aims to detect pathogenic Escherichia coli (E. coli) bacteria using non-destructive fluorescence microscopy and micro-Raman spectroscopy. RESULTS Raman vibrational spectroscopy provides additional information regarding biochemical changes at the cellular level. We have used two nanomaterials zinc oxide nanoparticles (ZnO-NPs) and gold nanoparticles (Au-NPs) to detect pathogenic E. coli. The scanning electron microscope (SEM) with energy dispersive X-ray (EDAX) spectroscopy exhibit surface morphology and the elemental composition of the synthesized NPs. The metal NPs are useful contrast agents due to the surface plasmon resonance (SPR) to detect the signal intensity and hence the bacterial cells. The changes due to the interaction between cells and NPs are further correlated to the change in the surface charge and stiffness of the cell surface with the help of the fluorescence microscopic assay. CONCLUSIONS We conclude that when two E. coli strains (MTCC723 and MTCC443) and NPs are respectively mixed and kept overnight, the growth of bacteria are inhibited by ZnO-NPs due to changes in cell membrane permeability and intracellular metabolic system under fluorescence microscopy. However, SPR possessed Au-NPs result in enhanced fluorescence of both pathogens. In addition, with the help of Raman microscopy and element analysis, significant changes are observed when Au-NPs are added with the two strains as compared to ZnO-NPs due to protein, lipid and DNA/RNA induced conformational changes.
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Affiliation(s)
- Gargibala Satpathy
- Central Research Laboratory, Sree Balaji Medical College & Hospital (SBMCH), Bharath Institute for Higher Education & Research (BIHER), Bharath University, Chennai, Tamil Nadu, 600073, India.,Laboratory of Integrative Multiscale Engineering Materials and Systems, Department of Aerospace Engineering, Indian Institute of Science, Bangalore, 560012, India
| | | | - E Manikandan
- Central Research Laboratory, Sree Balaji Medical College & Hospital (SBMCH), Bharath Institute for Higher Education & Research (BIHER), Bharath University, Chennai, Tamil Nadu, 600073, India. .,Solid-State Nanoscale Laboratory, Department of Physics, TUCAS Campus, Thiruvalluvar University, Thennangur, Vellore, 604408, India.
| | - D Roy Mahapatra
- Laboratory of Integrative Multiscale Engineering Materials and Systems, Department of Aerospace Engineering, Indian Institute of Science, Bangalore, 560012, India.
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India. .,Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, 462066, India.
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7
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Lin L, Zheng Q, Lin J, Yuk HG, Guo L. Immuno- and nucleic acid-based current technique for Salmonella detection in food. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-019-03423-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Sub-femtomolar detection of DNA and discrimination of mutant strands using microwell-array assisted digital enzyme-linked oligonucleotide assay. Anal Chim Acta 2018; 1041:122-130. [PMID: 30340684 DOI: 10.1016/j.aca.2018.08.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/12/2018] [Accepted: 08/28/2018] [Indexed: 02/01/2023]
Abstract
Detection methods that do not rely on the amplification of DNA but can reach sensitivity, specificity and throughput of gold standard methods, such as qPCR, have been extensively explored in recent years. Here, we present a hydrophilic-in-hydrophobic (HIH)-microwell array platform that empowers a panel of different amplification-free DNA bioassays: digital enzyme-linked oligonucleotide assay (ELONA), ligation-assisted (LA) digital ELONA and so-called 'analog' bioassays. We developed all three bioassays by using magnetic beads for capturing DNA target, followed by hybridization of enzyme-labelled detection probes and sealing of the built complexes into the femtoliter HIH microwells to achieve the fluorescent readout of single DNA molecules. With the optimized digital ELONA bioassay, we successfully detected 97 and 200 nt-long ssDNA molecules down to 68 and 92 aM, respectively, demonstrating extremely high sensitivity of the bioassay and its flexibility towards targets of different lengths. Importantly, we also proved that the same bioassay concept was suited to detect substantially higher concentrations of ssDNA (up to picomolar levels) by quantifying the total fluorescent intensity rather than counting fluorescent events for digital quantification. Finally, we advanced this concept towards LA digital ELONA capable of differentiating wildtype strands from those carrying single-point mutations even when the former were constituting only 1% of the DNA mixture and were present at 2 fM concentration. In conclusion, the developed platform showed remarkably high sensitivity, specificity and versatility for amplification-free detection of DNA and as such can be valuable for numerous applications in medical diagnostics, gene analysis, food safety and environmental monitoring.
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9
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Hasan MR, Pulingam T, Appaturi JN, Zifruddin AN, Teh SJ, Lim TW, Ibrahim F, Leo BF, Thong KL. Carbon nanotube-based aptasensor for sensitive electrochemical detection of whole-cell Salmonella. Anal Biochem 2018; 554:34-43. [PMID: 29870692 DOI: 10.1016/j.ab.2018.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
In this study, an amino-modified aptasensor using multi-walled carbon nanotubes (MWCNTs)-deposited ITO electrode was prepared and evaluated for the detection of pathogenic Salmonella bacteria. An amino-modified aptamer (ssDNA) which binds selectively to whole-cell Salmonella was immobilised on the COOH-rich MWCNTs to produce the ssDNA/MWCNT/ITO electrode. The morphology of the MWCNT before and after interaction with the aptamers were observed using scanning electron microscopy (SEM). Cyclic voltammetry and electrochemical impedance spectroscopy techniques were used to investigate the electrochemical properties and conductivity of the aptasensor. The results showed that the impedance measured at the ssDNA/MWCNT/ITO electrode surface increased after exposure to Salmonella cells, which indicated successful binding of Salmonella on the aptamer-functionalised surface. The developed ssDNA/MWCNT/ITO aptasensor was stable and maintained linearity when the scan rate was increased from 10 mV s-1 to 90 mV s-1. The detection limit of the ssDNA/MWCNT/ITO aptasensor, determined from the sensitivity analysis, was found to be 5.5 × 101 cfu mL-1 and 6.7 × 101 cfu mL-1 for S. Enteritidis and S. Typhimurium, respectively. The specificity test demonstrated that Salmonella bound specifically to the ssDNA/MWCNT/ITO aptasensor surface, when compared with non-Salmonella spp. The prepared aptasensor was successfully applied for the detection of Salmonella in food samples.
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Affiliation(s)
- Md Rakibul Hasan
- Nanotechnology & Catalysis Research Centre (NANOCAT), Institute of Graduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Thiruchelvi Pulingam
- Nanotechnology & Catalysis Research Centre (NANOCAT), Institute of Graduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jimmy Nelson Appaturi
- Nanotechnology & Catalysis Research Centre (NANOCAT), Institute of Graduate Studies, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Anis Nadyra Zifruddin
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Swe Jyan Teh
- Centre for Innovation in Medical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Teck Wei Lim
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Fatimah Ibrahim
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Bey Fen Leo
- Centre for Innovation in Medical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia; Department of Biomedical Imaging, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kwai Lin Thong
- Institute of Biological Science, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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10
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Cimaglia F, Tristezza M, Saccomanno A, Rampino P, Perrotta C, Capozzi V, Spano G, Chiesa M, Mita G, Grieco F. An innovative oligonucleotide microarray to detect spoilage microorganisms in wine. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.12.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Elucidating Waterborne Pathogen Presence and Aiding Source Apportionment in an Impaired Stream. Appl Environ Microbiol 2018; 84:AEM.02510-17. [PMID: 29305503 DOI: 10.1128/aem.02510-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/20/2017] [Indexed: 11/20/2022] Open
Abstract
Fecal indicator bacteria (FIB) are the basis for water quality regulations and are considered proxies for waterborne pathogens when conducting human health risk assessments. The direct detection of pathogens in water and simultaneous identification of the source of fecal contamination are possible with microarrays, circumventing the drawbacks to FIB approaches. A multigene target microarray was used to assess the prevalence of waterborne pathogens in a fecally impaired mixed-use watershed. The results indicate that fecal coliforms have improved substantially in the watershed since its listing as a 303(d) impaired stream in 2002 and are now near United States recreational water criterion standards. However, waterborne pathogens are still prevalent in the watershed, as viruses (bocavirus, hepatitis E and A viruses, norovirus, and enterovirus G), bacteria (Campylobacter spp., Clostridium spp., enterohemorrhagic and enterotoxigenic Escherichia coli, uropathogenic E. coli, Enterococcus faecalis, Helicobacter spp., Salmonella spp., and Vibrio spp.), and eukaryotes (Acanthamoeba spp., Entamoeba histolytica, and Naegleria fowleri) were detected. A comparison of the stream microbial ecology with that of sewage, cattle, and swine fecal samples revealed that human sources of fecal contamination dominate in the watershed. The methodology presented is applicable to a wide range of impaired streams for the identification of human health risk due to waterborne pathogens and for the identification of areas for remediation efforts.IMPORTANCE The direct detection of waterborne pathogens in water overcomes many of the limitations of the fecal indicator paradigm. Furthermore, the identification of the source of fecal impairment aids in identifying areas for remediation efforts. Multitarget gene microarrays are shown to simultaneously identify waterborne pathogens and aid in determining the sources of impairment, enabling further focused investigations. This study shows the use of this methodology in a historically impaired watershed in which total maximum daily load reductions have been successfully implemented to reduce risk. The results suggest that while the fecal indicators have been reduced more than 96% and are nearing recreational water criterion levels, pathogens are still detectable in the watershed. Microbial source tracking results show that additional remediation efforts are needed to reduce the impact of human sewage in the watershed.
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12
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Rohde A, Hammerl JA, Boone I, Jansen W, Fohler S, Klein G, Dieckmann R, Al Dahouk S. Overview of validated alternative methods for the detection of foodborne bacterial pathogens. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.02.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Valderrama WB, Dudley EG, Doores S, Cutter CN. Commercially Available Rapid Methods for Detection of Selected Food-borne Pathogens. Crit Rev Food Sci Nutr 2017; 56:1519-31. [PMID: 25749054 DOI: 10.1080/10408398.2013.775567] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Generally, the enumeration and isolation of food-borne pathogens is performed using culture-dependent methods. These methods are sensitive, inexpensive, and provide both qualitative and quantitative assessment of the microorganisms present in a sample, but these are time-consuming. For this reason, researchers are developing new techniques that allow detection of food pathogens in shorter period of time. This review identifies commercially available methods for rapid detection and quantification of Listeria monocytogenes, Salmonella spp., Staphylococcus aureus, and Shiga toxin-producing Escherichia coli in food samples. Three categories are discussed: immunologically based methods, nucleic acid-based assays, and biosensors. This review describes the basic mechanism and capabilities of each method, discusses the difficulties of choosing the most convenient method, and provides an overview of the future challenges for the technology for rapid detection of microorganisms.
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Affiliation(s)
- Wladir B Valderrama
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
| | - Edward G Dudley
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
| | - Stephanie Doores
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
| | - Catherine N Cutter
- a Department of Food Science , Pennsylvania State University , University Park , Pennsylvania , USA
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14
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Pandey A, Gurbuz Y, Ozguz V, Niazi JH, Qureshi A. Graphene-interfaced electrical biosensor for label-free and sensitive detection of foodborne pathogenic E. coli O157:H7. Biosens Bioelectron 2016; 91:225-231. [PMID: 28012318 DOI: 10.1016/j.bios.2016.12.041] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/01/2016] [Accepted: 12/15/2016] [Indexed: 01/07/2023]
Abstract
E. coli O157:H7 is an enterohemorrhagic bacteria responsible for serious foodborne outbreaks that causes diarrhoea, fever and vomiting in humans. Recent foodborne E. coli outbreaks has left a serious concern to public health. Therefore, there is an increasing demand for a simple, rapid and sensitive method for pathogen detection in contaminated foods. In this study, we developed a label-free electrical biosensor interfaced with graphene for sensitive detection of pathogenic bacteria. This biosensor was fabricated by interfacing graphene with interdigitated microelectrodes of capacitors that were biofunctionalized with E. coli O157:H7 specific antibodies for sensitive pathogenic bacteria detection. Here, graphene nanostructures on the sensor surface provided superior chemical properties such as high carrier mobility and biocompatibility with antibodies and bacteria. The sensors transduced the signal based on changes in dielectric properties (capacitance) through (i) polarization of captured cell-surface charges, (ii) cells' internal bioactivity, (iii) cell-wall's electronegativity or dipole moment and their relaxation and (iv) charge carrier mobility of graphene that modulated the electrical properties once the pathogenic E. coli O157:H7 captured on the sensor surface. Sensitive capacitance changes thus observed with graphene based capacitors were specific to E. coli O157:H7 strain with a sensitivity as low as 10-100 cells/ml. The proposed graphene based electrical biosensor provided advantages of speed, sensitivity, specificity and in-situ bacterial detection with no chemical mediators, represents a versatile approach for detection of a wide variety of other pathogens.
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Affiliation(s)
- Ashish Pandey
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey
| | - Yasar Gurbuz
- Faculty of Engineering and Natural Science, Sabanci University, Orhanli, Tuzla, 34956 Istanbul, Turkey
| | - Volkan Ozguz
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey
| | - Javed H Niazi
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey.
| | - Anjum Qureshi
- Sabanci University Nanotechnology Research and Application Center, Orta Mah., 34956 Istanbul, Turkey.
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15
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CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems. BMC Genomics 2016; 17:671. [PMID: 27552843 PMCID: PMC4994258 DOI: 10.1186/s12864-016-2988-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/02/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans. RESULTS This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota. CONCLUSIONS The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.
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Hybrid microarray based on double biomolecular markers of DNA and carbohydrate for simultaneous genotypic and phenotypic detection of cholera toxin-producing Vibrio cholerae. Biosens Bioelectron 2016; 79:398-405. [DOI: 10.1016/j.bios.2015.12.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 12/18/2015] [Accepted: 12/20/2015] [Indexed: 02/07/2023]
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Wang Y, Salazar JK. Culture-Independent Rapid Detection Methods for Bacterial Pathogens and Toxins in Food Matrices. Compr Rev Food Sci Food Saf 2015; 15:183-205. [DOI: 10.1111/1541-4337.12175] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/14/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Yun Wang
- Div. of Food Processing Science and Technology; U.S. Food and Drug Administration; Bedford Park IL U.S.A
| | - Joelle K. Salazar
- Div. of Food Processing Science and Technology; U.S. Food and Drug Administration; Bedford Park IL U.S.A
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Fluorescence-based bioassays for the detection and evaluation of food materials. SENSORS 2015; 15:25831-67. [PMID: 26473869 PMCID: PMC4634490 DOI: 10.3390/s151025831] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.
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Li X, Harwood VJ, Nayak B, Staley C, Sadowsky MJ, Weidhaas J. A novel microbial source tracking microarray for pathogen detection and fecal source identification in environmental systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:7319-7329. [PMID: 25970344 DOI: 10.1021/acs.est.5b00980] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pathogen detection and the identification of fecal contamination sources are challenging in environmental waters. Factors including pathogen diversity and ubiquity of fecal indicator bacteria hamper risk assessment and remediation of contamination sources. A custom microarray targeting pathogens (viruses, bacteria, protozoa), microbial source tracking (MST) markers, and antibiotic resistance genes was tested against DNA obtained from whole genome amplification (WGA) of RNA and DNA from sewage and animal (avian, cattle, poultry, and swine) feces. Perfect and mismatch probes established the specificity of the microarray in sewage, and fluorescence decrease of positive probes over a 1:10 dilution series demonstrated semiquantitative measurement. Pathogens, including norovirus, Campylobacter fetus, Helicobacter pylori, Salmonella enterica, and Giardia lamblia were detected in sewage, as well as MST markers and resistance genes to aminoglycosides, beta-lactams, and tetracycline. Sensitivity (percentage true positives) of MST results in sewage and animal waste samples (21-33%) was lower than specificity (83-90%, percentage of true negatives). Next generation DNA sequencing revealed two dominant bacterial families that were common to all sample types: Ruminococcaceae and Lachnospiraceae. Five dominant phyla and 15 dominant families comprised 97% and 74%, respectively, of sequences from all fecal sources. Phyla and families not represented on the microarray are possible candidates for inclusion in subsequent array designs.
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Affiliation(s)
- Xiang Li
- †Department of Civil and Environmental Engineering, West Virginia University, P.O. Box 6103, Morgantown, West Virginia 26506, United States
| | - Valerie J Harwood
- ‡Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Bina Nayak
- ‡Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Christopher Staley
- §BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Michael J Sadowsky
- ∥Department of Soil, Water, and Climate, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Jennifer Weidhaas
- †Department of Civil and Environmental Engineering, West Virginia University, P.O. Box 6103, Morgantown, West Virginia 26506, United States
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Mangal M, Bansal S, Sharma SK, Gupta RK. Molecular Detection of Foodborne Pathogens: A Rapid and Accurate Answer to Food Safety. Crit Rev Food Sci Nutr 2015; 56:1568-84. [DOI: 10.1080/10408398.2013.782483] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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21
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A portable automatic endpoint detection system for amplicons of loop mediated isothermal amplification on microfluidic compact disk platform. SENSORS 2015; 15:5376-89. [PMID: 25751077 PMCID: PMC4435121 DOI: 10.3390/s150305376] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/19/2015] [Accepted: 01/28/2015] [Indexed: 11/17/2022]
Abstract
In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP) on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV) emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD). The sensitivity test has been performed with detection limit up to 2.5 × 10−3 ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment.
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Law JWF, Ab Mutalib NS, Chan KG, Lee LH. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front Microbiol 2015. [PMID: 25628612 DOI: 10.3389/fmicb.2014.00770.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.
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Affiliation(s)
- Jodi Woan-Fei Law
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Selangor Darul Ehsan, Malaysia ; School of Science, Monash University Malaysia Selangor Darul Ehsan, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Bandar Tun Razak Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Selangor Darul Ehsan, Malaysia
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Law JWF, Ab Mutalib NS, Chan KG, Lee LH. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations. Front Microbiol 2015; 5:770. [PMID: 25628612 PMCID: PMC4290631 DOI: 10.3389/fmicb.2014.00770] [Citation(s) in RCA: 517] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/17/2014] [Indexed: 12/11/2022] Open
Abstract
The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.
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Affiliation(s)
- Jodi Woan-Fei Law
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
- School of Science, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Bandar Tun RazakKuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of MalayaKuala Lumpur, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University MalaysiaSelangor Darul Ehsan, Malaysia
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24
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Kiyama R, Zhu Y. DNA microarray-based gene expression profiling of estrogenic chemicals. Cell Mol Life Sci 2014; 71:2065-82. [PMID: 24399289 PMCID: PMC11113397 DOI: 10.1007/s00018-013-1544-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/06/2013] [Accepted: 12/16/2013] [Indexed: 12/31/2022]
Abstract
We summarize updated information about DNA microarray-based gene expression profiling by focusing on its application to estrogenic chemicals. First, estrogenic chemicals, including natural/industrial estrogens and phytoestrogens, and the methods for detection and evaluation of estrogenic chemicals were overviewed along with a comprehensive list of estrogenic chemicals of natural or industrial origin. Second, gene expression profiling of chemicals using a focused microarray containing estrogen-responsive genes is summarized. Third, silent estrogens, a new type of estrogenic chemicals characterized by their estrogenic gene expression profiles without growth stimulative or inhibitory effects, have been identified so far exclusively by DNA microarray assay. Lastly, the prospect of a microarray assay is discussed, including issues such as commercialization, future directions of applications and quality control methods.
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Affiliation(s)
- Ryoiti Kiyama
- Signaling Molecules Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan,
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High-throughput detection of food-borne pathogenic bacteria using oligonucleotide microarray with quantum dots as fluorescent labels. Int J Food Microbiol 2014; 185:27-32. [PMID: 24927399 DOI: 10.1016/j.ijfoodmicro.2014.05.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 04/16/2014] [Accepted: 05/14/2014] [Indexed: 01/10/2023]
Abstract
Bacterial pathogens are mostly responsible for food-borne diseases, and there is still substantial room for improvement in the effective detection of these organisms. In the present study, we explored a new method to detect target pathogens easily and rapidly with high sensitivity and specificity. This method uses an oligonucleotide microarray combined with quantum dots as fluorescent labels. Oligonucleotide probes targeting the 16SrRNA gene were synthesized to create an oligonucleotide microarray. The PCR products labeled with biotin were subsequently hybridized using an oligonucleotide microarray. Following incubation with CdSe/ZnS quantum dots coated with streptavidin, fluorescent signals were detected with a PerkinElmer Gx Microarray Scanner. The results clearly showed specific hybridization profiles corresponding to the bacterial species assessed. Two hundred and sixteen strains of food-borne bacterial pathogens, including standard strains and isolated strains from food samples, were used to test the specificity, stability, and sensitivity of the microarray system. We found that the oligonucleotide microarray combined with quantum dots used as fluorescent labels can successfully discriminate the bacterial organisms at the genera or species level, with high specificity and stability as well as a sensitivity of 10 colony forming units (CFU)/mL of pure culture. We further tested 105 mock-contaminated food samples and achieved consistent results as those obtained from traditional biochemical methods. Together, these results indicate that the quantum dot-based oligonucleotide microarray has the potential to be a powerful tool in the detection and identification of pathogenic bacteria in foods.
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26
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Kim TH, Park J, Kim CJ, Cho YK. Fully integrated lab-on-a-disc for nucleic acid analysis of food-borne pathogens. Anal Chem 2014; 86:3841-8. [PMID: 24635032 DOI: 10.1021/ac403971h] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This paper describes a micro total analysis system for molecular analysis of Salmonella, a major food-borne pathogen. We developed a centrifugal microfluidic device, which integrated the three main steps of pathogen detection, DNA extraction, isothermal recombinase polymerase amplification (RPA), and detection, onto a single disc. A single laser diode was utilized for wireless control of valve actuation, cell lysis, and noncontact heating in the isothermal amplification step, thereby yielding a compact and miniaturized system. To achieve high detection sensitivity, rare cells in large volumes of phosphate-buffered saline (PBS) and milk samples were enriched before loading onto the disc by using antibody-coated magnetic beads. The entire procedure, from DNA extraction through to detection, was completed within 30 min in a fully automated fashion. The final detection was carried out using lateral flow strips by direct visual observation; detection limit was 10 cfu/mL and 10(2) cfu/mL in PBS and milk, respectively. Our device allows rapid molecular diagnostic analysis and does not require specially trained personnel or expensive equipment. Thus, we expect that it would have an array of potential applications, including in the detection of food-borne pathogens, environmental monitoring, and molecular diagnostics in resource-limited settings.
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Affiliation(s)
- Tae-Hyeong Kim
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST) , UNIST-gil 50, Ulsan, 689-798, Republic of Korea
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27
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Pöhlmann C, Dieser I, Sprinzl M. A lateral flow assay for identification of Escherichia coli by ribosomal RNA hybridisation. Analyst 2014; 139:1063-71. [PMID: 24443718 DOI: 10.1039/c3an02059b] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Existing technologies for analysis of microbiological contaminants in food or clinical samples are often expensive and require laboratory settings and trained personnel. Here we present a lateral flow assay employing gold nanoparticle-oligodeoxynucleotide conjugates and four-component sandwich hybridisation for direct detection of specific sequences in bacterial 16S ribosomal RNA. Combined with rapid "one step" lysis the developed procedure allows detection of 5 × 10(4) colony forming units per mL Escherichia coli within less than 25 minutes. Several Escherichia coli strains were detected successfully, whereas non-related as well as closely related bacterial species produced no signal. The developed nucleic acid lateral flow assay is inexpensive, rapid to perform and requires no nucleic acid amplification step.
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Affiliation(s)
- Christopher Pöhlmann
- University of Bayreuth, Department of Biochemistry, Universitätsstr. 30, 95440 Bayreuth, Germany.
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28
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Duplex PCR methods for the molecular detection of Escherichia fergusonii isolates from broiler chickens. Appl Environ Microbiol 2014; 80:1941-8. [PMID: 24441160 DOI: 10.1128/aem.04169-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia fergusonii is an emerging pathogen that has been isolated from a wide range of infections in animals and humans. Primers targeting specific genes, including yliE (encoding a conserved hypothetical protein of the cellulose synthase and regulator of cellulose synthase island), EFER_1569 (encoding a hypothetical protein, putative transcriptional activator for multiple antibiotic resistance), and EFER_3126 (encoding a putative triphosphoribosyl-dephospho-coenzyme A [CoA]), were designed for the detection of E. fergusonii by conventional and real-time PCR methods. Primers were screened by in silico PCR against 489 bacterial genomic sequences and by both PCR methods on 55 reference and field strains. Both methods were specific and sensitive for E. fergusonii, showing amplification only for this bacterium. Conventional PCR required a minimum bacterial concentration of approximately 10(2) CFU/ml, while real-time PCR required a minimum of 0.3 pg of DNA for consistent detection. Standard curves showed an efficiency of 98.5%, with an R(2) value of 0.99 for the real-time PCR assay. Cecal and cloacal contents from 580 chickens were sampled from broiler farms located in the Fraser Valley (British Columbia, Canada). Presumptive E. fergusonii isolates were recovered by enrichment and plating on differential and selective media. Of 301 total presumptive isolates, 140 (46.5%) were identified as E. fergusonii by biochemical profiling with the API 20E system and 268 (89.0%) using PCR methods. E. fergusonii detection directly from cecal and cloacal samples without preenrichment was achieved with both PCR methods. Hence, the PCR methods developed in this work significantly improve the detection of E. fergusonii.
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Zuo P, Li X, Dominguez DC, Ye BC. A PDMS/paper/glass hybrid microfluidic biochip integrated with aptamer-functionalized graphene oxide nano-biosensors for one-step multiplexed pathogen detection. LAB ON A CHIP 2013; 13:3921-8. [PMID: 23929394 PMCID: PMC3913183 DOI: 10.1039/c3lc50654a] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Infectious pathogens often cause serious public health concerns throughout the world. There is an increasing demand for simple, rapid and sensitive approaches for multiplexed pathogen detection. In this paper we have developed a polydimethylsiloxane (PDMS)/paper/glass hybrid microfluidic system integrated with aptamer-functionalized graphene oxide (GO) nano-biosensors for simple, one-step, multiplexed pathogen detection. The paper substrate used in this hybrid microfluidic system facilitated the integration of aptamer biosensors on the microfluidic biochip, and avoided complicated surface treatment and aptamer probe immobilization in a PDMS or glass-only microfluidic system. Lactobacillus acidophilus was used as a bacterium model to develop the microfluidic platform with a detection limit of 11.0 cfu mL(-1). We have also successfully extended this method to the simultaneous detection of two infectious pathogens - Staphylococcus aureus and Salmonella enterica. This method is simple and fast. The one-step 'turn on' pathogen assay in a ready-to-use microfluidic device only takes ~10 min to complete on the biochip. Furthermore, this microfluidic device has great potential in rapid detection of a wide variety of different other bacterial and viral pathogens.
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Affiliation(s)
- Peng Zuo
- Department of Chemistry, University of Texas at El Paso, 500 West University Ave, El Paso, Texas, 79968, USA.
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Brinkman NE, Francisco R, Nichols TL, Robinson D, Schaefer FW, Schaudies RP, Villegas EN. Detection of multiple waterborne pathogens using microsequencing arrays. J Appl Microbiol 2012; 114:564-73. [PMID: 23167710 DOI: 10.1111/jam.12073] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 10/10/2012] [Accepted: 10/31/2012] [Indexed: 11/25/2022]
Abstract
AIMS A microarray was developed to simultaneously detect Cryptosporidium parvum, Cryptosporidium hominis, Enterococcus faecium, Bacillus anthracis and Francisella tularensis in water. METHODS AND RESULTS A DNA microarray was designed to contain probes that specifically detected C. parvum, C. hominis, Ent. faecium, B. anthracis and F. tularensis. The microarray was then evaluated with samples containing target and nontarget DNA from near-neighbour micro-organisms, and tap water spiked with multiple organisms. Results demonstrated that the microarray consistently detected Ent. faecium, B. anthracis, F. tularensis and C. parvum when present in samples. Cryptosporidium hominis was only consistently detected through the use of shared probes between C. hominis and C. parvum. CONCLUSIONS This study successfully developed and tested a microarray-based assay that can specifically detect faecal indicator bacteria and human pathogens in tap water. SIGNIFICANCE AND IMPACT OF THE STUDY The use of indicator organisms has become a practical solution for monitoring for water quality. However, they do not always correlate well with the presence of many microbial pathogens, thus necessitating direct monitoring for most pathogens. This microarray can be used to simultaneously detect multiple organisms in a single sample. More importantly, it can provide occurrence information that may be used in assessing potential exposure risks to waterborne pathogens.
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Affiliation(s)
- N E Brinkman
- National Exposure Research Laboratory, US Environmental Protection Agency, Cincinnati, OH, USA
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Leski TA, Lin B, Malanoski AP, Stenger DA. Application of resequencing microarrays in microbial detection and characterization. Future Microbiol 2012; 7:625-37. [PMID: 22568717 DOI: 10.2217/fmb.12.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microarrays are powerful, highly parallel assays that are transforming microbiological diagnostics and research. The adaptation of microarray-based resequencing technology for microbial detection and characterization resulted in the development of a number assays that have unique advantages over other existing technologies. This technological platform seems to be especially useful for sensitive and high-resolution multiplexed diagnostics for clinical syndromes with similar symptoms, screening environmental samples for biothreat agents, as well as genotyping and whole-genome analysis of single pathogens.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, SW, Washington, DC 20375, USA.
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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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González I, García T, Fernández S, Martín R. Current Status on Arcobacter Research: An Update on DNA-Based Identification and Typing Methodologies. FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-011-9343-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Kostić T, Sessitsch A. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens. ACTA ACUST UNITED AC 2011; 1:3-24. [PMID: 27605332 PMCID: PMC5007712 DOI: 10.3390/microarrays1010003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 01/02/2023]
Abstract
Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.
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Affiliation(s)
- Tanja Kostić
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln an der Donau, Austria.
- Christian Doppler Laboratory for Molecular Food Analytics, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria.
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln an der Donau, Austria
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Hébrard M, Kröger C, Sivasankaran SK, Händler K, Hinton JCD. The challenge of relating gene expression to the virulence of Salmonella enterica serovar Typhimurium. Curr Opin Biotechnol 2011; 22:200-10. [PMID: 21388802 DOI: 10.1016/j.copbio.2011.02.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/04/2011] [Accepted: 02/10/2011] [Indexed: 12/15/2022]
Abstract
The first decade of transcriptomic studies of Salmonella enterica serovar Typhimurium focused upon gene expression in vitro, and during the infection of mammalian cells. The published regulons and stimulons show that the three Type Three Secretion Systems of S. Typhimurium respond to a diverse range of environmental conditions, and are controlled by a hierarchy of regulatory proteins. The integration of in vitro generated transcriptomic data with global gene expression of S. Typhimurium during infection is beginning to yield valuable information. The coordinated regulation of Salmonella gene expression is a key process for survival, adaptation and virulence capacities of the pathogen.
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Affiliation(s)
- Magali Hébrard
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics & Microbiology, Trinity College, Dublin 2, Ireland
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Koyuncu S, Andersson G, Vos P, Häggblom P. DNA microarray for tracing Salmonella in the feed chain. Int J Food Microbiol 2011; 145 Suppl 1:S18-22. [DOI: 10.1016/j.ijfoodmicro.2010.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 07/08/2010] [Accepted: 07/09/2010] [Indexed: 10/19/2022]
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Lee JY, Kim BC, Chang KJ, Ahn JM, Ryu JH, Chang HI, Gu MB. A subtractively optimized DNA microarray using non-sequenced genomic probes for the detection of food-borne pathogens. Appl Biochem Biotechnol 2010; 164:183-93. [PMID: 21116735 DOI: 10.1007/s12010-010-9126-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
Abstract
In this study, we present the successful detection of food-borne pathogens using randomly selected non-sequenced genomic DNA probes-based DNA microarray chips. Three food-borne pathogens, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), and Bacillus cereus, were subjected for the preparation of the DNA microarray probes. Initially, about 50 DNA probes selected randomly from non-sequenced genomic DNA of each pathogen were prepared by using a set of restriction enzyme pairs. The proto-type of DNA microarray chip for detecting three different pathogens simultaneously was fabricated by using those DNA probes prepared for each pathogen. This proto-type DNA microarray has been tested with three target pathogens and additional seven bacteria, and successfully verified with a few cross-hybridized probes. After this primary verification of the DNA microarray hybridization, this proto-type DNA microarray chip was redesigned and successfully optimized by eliminating a few cross-hybridized probes. The specificity of this redesigned DNA microarray chip to each pathogen was confirmed without any serious cross-hybridizations, and its multiplexing capability in its pathogen detection was found to be possible. This randomly selected non-sequenced genomic DNA probes-based DNA microarray was successfully proved to be the high-throughput simultaneous detection chip for the detection of food-borne pathogens, without knowing the exact sequence information of the target bacteria. This could be the first fabrication of DNA microarray chip for the simultaneous detection of different kinds of food-borne pathogens.
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Affiliation(s)
- Jin Yong Lee
- School of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul 136-701, Republic of Korea
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Distribution of antimicrobial resistance and virulence genes in Enterococcus spp. and characterization of isolates from broiler chickens. Appl Environ Microbiol 2010; 76:8033-43. [PMID: 20971861 DOI: 10.1128/aem.01545-10] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are now frequent causative agents of nosocomial infections. In this study, we analyzed the frequency and distribution of antibiotic resistance and virulence genotypes of Enterococcus isolates from broiler chickens. Fecal and cecal samples from nine commercial poultry farms were collected to quantify total enterococci. Sixty-nine presumptive enterococci were isolated and identified by API 20 Strep, and their susceptibilities to antibiotics were determined. Genotypes were assessed through the use of a novel DNA microarray carrying 70 taxonomic, 17 virulence, and 174 antibiotic resistance gene probes. Total enterococcal counts were different from farm to farm and between sample sources (P < 0.01). Fifty-one (74%) of the isolates were identified as E. faecium, whereas nine (13%), seven (10%), and two (3%) isolates were identified as E. hirae, E. faecalis, and E. gallinarum, respectively. Multiple-antibiotic resistance was evident in E. faecium and E. faecalis isolates. The most common multiple-antibiotic resistance phenotype was Bac Ery Tyl Lin Str Gen Tet Cip. Genes conferring resistance to aminoglycoside (aac, aacA-aphD, aadB, aphA, sat4), macrolide (ermA, ermB, ermAM, msrC), tetracycline (tetL, tetM, tetO), streptogramin (satG_vatE8), bacitracin (bcrR), and lincosamide (linB) antibiotics were detected in corresponding phenotypes. A range of 9 to 12 different virulence genes was found in E. faecalis, including ace, agg, agrB(Efs) (agrB gene of E. faecalis), cad1, the cAM373 and cCF10 genes, cob, cpd1, cylAB, efaA(Efs), and gelE. All seven E. faecalis isolates were found to carry the gelE gene and to hydrolize gelatin and bile salts. Results from this study showed the presence of enterococci of public and environmental health concerns in broiler chicken farms and demonstrated the utility of a microarray to quickly and reliably analyze resistance and virulence genotypes of Enterococcus spp.
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Boxrud D. Advances in subtyping methods of foodborne disease pathogens. Curr Opin Biotechnol 2010; 21:137-41. [PMID: 20299203 DOI: 10.1016/j.copbio.2010.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 02/17/2010] [Accepted: 02/17/2010] [Indexed: 01/26/2023]
Abstract
Current subtyping methods for the detection of foodborne disease outbreaks have limitations that reduce their use by public health laboratories. Recent advances in subtyping of foodborne disease pathogens utilize techniques that identify nucleic acid polymorphisms. Recent methods of nucleic acid characterization such as microarrays and mass spectrometry (MS) may provide improvements such as increasing speed and data portability while decreasing labor compared to current methods. This article discusses multiple-locus variable-number tandem-repeat analysis, single-nucleotide polymorphisms, nucleic acid sequencing, whole genome sequencing, variable absent or present loci, microarrays and MS as potential subtyping methods to enhance our ability to detect foodborne disease outbreaks.
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Leski TA, Malanoski AP, Stenger DA, Lin B. Target amplification for broad spectrum microbial diagnostics and detection. Future Microbiol 2010; 5:191-203. [DOI: 10.2217/fmb.09.126] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Microarrays are massively parallel detection platforms that were first used extensively for gene expression studies, but have also been successfully applied to microbial detection in a number of diverse fields requiring broad-range microbial identification. This technology has enabled researchers to gain an insight into the microbial diversity of environmental samples, facilitated discovery of a number of new pathogens and enabled studies of multipathogen infections. In contrast to gene expression studies, the concentrations of targets in analyzed samples for microbial detection are usually much lower, and require the use of nucleic acid amplification techniques. The rapid advancement of manufacturing technologies has increased the content of the microarrays; thus, the required amplification is a challenging problem. The constant parallel improvements in both microarray and sample amplification techniques in the near future may lead to a radical progression in medical diagnostics and systems for efficient detection of microorganisms in the environment.
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Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA and Nova Research Inc., 1900 Elkin Street, Suite 230, Alexandria, VA, USA
| | - Anthony P Malanoski
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - David A Stenger
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
| | - Baochuan Lin
- Center for Bio/Molecular Science & Engineering, Code 6900, Naval Research Laboratory, Washington, DC, USA
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Detection of Enterobacter sakazakii and other pathogens associated with infant formula powder by use of a DNA microarray. J Clin Microbiol 2009; 47:3178-84. [PMID: 19641057 PMCID: PMC2756907 DOI: 10.1128/jcm.00366-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogen detection is critical to the process of generating and testing powdered infant formula (PIF). An obstacle associated with PIF microbial surveillance is that most current procedures are time-consuming and labor-intensive. We have developed a rapid, DNA microarray-based detection technique to identify 10 different pathogenic bacteria associated with PIF contamination based on the 16S-23S rRNA gene internal transcribed spacer (ITS) sequences and wzy (O antigen polymerase) gene. Using this procedure, Enterobacter sakazakii, Salmonella enterica, Klebsiella pneumoniae, Klebsiella oxytoca, Serratia marcescens, Acinetobacter baumannii, Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli O157 were identified. One hundred eighty-five strains were used to validate the microarray assay (including 134 target pathogen strains and 51 closely related bacteria). Twenty-seven probes reproducibly detected multiple pathogens with high specificity and sensitivity (0.100 ng genomic DNA or 10(4) CFU/ml). Twenty-one real PIF samples were tested by the microarray with 100% accuracy. The data presented reveal that the designed oligonucleotide microarray is a promising method for basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance.
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