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Umesha S, Manukumar HM. Advanced molecular diagnostic techniques for detection of food-borne pathogens: Current applications and future challenges. Crit Rev Food Sci Nutr 2017; 58:84-104. [PMID: 26745757 DOI: 10.1080/10408398.2015.1126701] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The elimination of disease-causing microbes from the food supply is a primary goal and this review deals with the overall techniques available for detection of food-borne pathogens. Now-a-days conventional methods are replaced by advanced methods like Biosensors, Nucleic Acid-based Tests (NAT), and different PCR-based techniques used in molecular biology to identify specific pathogens. Bacillus cereus, Staphylococcus aureus, Proteus vulgaris, Escherichia coli, Campylobacter, Listeria monocytogenes, Salmonella spp., Aspergillus spp., Fusarium spp., Penicillium spp., and pathogens are detected in contaminated food items that cause always diseases in human in any one or the other way. Identification of food-borne pathogens in a short period of time is still a challenge to the scientific field in general and food technology in particular. The low level of food contamination by major pathogens requires specific sensitive detection platforms and the present area of hot research looking forward to new nanomolecular techniques for nanomaterials, make them suitable for the development of assays with high sensitivity, response time, and portability. With the sound of these, we attempt to highlight a comprehensive overview about food-borne pathogen detection by rapid, sensitive, accurate, and cost affordable in situ analytical methods from conventional methods to recent molecular approaches for advanced food and microbiology research.
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Affiliation(s)
- S Umesha
- a Department of Studies in Biotechnology , University of Mysore, Manasagangotri , Mysore , Karnataka , India
| | - H M Manukumar
- a Department of Studies in Biotechnology , University of Mysore, Manasagangotri , Mysore , Karnataka , India
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Ishii K, Onishi Y, Miyamura N, Fukuhara N, Ishizawa K, Nakanishi M, Ohnaka S, Miyasaka T, Kanno E, Kawakami K, Harigae H, Kaku M. Development and evaluation of a quantitative assay detecting cytomegalovirus transcripts for preemptive therapy in allogeneic hematopoietic stem cell transplant recipients. J Med Virol 2017; 89:1265-1273. [DOI: 10.1002/jmv.24775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/28/2016] [Accepted: 01/06/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Keiko Ishii
- Department of Medical Microbiology, Mycology and Immunology; Tohoku University Graduate School of Medicine; Sendai Japan
| | - Yasushi Onishi
- Department of Hematology and Rheumatology; Tohoku University Hospital; Sendai Japan
| | - Namiko Miyamura
- Department of Medical Microbiology, Mycology and Immunology; Tohoku University Graduate School of Medicine; Sendai Japan
| | - Noriko Fukuhara
- Department of Hematology and Rheumatology; Tohoku University Hospital; Sendai Japan
| | - Kenichi Ishizawa
- Department of Hematology and Rheumatology; Tohoku University Hospital; Sendai Japan
| | | | | | - Tomomitsu Miyasaka
- Department of Medical Microbiology, Mycology and Immunology; Tohoku University Graduate School of Medicine; Sendai Japan
| | - Emi Kanno
- Department of Science of Nursing Practice; Tohoku University Graduate School of Medicine; Sendai Japan
| | - Kazuyoshi Kawakami
- Department of Medical Microbiology, Mycology and Immunology; Tohoku University Graduate School of Medicine; Sendai Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology; Tohoku University Hospital; Sendai Japan
| | - Mitsuo Kaku
- Department of Infection Control and Laboratory Diagnostics, Internal Medicine; Tohoku University Graduate School of Medicine; Sendai Japan
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Suffredini E, Cozzi L, Ciccaglioni G, Croci L. Development of a colony hybridization method for the enumeration of total and potentially enteropathogenic Vibrio parahaemolyticus in shellfish. Int J Food Microbiol 2014; 186:22-31. [PMID: 24984219 DOI: 10.1016/j.ijfoodmicro.2014.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 05/07/2014] [Accepted: 06/10/2014] [Indexed: 01/30/2023]
Abstract
Vibrio parahaemolyticus is a marine microorganism, recognized as cause of gastroenteritis outbreaks associated with seafood consumption. In this study the development and the in-house validation of a colony hybridization method for the enumeration of total and potentially pathogenic V. parahaemolyticus is reported. The method included a set of three controls (process, hybridization and detection control) for the full monitoring of the analytical procedure. Four digoxigenin-labeled probes were designed for pathogenic strains enumeration (tdh1, tdh2, trh1 and trh2 probes) and one for total V. parahaemolyticus count (toxR probe). Probes were tested on a panel of 70 reference strains and 356 environmental, food and clinical isolates, determining the inclusivity (tdh: 96.7%, trh: 97.8%, toxR: 99.4%) and the exclusivity (100% for all probes). Accuracy and linearity of the enumeration were evaluated on pure and mixed cultures: slopes of the regression lines ranged from 0.957 to 1.058 depending on the target gene and R(2) was greater than or equal to 0.989 for all reactions. Evaluation was also carried on using four experimentally contaminated seafood matrices (shellfish, finfish, crustaceans and cephalopods) and the slopes of the curves varied from 0.895 (finfish) to 0.987 (cephalopods) for the counts of potentially pathogenic V. parahaemolyticus (R(2)≥0.965) and from 0.965 to 1.073 for total V. parahaemolyticus enumeration (R(2)≥0.981). Validation was performed on 104 naturally contaminated shellfish samples, analyzed in parallel by colony hybridization, ISO/TS 21872-1 and MPN enumeration. Colony hybridization and ISO method showed a relative accuracy of 86.7%, and a statistically significant correlation was present between colony hybridization enumeration and MPN results (r=0.744, p<0.001). The proposed colony hybridization can be a suitable alternative method for the enumeration of total and potentially pathogenic V. parahaemolyticus in seafood.
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Affiliation(s)
- Elisabetta Suffredini
- Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, v.le Regina Elena 299, 00161 Rome, Italy.
| | - Loredana Cozzi
- Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, v.le Regina Elena 299, 00161 Rome, Italy
| | - Gianni Ciccaglioni
- Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, v.le Regina Elena 299, 00161 Rome, Italy
| | - Luciana Croci
- Istituto Superiore di Sanità, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, v.le Regina Elena 299, 00161 Rome, Italy
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Evaluation of the TRCRtest NV-W for norovirus detection in stools by the Transcription-Reverse Transcription Concerted method. J Virol Methods 2013; 193:620-6. [DOI: 10.1016/j.jviromet.2013.07.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 07/11/2013] [Accepted: 07/18/2013] [Indexed: 11/20/2022]
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Gavilan RG, Zamudio ML, Martinez-Urtaza J. Molecular epidemiology and genetic variation of pathogenic Vibrio parahaemolyticus in Peru. PLoS Negl Trop Dis 2013; 7:e2210. [PMID: 23696906 PMCID: PMC3656152 DOI: 10.1371/journal.pntd.0002210] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/29/2013] [Indexed: 11/17/2022] Open
Abstract
Vibrio parahaemolyticus is a foodborne pathogen that has become a public health concern at the global scale. The epidemiological significance of V. parahaemolyticus infections in Latin America received little attention until the winter of 1997 when cases related to the pandemic clone were detected in the region, changing the epidemic dynamics of this pathogen in Peru. With the aim to assess the impact of the arrival of the pandemic clone on local populations of pathogenic V. parahaemolyticus in Peru, we investigated the population genetics and genomic variation in a complete collection of non-pandemic strains recovered from clinical sources in Peru during the pre- and post-emergence periods of the pandemic clone. A total of 56 clinical strains isolated in Peru during the period 1994 to 2007, 13 strains from Chile and 20 strains from Asia were characterized by Multilocus Sequence Typing (MLST) and checked for the presence of Variable Genomic Regions (VGRs). The emergence of O3:K6 cases in Peru implied a drastic disruption of the seasonal dynamics of infections and a shift in the serotype dominance of pathogenic V. parahaemolyticus. After the arrival of the pandemic clone, a great diversity of serovars not previously reported was detected in the country, which supports the introduction of additional populations cohabitating with the pandemic group. Moreover, the presence of genomic regions characteristic of the pandemic clone in other non-pandemic strains may represent early evidence of genetic transfer from the introduced population to the local communities. Finally, the results of this study stress the importance of population admixture, horizontal genetic transfer and homologous recombination as major events shaping the structure and diversity of pathogenic V. parahaemolyticus.
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Affiliation(s)
- Ronnie G Gavilan
- Instituto de Acuicultura, Universidad de Santiago de Compostela, Campus Universitario Sur, Santiago de Compostela, Spain
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Singh A, Arutyunov D, Szymanski CM, Evoy S. Bacteriophage based probes for pathogen detection. Analyst 2012; 137:3405-21. [PMID: 22724121 DOI: 10.1039/c2an35371g] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid and specific detection of pathogenic bacteria is important for the proper treatment, containment and prevention of human, animal and plant diseases. Identifying unique biological probes to achieve a high degree of specificity and minimize false positives has therefore garnered much interest in recent years. Bacteriophages are obligate intracellular parasites that subvert bacterial cell resources for their own multiplication and production of disseminative new virions, which repeat the cycle by binding specifically to the host surface receptors and injecting genetic material into the bacterial cells. The precision of host recognition in phages is imparted by the receptor binding proteins (RBPs) that are often located in the tail-spike or tail fiber protein assemblies of the virions. Phage host recognition specificity has been traditionally exploited for bacterial typing using laborious and time consuming bacterial growth assays. At the same time this feature makes phage virions or RBPs an excellent choice for the development of probes capable of selectively capturing bacteria on solid surfaces with subsequent quick and automatic detection of the binding event. This review focuses on the description of pathogen detection approaches based on immobilized phage virions as well as pure recombinant RBPs. Specific advantages of RBP-based molecular probes are also discussed.
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Affiliation(s)
- Amit Singh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada.
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Garrido A, Chapela MJ, Ferreira M, Atanassova M, Fajardo P, Lago J, Vieites JM, Cabado AG. Development of a multiplex real-time PCR method for pathogenic Vibrio parahaemolyticus detection (tdh+ and trh+). Food Control 2012. [DOI: 10.1016/j.foodcont.2011.09.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Su J, Zhang H, Jiang B, Zheng H, Chai Y, Yuan R, Xiang Y. Dual signal amplification for highly sensitive electrochemical detection of uropathogens via enzyme-based catalytic target recycling. Biosens Bioelectron 2011; 29:184-8. [DOI: 10.1016/j.bios.2011.08.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/18/2011] [Accepted: 08/10/2011] [Indexed: 10/17/2022]
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A novel genotyping scheme for Vibrio parahaemolyticus with combined use of large variably-presented gene clusters (LVPCs) and variable-number tandem repeats (VNTRs). Int J Food Microbiol 2011; 149:143-51. [PMID: 21742395 DOI: 10.1016/j.ijfoodmicro.2011.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 06/17/2011] [Accepted: 06/18/2011] [Indexed: 11/24/2022]
Abstract
A total of 18 variably-presented gene clusters (LVPCs) and nine previously characterized variable-number tandem repeats (VNTRs), and all known virulence markers were screened for their frequency and/or copy number in 251 global strains of Vibrio parahaemolyticus using PCR and gel or capillary electrophoresis. A two-step genotyping approach combining the use of LVPCs and VNTRs was established accordingly. The frequency profiles of LVPCs and virulence markers were primarily used to group the strains into six distinct complexes with different potential pathogenicity natures. The strains from each of these complexes were further analyzed with VNTRs to give a much more detailed discrimination of the strains. A genetic fingerprint-like database of a large collection of strains established with this two-stage approach would be very useful for identification, genotyping, origin tracing, and risk estimation of V. parahaemolyticus.
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Kamruzzaman M, Bhoopong P, Vuddhakul V, Nishibuchi M. Detection of a functional insertion sequence responsible for deletion of the thermostable direct hemolysin gene (tdh) in Vibrio parahaemolyticus. Gene 2008; 421:67-73. [DOI: 10.1016/j.gene.2008.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/28/2008] [Accepted: 06/02/2008] [Indexed: 10/22/2022]
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Mothershed EA, Whitney AM. Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory. Clin Chim Acta 2006; 363:206-20. [PMID: 16139259 DOI: 10.1016/j.cccn.2005.05.050] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 05/25/2005] [Accepted: 05/26/2005] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in nucleic acid-based methods to detect bacteria offer increased sensitivity and specificity over traditional microbiological techniques. The potential benefit of nucleic acid-based testing to the clinical laboratory is reduced time to diagnosis, high throughput, and accurate and reliable results. METHODS Several PCR and hybridization tests are commercially available for specific organism detection. Furthermore, hundreds of nucleic acid-based bacterial detection tests have been published in the literature and could be adapted for use in the clinical setting. Contamination potential, lack of standardization or validation for some assays, complex interpretation of results, and increased cost are possible limitations of these tests, however, and must be carefully considered before implementing them in the clinical laboratory. CONCLUSIONS A major area of advancement in nucleic acid-based assay development has been for specific and broad-range detection of bacterial pathogens.
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Affiliation(s)
- Elizabeth A Mothershed
- Meningitis and Special Pathogens Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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Takakura S, Tsuchiya S, Isawa Y, Yasukawa K, Hayashi T, Tomita M, Suzuki K, Hasegawa T, Tagami T, Kurashima A, Ichiyama S. Rapid detection of Mycobacterium tuberculosis in respiratory samples by transcription-reverse transcription concerted reaction with an automated system. J Clin Microbiol 2005; 43:5435-9. [PMID: 16272466 PMCID: PMC1287819 DOI: 10.1128/jcm.43.11.5435-5439.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to evaluate the performance of the transcription-reverse transcription concerted (TRC) method for the detection of Mycobacterium tuberculosis complex (MTC) 16S rRNA in clinical respiratory samples for the diagnosis of pulmonary tuberculosis. TRC is a novel method that enables the rapid and the completely homogeneous real-time monitoring of isothermal sequence RNA amplification without any postamplification procedure. The detection limit of the TRC method for MTC was one organism per 100 mul of sputum. The specificity of the method was confirmed by the absence of positive signals for sputum containing 10(6) M. avium or M. kansasii organisms per 100 microl. A total of 201 respiratory samples from patients diagnosed with or suspected of having tuberculosis were tested. Of the 72 MTC culture-positive samples, the TRC method was positive for 52 (sensitivity, 72.2%), whereas the Roche COBAS AMPLICOR PCR was positive for 58 (sensitivity, 80.6%). Both the TRC method and the COBAS AMPLICOR PCR showed no positive identification for any of the 129 culture-negative samples. The percent agreement between the two methods was 95% (191 of 201 samples). The high sensitivity and specificity together with shorter detection time (within 1 h) of the TRC method allow it to be proposed as a useful method for the rapid detection of MTC in respiratory samples.
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Affiliation(s)
- Shunji Takakura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 6068507, Japan.
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Masuda N, Yasukawa K, Isawa Y, Horie R, Saitoh J, Ishiguro T, Nakaguchi Y, Nishibuchi M, Hayashi T. Rapid detection of tdh and trh mRNAs of Vibrio parahaemolyticus by the transcription-reverse transcription concerted (TRC) method. J Biosci Bioeng 2004; 98:236-43. [PMID: 16233699 DOI: 10.1016/s1389-1723(04)00275-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Accepted: 06/28/2004] [Indexed: 11/29/2022]
Abstract
We developed a novel method named the transcription-reverse transcription concerted (TRC) method and an instrument that allowed rapid and completely homogeneous real-time monitoring of RNA isothermal sequence amplification without any post-amplification analysis in our previous study [Ishiguro et al., Anal. Biochem., 314, 77-86 (2003)]. In this study, we newly established rapid and sensitive TRC systems for the detection of the mRNAs transcribed from two major virulence genes of Vibrio parahaemolyticus: the tdh gene encoding the thermostable direct hemolysin (tdh) and the trh gene encoding the thermostable direct hemolysin-related hemolysin. Examination of the standard RNAs prepared in vitro showed that a positive result, increase in the fluorescence intensity to the cut-off value within 25 min, was obtained for as few as 100 copies of RNA. The TRC method specific to the trh mRNA detected the mRNAs transcribed from the trh1 and trh2 genes, two representative trh variants sharing 84% sequence identity. The detection time gave a linear relationship to the logarithm of starting RNA copies ranging from 10(3) to 10(7) copies, showing that quantitative analysis is possible. The detection time for 10(3) copies of the standard RNAs ranged from 11 to 15 min. Examination of the total RNAs extracted from the standard strains of V. parahaemolyticus demonstrated that the new TRC systems are sufficiently sensitive to detect as few as 100 CFUs of the strains carrying the target genes. Total RNA preparations extracted from 24 strains of V. parahaemolyticus, 52 strains belonging to 31 other species of the genus Vibrio and 11 strains belonging to 8 species of non-Vibrio genera were examined. The results of the detection of tdh- and trh-specific mRNAs by the two TRC systems and those of the respective genes by the DNA colony hybridization method agreed. We conclude that the new TRC systems are rapid, highly sensitive, easy to manipulate, and are suitable for routine examination of virulent strains of V. parahaemolyticus in microbiological laboratories.
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Affiliation(s)
- Noriyoshi Masuda
- Scientific Instruments Division, Tosoh Corporation, 2743-1 Hayakawa, Ayase-shi, Kanagawa 252-1123, Japan
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