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Zhong Y, Liu M, Ding Y, Wu Q, Zhang J, Ma G, Xu T, Wang Z, Chen M, Xue L, Ye Q, Wang J. Rapid fluorescence visualization of Yersinia enterocolitica by CRISPR/Cas12a using novel specific target obtained by pan-genome analysis. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Jin J, Duan L, Fu J, Chai F, Zhou Q, Wang Y, Shao X, Wang L, Yan M, Su X, Zhang Y, Pan J, Chen J. A real-time LAMP-based dual-sample microfluidic chip for rapid and simultaneous detection of multiple waterborne pathogenic bacteria from coastal waters. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2710-2721. [PMID: 34041513 DOI: 10.1039/d1ay00492a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Waterborne pathogens are becoming a serious worldwide health hazard; thus, the regular monitoring of epidemic pathogens is urgently required for public safety. In the present study, we developed a microfluidic chip integrated loop-mediated isothermal amplification technique (on-chip LAMP) to simultaneously detect 10 waterborne pathogenic bacteria, Campylobacter jejuni, Listeria monocytogenes, Salmonella enterica, Shigella flexneri, Staphylococcus aureus, Vibrio alginolyticus, V. cholerae, V. parahemolyticus, V. vulnificus, and Yersinia enterocolitica. This method was capable of simultaneously completing 22 genetic analyses of two specimens and achieved limits of detection ranging from 7.92 × 10-3 to 9.54 × 10-1 pg of genomic DNA of pure bacteria per reaction. The processes from sample loading to microfluidic operation were in a highly automated format, and the LAMP reaction ran to completion within 35 minutes, with a minimal volume of 22 μl per each half of a single chip. The coefficient of variation for the time-to-positive value was less than 0.1, indicating an excellent reproducibility of the dual-sample on-chip LAMP assay. The clinical sensitivity and specificity in analyses of coastal water samples were 93.1% and 98.0%, respectively, in comparison with traditional microbiological methods. Our established dual-sample on-chip LAMP assay provides an effective multiple-pathogen analysis of waterborne bacterial pathogens. This indicates that the method is applicable for on-site detection and routine monitoring of waterborne bacteria in aquatic environments.
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Affiliation(s)
- Jinglei Jin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Lijun Duan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China. and Ningbo Haishu District Animal Husbandry and Veterinary Medicine Technical Management Service Station, Ningbo 315153, China
| | - Jiali Fu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Fangchao Chai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Qianjin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Yaohua Wang
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Xinbin Shao
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Lei Wang
- CapitalBio Corporation, 18 Life Science Parkway, Changping District, Beijing 102206, China
| | - Maocang Yan
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310009, China
| | - Junhang Pan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310009, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China. and Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, China
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Shoaib M, Shehzad A, Raza H, Niazi S, Khan IM, Akhtar W, Safdar W, Wang Z. A comprehensive review on the prevalence, pathogenesis and detection ofYersinia enterocolitica. RSC Adv 2019; 9:41010-41021. [PMID: 35540058 PMCID: PMC9076465 DOI: 10.1039/c9ra06988g] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/31/2019] [Indexed: 01/23/2023] Open
Abstract
Food safety is imperative for a healthy life, but pathogens are still posing a significant life threat. “Yersiniosis” is caused by a pathogen named Yersinia enterocolitica and is characterized by diarrheal, ileitis, and mesenteric lymphadenitis types of sicknesses. This neglected pathogen starts its pathogenic activity by colonizing inside the intestinal tract of the host upon the ingestion of contaminated food. Y. enterocolitica remains a challenge for researchers and food handlers due to its growth habits, low concentrations in samples, morphological similarities with other bacteria and lack of rapid, cost-effective, and accurate detection methods. In this review, we presented recent information about its prevalence, biology, pathogenesis, and existing cultural, immunological, and molecular detection approaches. Our ultimate goal is to provide updated knowledge regarding this pathogen for the development of quick, effective, automated, and sensitive detection methods for the systematic detection of Y. enterocolitica. Food safety is imperative for a healthy life, but pathogens are still posing a significant life threat.![]()
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Affiliation(s)
- Muhammad Shoaib
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- China
- Synergetic Innovation Center of Food Safety and Nutrition
| | - Aamir Shehzad
- UniLaSalle
- Transformations & Agroressources Research Unit
- France
- National Institute of Food Science and Technology
- FFNHS
| | - Husnain Raza
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- China
- National Institute of Food Science and Technology
| | - Sobia Niazi
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- China
- National Institute of Food Science and Technology
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- China
- Synergetic Innovation Center of Food Safety and Nutrition
| | - Wasim Akhtar
- Synergetic Innovation Center of Food Safety and Nutrition
- Jiangnan University
- Wuxi 214122
- People's Republic of China
| | - Waseem Safdar
- University Institute of Diet and Nutritional Sciences
- The University of Lahore-Islamabad Campus
- Islamabad
- Pakistan
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi
- China
- Synergetic Innovation Center of Food Safety and Nutrition
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Petsios S, Fredriksson-Ahomaa M, Sakkas H, Papadopoulou C. Conventional and molecular methods used in the detection and subtyping of Yersinia enterocolitica in food. Int J Food Microbiol 2016; 237:55-72. [DOI: 10.1016/j.ijfoodmicro.2016.08.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 07/28/2016] [Accepted: 08/11/2016] [Indexed: 01/08/2023]
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Kalia VC, Kumar P. Genome Wide Search for Biomarkers to Diagnose Yersinia Infections. Indian J Microbiol 2015; 55:366-74. [PMID: 26543261 DOI: 10.1007/s12088-015-0552-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/01/2015] [Indexed: 01/12/2023] Open
Abstract
Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4-6 base cutters). Yersinia species have 6-7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences-carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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Zhou C, Sun C, Ruan J, Zou H, Li Y. Determination of Yersinia enterocoliticain Food by Capillary Electrophoresis with Laser Induced Fluorescence Detection. ANAL LETT 2015. [DOI: 10.1080/00032719.2015.1012676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Tiwari S, da Costa MP, Almeida S, Hassan SS, Jamal SB, Oliveira A, Folador EL, Rocha F, de Abreu VAC, Dorella F, Hirata R, de Oliveira DM, da Silva Teixeira MF, Silva A, Barh D, Azevedo V. C. pseudotuberculosis Phop confers virulence and may be targeted by natural compounds. Integr Biol (Camb) 2015; 6:1088-99. [PMID: 25212181 DOI: 10.1039/c4ib00140k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bacterial two-component system (TCS) regulates genes that are crucial for virulence in several pathogens. One of such TCS, the PhoPR system, consisting of a transmembrane sensory histidine kinase protein (PhoR) and an intracellular response regulator protein (PhoP), has been reported to have a major role in mycobacterial pathogenesis. We knocked out the phoP in C. pseudotuberculosis, the causal organism of caseous lymphadenitis (CLA), and using a combination of in vitro and in vivo mouse system, we showed for the first time, that the PhoP of C. pseudotuberculosis plays an important role in the virulence and pathogenicity of this bacterium. Furthermore, we modeled the PhoP of C. pseudotuberculosis and our docking results showed that several natural compounds including Rhein, an anthraquinone from Rheum undulatum, and some drug-like molecules may target PhoP to inhibit the TCS of C. pseudotuberculosis, and therefore may facilitate a remarkable attenuation of bacterial pathogenicity being the CLA. Experiments are currently underway to validate these in silico docking results.
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Affiliation(s)
- Sandeep Tiwari
- PG Program in Bioinformatics, Laboratory of Cellular and Molecular Genetics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil.
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Gupta V, Gulati P, Bhagat N, Dhar MS, Virdi JS. Detection of Yersinia enterocolitica in food: an overview. Eur J Clin Microbiol Infect Dis 2014; 34:641-50. [PMID: 25410144 DOI: 10.1007/s10096-014-2276-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/04/2014] [Indexed: 01/30/2023]
Abstract
Yersinia enterocolitica is a gastrointestinal pathogen which causes yersiniosis, an illness characterized by diarrhea, ileitis, and mesenteric lymphadenitis. Y. enterocolitica is transmitted via the feco-oral route by the consumption of contaminated food or water. Several phenotypic and genotypic methods have been developed to reliably detect Y. enterocolitica in food. However, the source of infection of many recently reported foodborne outbreaks remains obscure. The detection of this pathogen in food is a challenging task, since it shares similarities with other enteric bacteria. The presence of other microorganisms in the food samples makes it even more difficult to identify this slow-growing pathogen. Therefore, the present-day emphasis is on the development of sensitive, easily automated methods suitable for in-situ detection, allowing quick and cost-effective characterization of food samples. This review summarizes and compares the currently available cultural, immunological, and molecular methods, particularly in relation to their specific merits or demerits when implemented for the detection of Y. enterocolitica in food.
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Affiliation(s)
- V Gupta
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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Mortari A, Lorenzelli L. Recent sensing technologies for pathogen detection in milk: A review. Biosens Bioelectron 2014; 60:8-21. [DOI: 10.1016/j.bios.2014.03.063] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 03/07/2014] [Accepted: 03/26/2014] [Indexed: 01/30/2023]
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Niessen L, Luo J, Denschlag C, Vogel RF. The application of loop-mediated isothermal amplification (LAMP) in food testing for bacterial pathogens and fungal contaminants. Food Microbiol 2013; 36:191-206. [DOI: 10.1016/j.fm.2013.04.017] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
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Gurtler V, Grando D, Mayall BC, Wang J, Ghaly-Derias S. A novel method for simultaneous Enterococcus species identification/typing and van genotyping by high resolution melt analysis. J Microbiol Methods 2012; 90:167-81. [PMID: 22658426 DOI: 10.1016/j.mimet.2012.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/30/2012] [Accepted: 05/04/2012] [Indexed: 11/19/2022]
Abstract
In order to develop a typing and identification method for van gene containing Enterococcus faecium, two multiplex PCR reactions were developed for use in HRM-PCR (High Resolution Melt-PCR): (i) vanA, vanB, vanC, vanC23 to detect van genes from different Enterococcus species; (ii) ISR (intergenic spacer region between the 16S and 23S rRNA genes) to detect all Enterococcus species and obtain species and isolate specific HRM curves. To test and validate the method three groups of isolates were tested: (i) 1672 Enterococcus species isolates from January 2009 to December 2009; (ii) 71 isolates previously identified and typed by PFGE (pulsed-field gel electrophoresis) and MLST (multi-locus sequence typing); and (iii) 18 of the isolates from (i) for which ISR sequencing was done. As well as successfully identifying 2 common genotypes by HRM from the Austin Hospital clinical isolates, this study analysed the sequences of all the vanB genes deposited in GenBank and developed a numerical classification scheme for the standardised naming of these vanB genotypes. The identification of Enterococcus faecalis from E. faecium was reliable and stable using ISR PCR. The typing of E. faecium by ISR PCR: (i) detected two variable peaks corresponding to different copy numbers of insertion sequences I and II corresponding to peak I and II respectively; (ii) produced 7 melt profiles for E. faecium with variable copy numbers of sequences I and II; (iii) demonstrated stability and instability of peak heights with equal frequency within the patient sample (36.4±4.5 days and 38.6±5.8 days respectively for 192 patients); (iv) detected ISR-HRM types with as much discrimination as PFGE and more than MLST; and (v) detected ISR-HRM types that differentiated some isolates that were identical by PFGE and MLST. In conjunction with the rapid and accurate van genotyping method described here, this ISR-HRM typing and identification method can be used as a stable identification and typing method with predictable instability based on recombination and concerted evolution of the rrn operon that will complement existing typing methods.
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Affiliation(s)
- Volker Gurtler
- Department of Pathology, Austin Hospital, Heidelberg 3084, Australia.
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Tang MJ, Zhou S, Zhang XY, Pu JH, Ge QL, Tang XJ, Gao YS. Rapid and Sensitive Detection of Listeria monocytogenes by Loop-Mediated Isothermal Amplification. Curr Microbiol 2011; 63:511-6. [DOI: 10.1007/s00284-011-0013-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 08/30/2011] [Indexed: 02/02/2023]
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