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Shan S, Li R, Xia W, Tong X, Huang Y, Tan Y, Peng S, Liu C, Wang S, Liu D. High-resolution melting real-time polymerase chain reaction assays for subtyping of five diarrheagenic Escherichia coli by a single well in milk. J Dairy Sci 2024; 107:5416-5426. [PMID: 38490558 DOI: 10.3168/jds.2024-24331] [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: 10/19/2023] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
Diarrheagenic Escherichia coli (DEC) is a kind of foodborne pathogen that poses a significant threat to both food safety and human health. To address the current challenges of high prevalence and difficult subtyping of DEC, this study developed a method that combined multiplex PCR with high-resolution melting (HRM) analysis for subtyping 5 kinds of DEC. The target genes are amplified by multiplex PCR in a single well, and HRM curve analysis was applied for distinct amplicons based on different melting temperature (Tm) values. The method enables discrimination of different DEC types based on characteristic peaks and distinct Tm values in the thermal melting curve. The assay exhibited 100% sensitivity and 100% specificity with a detection limit of 0.5 to 1 ng/μL. The results showed that different DNA concentrations did not influence the subtyping results, demonstrating this method owed high reliability and stability. In addition, the method was also used for the detection and subtyping of DEC in milk. This method streamlines operational procedures, shorts the detection time, and offers a novel tool for subtyping DEC.
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Affiliation(s)
- Shan Shan
- College of Life Science, National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China; Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, China
| | - Rui Li
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, China; Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang 330019, China
| | - Weicheng Xia
- Center for Life Sciences, Yunnan University, Kunming 650031, China
| | - Xiaoyu Tong
- College of Life Science, National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China
| | - Yanmei Huang
- Jiangxi YeLi Medical Device Co. Ltd., Nanchang 330008, China
| | - Yucheng Tan
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, China; Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang 330019, China
| | - Silu Peng
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, China
| | - Chengwei Liu
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, China
| | - Shuanglong Wang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China
| | - Daofeng Liu
- Jiangxi Province Key Laboratory of Diagnosing and Tracing of Foodborne Disease, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang 330029, China.
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Akinlabi OC, Dada RA, Nwoko ESQA, Okeke IN. PCR diagnostics are insufficient for the detection of Diarrhoeagenic Escherichia coli in Ibadan, Nigeria. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001539. [PMID: 37549136 PMCID: PMC10406320 DOI: 10.1371/journal.pgph.0001539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Understanding the contribution of different diarrhoeagenic Escherichia coli pathotypes to disease burden is critical to mapping risk and informing vaccine development. Targeting select virulence genes by PCR is the diagnostic approach of choice in high-burden, least-resourced African settings. We compared the performance of a commonly-used multiplex protocol to whole genome sequencing (WGS). PCR was applied to 3,815 E. coli isolates from 120 children with diarrhoea and 357 healthy controls. Three or more isolates per specimen were also Illumina-sequenced. Following quality assurance, ARIBA and Virulencefinder database were used to identify virulence targets. Root cause analysis of deviant PCR results was performed by examining target sensitivity using BLAST, Sanger sequencing false-positive amplicons, and identifying lineages prone to false-positivity using in-silico multilocus sequence typing and a Single Nucleotide Polymorphism phylogeny constructed using IQTree. The sensitivity and positive predictive value of PCR compared to WGS ranged from 0-77.8% while specificity ranged from 74.5-94.7% for different pathotypes. WGS identified more enteroaggregative E. coli (EAEC), fewer enterotoxigenic E. coli (ETEC) and none of the Shiga toxin-producing E. coli detected by PCR, painting a considerably different epidemiological picture. Use of the CVD432 target resulted in EAEC under-detection, and enteropathogenic E. coli eae primers mismatched more recently described intimin alleles common in our setting. False positive ETEC were over-represented among West Africa-predominant ST8746 complex strains. PCR precision varies with pathogen genome so primers optimized for use in one part of the world may have noticeably lower sensitivity and specificity in settings where different pathogen lineages predominate.
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Affiliation(s)
- Olabisi C. Akinlabi
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, University of Ibadan, Oyo, Nigeria
| | - Rotimi A. Dada
- Faculty of Pharmacy, Bowen University Iwo and Department of Pharmaceutical Microbiology, College of Health Sciences, Medical Laboratory Science Programme, Ahmadu Bello University, Zaria, Nigeria
| | - El-shama Q. A. Nwoko
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, University of Ibadan, Oyo, Nigeria
| | - Iruka N. Okeke
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, University of Ibadan, Oyo, Nigeria
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Abolarinwa TO, Ajose DJ, Oluwarinde BO, Fri J, Montso KP, Fayemi OE, Aremu AO, Ateba CN. Plant-derived nanoparticles as alternative therapy against Diarrheal pathogens in the era of antimicrobial resistance: A review. Front Microbiol 2022; 13:1007115. [PMID: 36590407 PMCID: PMC9797601 DOI: 10.3389/fmicb.2022.1007115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Diarrhea is a condition in which feces is discharged from the bowels frequently and in a liquid form. It is one of the frequent causes of morbidity and mortality in developing countries. The impact of Diarrhea is worsened by the increasing incidence of antimicrobial resistance among the causative agents, and this is now categorized as a global healthcare challenge. Antimicrobial resistance among Diarrheal pathogens also contributes to extended infection durations, and huge economic loss even in countries with advanced public health policies. The ever-increasing incidence of antimicrobial resistance including the contraindications arising from the administration of antibiotics in some Diarrheal cases highlights a crucial need for the development of novel non-antibiotic alternative agents for therapeutic and biocontrol applications. One such intervention includes the application of plant-derived nanoparticles (PDNPs) with novel antimicrobial properties. Given their small size and large surface area to volume ratio, PDNPs can attack target bacterial cell walls to generate reactive oxygen species that may simultaneously disrupt bacteria cell components such as DNA and proteins leading to cell damage or death. This potential can make it very difficult for pathogenic organisms to develop resistance against these antibacterial agents. In this review, we provide a critical overview on the antimicrobial resistance crisis among Diarrheagenic bacteria. We also discuss the evidence from the existing literature to support the potential associated with the use of PDNPs as alternative therapeutic agents for multidrug resistant and antibiotics administer contraindicated bacteria that are associated with Diarrhea.
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Affiliation(s)
- Tesleem Olatunde Abolarinwa
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Daniel Jesuwenu Ajose
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Bukola Opeyemi Oluwarinde
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Justine Fri
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Kotsoana Peter Montso
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Omolola Esther Fayemi
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Adeyemi Oladapo Aremu
- Indigenous Knowledge Systems Center, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Collins Njie Ateba
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa,*Correspondence: Collins Njie Ateba,
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Enciso-Martínez Y, González-Aguilar GA, Martínez-Téllez MA, González-Pérez CJ, Valencia-Rivera DE, Barrios-Villa E, Ayala-Zavala JF. Relevance of tracking the diversity of Escherichia coli pathotypes to reinforce food safety. Int J Food Microbiol 2022; 374:109736. [DOI: 10.1016/j.ijfoodmicro.2022.109736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/21/2022]
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A surface-enhanced Raman scattering aptasensor for Escherichia coli detection based on high-performance 3D substrate and hot spot effect. Anal Chim Acta 2022; 1221:340141. [DOI: 10.1016/j.aca.2022.340141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022]
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Hong T, Liu X, Zhou Q, Liu Y, Guo J, Zhou W, Tan S, Cai Z. What the Microscale Systems "See" In Biological Assemblies: Cells and Viruses? Anal Chem 2021; 94:59-74. [PMID: 34812604 DOI: 10.1021/acs.analchem.1c04244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Xing Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Qi Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Yilian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Jing Guo
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China.,Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu 213100, China
| | - Zhiqiang Cai
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.,Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu 213100, China
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Valdés A, Álvarez-Rivera G, Socas-Rodríguez B, Herrero M, Cifuentes A. Capillary electromigration methods for food analysis and Foodomics: Advances and applications in the period February 2019-February 2021. Electrophoresis 2021; 43:37-56. [PMID: 34473359 DOI: 10.1002/elps.202100201] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/17/2021] [Accepted: 08/30/2021] [Indexed: 12/11/2022]
Abstract
This work presents a revision of the main applications of capillary electromigration methods in food analysis and Foodomics. Articles that were published during the period February 2019-February 2021 are included. The work shows the multiple CE methods that have been developed and applied to analyze different types of molecules in foods. Namely, CE methods have been applied to analyze amino acids, biogenic amines, carbohydrates, chiral compounds, contaminants, DNAs, food additives, heterocyclic amines, lipids, secondary metabolites, peptides, pesticides, phenols, pigments, polyphenols, proteins, residues, toxins, vitamins, small organic and inorganic compounds, as well as other minor compounds. The last results on the use of CE for monitoring food interactions and food processing, including recent microchips developments and new applications of CE in Foodomics, are discussed too. The new procedures of CE to investigate food quality and safety, nutritional value, storage and bioactivity are also included in the present review work.
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Shan S, Huang Y, Huang Z, Long Z, Liu C, Zhao X, Xing K, Xiao X, Liu J, Huang Y, Lai W, Liu D. Detection of stx1 and stx2 and subtyping of Shiga toxin-producing Escherichia coli using asymmetric PCR combined with lateral flow immunoassay. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Guan H, Xue P, Zhou H, Sha D, Wang D, Gao H, Li J, Diao B, Zhao H, Kan B, Zhang J. A multiplex PCR assay for the detection of five human pathogenic Vibrio species and Plesiomonas. Mol Cell Probes 2020; 55:101689. [PMID: 33338586 DOI: 10.1016/j.mcp.2020.101689] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 01/07/2023]
Abstract
A multiplex PCR (mPCR) assay was established to detect five pathogenic Vibrio species and Plesiomonas shigelloides. Twelve genes were included: ompW, ctxA, rfbN, and wbfR from V. cholerae; tl, tdh, and trh from V. parahaemolyticus; toxR and vmhA from V. mimicus; toxR from V. fluvialis; vvhA from V. vulnificus; and the 23S rRNA gene from P. shigelloides. The specificity of the mPCR assay was 100% for the detection of 136 strains and the limits of detection (LoD) were 12.5-50 pg/reaction. The assay exhibited higher sensitivity than cultivation methods in the detection of APW cultures of 113 diarrhea samples. In the analysis of 369 suspected Vibrio populations from estuarine water samples, the specificity of the mPCR for V. cholerae and V. parahaemolyticus was 100% for both, while the sensitivities were 100% and 96.1%, respectively. The assay can be applied to screen enrichment cultures and suspected colonies from environmental and clinical samples.
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Affiliation(s)
- Hongxia Guan
- Wuxi Center for Disease Control and Prevention, Jiangsu, 214023, China
| | - Panpan Xue
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dan Sha
- Wuxi Center for Disease Control and Prevention, Jiangsu, 214023, China
| | - Duochun Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - He Gao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Baowei Diao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hongqun Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Pazhoohan M, Sadeghi F, Moghadami M, Soltanmoradi H, Davoodabadi A. Antimicrobial and antiadhesive effects of Lactobacillus isolates of healthy human gut origin on Enterotoxigenic Escherichia coli (ETEC) and Enteroaggregative Escherichia coli (EAEC). Microb Pathog 2020; 148:104271. [PMID: 32835777 DOI: 10.1016/j.micpath.2020.104271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Diarrhea is one of the five leading causes of mortality in children under the age of five, especially in developing countries. Nowadays, by increasing the resistance of pathogens to antibiotics, employment of probiotics as novel therapeutic method, could be considered as a necessity.The aim of this study was to examine the features and antagonistic action of Lactobacillus strains, against the growth and adhesion of Enterotoxigenic Escherichia coli (ETEC) and Enteroaggregative Escherichia coli (EAEC) strains creating diarrhea in children. Then, we introduced new strains of Lactobacillus as probiotic candidates, to prevent diarrheal infections in children. METHODS Stool samples were collected from healthy individuals, and Lactobacillus strains were isolated. The antimicrobial effect of the isolates against ETEC and EAEC strains investigated by agar well diffusion method and their resistance to acidic and bile conditions. The potency of selected isolates in adhesion to HT-29 epithelial cells and their ability to inhibit the adhesion of ETEC and EAEC strains to this cell were measured. At the end, identification of the optimally efficient Lactobacillus isolates was performed by 16S rDNA sequencing and making Phylogenetic tree using MEGA (version 4.0) software. RESULTS In total, 157 isolates suspected to Lactobacillus were isolated from 115 stool samples. In antimicrobial activity test, ETEC and EAEC growth was inhibited by 132 and 84 isolates respectively, while 17 isolates showed resistance to Bile. Of 17 Bile resistant Lactobacillus isolates, 15 isolates were resistant to pH: 3.2. Further, among 15 isolates, only two isolates, were resistant to pH: 2.5. In the adhesion assay, five isolates had more adhesion tendency to HT-29 epithelial cells than L. rhamnosus GG, which was considered as a positive control. Investigation of isolates that inhibit adhesion of ETEC and EAEC strains to HT-29 cells showed that four isolates were able to inhibit ETEC adhesion. However, only one out of four isolates was relatively able to have an impact on EAEC adhesion. CONCLUSION In conclusion, three species of Lactobacillus including L. paracasei (two strain), L. fermentum (two strain) and L. plantarum showed good probiotic properties compared to other isolates that were identified by sequencing. In this study, strain L. fermentum 61.1 had the highest adhesion ability to HT-29 cells and strain L. paracasei 47.2 had the highest potency to inhibit ETEC adhesion to HT-29 cells. These isolates have good probiotic properties and are likely to be effective in preventing or treating diarrheal infections, especially in children.
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Affiliation(s)
- Maryam Pazhoohan
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
| | - Farzin Sadeghi
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran; Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Morteza Moghadami
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Hossein Soltanmoradi
- Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Abolfazl Davoodabadi
- Infectious Diseases & Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran; Department of Microbiology, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
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