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Wu S, Ji J, Carole NVD, Yang J, Yang Y, Sun J, Ye Y, Zhang Y, Sun X. Combined metabolomics and transcriptomics analysis reveals the mechanism of antibiotic resistance of Salmonella enterica serovar Typhimurium after acidic stress. Food Microbiol 2023; 115:104328. [PMID: 37567621 DOI: 10.1016/j.fm.2023.104328] [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: 09/12/2022] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 08/13/2023]
Abstract
Drug-resistant Salmonella is widely distributed in the meat production chain, endangering food safety and public health. Acidification of meat products during processing can induce acid stress, which may alter antibiotic resistance. Our study investigated the effects of acid stress on the antibiotic resistance and metabolic profile of Salmonella Typhimurium, and explored the underlying mechanisms using metabolomic and transcriptomic analysis. We found that acid-stressed 14028s was more sensitive to small molecule hydrophobic antibiotics (SMHA) while more resistant to meropenem (MERO). Metabolomic analysis revealed that enhanced sensitivity to SMHA was correlated with increased purine metabolism and tricarboxylic acid cycle. Transcriptomic analysis revealed the downregulation of chemotaxis-related genes, which are also associated with SMHA sensitivity. We also found a significant downregulation of the ompF gene, which encodes a major outer membrane protein OmpF of Salmonella. The decreased expression of OmpF porin hindered the influx of MERO, leading to enhanced resistance of the bacteria to the drug. Our findings contribute to greatly improve the understanding of the relationship between Salmonella metabolism, gene expression, and changes in drug resistance after acid stress, while providing a structural framework for exploring the relationship between bacterial stress responses and antibiotic resistance.
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Affiliation(s)
- Shang Wu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Nanfack V D Carole
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jia Yang
- Yangzhou Center for Food and Drug Control, Yangzhou, 225000, China
| | - Yang Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jiadi Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yongli Ye
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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Xiong D, Yuan L, Song L, Jiao X, Pan Z. A new multiplex PCR for the accurate identification and differentiation of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum. Front Microbiol 2022; 13:983942. [PMID: 36147848 PMCID: PMC9485580 DOI: 10.3389/fmicb.2022.983942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Salmonella enterica serovar Gallinarum biovars Gallinarum and Pullorum cause severe chicken salmonellosis, a disease associated with high mortality and morbidity among chickens worldwide. The conventional serotyping and biochemical reactions have been used to identify Salmonella serovars. However, the conventional methods are complicated, time-consuming, laborious, and expensive. Furthermore, it is challenging to distinguish S. Gallinarum and S. Pullorum via biochemical assays and serotyping because of their antigenic similarity. Although various PCR methods were established, a PCR protocol to detect and discriminate S. Gallinarum and S. Pullorum simultaneously is lacking. Herein, a one-step multiplex PCR method was established for the accurate identification and discrimination of S. Pullorum and S. Gallinarum. Three specific genes were used for the multiplex PCR method, with the I137_14445 and ybgL genes being the key targets to identify and differentiate S. Gallinarum and S. Pullorum, and stn being included as a reference gene for the Salmonella genus. In silico analysis showed that the I137_14445 gene is present in all Salmonella serovars, except for S. Gallinarum, and could therefore be used for the identification of S. Gallinarum. A 68-bp sequence deficiency in ybgL was found only in S. Pullorum compared to other Salmonella serovars, and this could therefore be used for the specific identification of S. Pullorum. The developed PCR assay was able to distinguish S. Gallinarum and S. Pullorum among 75 various Salmonella strains and 43 various non-Salmonella pathogens with excellent specificity. The detection limit for the genomic DNA of S. Gallinarum and S. Pullorum was 21.4 pg./μL, and the detectable limit for bacterial cells was 100 CFU. The developed PCR method was used for the analysis of Salmonella isolates in a chicken farm. This PCR system successfully discriminated S. Gallinarum and S. Pullorum from other different Salmonella serovars. The PCR results were confirmed by the conventional serotyping method. The newly established multiplex PCR is a simple, accurate, and cost-effective method for the timely identification and differentiation of S. Pullorum and S. Gallinarum.
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Affiliation(s)
- Dan Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Yuan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Song
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- *Correspondence: Xinan Jiao,
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
- Zhiming Pan,
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Jin L, Wang S, Shao Q, Cheng Y. A rapid and facile analytical approach to detecting Salmonella Enteritidis with aptamer-based surface-enhanced Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120625. [PMID: 34840047 DOI: 10.1016/j.saa.2021.120625] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/21/2021] [Accepted: 11/11/2021] [Indexed: 05/22/2023]
Abstract
Salmonella should be absence in pharmaceutical preparations and foods according to regulations in many countries. Up to now, rapidly detecting Salmonella at 1 CFU·[10 g (mL) ]-1 in pharmaceutical preparation or 1 CFU·[25 g (mL) ]-1 in food samples is still a challenge. Herein, we present an aptamer-based surface-enhanced Raman spectroscopy (SERS) method for rapidly detecting Salmonella Enteritidis by using a handheld Raman instrument. The aptamer could specifically recognize S. Enteritidis, and 4-MBA self-assembled on the surface of Au@Ag NPs was used as a Raman reporter molecule. The method was validated to be high specific with no interference from other five pathogenic bacteria. It could identify S. Enteritidis contaminant at ∼ 1 CFU·(10 g)-1 spiked level in a real sample (Wenxin granule, a botanical drug) after 6 h of enrichment. The detection time was much shorter than that of the methods (more than 54 ∼ 96 h) in the standards of pharmaceutical preparations and foods. In addition, the method could quantitatively determinate S. Enteritidis with satisfactory results. The SERS peak intensities of 4-MBA at 1072 cm-1 showed a good linear correlation (R2 = 0.9873) with the logarithms of S. Enteritidis concentrations ranging from 4.17 × 102 to 1.39 × 107 CFU·mL-1. T-test result (P = 0.425) revealed that there was no significant difference between the determination results obtained by the SERS method and the plate counting method. Therefore, the study indicated that the method was practical and reliable, and it could be a promising alternative for the on-site detection of S. Enteritidis.
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Affiliation(s)
- Lei Jin
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Shufang Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China.
| | - Qing Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yiyu Cheng
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, PR China
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Xin S, Zhu H, Tao C, Zhang B, Yao L, Zhang Y, Afayibo DJA, Li T, Tian M, Qi J, Ding C, Yu S, Wang S. Rapid Detection and Differentiating of the Predominant Salmonella Serovars in Chicken Farm by TaqMan Multiplex Real-Time PCR Assay. Front Cell Infect Microbiol 2021; 11:759965. [PMID: 34660351 PMCID: PMC8512842 DOI: 10.3389/fcimb.2021.759965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/10/2021] [Indexed: 01/27/2023] Open
Abstract
Salmonella has been known as an important zoonotic pathogen that can cause a variety of diseases in both animals and humans. Poultry are the main reservoir for the Salmonella serovars Salmonella Pullorum (S. Pullorum), Salmonella Gallinarum (S. Gallinarum), Salmonella Enteritidis (S. Enteritidis), and Salmonella Typhimurium (S. Typhimurium). The conventional serotyping methods for differentiating Salmonella serovars are complicated, time-consuming, laborious, and expensive; therefore, rapid and accurate molecular diagnostic methods are needed for effective detection and prevention of contamination. This study developed and evaluated a TaqMan multiplex real-time PCR assay for simultaneous detection and differentiation of the S. Pullorum, S. Gallinarum, S. Enteritidis, and S. Typhimurium. In results, the optimized multiplex real-time PCR assay was highly specific and reliable for all four target genes. The analytical sensitivity corresponded to three colony-forming units (CFUs) for these four Salmonella serovars, respectively. The detection limit for the multiplex real-time PCR assay in artificially contaminated samples was 500 CFU/g without enrichment, while 10 CFU/g after pre-enrichment. Moreover, the multiplex real-time PCR was applied to the poultry clinical samples, which achieved comparable results to the traditional bacteriological examination. Taken together, these results indicated that the optimized TaqMan multiplex real-time PCR assay will be a promising tool for clinical diagnostics and epidemiologic study of Salmonella in chicken farm and poultry products.
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Affiliation(s)
- Suhua Xin
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hong Zhu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chenglin Tao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Beibei Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lan Yao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yaodong Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | | | - Tao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Mingxing Tian
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jingjing Qi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Shengqing Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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Wu S, Yang Y, Wang T, Sun J, Zhang Y, Ji J, Sun X. Effects of acid, alkaline, cold, and heat environmental stresses on the antibiotic resistance of the Salmonella enterica serovar Typhimurium. Food Res Int 2021; 144:110359. [PMID: 34053552 DOI: 10.1016/j.foodres.2021.110359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Antibiotic resistance in Salmonella enterica serovar Typhimurium (S. ser. Typhimurium) has become a critical safety hazard in food. Sublethal environmental stresses can influence resistance in Salmonella during food processing. This study simulated environmental stresses in food processing. The antibiotic resistance of three strains of S. ser. Typhimurium (the ATCC 14028 strain and two wild-type isolates from chicken and pork product processing) was evaluated under different pH levels (5.0, 5.5, 6.0, 8.0, and 9.0). Also, dynamic changes in resistance with treatment duration under cold (4 °C, -20 °C) and heat (55 °C) treatment were studied. The results showed that acid and alkaline stresses reduced the resistance of S. ser. Typhimurium to eight antibiotics; meanwhile, the resistance of meropenem (MERO) increased. The minimal inhibitory concentration (MIC) of MERO was increased 16- to 64-fold. With acid or alkaline stress, the extracellular ATP content increased, and the scanning electron microscopy (SEM) result clearly revealed the appearance of wrinkles and holes on the outer membrane of Salmonella. These observations imply changes in membrane permeability, which may decrease the antibiotic resistance of Salmonella. Cold or heat stress increased the resistance of S. ser. Typhimurium to tetracycline, cefotaxime, ceftazidime, nalidixic acid, azithromycin, and ampicillin; the MIC increased 2- to 4-fold. The antibiotic resistance only changed when cold and heat stresses occurred over a certain period of time and remained unchanged when the stress persisted. This study reports on the ability of S. ser. Typhimurium to develop antibiotic resistance after environmental stresses. It can provide valuable information for meat processing to improve interventions and risk management.
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Affiliation(s)
- Shang Wu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Yang Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Tingwei Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jiadi Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
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Shi Y, Li C, Yang G, Xia X, Mao X, Fang Y, Zhang AM, Song Y. A rapid and accurate method for the detection of four aminoglycoside modifying enzyme drug resistance gene in clinical strains of Escherichia coli by a multiplex polymerase chain reaction. PeerJ 2020; 8:e8944. [PMID: 32309051 PMCID: PMC7153551 DOI: 10.7717/peerj.8944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/18/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Antibiotics are highly effective drugs used in the treatment of infectious diseases. Aminoglycoside antibiotics are one of the most common antibiotics in the treatment of bacterial infections. However, the development of drug resistance against those medicines is becoming a serious concern. AIM This study aimed to develop an efficient, rapid, accurate, and sensitive detection method that is applicable for routine clinical use. METHODS Escherichia coli was used as a model organism to develop a rapid, accurate, and reliable multiplex polymerase chain reaction (M-PCR) for the detection of four aminoglycoside modifying enzyme (AME) resistance genes Aac(6')-Ib, Aac(3)-II, Ant(3″)-Ia, and Aph(3')-Ia. M-PCR was used to detect the distribution of AME resistance genes in 237 clinical strains of E. coli. The results were verified by simplex polymerase chain reaction (S-PCR). RESULTS Results of M-PCR and S-PCR showed that the detection rates of Aac(6')-Ib, Aac(3)-II, Ant(3″)-Ia, and Aph(3')-Ia were 32.7%, 59.2%, 23.5%, and 16.8%, respectively, in 237 clinical strains of E. coli. Compared with the traditional methods for detection and identification, the rapid and accurate M-PCR detection method was established to detect AME drug resistance genes. This technique can be used for the clinical detection as well as the surveillance and monitoring of the spread of those specific antibiotic resistance genes.
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Affiliation(s)
- Yaoqiang Shi
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Molecular Medicine Center of Yunnan Province, Kunming, Yunnan, China
| | - Chao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Molecular Medicine Center of Yunnan Province, Kunming, Yunnan, China
| | - Guangying Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Molecular Medicine Center of Yunnan Province, Kunming, Yunnan, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Molecular Medicine Center of Yunnan Province, Kunming, Yunnan, China
| | - Xiaoqin Mao
- The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yue Fang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Molecular Medicine Center of Yunnan Province, Kunming, Yunnan, China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Molecular Medicine Center of Yunnan Province, Kunming, Yunnan, China
| | - Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- Molecular Medicine Center of Yunnan Province, Kunming, Yunnan, China
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Miao G, Zhang L, Zhang J, Ge S, Xia N, Qian S, Yu D, Qiu X. Free convective PCR: From principle study to commercial applications-A critical review. Anal Chim Acta 2020; 1108:177-197. [PMID: 32222239 DOI: 10.1016/j.aca.2020.01.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022]
Abstract
Polymerase chain reaction (PCR) is an extremely important tool for molecular diagnosis, as it can specifically amplify nucleic acid templates for sensitive detection. As another division of PCR, free convective PCR was invented in 2001, which can be performed in a capillary tube pseudo-isothermally within a significantly short time. Convective PCR thermal cycling is implemented by inducing thermal convection inside the capillary tube, which stratifies the reaction into spatially separate and stable melting, annealing, and extension zones created by the temperature gradient. Convective PCR is a promising tool that can be used for nucleic acid diagnosis as a point-of-care test (POCT) due to the significantly simplified heating strategy, reduced cost, and shortened detection time without sacrificing sensitivity and accuracy. Here, we review the history of free convective PCR from its invention to development and its commercial applications.
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Affiliation(s)
- Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Jing Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China.
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China.
| | - Shizhi Qian
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, 23529, USA.
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029, China.
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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Quintela IA, de Los Reyes BG, Lin CS, Wu VCH. Simultaneous Colorimetric Detection of a Variety of Salmonella spp. in Food and Environmental Samples by Optical Biosensing Using Oligonucleotide-Gold Nanoparticles. Front Microbiol 2019; 10:1138. [PMID: 31214132 PMCID: PMC6554661 DOI: 10.3389/fmicb.2019.01138] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/06/2019] [Indexed: 01/17/2023] Open
Abstract
Optical biosensors for rapid detection of significant foodborne pathogens are steadily gaining popularity due to its simplicity and sensitivity. While nanomaterials such as gold nanoparticles (AuNPs) are commonly used as signal amplifiers for optical biosensors, AuNPs can also be utilized as a robust biosensing platform. Many reported optical biosensors were designed for individual pathogen detection in a single assay and have high detection limit (DL). Salmonella spp. is one of the major causative agents of foodborne sickness, hospitalization and deaths. Unfortunately, there are around 2,000 serotypes of Salmonella worldwide, and rapid and simultaneous detection of multiple strains in a single assay is lacking. In this study, a comprehensive and highly sensitive simultaneous colorimetric detection of nineteen (19) environmental and outbreak Salmonella spp. strains was achieved by a novel optical biosensing platform using oligonucleotide-functionalized AuNPs. A pair of newly designed single stranded oligonucleotides (30-mer) was displayed onto the surface of AuNPs (13 nm) as detection probes to hybridize with a conserved genomic region (192-bases) of ttrRSBCA found on a broad range of Salmonella spp. strains. The sandwich hybridization (30 min, 55°C) resulted in a structural formation of highly stable oligonucleotide/AuNPs-DNA complexes which remained undisturbed even after subjecting to an increased salt concentration (2 M, final), thus allowing a direct discrimination via color change of target (red color) from non-target (purplish-blue color) reaction mixtures by direct observation using the naked eye. In food matrices (blueberries and chicken meat), nineteen different Salmonella spp. strains were concentrated using immunomagnetic separation and then simultaneously detected in a 96-well microplate by oligonucleotide-functionalized AuNPs after DNA preparation. Successful oligonucleotide/AuNPs-DNA hybridization was confirmed by gel electrophoresis while AuNPs aggregation in non-target and control reaction mixtures was verified by both spectrophotometric analysis and TEM images. Results showed that the optical AuNP biosensing platform can simultaneously screen nineteen (19) viable Salmonella spp. strains tested with 100% specificity and a superior detection limit of <10 CFU/mL or g for both pure culture and complex matrices setups. The highly sensitive colorimetric detection system can significantly improve the screening and detection of viable Salmonella spp. strains present in complex food and environmental matrices, therefore reducing the risks of contamination and incidence of foodborne diseases.
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Affiliation(s)
- Irwin A Quintela
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Services, Western Regional Research Center, Albany, CA, United States.,School of Food and Agriculture, University of Maine, Orono, ME, United States
| | | | - Chih-Sheng Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Vivian C H Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Services, Western Regional Research Center, Albany, CA, United States.,Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
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9
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Kim TH, Hwang HJ, Kim JH. Ultra-Fast On-Site Molecular Detection of Foodborne Pathogens Using a Combination of Convection Polymerase Chain Reaction and Nucleic Acid Lateral Flow Immunoassay. Foodborne Pathog Dis 2019; 16:144-151. [DOI: 10.1089/fpd.2018.2500] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Tae-Hoon Kim
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Korea
| | | | - Jeong Hee Kim
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Korea
- Department of Oral Biochemistry and Molecular Biology, School of Dentistry, Kyung Hee University, Seoul, Korea
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10
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Effect of tris(2-carboxyethyl)phosphine and tertiary butyl alcohol on the performance of convection polymerase chain reaction. Mol Biol Rep 2018; 46:639-645. [PMID: 30484105 DOI: 10.1007/s11033-018-4519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/22/2018] [Indexed: 10/27/2022]
Abstract
Rapid and on-site DNA-based molecular detection has become increasingly important for sensitive, specific, and timely detection and treatment of various diseases. To prepare and store biomolecule-containing reagents stably, reducing agents are used during protein preparation, and freeze-drying technology has been applied to the protein reagents. Some of the additives used during these processes may affect subsequent processes such as polymerase chain reaction (PCR). In this study, we evaluated the impact of TCEP, a reducing agent, and TBA, a freeze-drying medium, on the performance of convection PCR (cPCR) using a battery-operable PCR device. Singleplex cPCR detection of a 249 bp amplicon from human genomic DNA suggested that approximately 82% of performance was achieved in the presence of 0.1 mM TCEP and 1% TBA. The limit of detection and the minimum number of cycles at which amplicons began to appear was a little lower (~ 82% efficiency) or higher (20 vs 15 cycles), respectively, in the chemical-treated group than in the control group. With larger amplicons of 500 bp, the chemical-treated group revealed approximately 78% of performance and amplicons started to appear at 20 cycles of cPCR in both groups. Similar results were obtained with multiplex cPCR amplification.
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Taşkale Karatuğ N, Yüksel FN, Akçelik N, Akçelik M. Genetic diversity of food originated Salmonella isolates. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1451779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
| | | | - Nefise Akçelik
- Institute of Biotechnology, Central Laboratory, Ankara University, Turkey
| | - Mustafa Akçelik
- Department of Biology, Faculty of Science, Ankara University, Turkey
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