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Fang Z, Zhou X, Wang X, Shi X. Development of a 3-plex droplet digital PCR for identification and absolute quantification of Salmonella and its two important serovars in various food samples. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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2
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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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Wang C, Ye Q, Ding Y, Zhang J, Gu Q, Pang R, Zhao H, Wang J, Wu Q. Detection of Pseudomonas aeruginosa Serogroup G Using Real-Time PCR for Novel Target Genes Identified Through Comparative Genomics. Front Microbiol 2022; 13:928154. [PMID: 35814691 PMCID: PMC9263582 DOI: 10.3389/fmicb.2022.928154] [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: 04/25/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
Accurate serotyping is essential for effective infection control. Pseudomonas aeruginosa serogroup G is one of the most common serogroups found in water. Conventional serotyping methods are not standardized and have several shortcomings. Therefore, a robust method for rapidly identifying P. aeruginosa serotypes is required. This study established a real-time PCR method for identifying P. aeruginosa serogroup G strains using novel target gene primers based on comparative genomic analysis. A total of 343 genome sequences, including 16 P. aeruginosa serogroups and 67 other species, were analyzed. Target genes identified were amplified using real-time PCR for detecting P. aeruginosa serogroup G strains. Eight serogroup G genes, PA59_01276, PA59_01887, PA59_01888, PA59_01891, PA59_01894, PA59_04268, PA59_01892, and PA59_01896, were analyzed to determine specific targets. A real-time fluorescence quantitative PCR method, based on the novel target PA59_01276, was established to detect and identify serogroup G strains. The specificity of this method was confirmed using P. aeruginosa serogroups and non-P. aeruginosa species. The sensitivity of this real-time PCR method was 4 × 102 CFU/mL, and it could differentiate and detect P. aeruginosa serogroup G in the range of 4.0 × 103–4.0 × 108 CFU/mL in artificially contaminated drinking water samples without enrichment. The sensitivity of these detection limits was higher by 1–3 folds compared to that of the previously reported PCR methods. In addition, the G serum group was accurately detected using this real-time PCR method without interference by high concentrations of artificially contaminated serum groups F and D. These results indicate that this method has high sensitivity and accuracy and is promising for identifying and rapidly detecting P. aeruginosa serogroup G in water samples. Moreover, this research will contribute to the development of effective vaccines and therapies for infections caused by multidrug-resistant P. aeruginosa.
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Affiliation(s)
- Chufang Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
| | - Qihui Gu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
| | - Hui Zhao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Juan Wang,
| | - Qingping Wu
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Academy of Sciences, Guangzhou, China
- Qingping Wu,
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Brown EW, Bell R, Zhang G, Timme R, Zheng J, Hammack TS, Allard MW. Salmonella Genomics in Public Health and Food Safety. EcoSal Plus 2021; 9:eESP00082020. [PMID: 34125583 PMCID: PMC11163839 DOI: 10.1128/ecosalplus.esp-0008-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 12/26/2022]
Abstract
The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.
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Affiliation(s)
- Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Ruth Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Thomas S. Hammack
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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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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Zhou X, Liu B, Liu Y, Shi C, Fratamico PM, Zhang L, Wang D, Zhang J, Cui Y, Xu P, Shi X. Two homologous Salmonella serogroup C1-specific genes are required for flagellar motility and cell invasion. BMC Genomics 2021; 22:507. [PMID: 34225670 PMCID: PMC8259012 DOI: 10.1186/s12864-021-07759-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Background Salmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella ser. Choleraesuis is a prominent cause of invasive infections in Asia. Comparative genomic analysis in our previous study showed that two homologous genes, SC0368 and SC0595 in Salmonella ser. Choleraesuis were unique to serogroup C1. In this study, two single-deletion mutants (Δ0368 and Δ0595) and one double-deletion mutant (Δ0368Δ0595) were constructed based on the genome. All these mutants and the wild-type strain were subjected to RNA-Seq analysis to reveal functional relationships of the two serogroup C1-specific genes. Results Data from RNA-Seq indicated that deletion of SC0368 resulted in defects in motility through repression of σ28 in flagellar regulation Class 3. Consistent with RNA-Seq data, results from transmission electron microcopy (TEM) showed that flagella were not present in △0368 and △0368△0595 mutants resulting in both swimming and swarming defects. Interestingly, the growth rates of two non-motile mutants △0368 and △0368△0595 were significantly greater than the wild-type, which may be associated with up-regulation of genes encoding cytochromes, enhancing bacterial proliferation. Moreover, the △0595 mutant was significantly more invasive in Caco-2 cells as shown by bacterial enumeration assays, and the expression of lipopolysaccharide (LPS) core synthesis-related genes (rfaB, rfaI, rfaQ, rfaY, rfaK, rfaZ) was down-regulated only in the △0368△0595 mutant. In addition, this study also speculated that these two genes might be contributing to serotype conversion for Salmonella C1 serogroup based on their apparent roles in biosynthesis of LPS and the flagella. Conclusion A combination of biological and transcriptomic (RNA-Seq) analyses has shown that the SC0368 and SC0595 genes are involved in biosynthesis of flagella and complete LPS, as well as in bacterial growth and virulence. Such information will aid to revealing the role of these specific genes in bacterial physiology and evolution within the serogroup C1. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07759-z.
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Affiliation(s)
- Xiujuan Zhou
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bin Liu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Yangling, 712100, Shaanxi, China
| | - Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pina M Fratamico
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Lida Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dapeng Wang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianhua Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Cui
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Xu
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Shang Y, Ye Q, Wu Q, Pang R, Zhou B, Wang C, Xiang X, Li F, Wang J, Zhang Y, Wang J, Sun X, Zhang J. PCR and multiplex PCR assays for the detection of Cronobacter species using specific targets obtained by a bioinformatics approach. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ye Q, Shang Y, Chen M, Pang R, Li F, Wang C, Xiang X, Zhou B, Zhang S, Zhang J, Wu S, Xue L, Ding Y, Wu Q. Identification of new serovar-specific detection targets against salmonella B serogroup using large-scale comparative genomics. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Shang Y, Ye Q, Wu Q, Pang R, Xiang X, Wang C, Li F, Zhou B, Xue L, Zhang Y, Sun X, Zhang J. PCR identification of Salmonella serovars for the E serogroup based on novel specific targets obtained by pan-genome analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Loop-mediated isothermal amplification (LAMP) for rapid detection of Salmonella in foods based on new molecular targets. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110999] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ye Q, Shang Y, Chen M, Pang R, Li F, Xiang X, Zhou B, Wang C, Zhang S, Zhang J, Wang J, Xue L, Ding Y, Wu Q. Mining and evaluating novel serovar-specific Salmonella C1 serogroup genes by polymerase chain reaction analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ye Q, Shang Y, Chen M, Pang R, Li F, Xiang X, Wang C, Zhou B, Zhang S, Zhang J, Yang X, Xue L, Ding Y, Wu Q. Identification of Novel Sensitive and Reliable Serovar-Specific Targets for PCR Detection of Salmonella Serovars Hadar and Albany by Pan-Genome Analysis. Front Microbiol 2021; 12:605984. [PMID: 33815306 PMCID: PMC8011537 DOI: 10.3389/fmicb.2021.605984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/22/2021] [Indexed: 01/16/2023] Open
Abstract
The accurate and rapid classification of Salmonella serovars is an essential focus for the identification of isolates involved in disease in humans and animals. The purpose of current research was to identify novel sensitive and reliable serovar-specific targets and to develop PCR method for Salmonella C2 serogroups (O:8 epitopes) in food samples to facilitate timely treatment. A total of 575 genomic sequences of 16 target serovars belonging to serogroup C2 and 150 genomic sequences of non-target serovars were analysed by pan-genome analysis. As a result, four and three specific genes were found for serovars Albany and Hadar, respectively. Primer sets for PCR targeting these serovar-specific genes were designed and evaluated based on their specificity; the results showed high specificity (100%). The sensitivity of the specific PCR was 2.8 × 101–103 CFU/mL and 2.3 × 103–104 CFU/mL for serovars Albany and Hadar, respectively, and the detection limits were 1.04 × 103–104 CFU/g and 1.16 × 104–105 CFU/g in artificially contaminated raw pork samples. Furthermore, the potential functions of these serovar-specific genes were analysed; all of the genes were functionally unknown, except for one specific serovar Albany gene known to be a encoded secreted protein and one specific gene for serovars Hadar and Albany that is a encoded membrane protein. Thus, these findings demonstrate that pan-genome analysis is a precious method for mining new high-quality serovar-targets for PCR assays or other molecular methods that are highly sensitive and can be used for rapid detection of Salmonella serovars.
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Affiliation(s)
- Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuting Shang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Moutong Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rui Pang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Fan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinran Xiang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chufang Wang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Baoqing Zhou
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuhong Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Liang Xue
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yu Ding
- Department of Food Science & Technology, Jinan University, Institute of Food Safety & Nutrition, Jinan University, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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Real-time PCR identification of Listeria monocytogenes serotype 4c using primers for novel target genes obtained by comparative genomic analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110774] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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A method based on amino-modified magnetic nanoparticles to extract DNA for PCR-based analysis. Colloids Surf B Biointerfaces 2019; 179:87-93. [DOI: 10.1016/j.colsurfb.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/15/2019] [Accepted: 03/03/2019] [Indexed: 01/10/2023]
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15
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Zhang P, Zhuang L, Zhang D, Xu J, Dou X, Wang C, Gong J. Serovar-Specific Polymerase Chain Reaction for Detection of Salmonella enterica Serovar Indiana. Foodborne Pathog Dis 2018; 15:776-781. [PMID: 30183348 DOI: 10.1089/fpd.2018.2492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Salmonella enterica serovar Indiana (S. Indiana) is a newly emerging pathogen with high levels of drug resistance. It has become one of the most common Salmonella serovars in China with a worldwide distribution, posing significant public health concerns. Detection of S. Indiana by traditional bacteriological methods is time-consuming and laborious, which prevents timely surveillance and effective control of the pathogen. In this study, comparative genomics was used to identify an A7P63_13850 gene that is uniquely present in S. Indiana, but not in other Salmonella serovars or any non-Salmonella bacteria. Then, a polymerase chain reaction (PCR) assay targeting this serovar-specific gene was established for specific detection of S. Indiana. The detection limit of this method is 10 pg per reaction for bacterial genomic DNA, being equivalent to 100 colony-forming units (CFU) per reaction. The established PCR amplifies all S. Indiana strains (n = 56), but none of other Salmonella serovars (n = 146) and non-Salmonella species (n = 14). The assay established in this study was also used to detect clinical samples from poultry, showed a positivity of 14.7% (23/156) for S. Indiana, which were verified by bacteriological methods. The highly sensitive and serovar-specific PCR for S. Indiana established in this study is suitable and convenient for detection of S. Indiana which aids in surveillance and control of the pathogen.
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Affiliation(s)
- Ping Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Linlin Zhuang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Di Zhang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Jingxiao Xu
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China
| | - Xinhong Dou
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
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16
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Aydin M, Carter-Conger J, Gao N, Gilmore DF, Ricke SC, Ahn S. Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array. Anal Bioanal Chem 2018; 410:2637-2646. [DOI: 10.1007/s00216-018-0938-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/25/2018] [Accepted: 02/02/2018] [Indexed: 12/15/2022]
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17
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Kumar Y, Bansal S, Jaiswal P. Loop-Mediated Isothermal Amplification (LAMP): A Rapid and Sensitive Tool for Quality Assessment of Meat Products. Compr Rev Food Sci Food Saf 2017; 16:1359-1378. [DOI: 10.1111/1541-4337.12309] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Yogesh Kumar
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Sangita Bansal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
| | - Pranita Jaiswal
- ICAR-Central Inst. of Post-Harvest Engineering and Technology (CIPHET); Ludhiana India
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18
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Iwu CJ, Iweriebor BC, Obi LC, Basson AK, Okoh AI. Multidrug-Resistant Salmonella Isolates from Swine in the Eastern Cape Province, South Africa. J Food Prot 2016; 79:1234-9. [PMID: 27357044 DOI: 10.4315/0362-028x.jfp-15-224] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The exposure of farm animals to antimicrobials for treatment, prophylaxis, or growth promotion can select for resistant bacteria that can be transmitted to humans, and Salmonella as an important zoonotic pathogen can act as a potential reservoir of antimicrobial resistance determinants. We assessed the antibiogram profiles of Salmonella species isolated from pig herds in two commercial farms in South Africa. Two hundred fifty-eight presumptive Salmonella isolates were recovered from the fecal samples of 500 adult pigs. Specific primers targeting Salmonella serogroups A, B, C1, C2, and D were used to determine the prevalence of different serogroups. Only serogroup A (n = 48) was detected, while others were not. Antimicrobial susceptibility of the confirmed Salmonella serogroup A isolates was performed by using the disk diffusion method against a panel of 18 antibiotics. All the 48 isolates were resistant to tetracycline and oxytetracycline, while 75% were resistant to ampicillin, sulphamethoxazole-trimethoprim, nalidixic acid, and streptomycin. All the isolates exhibited multidrug resistance, with the predominant phenotype being against 11 antibiotics, and multiple antibiotic resistance index ranged between 0.3 and 0.6. The incidence of genes encoding resistance against ampicillin (ampC), tetracycline (tetA), and streptomycin (strA) were 54, 61, and 44%, respectively. We conclude that healthy pigs are potential reservoirs of multidrug-resistant Salmonella that could be transmitted to humans through the food chain and, hence, a significant public health threat.
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Affiliation(s)
- Chinwe Juliana Iwu
- South African Medical Research Council Microbial Water Quality Monitoring Centre, , University of Fort Hare, Alice 5700, Eastern Cape, South Africa; Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, Eastern Cape, South Africa.
| | - Benson Chuks Iweriebor
- South African Medical Research Council Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, Eastern Cape, South Africa;Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, Eastern Cape, South Africa
| | - Larry Chikwelu Obi
- Academic and Research Division, University of Fort Hare, Alice 5700, Eastern Cape, South Africa
| | - Albertus Kotze Basson
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Anthony Ifeanyi Okoh
- South African Medical Research Council Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, Eastern Cape, South Africa; Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, Eastern Cape, South Africa
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19
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Identification of Salmonella enterica Typhimurium and variants using a novel multiplex PCR assay. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Zhou X, Zhang L, Shi C, Fratamico PM, Liu B, Paoli GC, Dan X, Zhuang X, Cui Y, Wang D, Shi X. Genome-Scale Screening and Validation of Targets for Identification of Salmonella enterica and Serovar Prediction. J Food Prot 2016; 79:376-83. [PMID: 26939647 DOI: 10.4315/0362-028x.jfp-15-286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Salmonella enterica is the most common foodborne pathogen worldwide, with 2,500 recognized serovars. Detection of S. enterica and its classification into serovars are essential for food safety surveillance and clinical diagnosis. The PCR method is useful for these applications because of its rapidity and high accuracy. We obtained 412 candidate detection targets for S. enterica using a comparative genomics mining approach. Gene ontology (GO) functional enrichment analysis of these candidate targets revealed that the GO term with the largest number of unigenes with known function (38 of 177, 21.5%) was significantly involved in pathogenesis (P < 10(-24)). All the candidate targets were then evaluated by PCR assays. Fifteen targets showed high specificity for the detection of S. enterica by verification with 151 S. enterica strains and 34 non-Salmonella strains. The phylogenetic trees of verified targets were highly comparable with those of housekeeping genes, especially for differentiating S. enterica strains into serovars. The serovar prediction ability was validated by sequencing one target (S9) for 39 S. enterica strains belonging to six serovars. Identical mutation sites existed in the same serovar, and different mutation sites were found in diverse serovars. Our findings revealed that 15 verified targets can be potentially used for molecular detection, and some of them can be used for serotyping of S. enterica strains.
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Affiliation(s)
- Xiujuan Zhou
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Lida Zhang
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Chunlei Shi
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Pina M Fratamico
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038, USA
| | - Bin Liu
- College of Food Science and Engineering, Northwest Agriculture and Forestry University, Shaanxi Yangling, People's Republic of China
| | - George C Paoli
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania 19038, USA
| | - Xianlong Dan
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xiaofei Zhuang
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yan Cui
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Dapeng Wang
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xianming Shi
- Chinese Ministry of Science and Technology and U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture and Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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21
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Dias MR, Cavicchioli VQ, Camargo AC, Lanna FGPA, Pinto PSDA, Bersot LDS, Nero LA. Molecular tracking of Salmonella spp. in chicken meat chain: from slaughterhouse reception to end cuts. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2016; 53:1084-91. [PMID: 27162388 PMCID: PMC4837711 DOI: 10.1007/s13197-015-2126-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/12/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
Abstract
Due to the importance of Salmonella spp. in poultry products, this study aimed to track its main contamination routes since slaughtering reception to processing of chicken end cuts. Samples from different steps of slaughtering and processing (n = 277) were collected from two chicken slaughterhouses (Sl1 and Sl2) located in Minas Gerais state, Brazil, and subjected to Salmonella spp. detection. The obtained isolates were subjected to serological identification and tested by PCR for specific Salmonella spp. genes (ompC and sifB). Also, Salmonella spp. isolates were subjected to XbaI macrorestriction and pulsed-field gel electrophoresis (PFGE). Sixty-eight samples were positive for Salmonella spp. and 172 isolates were obtained. Sl1 and Sl2 presented similar frequencies of Salmonella spp. positive samples during reception, slaughtering and processing (p > 0.05), except for higher frequencies in Sl1 for chicken carcasses after de-feathering and evisceration (p < 0.05). PFGE allowed the identification of cross contamination and persistence of Salmonella spp. strains in Sl1. The results highlighted the relevance of the initial steps of chicken slaughtering for Salmonella spp. contamination, and the pre-chilling of carcasses as an important controlling tool. In addition, the presence of Salmonella spp. in chicken end cuts samples represents a public health concern.
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Affiliation(s)
- Mariane Rezende Dias
- />Departamento de Veterinária, Universidade Federal de Viçosa, Campus UFV, Viçosa, MG 36570-900 Brazil
| | | | - Anderson Carlos Camargo
- />Departamento de Veterinária, Universidade Federal de Viçosa, Campus UFV, Viçosa, MG 36570-900 Brazil
| | | | | | | | - Luís Augusto Nero
- />Departamento de Veterinária, Universidade Federal de Viçosa, Campus UFV, Viçosa, MG 36570-900 Brazil
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22
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Nho SW, Abdelhamed H, Reddy S, Karsi A, Lawrence ML. Identification of high-risk Listeria monocytogenes serotypes in lineage I (serotype 1/2a, 1/2c, 3a and 3c) using multiplex PCR. J Appl Microbiol 2015; 119:845-52. [PMID: 26095922 DOI: 10.1111/jam.12876] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/21/2015] [Accepted: 06/04/2015] [Indexed: 01/08/2023]
Abstract
AIMS Using molecular subtyping techniques, Listeria monocytogenes is divided into three major phylogenetic lineages, and a multiplex PCR method can differentiate five L. monocytogenes subgroups: 1/2a-3a, 1/2c-3c, 1/2b-3b-7, 4b-4d-4e and 4a-4c. In this study, we conducted genome comparisons and evaluated serotype-associated genes for their utility as a multiplex PCR-based method for distinguishing high-risk serotypes 1/2a and 1/2c in lineage I from low-risk serotypes 3a and 3c. METHODS AND RESULTS Primer sets were developed that are specific for serotype 1/2c (LMOSLCC2372_0308) and serotype 3a (LMLG_0742). These primers were then tested in a multiplex format with primers specific for serotype 1/2a (flaA) to separate serotypes 1/2a, 1/2c, 3a and 3c using 25 strains of lineage I L. monocytogenes. CONCLUSIONS Here, for the first time, we report primers specific for L. monocytogenes serotype 1/2c and serotype 3a, and we demonstrate a multiplex PCR method for separating the four serotypes of lineage I L. monocytogenes. SIGNIFICANCE AND IMPACT OF THE STUDY The described multiplex PCR assay consistently showed successful separation of 1/2a and 1/2c strains from 3a and 3c strains. PCR is routinely performed in many diagnostic and epidemiologic investigations for L. monocytogenes, and these primers should increase the feasibility and accessibility of L. monocytogenes serotyping.
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Affiliation(s)
- S W Nho
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - H Abdelhamed
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - S Reddy
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - A Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - M L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
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23
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Zhou X, He S, Song Q, Zhuang X, Wang Y, Huang X, Shi C, Shi X. Phenotypic and Genotypic Characterization ofSalmonella entericaSerovar Enteritidis Isolates Associated with a Mousse Cake–Related Outbreak of Gastroenteritis in Ningbo, China. Foodborne Pathog Dis 2015; 12:433-40. [DOI: 10.1089/fpd.2014.1896] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiujuan Zhou
- Ministry of Science and Technology of China (MOST)–U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Shoukui He
- Ministry of Science and Technology of China (MOST)–U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Qifa Song
- Ningbo Center for Disease Control and Prevention, Ningbo, Zhejiang, China
| | - Xiaofei Zhuang
- Ministry of Science and Technology of China (MOST)–U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyan Wang
- Ministry of Science and Technology of China (MOST)–U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaozhen Huang
- Ministry of Science and Technology of China (MOST)–U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- Ministry of Science and Technology of China (MOST)–U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xianming Shi
- Ministry of Science and Technology of China (MOST)–U.S. Department of Agriculture Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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24
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Zhou X, Liu B, Shi C, Shi X. Mutation of a Salmonella serogroup-C1-specific gene abrogates O7-antigen biosynthesis and triggers NaCl-dependent motility deficiency. PLoS One 2014; 9:e106708. [PMID: 25211341 PMCID: PMC4161368 DOI: 10.1371/journal.pone.0106708] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 08/04/2014] [Indexed: 01/12/2023] Open
Abstract
Several molecular detection marker genes specific for a number of individual Salmonella serogroups have been recently identified in our lab by comparative genomics for the genotyping of diverse serogroups. To further understand the correlation between serotype and genotype, the function of a Salmonella serogroup-C1-specific gene (SC_2092) was analyzed in this study. It was indicated from the topological prediction using the deduced amino acid sequence of SC_2092 that this putative protein was highly similar to the confirmed Wzx flippases. Furthermore, SDS-PAGE revealed that lipopolysaccharide (LPS) biosynthesis, specifically O-antigen synthesis, was incomplete in an SC_2092 in-frame deletion mutant, and no agglutination reaction with the O7 antibody was exhibited in this mutant. Therefore, it was revealed that this Salmonella serogroup-C1-specific gene SC_2092 encoded a putative flippase, which was required for O7-polysaccharide biosynthesis, and was designated here as wzxC1. Subsequently, the effects of the deletion of wzxC1 on bacterial motility and sodium chloride (NaCl) tolerance were evaluated. The wzxC1 mutant lacked swarming motility on solid surfaces and was impaired in swimming motility in soft agar. Moreover, microscopic examination and RT-qPCR exhibited that an increased auto-aggregation and a strong defect in flagella expression, respectively, were responsible for the reduced motility in this mutant. In addition, the wzxC1 mutant was more sensitive than the wild-type strain to NaCl, and auto-aggregation of mutant cells was observed immediately up on the addition of 1% NaCl to the medium. Interestingly, the motility deficiency of the mutant strain, as well as the cell agglomeration and the decrease in flagellar expression, were relieved in a NaCl-free medium. This is the first study to experimentally demonstrate a connection between a Salmonella serogroup specific gene identified by comparative genomics with the synthesis of a specific O-antigen biosynthesis. Also, our results show that the mutation of wzxC1 triggers a NaCl-dependent motility deficiency.
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Affiliation(s)
- Xiujuan Zhou
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bin Liu
- College of Food Science and Engineering, Northwest Agriculture & Forestry University, Shaanxi, Yangling, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (CS); (XS)
| | - Xianming Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture & Biology, and State Key Lab of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (CS); (XS)
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25
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Fusco V, Quero GM. Culture-Dependent and Culture-Independent Nucleic-Acid-Based Methods Used in the Microbial Safety Assessment of Milk and Dairy Products. Compr Rev Food Sci Food Saf 2014; 13:493-537. [DOI: 10.1111/1541-4337.12074] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Vincenzina Fusco
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
| | - Grazia Marina Quero
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
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26
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Zhai L, Yu Q, Bie X, Lu Z, Lv F, Zhang C, Kong X, Zhao H. Development of a PCR test system for specific detection of Salmonella Paratyphi B in foods. FEMS Microbiol Lett 2014; 355:83-9. [PMID: 24725227 DOI: 10.1111/1574-6968.12443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/10/2014] [Accepted: 04/10/2014] [Indexed: 01/02/2023] Open
Abstract
Salmonella enterica serotype Paratyphi B is a globally distributed human-specific pathogen causing paratyphoid fever. The aim of this study was to develop a rapid and reliable polymerase chain reaction (PCR) assay for its detection in food. The SPAB_01124 gene was found to be unique to S. Paratyphi B using comparative genomics. Primers for fragments of the SPAB_01124 gene and the Salmonella-specific invA gene were used in combination to establish a multiplex PCR assay that showed 100% specificity across 45 Salmonella strains (representing 34 serotypes) and 18 non-Salmonella strains. The detection limit was 2.2 CFU mL(-1) of S. Paratyphi B after 12-h enrichment in pure culture. It was shown that co-culture with S. Typhimurium or Escherichia coli up to concentrations of 3.6 × 10(5) CFU and 3.3 × 10(4) CFU, respectively, did not interfere with PCR detection of S. Paratyphi B. In artificially contaminated milk, the assay could detect as few as 62 CFU mL(-1) after 8 h of enrichment. In conclusion, comparative genomics was found to be an efficient approach to the mining of pathogen-specific target genes, and the PCR assay that was developed from this provided a rapid, specific, and sensitive method for detection of S. Paratyphi B.
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Affiliation(s)
- Ligong Zhai
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, Nanjing, China
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27
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Zhai L, Kong X, Lu Z, Lv F, Zhang C, Bie X. Detection of Salmonella enterica serovar Dublin by polymerase chain reaction in multiplex format. J Microbiol Methods 2014; 100:52-7. [DOI: 10.1016/j.mimet.2014.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 11/28/2022]
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28
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29
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Cossi MVC, Burin RCK, Lopes DA, Dias MR, Castilho NPAD, de Arruda Pinto PS, Nero LA. Antimicrobial resistance and virulence profiles of Salmonella isolated from butcher shops in Minas Gerais, Brazil. J Food Prot 2013; 76:1633-7. [PMID: 23992511 DOI: 10.4315/0362-028x.jfp-13-119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Salmonella can contaminate finished products of butcher shops, mainly through cross-contamination of utensils exposed to raw materials. To identify the main sources of contamination with this foodborne pathogen in four butcher shop environments, surface samples were obtained from employees' hands, cutting boards, knives, floor of the refrigeration room, meat grinders, and meat tenderizers (32 samples per area) and analyzed for Salmonella using the International Organization for Standardization method 6579, with modifications. Suspect isolates were identified by PCR (targeting ompC), and confirmed Salmonella isolates were subjected to pulsed-field gel electrophoresis (after treatment with restriction enzyme XbaI), analyzed for the presence of virulence genes (invA, sefA, and spvC), and screened for resistance to 12 antimicrobials. Salmonella isolates was identified only on cutting boards (five samples) from three butcher shops. Fifteen isolates were confirmed as Salmonella belonging to four pulse types (similarity of 71.1 to 100%). The invA gene was detected in 13 isolates, and the sefA was found in 8 isolates; no isolate carried spvC. All tested isolates were resistant to clindamycin and sensitive to amikacin and cefotaxine, and all isolates were resistant to at least 3 of the 12 antimicrobials tested. The results indicate the importance of cutting boards as a source of Salmonella contamination in butcher shops. The presence of multidrug-resistant Salmonella strains possessing virulence genes highlights the health risks for consumers.
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Affiliation(s)
- Marcus Vinícius Coutinho Cossi
- Departamento de Veterinária, Universidade Federal de Viçosa, Campus Universitário, 36570-000 Viçosa, Minas Gerais, Brazil
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30
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Kupradit C, Rodtong S, Ketudat-Cairns M. Development of a DNA macroarray for simultaneous detection of multiple foodborne pathogenic bacteria in fresh chicken meat. World J Microbiol Biotechnol 2013; 29:2281-91. [DOI: 10.1007/s11274-013-1394-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 05/31/2013] [Indexed: 10/26/2022]
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Liu B, Zhou X, Zhang L, Liu W, Dan X, Shi C, Shi X. Development of a novel multiplex PCR assay for the identification of Salmonella enterica Typhimurium and Enteritidis. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.01.062] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ravan H, Yazdanparast R. Development and evaluation of a loop-mediated isothermal amplification method in conjunction with an enzyme-linked immunosorbent assay for specific detection of Salmonella serogroup D. Anal Chim Acta 2012; 733:64-70. [DOI: 10.1016/j.aca.2012.04.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/24/2012] [Accepted: 04/26/2012] [Indexed: 11/25/2022]
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Ravan H, Yazdanparast R. Development of a new loop-mediated isothermal amplification assay for prt (rfbS) gene to improve the identification of Salmonella serogroup D. World J Microbiol Biotechnol 2012; 28:2101-6. [PMID: 22806032 DOI: 10.1007/s11274-012-1014-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 01/30/2012] [Indexed: 12/14/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a promising nucleic acid assay for rapid and cost-effective detection of pathogen-specific sequences within a sample. Development of an appropriate taxonomic group-specific LAMP assay highly relies on the design of proper primers to cover all major members of the taxon. Regarding this fact, we designed and evaluated a new LAMP primer set specific to prt (rfbS) gene for rapid identification of Salmonella serogroup D serotypes. Unlike the previously reported LAMP assay for serogroup D which detects solely the non-typhoidal serotypes; the new LAMP primers set detects both typhoidal and non-typhoidal serotypes of this serogroup with a detection limit of 10 CFU/rection. Furthermore, the technique was successfully applied to artificially contaminated meat samples with an inoculation level of 1-5 CFU/250 ml of Salmonella Enteritidis, following a 5-h pre-enrichment step in tryptic soy broth. Overall, the new LAMP assay and its optimized setup would be useful for fast diagnosis of food poisoning incidents caused by these bacteria.
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Affiliation(s)
- Hadi Ravan
- Institute of Biochemistry and Biophysics, University of Tehran, P. O. Box 13145-1384, Tehran, Iran
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