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Pan J, Zeng M, Zhao M, Huang L. Research Progress on the detection methods of porcine reproductive and respiratory syndrome virus. Front Microbiol 2023; 14:1097905. [PMID: 36970703 PMCID: PMC10033578 DOI: 10.3389/fmicb.2023.1097905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) causes clinical syndromes typified as reproductive disorders in sows and respiratory diseases in piglets. PRRSV remains one of the most prevalent pathogens affecting the pig industry, because of its complex infection profile and highly heterogeneous genetic and recombination characteristics. Therefore, a rapid and effective PRRSV detection method is important for the prevention and control of PRRS. With extensive in-depth research on PRRSV detection methods, many detection methods have been improved and promoted. Laboratory methods include techniques based on virus isolation (VI), enzyme-linked immunosorbent assays (ELISA), indirect immunofluorescence assays (IFA), immunoperoxidase monolayer assays (IPMA), polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), digital PCR (dPCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), clustered regularly interspaced short palindromic repeats (CRISPR), metagenomic next-generation sequencing (mNGS), and other methods. This study reviews the latest research on improving the main PRRSV detection methods and discusses their advantages and disadvantages.
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Affiliation(s)
- Jinghua Pan
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Mengyi Zeng
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Mengmeng Zhao
- School of Life Science and Engineering, Foshan University, Foshan, China
- Veterinary Teaching Hospital, Foshan University, Foshan, China
- *Correspondence: Mengmeng Zhao,
| | - Liangzong Huang
- School of Life Science and Engineering, Foshan University, Foshan, China
- Veterinary Teaching Hospital, Foshan University, Foshan, China
- Liangzong Huang,
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Oliveira M, Truchado P, Cordero-García R, Gil MI, Soler MA, Rancaño A, García F, Álvarez-Ordóñez A, Allende A. Surveillance on ESBL- Escherichia coli and Indicator ARG in Wastewater and Reclaimed Water of Four Regions of Spain: Impact of Different Disinfection Treatments. Antibiotics (Basel) 2023; 12:antibiotics12020400. [PMID: 36830310 PMCID: PMC9952245 DOI: 10.3390/antibiotics12020400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
In the present study, the occurrence of indicator antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) both in the influent and the effluent of four Spanish wastewater treatment plants (WWTPs) was monitored for 12 months, and the susceptibility profiles of 89 recovered extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolates were obtained against a wide range of antimicrobials. The aim of the study was to better understand whether the current wastewater treatment practices allow us to obtain safe reclaimed water mitigating the spread of ARB and ARGs to the environment. Results showed high concentrations of ESBL-producing E. coli as well as a high prevalence of a range of ARGs in the influent samples. The reclamation treatments implemented in the WWTPs were effective in reducing both the occurrence of ESBL E. coli and ARGs, although significant differences were observed among WWTPs. Despite these reductions in occurrence observed upon wastewater treatment, our findings suggest that WWTP effluents may represent an important source of ARGs, which could be transferred among environmental bacteria and disseminate antimicrobial resistance through the food chain. Remarkably, no major differences were observed in the susceptibility profiles of the ESBL E. coli isolated from influent and effluent waters, indicating that water treatments do not give rise to the emergence of new resistance phenotypes.
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Affiliation(s)
- Márcia Oliveira
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Correspondence: ; Tel.: +34-987291182
| | - Pilar Truchado
- Research Group on Microbiology and Quality of Fruit and Vegetables, Food Science and Technology Department, CEBAS-CSIC, 25, Espinardo, 30100 Murcia, Spain
| | | | - María I. Gil
- Research Group on Microbiology and Quality of Fruit and Vegetables, Food Science and Technology Department, CEBAS-CSIC, 25, Espinardo, 30100 Murcia, Spain
| | - Manuel Abellán Soler
- Entidad Regional de Saneamiento y Depuración de Murcia (ESAMUR), Avda. Juan Carlos I, s/n. Ed. Torre Jemeca, 30009 Murcia, Spain
| | - Amador Rancaño
- Acciona Agua, S.A.U., Avda. de Europa, 18, Parque Empresarial La Moraleja, 28108 Alcobendas, Spain
| | - Francisca García
- Acciona Agua, S.A.U., Avda. de Europa, 18, Parque Empresarial La Moraleja, 28108 Alcobendas, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Institute of Food Science and Technology, Universidad de León, 24007 León, Spain
| | - Ana Allende
- Research Group on Microbiology and Quality of Fruit and Vegetables, Food Science and Technology Department, CEBAS-CSIC, 25, Espinardo, 30100 Murcia, Spain
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Akshay SD, Anupama KP, Deekshit VK, Rohit A, Maiti B. Effect of sub-minimum inhibitory concentration of ceftriaxone on the expression of outer membrane proteins in Salmonella enterica serovar Typhi. World J Microbiol Biotechnol 2022; 38:190. [PMID: 35972699 DOI: 10.1007/s11274-022-03383-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 01/22/2023]
Abstract
Multi-drug resistance (MDR) in Salmonella is one of the major reasons for foodborne outbreaks worldwide. Decreased susceptibility of Salmonella Typhi to first-line drugs such as ceftriaxone, ciprofloxacin, and azithromycin has raised concern. Reduced outer membrane proteins (OMPs) permeability and increased efflux pump transportation are considered to be the main reasons for the emergence of antibiotic resistance in Salmonella. The present study aimed to assess the expression of OMPs at sub-lethal concentrations of ceftriaxone in S. Typhi (Sl5037/BC, and Sl05). The S. Typhi strains were exposed to sub-MIC and half of the sub-MIC concentrations of ceftriaxone at three different time intervals (0 min, 40 min, and 180 min) and analyzed for differential expression of OMPs. Further, the expression variation of OMP encoding genes (yaeT, ompX, lamb, ompA, and ybfM) in response to ceftriaxone was evaluated using real-time PCR. The genes like lamB, ompX, and yaeT showed significant downregulation (p < 0.05) compared to the control without antibiotic exposure, whereas ybfM and ompA showed a moderate downregulation. The expression of omp genes such as lamB, ompA, ompX, ybfM, and yaeT were found to be low in the presence of ceftriaxone, followed by time and dose-dependent. The study provides insights into the possible involvement of OMPs in drug resistance of S. Typhi, which could help develop a therapeutic strategy to combat MDR isolates of S. Typhi.
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Affiliation(s)
- Sadanand Dangari Akshay
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Karanth Padyana Anupama
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Vijaya Kumar Deekshit
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Anusha Rohit
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India.,Department of Microbiology, The Madras Medical Mission, 4-A, Dr, Mogappair, Chennai, Tamil Nadu, 600037, India
| | - Biswajit Maiti
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India.
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Giglioti R, Polli H, Tainá Azevedo B, Morita Katiki L, Eugênio Vercesi Filho A. Detection and quantification of adulteration in milk and dairy products: A novel and sensitive qPCR-based method. FOOD CHEMISTRY. MOLECULAR SCIENCES 2022; 4:100074. [PMID: 35415677 PMCID: PMC8991746 DOI: 10.1016/j.fochms.2022.100074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
A novel qPCR method was able to detect and quantify cow, buffalo, goat and sheep DNA in milk and dairy products. Established detection limit was 0.016 ng for the four species. The limit of detection of cow DNA in buffalo, goat and sheep DNA samples was 0.1% (0.01 ng) This method is able to detect and quantify adulteration between cows, buffaloes, goats and sheep dairy samples.
Species identification in dairy products has a notable importance in food traceability and adulteration control and consequently has a significant effect on the final economic value of foods. In the present study, we developed a method based on real-time quantitative PCR (qPCR) for detection and quantification of cow DNA in DNA samples from milk and dairy products from buffaloes, goats, and sheep. The qPCR reactions showed high specificity, and the amplifications only occurred to species-specific primers. The calibration curves allowed for the quantification of the amount of DNA of each species-specific primer, and the established detection limit was 0.016 ng for the four species. The detection limit of cow DNA in buffalo, goat and sheep DNA samples was 0.1% (0.01 ng). Although the present study aimed to detect and quantify cow DNA in buffalo, goat, and sheep dairy products, we believe that the qPCR assays can also be directed to differentiate and quantify goat × sheep, and/or buffalo × goat/sheep.
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Affiliation(s)
- Rodrigo Giglioti
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
| | - Hiago Polli
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
| | - Bianca Tainá Azevedo
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
| | - Luciana Morita Katiki
- Instituto de Zootecnia, Rua Heitor Penteado, n. 56, Nova Odessa, São Paulo 13380-011, Brazil
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Ghorbani J, Hashemi FB, Jabalameli F, Emaneini M, Beigverdi R. Multiplex detection of five common respiratory pathogens from bronchoalveolar lavages using high resolution melting curve analysis. BMC Microbiol 2022; 22:141. [PMID: 35590256 PMCID: PMC9118692 DOI: 10.1186/s12866-022-02558-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
Background The study describes the application of the multiplex high-resolution melting curve (MHRM) assay for the simultaneous detection of five common bacterial pathogens (Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii and Escherichia coli) directly from bronchoalveolar lavage samples. Results Our MHRM assay successfully identified all five respiratory pathogens in less than 5 h, with five separate melting curves with specific melt peak temperatures (Tm). The different Tm were characterized by peaks of 78.1 ± 0.4 °C for S. aureus, 83.3 ± 0.1 °C for A. baumannii, 86.7 ± 0.2 °C for E. coli, 90.5 ± 0.1 °C for K. pneumoniae, 94.5 ± 0.2 °C for P. aeruginosa. The overall sensitivity and specificity of MHRM were 100% and 88.8–100%, respectively. Conclusions Our MHRM assay offers a simple and fast alternative to culture approach for simultaneous detection of five major bacterial lower respiratory tract infection pathogens. Utilization of this assay can help clinicians initiate prompt and appropriate antimicrobial treatment, towards reducing the morbidity and mortality of severe respiratory infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02558-2.
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Affiliation(s)
- Jaber Ghorbani
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Farhad Bonakdar Hashemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran.,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 6, 100 Poursina St., Keshavarz Blvd., Tehran, Iran. .,Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran.
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Li Q, Li Z, Wang Y, Chen Y, Sun J, Yang Y, Si H. Antimicrobial Resistance and Transconjugants Characteristics of sul3 Positive Escherichia coli Isolated from Animals in Nanning, Guangxi Province. Animals (Basel) 2022; 12:ani12080976. [PMID: 35454223 PMCID: PMC9025041 DOI: 10.3390/ani12080976] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 01/27/2023] Open
Abstract
Sulfonamides are the second most popular antibiotic in many countries, which leads to the widespread emergence of sulfonamides resistance. sul3 is a more recent version of the gene associated with sulfonamide resistance, whose research is relatively little. In order to comprehend the prevalence of sul3 positive E. coli from animals in Nanning, a total of 146 strains of E. coli were identified from some farms and pet hospitals from 2015 to 2017. The drug resistance and prevalence of sul3 E. coli were analyzed by polymerase chain reaction (PCR) identification, multi-site sequence typing (MLST), drug sensitivity test, and drug resistance gene detection, and then the plasmid containing sul3 was conjugated with the recipient strain (C600). The effect of sul3 plasmid on the recipient was analyzed by stability, drug resistance, and competitive test. In this study, forty-six sul3 positive E. coli strains were separated. A total of 12 ST types were observed, and 1 of those was a previously unknown type. The ST350 is the most numerous type. All isolates were multidrug-resistant E. coli, with high resistant rates to penicillin, ceftriaxone sodium, streptomycin, tetracycline, ciprofloxacin, gatifloxacin, and chloramphenicol (100%, 73.9%, 82.6%, 100%, 80.4%, 71.7%, and 97.8%, respectively). They had at least three antibiotic resistance genes (ARGs) in addition to sul3. The plasmids transferred from three sul3-positive isolates to C600, most of which brought seven antimicrobial resistance (AMR) and increased ARGs to C600. The transferred sul3 gene and the plasmid carrying sul3 could be stably inherited in the recipient bacteria for at least 20 days. These plasmids had no effect on the growth of the recipient bacteria but greatly reduced the competitiveness of the strain at least 60 times in vitro. In Nanning, these sul3-positive E. coli had such strong AMR, and the plasmid carrying sul3 had the ability to transfer multiple resistance genes that long-term monitoring was necessary. Since the transferred plasmid would greatly reduce the competitiveness of the strain in vitro, we could consider limiting the spread of drug-resistant isolates in this respect.
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Detection of Eight Respiratory Bacterial Pathogens Based on Multiplex Real-Time PCR with Fluorescence Melting Curve Analysis. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:2697230. [PMID: 32184908 PMCID: PMC7061119 DOI: 10.1155/2020/2697230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 01/23/2023]
Abstract
Background and Objective. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis are primary respiratory bacterial pathogens contributing to morbidity and mortality in developing countries. This study evaluated the diagnostic performance of multiplex real-time PCR with fluorescence melting curve analysis (MCA) assay, which was used to detect eight respiratory bacterial pathogens simultaneously. Methods A total of 157 sputum specimens were examined by multiplex real-time with fluorescence MCA, and the results were compared with the conventional culture method. Results Multiplex real-time PCR with fluorescence MCA specifically detected and differentiated eight respiratory bacterial pathogens by different melting curve peaks for each amplification product within 2 hours and exhibited high repeatability. The limit of detection ranged from 64 to 102 CFU/mL in the multiplex PCR system. Multiplex real-time PCR with fluorescence MCA showed a sensitivity greater than 80% and a 100% specificity for each pathogen. The kappa correlation of eight bacteria ranged from 0.89 to 1.00, and the coefficient of variation ranged from 0.05% to 0.80%. Conclusions Multiplex real-time PCR with fluorescence MCA assay is a sensitive, specific, high-throughput, and cost-effective method to detect multiple bacterial pathogens simultaneously.
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Dehbashi S, Tahmasebi H, Sedighi P, Davarian F, Arabestani MR. Development of high-resolution melting curve analysis in rapid detection of vanA gene, Enterococcus faecalis, and Enterococcus faecium from clinical isolates. Trop Med Health 2020; 48:8. [PMID: 32099522 PMCID: PMC7027104 DOI: 10.1186/s41182-020-00197-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
Background High-resolution melting analysis (HRMA) is a novel molecular technique based on the real-time PCR that can be used to detect vancomycin resistance Enterococcus (VRE). The purpose of this study was to identify VRE species with HRMA in clinical isolates. Results Out of 49 Enterococcus isolates, 11 (22.44%) E. faecium isolates and 19 (38.77%) E. faecalis isolates were detected. Average melting temperatures for divIVA in E.faecalis, alanine racemase in E.faecium, and vanA in VRE strains were obtained as 79.9 ± 0.5 °C, 85.4 ± 0.5 °C, and 82.99 ± 0.5 °C, respectively. Furthermore, the data showed that the HRMA method was sensitive to detect 100 CFU/ml for the divIVA, alanine racemase, and vanA genes. Also, out of 49 Enterococcus spp., which were isolated by HRMA assay, 8 isolates (16.32%) of E. faecium and 18 isolates (36.73%) of E. faecalis were detected. The vanA gene was reported in 2 isolates (25%) of E. faecium and 9 isolates (50%) of E. faecalis. Conclusions This study demonstrated that using the HRMA method, we can detect E. faecium, E. faecalis, and the vanA gene with high sensitivity and specificity.
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Affiliation(s)
- Sanaz Dehbashi
- 1Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Pajoohesh junction, Hamadan, Iran
| | - Hamed Tahmasebi
- 2Department of Microbiology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Faeze Davarian
- 4School of Paramedical, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Reza Arabestani
- 1Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Pajoohesh junction, Hamadan, Iran.,5Nutritious Research Center, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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Xiong L, Sun Y, Shi L, Yan H. Characterization of antimicrobial resistance genes and class 1 integrase gene in raw meat and aquatic product, fresh vegetable and fruit, and swine manure in southern China. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lapa SA, Pavlov AS, Kuznetsova VE, Shershov VE, Spitsyn MA, Guseinov TO, Radko SP, Zasedatelev AS, Lisitsa AV, Chudinov AV. Enzymatic Preparation of Modified DNA: Study of the Kinetics by Real-Time PCR. Mol Biol 2019. [DOI: 10.1134/s0026893319030099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Handrova L, Kmet V. Antibiotic resistance and virulence factors of Escherichia coli from eagles and goshawks. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2019; 54:605-614. [PMID: 31046564 DOI: 10.1080/03601234.2019.1608103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
One of the major global problems in medicine is microbial resistance to antibiotics (antimicrobial resistance) and this has become an increasingly frequent research topic. This study focuses on antimicrobial resistance, phylogenetic and genetic characterization of Escherichia coli from wild birds: ten isolates from eagles (Aquila chrysaetos), nine from goshawks (Accipiter gentilis) and 24 from broilers in the Slovak Republic. Twenty-two strains with presence of int1 gene were selected and examined for the presence or absence of transposon gene (tn3), genes of antibiotic resistance and virulence factors. We detected sequence type (ST) in eagles ST 442 with genes iss, papC, iutA, cvaC, tsh, fyuA, iroN, kps, feoB, sitA, irp2, ireA for virulence factors and tetA, sul1, sul2, dfrA, aadA for antibiotic resistance; in goshawks ST 1011 with iss, papC, fyuA, iroN, feoB, sitA and qnrS1, tetA, sul1, sul2, dfrA, aadA, respectively. These ST types have been found in humans too and should be evaluated further for possible zoonotic potential and transfer of resistance genes from the environment.
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Affiliation(s)
- Livia Handrova
- a Centre of biosciences of the SAS , Institute of Animal Physiology , Kosice , Slovak Republic
| | - Vladimir Kmet
- a Centre of biosciences of the SAS , Institute of Animal Physiology , Kosice , Slovak Republic
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Domínguez-Zepahua M, Hernández-Arteaga S, López-Revilla R. Genotyping based on thermal denaturation of amplification products identifies species of the Mycobacterium tuberculosis complex. J Med Microbiol 2018; 67:1310-1320. [PMID: 30074475 DOI: 10.1099/jmm.0.000816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To develop a fast and inexpensive genotyping assay to identify the Mycobacterium tuberculosis complex (MTC) species most prevalent in human tuberculosis (TB), based on the thermal denaturation profiles of PCR products from mycobacterial 16S rDNA and three MTC genomic regions of difference (RD). METHODOLOGY Genotypes were determined by the presence and thermal denaturation profiles of the amplicons generated in the 'preliminary' PCR mixture (16S rDNA), followed by those of the simultaneous D1 (RD9+, RD1-) and D2 (RD4+, RD4-) PCR mixtures. The 16S rDNA profile identifies the genus Mycobacterium; the absence of any additional RD profile identifies Mycobacterium non-tuberculous (MNT) strains; additional RD4+ and RD9+ profiles without RD1- identify M. tuberculosis; an additional RD4+ profile per se identifies M. africanum; an additional RD4- profile per se identifies Mycobaterium bovis; additional RD1- and RD4- profiles identify M. bovis BCG. RESULTS Genotypes of a panel with 44 mycobacterial strains coincided in 16 MB and five non-MTC strains; in the remaining 23 MTC strains, 17 MTB and five MA concordant genotypes and one discordant MB genotype were resolved. The genotypes of 13 human and bovine MTC isolates coincided in all four MB and eight of the nine MTB isolates. CONCLUSION Sensitivity, specificity and positive and negative predictive values of the method are 100 % for the genus Mycobacterium, which resolves MB, MTB and MA genotypes. Species/genotype agreement is 97.7 % for the panel and 92.3 % for the MTC isolates. This method may be advantageously used to identify the most prevalent MTC species in humans.
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Affiliation(s)
- Mariel Domínguez-Zepahua
- 1División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa de San José 2055, 78216 San Luis Potosí, S.L.P., Mexico
| | - Socorro Hernández-Arteaga
- 2Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Carretera San Luis-Matehuala km 14.5, 78321 Soledad de Graciano Sánchez, S.L.P., Mexico
| | - Rubén López-Revilla
- 1División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa de San José 2055, 78216 San Luis Potosí, S.L.P., Mexico
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Aloisio M, Morelli M, Elicio V, Saldarelli P, Ura B, Bortot B, Severini G, Minafra A. Detection of four regulated grapevine viruses in a qualitative, single tube real-time PCR with melting curve analysis. J Virol Methods 2018; 257:42-47. [DOI: 10.1016/j.jviromet.2018.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 10/17/2022]
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Hasanpour M, Najafi A. Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli. J Microbiol Methods 2017; 137:25-29. [PMID: 28359738 DOI: 10.1016/j.mimet.2017.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 11/15/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (Tm) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains.
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Affiliation(s)
- Mojtaba Hasanpour
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Akram Najafi
- The Persian Gulf Marine Biotechnology Research Center, Bushehr University of Medical Sciences, Bushehr, Iran.
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Yang HC, Haudenshield JS, Hartman GL. Multiplex Real-time PCR Detection and Differentiation of Colletotrichum Species Infecting Soybean. PLANT DISEASE 2015; 99:1559-1568. [PMID: 30695948 DOI: 10.1094/pdis-11-14-1189-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Colletotrichum species are fungal plant pathogens of worldwide significance. Colletotrichum species were isolated from soybean with anthracnose symptoms in five states in the United States from 2009 to 2013. Among 240 isolates collected, four Colletotrichum species were initially identified by morphological and sequence analysis, including C. chlorophyti, C. incanum, C. truncatum, and Colletotrichum sp. (henceforth Glomerella glycines, the name of its sexual state). To increase diagnostic efficiency and accuracy, real-time multiplex PCR assays based on a double-stranded DNA-binding dye coupled with dissociation curve analysis were designed, using a region of the cytochrome c oxidase subunit 1 (cox1) gene to discern these four Colletotrichum species. Two sets of duplex, real-time PCR assays were established and species differentiation was based upon amplicon melting point temperatures (Tm) in the dissociation curve analysis. The Set 1 duplex assay distinguished C. chlorophyti and G. glycines, and the Set 2 duplex assay distinguished C. incanum and C. truncatum. Successful detection was achieved with as little as 1 pg DNA. The assays were especially useful for differentiating C. chlorophyti, C. incanum, and C. truncatum, which have similar morphological features. Colletotrichum gloeosporioides, another pathogen associated with soybean anthracnose, was not resolved from G. glycines by the melting curve analysis. The two duplex real-time PCR assays were used to screen more than 200 purified Colletotrichum isolates, showing that they were rapid and effective methods to detect and differentiate Colletotrichum species infecting soybean.
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Affiliation(s)
- Hui-Ching Yang
- Department of Natural Resources and Environmental Sciences
| | | | - Glen L Hartman
- USDA Agricultural Research Service, Department of Crop Sciences, and Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA
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Safdar M, Junejo Y, Arman K, Abasıyanık MF. Rapid bovine and caprine species identification in ruminant feeds by duplex real-time PCR melting curve analysis using EvaGreen fluorescence dye. Mol Biotechnol 2015; 56:770-6. [PMID: 24770990 DOI: 10.1007/s12033-014-9756-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A duplex real-time PCR assay with melting curve analysis, using the EvaGreen fluorescence dye, was developed for rapid and reliable identification of bovine and caprine in ruminant feeds. The method merges the use of bovine (Bos taurus) and caprine (Capra hircus) specific primers that amplify small fragments (bovine 96 bp and caprine 142 bp) of the mitochondrial 16S rRNA and 12S rRNA genes, respectively. DNA was isolated from heat-treated meats (133 °C/3 bar for 20 min) mixtures of bovine and caprine and was used to optimize the assay. Gene products of caprine and bovine produced two distinct melting peaks simultaneously at 82 and 86.8 °C, respectively. Duplex analysis of the reference samples showed that the detection limit of the assay was 0.003 % for bovine and 0.005 % for caprine species. The aim of this study was to develop a duplex real-time PCR assay followed by a melt curve step for sensitive, rapid, specific, and cost-effective detection of bovine and caprine species based on the amplicon melting peak in ruminant feeds to prevent Transmissible Spongiform Encephalopathies.
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Affiliation(s)
- M Safdar
- Department of Medical Biology and Genetics, University of Gaziantep, Gaziantep, Turkey,
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Rapid Genotyping of Shigella sonnei by Use of Multiplex High-Resolution Melting. J Clin Microbiol 2015; 53:2389-91. [PMID: 25926492 DOI: 10.1128/jcm.00874-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Development and validation of fast duplex real-time PCR assays based on SYBER Green florescence for detection of bovine and poultry origins in feedstuffs. Food Chem 2015; 173:660-4. [DOI: 10.1016/j.foodchem.2014.10.088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 06/15/2014] [Accepted: 10/17/2014] [Indexed: 11/15/2022]
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Singh P, Mustapha A. Development of a real-time PCR melt curve assay for simultaneous detection of virulent and antibiotic resistant Salmonella. Food Microbiol 2014; 44:6-14. [DOI: 10.1016/j.fm.2014.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 04/04/2014] [Accepted: 04/25/2014] [Indexed: 12/11/2022]
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Rao P, Wu H, Jiang Y, Opriessnig T, Zheng X, Mo Y, Yang Z. Development of an EvaGreen-based multiplex real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of six viral pathogens of porcine reproductive and respiratory disorder. J Virol Methods 2014; 208:56-62. [DOI: 10.1016/j.jviromet.2014.06.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/17/2014] [Accepted: 06/20/2014] [Indexed: 11/27/2022]
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Hu Z, Zhu C, Chang H, Guo W, Liu D, Xiang W, Wang X. Development of a single-tube duplex EvaGreen real-time PCR for the detection and identification of EHV-1 and EHV-4. Appl Microbiol Biotechnol 2014; 98:4179-86. [PMID: 24615388 DOI: 10.1007/s00253-014-5626-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/15/2014] [Accepted: 02/17/2014] [Indexed: 12/24/2022]
Abstract
The objective of this study was to develop a novel EvaGreen (EG) based real-time PCR technique for the simultaneous detection of Equine herpesvirus 1 (EHV-1) and Equine herpesvirus 4 (EHV-4) genomes from equine nasal swabs. Viral genomes were identified based on their specific melting temperatures (T m), which are 88.0 and 84.4 °C for EHV-1 and EHV-4, respectively. The detection limitation of this method was 50 copies/μl or 0.15 pg/μl for EHV-1 and 5 copies/μl or 2.5 fg/μl for EHV-4. This assay was 50-1,000 times more sensitive than the SYBR Green (SG)-based assay using the same primer pairs and as sensitive as the TaqMan-MGB probe-based assay. The validity of the real-time PCR assays was confirmed by testing 13 clinical samples. When all results of the EG, SG, and TaqMan probe-based singleplex and duplex real-time PCRs were considered together, a total of 84.6 % (11/13) horses and donkeys were positive for at least one virus. EHV-1 and EHV-4 coexisted in 81.8 % (9/11) horses. Overall, we report that the EvaGreen duplex real-time PCR is an economical and alternative diagnostic method for the rapid differentiation of EHV-1 and EHV-4 in nasal swabs.
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Affiliation(s)
- Zhe Hu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agriculture Sciences, 427 Maduan Street, Harbin, 150001, People's Republic of China
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Singh P, Mustapha A. Multiplex TaqMan® detection of pathogenic and multi-drug resistant Salmonella. Int J Food Microbiol 2013; 166:213-8. [PMID: 23973830 DOI: 10.1016/j.ijfoodmicro.2013.07.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 06/26/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
Overuse of antibiotics in the medical and animal industries is one of the major causes for the development of multi-drug-resistant (MDR) food pathogens that are often difficult to treat. In the past few years, higher incidences of outbreaks caused by MDR Salmonella have been increasingly documented. The objective of this study was to develop a rapid multiplex real-time polymerase chain reaction (PCR) assay for simultaneous detection of pathogenic and MDR Salmonella spp. A multiplex TaqMan®real-time PCR was designed by targeting the invasin virulence gene (invA), and four commonly found antibiotic resistance genes, viz. ampicillin, chloramphenicol, streptomycin and tetracycline. To avoid false negative results and to increase the reliability of the assay, an internal amplification control (IAC) was added which was detected using a locked nucleic acid (LNA) probe. In serially diluted (5 ng-50 fg) DNA samples, the assay was able to detect 100 genomic equivalents of Salmonella, while in a multiplex format, the sensitivity was 1000 genomic equivalents. The assay performed equally well on artificially contaminated samples of beef trim, ground beef of different fat contents (73:27, 80:20, 85:15 and 93:7), chicken rinse, ground chicken, ground turkey, egg, spinach and tomato. While the detection limit for un-enriched inoculated food samples was 10(4) CFU/g, this was improved to 10 CFU/g after a 12-h enrichment in buffered peptone water, with 100% reproducibility. The multiplex real-time assay developed in this study can be used as a valuable tool to detect MDR virulent Salmonella, thus enhancing the safety of food.
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Affiliation(s)
- Prashant Singh
- Food Science Program, University of Missouri, Columbia, MO 65211, USA
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Marie A, Boissière A, Tsapi MT, Poinsignon A, Awono-Ambéné PH, Morlais I, Remoue F, Cornelie S. Evaluation of a real-time quantitative PCR to measure the wild Plasmodium falciparum infectivity rate in salivary glands of Anopheles gambiae. Malar J 2013; 12:224. [PMID: 23819831 PMCID: PMC3707787 DOI: 10.1186/1475-2875-12-224] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/04/2013] [Indexed: 12/15/2022] Open
Abstract
Background Evaluation of malaria sporozoite rates in the salivary glands of Anopheles gambiae is essential for estimating the number of infective mosquitoes, and consequently, the entomological inoculation rate (EIR). EIR is a key indicator for evaluating the risk of malaria transmission. Although the enzyme-linked immunosorbent assay specific for detecting the circumsporozoite protein (CSP-ELISA) is routinely used in the field, it presents several limitations. A multiplex PCR can also be used to detect the four species of Plasmodium in salivary glands. The aim of this study was to evaluate the efficacy of a real-time quantitative PCR in detecting and quantifying wild Plasmodium falciparum in the salivary glands of An. gambiae. Methods Anopheles gambiae (n=364) were experimentally infected with blood from P. falciparum gametocyte carriers, and P. falciparum in the sporozoite stage were detected in salivary glands by using a real-time quantitative PCR (qPCR) assay. The sensitivity and specificity of this qPCR were compared with the multiplex PCR applied from the Padley method. CSP-ELISA was also performed on carcasses of the same mosquitoes. Results The prevalence of P. falciparum and the intensity of infection were evaluated using qPCR. This method had a limit of detection of six sporozoites per μL based on standard curves. The number of P. falciparum genomes in the salivary gland samples reached 9,262 parasites/μL (mean: 254.5; 95% CI: 163.5-345.6). The qPCR showed a similar sensitivity (100%) and a high specificity (60%) compared to the multiplex PCR. The agreement between the two methods was “substantial” (κ = 0.63, P <0.05). The number of P. falciparum-positive mosquitoes evaluated with the qPCR (76%), multiplex PCR (59%), and CSP-ELISA (83%) was significantly different (P <0.005). Conclusions The qPCR assay can be used to detect P. falciparum in salivary glands of An. gambiae. The qPCR is highly sensitive and is more specific than multiplex PCR, allowing an accurate measure of infective An. gambiae. The results also showed that the CSP-ELISA overestimates the sporozoite rate, detecting sporozoites in the haemolymph in addition to the salivary glands.
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Affiliation(s)
- Alexandra Marie
- Laboratoire MIVEGEC (UMR IRD 224 CNRS 5290 UM1-UM2), 911 Av, Agropolis, 34394 Montpellier Cedex 5, France.
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Sang F, Zhang Z, Xu Z, Ju X, Wang H, Zhang S, Guo C. CdTe Quantum Dots Enhance Feasibility of EvaGreen-Based Real-Time PCR with Decent Amplification Fidelity. Mol Biotechnol 2013; 54:969-76. [DOI: 10.1007/s12033-013-9650-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cheng J, Jiang Y, Rao P, Wu H, Dong Q, Wu Z, Ding X, Guo J. Development of a single-tube multiplex real-time PCR for detection and identification of five pathogenic targets by using melting-curve analysis with EvaGreen. Arch Virol 2012; 158:379-86. [PMID: 23053522 DOI: 10.1007/s00705-012-1493-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/21/2012] [Indexed: 12/18/2022]
Abstract
SYBR Green I (SG) is widely used in real-time PCR applications as an intercalating dye. Preferential binding of SG during PCR and inhibition of PCR often result in failure to detect multiple amplicons in multiplex reactions. In the present study, a novel single-tube, multiplex real-time PCR with EvaGreen dye (EG) was developed and evaluated for simultaneous detection of pathogenic targets by using five potato viruses as models. The PCR products obtained using five sets of specific primers were analyzed by melting curve analysis. The assay could specifically detect and differentiate the five potato viruses by producing a distinct peak for each amplification product and exhibited a high reproducibility with coefficients of variation from 0.01 to 0.25 %. Detection sensitivity of the assay ranged from 100 to 500 copies/μL for each virus. The results of this study demonstrate that multiplex real-time PCR and melting-curve analysis with EG is a sensitive, specific and inexpensive method for simultaneous detection of multiple pathogens.
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Affiliation(s)
- Juhui Cheng
- College of Life Sciences, Zhejiang Sci-Tech University, 2nd street, Xiasha, Hangzhou, 310018, China
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Gurtler V, Grando D, Mayall BC, Wang J, Ghaly-Derias S. A novel method for simultaneous Enterococcus species identification/typing and van genotyping by high resolution melt analysis. J Microbiol Methods 2012; 90:167-81. [PMID: 22658426 DOI: 10.1016/j.mimet.2012.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/30/2012] [Accepted: 05/04/2012] [Indexed: 11/19/2022]
Abstract
In order to develop a typing and identification method for van gene containing Enterococcus faecium, two multiplex PCR reactions were developed for use in HRM-PCR (High Resolution Melt-PCR): (i) vanA, vanB, vanC, vanC23 to detect van genes from different Enterococcus species; (ii) ISR (intergenic spacer region between the 16S and 23S rRNA genes) to detect all Enterococcus species and obtain species and isolate specific HRM curves. To test and validate the method three groups of isolates were tested: (i) 1672 Enterococcus species isolates from January 2009 to December 2009; (ii) 71 isolates previously identified and typed by PFGE (pulsed-field gel electrophoresis) and MLST (multi-locus sequence typing); and (iii) 18 of the isolates from (i) for which ISR sequencing was done. As well as successfully identifying 2 common genotypes by HRM from the Austin Hospital clinical isolates, this study analysed the sequences of all the vanB genes deposited in GenBank and developed a numerical classification scheme for the standardised naming of these vanB genotypes. The identification of Enterococcus faecalis from E. faecium was reliable and stable using ISR PCR. The typing of E. faecium by ISR PCR: (i) detected two variable peaks corresponding to different copy numbers of insertion sequences I and II corresponding to peak I and II respectively; (ii) produced 7 melt profiles for E. faecium with variable copy numbers of sequences I and II; (iii) demonstrated stability and instability of peak heights with equal frequency within the patient sample (36.4±4.5 days and 38.6±5.8 days respectively for 192 patients); (iv) detected ISR-HRM types with as much discrimination as PFGE and more than MLST; and (v) detected ISR-HRM types that differentiated some isolates that were identical by PFGE and MLST. In conjunction with the rapid and accurate van genotyping method described here, this ISR-HRM typing and identification method can be used as a stable identification and typing method with predictable instability based on recombination and concerted evolution of the rrn operon that will complement existing typing methods.
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Affiliation(s)
- Volker Gurtler
- Department of Pathology, Austin Hospital, Heidelberg 3084, Australia.
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