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Yaghoobi A, Abiri R, Alvandi A, Arkan E, Jalalvand AR. A novel electrochemical biosensor as an efficient electronic device for impedimetric and amperometric quantification of the pneumococcus. SENSING AND BIO-SENSING RESEARCH 2022. [DOI: 10.1016/j.sbsr.2022.100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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A novel method of multiple nucleic acid detection: Real-time RT-PCR coupled with probe-melting curve analysis. Anal Biochem 2017; 537:50-55. [DOI: 10.1016/j.ab.2017.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 08/14/2017] [Accepted: 08/31/2017] [Indexed: 11/20/2022]
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Iraola G, Pérez R, Betancor L, Marandino A, Morsella C, Méndez A, Paolicchi F, Piccirillo A, Tomás G, Velilla A, Calleros L. A novel real-time PCR assay for quantitative detection of Campylobacter fetus based on ribosomal sequences. BMC Vet Res 2016; 12:286. [PMID: 27978826 PMCID: PMC5159996 DOI: 10.1186/s12917-016-0913-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 12/06/2016] [Indexed: 12/20/2022] Open
Abstract
Background Campylobacter fetus is a pathogen of major concern for animal and human health. The species shows a great intraspecific variation, with three subspecies: C. fetus subsp. fetus, C. fetus subsp. venerealis, and C. fetus subsp. testudinum. Campylobacter fetus fetus affects a broad range of hosts and induces abortion in sheep and cows. Campylobacter fetus venerealis is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus testudinum has been proposed recently based on genetically divergent strains isolated from reptiles and humans. Both C. fetus fetus and C. fetus testudinum are opportunistic pathogens for immune-compromised humans. Biochemical tests remain as the gold standard for identifying C. fetus but the fastidious growing requirements and the lack of reliability and reproducibility of some biochemical tests motivated the development of molecular diagnostic tools. These methods have been successfully tested on bovine isolates but fail to detect some genetically divergent strains isolated from other hosts. The aim of the present study was to develop a highly specific molecular assay to identify and quantify C. fetus strains. Results We developed a highly sensitive real-time PCR assay that targets a unique region of the 16S rRNA gene. This assay successfully detected all C. fetus strains, including those that were negative for the cstA gene-based assay used as a standard for molecular C. fetus identification. The assay showed high specificity and absence of cross-reactivity with other bacterial species. The analytical testing of the assay was determined using a standard curve. The assay demonstrated a wide dynamic range between 102 and 107 genome copies per reaction, and a good reproducibility with small intra- and inter-assay variability. Conclusions The possibility to characterize samples in a rapid, sensitive and reproducible way makes this assay a good option to establish a new standard in molecular identification and quantification of C. fetus species. Electronic supplementary material The online version of this article (doi:10.1186/s12917-016-0913-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregorio Iraola
- Sección Genética Evolutiva, Facultad de Ciencias, Iguá 4225, Montevideo, 11400, Uruguay.,Unidad de Bioinformática, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Iguá 4225, Montevideo, 11400, Uruguay
| | - Laura Betancor
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Facultad de Ciencias, Iguá 4225, Montevideo, 11400, Uruguay
| | - Claudia Morsella
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Alejandra Méndez
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Fernando Paolicchi
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Alessandra Piccirillo
- Dipartimento di Biomedicina Comparata e Alimentazione, Università degli Studi di Padova, Padova, Italy
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Facultad de Ciencias, Iguá 4225, Montevideo, 11400, Uruguay
| | - Alejandra Velilla
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Iguá 4225, Montevideo, 11400, Uruguay.
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Onseedaeng S, Ratthawongjirakul P. Rapid Detection of Genomic Mutations in gyrA and parC Genes of Escherichia coli by Multiplex Allele Specific Polymerase Chain Reaction. J Clin Lab Anal 2016; 30:947-955. [PMID: 27075845 DOI: 10.1002/jcla.21961] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/11/2015] [Accepted: 01/26/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Fluoroquinolone (FR) resistant Escherichia coli infection has become a global problem. The FR resistance usually occurs mainly due to specific point of mutations within the quinolone resistance-determining regions (QRDRs) at the gyrA codon of Ser83 and Asp87 and the parC codon of Ser80 and Glu84. Here, we appraised type and frequency of the QRDR mutations in FR-resistant E. coli isolates, and developed multiplex allele specific PCR (MAS-PCR) for the detection of "hot spot" mutations. METHODS A total of 111 ciprofloxacin-resistant E. coli from Ramathibodi Hospital in Bangkok, Thailand, were performed Minimum Inhibitory Concentration (MIC) by Etest® and investigated for gyrA and parC genes' mutations by MAS-PCR. Sensitivity and specificity of MAS-PCR were compared to the sequencing method's. RESULTS Ninety-nine of 111 (89.19%) E. coli isolates had mutation at least one point in the QRDRs. Six usual amino acid substitutes were reported, including Ser83-Lue, Asp87-Asn, Asp87-Tyr, Ser80-Ile, Glu84-Gly, and Glu84-Val. MAS-PCR detected codons 83 and 87 in gyrA and codons 80 and 84 in parC mutations, yielding 96.97%, 100%, 100%, and 93.33% sensitivity, respectively, and 100%, 100%, 100%, and 98.48% specificity, respectively. CONCLUSION MAS-PCR may be used for rapid detection of FR resistance in routine laboratory as well as in epidemiology study.
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Affiliation(s)
- Sukanlayanee Onseedaeng
- Molecular Science of Medical Microbiology and Immunology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Panan Ratthawongjirakul
- Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
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Li F, Yu Z, Xu Y, Ma H, Zhang G, Song Y, Yan H, He X. Using the synergism strategy for highly sensitive and specific electrochemical sensing of Streptococcus pneumoniae Lyt-1 gene sequence. Anal Chim Acta 2015; 886:175-81. [DOI: 10.1016/j.aca.2015.05.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
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Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin Microbiol Rev 2014. [PMID: 24696436 DOI: 10.1128/cmr.00101-13)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Streptococcus pyogenes, also known as group A Streptococcus (GAS), causes mild human infections such as pharyngitis and impetigo and serious infections such as necrotizing fasciitis and streptococcal toxic shock syndrome. Furthermore, repeated GAS infections may trigger autoimmune diseases, including acute poststreptococcal glomerulonephritis, acute rheumatic fever, and rheumatic heart disease. Combined, these diseases account for over half a million deaths per year globally. Genomic and molecular analyses have now characterized a large number of GAS virulence determinants, many of which exhibit overlap and redundancy in the processes of adhesion and colonization, innate immune resistance, and the capacity to facilitate tissue barrier degradation and spread within the human host. This improved understanding of the contribution of individual virulence determinants to the disease process has led to the formulation of models of GAS disease progression, which may lead to better treatment and intervention strategies. While GAS remains sensitive to all penicillins and cephalosporins, rising resistance to other antibiotics used in disease treatment is an increasing worldwide concern. Several GAS vaccine formulations that elicit protective immunity in animal models have shown promise in nonhuman primate and early-stage human trials. The development of a safe and efficacious commercial human vaccine for the prophylaxis of GAS disease remains a high priority.
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Walker MJ, Barnett TC, McArthur JD, Cole JN, Gillen CM, Henningham A, Sriprakash KS, Sanderson-Smith ML, Nizet V. Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin Microbiol Rev 2014; 27:264-301. [PMID: 24696436 PMCID: PMC3993104 DOI: 10.1128/cmr.00101-13] [Citation(s) in RCA: 556] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pyogenes, also known as group A Streptococcus (GAS), causes mild human infections such as pharyngitis and impetigo and serious infections such as necrotizing fasciitis and streptococcal toxic shock syndrome. Furthermore, repeated GAS infections may trigger autoimmune diseases, including acute poststreptococcal glomerulonephritis, acute rheumatic fever, and rheumatic heart disease. Combined, these diseases account for over half a million deaths per year globally. Genomic and molecular analyses have now characterized a large number of GAS virulence determinants, many of which exhibit overlap and redundancy in the processes of adhesion and colonization, innate immune resistance, and the capacity to facilitate tissue barrier degradation and spread within the human host. This improved understanding of the contribution of individual virulence determinants to the disease process has led to the formulation of models of GAS disease progression, which may lead to better treatment and intervention strategies. While GAS remains sensitive to all penicillins and cephalosporins, rising resistance to other antibiotics used in disease treatment is an increasing worldwide concern. Several GAS vaccine formulations that elicit protective immunity in animal models have shown promise in nonhuman primate and early-stage human trials. The development of a safe and efficacious commercial human vaccine for the prophylaxis of GAS disease remains a high priority.
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Affiliation(s)
- Mark J. Walker
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Timothy C. Barnett
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Jason D. McArthur
- School of Biological Sciences and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
| | - Jason N. Cole
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Christine M. Gillen
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Anna Henningham
- School of Chemistry and Molecular Biosciences and the Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - K. S. Sriprakash
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
| | - Martina L. Sanderson-Smith
- School of Biological Sciences and Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
| | - Victor Nizet
- Department of Pediatrics and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California, USA
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Kim J, Jeon S, Kim H, Park M, Kim S, Kim S. Multiplex Real-Time Polymerase Chain Reaction-Based Method for the Rapid Detection of gyrA and parC Mutations in Quinolone-Resistant Escherichia coli and Shigella spp. Osong Public Health Res Perspect 2013; 3:113-7. [PMID: 24159500 PMCID: PMC3747644 DOI: 10.1016/j.phrp.2012.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 01/10/2012] [Accepted: 01/16/2012] [Indexed: 11/26/2022] Open
Abstract
Two real-time polymerase chain reaction assays were developed to detect mutations in codons 83 and 87 in gyrA and in codons 80 and 91 in parC, the main sites that causes quinolone resistance in pathogenic Escherichia coli and Shigella spp. isolates. These assays can be employed as a useful method for controlling infections caused by quinolone-resistant E coli and Shigella isolates.
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Affiliation(s)
- Junyoung Kim
- Division of Enteric Bacterial Infections, Korea National Institute of Health, Osong, Korea
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Valera MJ, Torija MJ, Mas A, Mateo E. Acetobacter malorum and Acetobacter cerevisiae identification and quantification by Real-Time PCR with TaqMan-MGB probes. Food Microbiol 2013; 36:30-9. [PMID: 23764217 DOI: 10.1016/j.fm.2013.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/06/2013] [Accepted: 03/27/2013] [Indexed: 10/27/2022]
Abstract
The identification and quantification of Acetobacter malorum and Acetobacter cerevisiae in wine and vinegar were performed using the Real-Time PCR (RT-PCR) with two TaqMan-MGB probes designed to amplify the internal transcribed spacer (ITS) region between the 16S-23S rRNA genes. The primers and probes were highly specific, with a detection limit of 10² cells/ml for both species, and the efficiency of the technique was >80%. The RT-PCR technique with these two new TaqMan-MGB probes, together with the five (Acetobacter aceti, Acetobacter pasteurianus, Gluconobacter oxydans, Gluconacetobacter hansenii and Gluconacetobacter europaeus) that are already available (Torija et al., 2010), were validated on known concentrations of Acetic Acid Bacteria (AAB) grown in glucose medium (GY) and in inoculated matrices of wine and vinegar. Furthermore, this technique was applied to evaluate the AAB population in real wine samples collected in the Canary Islands. PCR enrichment performed prior to RT-PCR increased the accuracy of quantification and produced results similar to those detected with SYBR-Green. In real wine samples, the total AAB enumeration ranged from 9 × 10² to 10⁶ cells/ml, and the seven AAB species tested were detected in more than one sample. However, AAB recovery on plates was poor; the isolates obtained on plates were A. malorum, G. oxydans, A. cerevisiae and A. pasteurianus species. RT-PCR with TaqMan-MGB probes is an accurate, specific and fast method for the identification and quantification of AAB species commonly found in wine and vinegar.
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Affiliation(s)
- Maria José Valera
- Biotecnologia Enológica, Dept. Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, C/ Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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Torija M, Mateo E, Guillamón J, Mas A. Identification and quantification of acetic acid bacteria in wine and vinegar by TaqMan–MGB probes. Food Microbiol 2010; 27:257-65. [DOI: 10.1016/j.fm.2009.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/28/2009] [Accepted: 10/05/2009] [Indexed: 11/29/2022]
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