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Alvaro A, Piazza A, Papaleo S, Perini M, Pasala AR, Panelli S, Nardi T, Nodari R, Sterzi L, Pagani C, Merla C, Castelli D, Olivieri E, Bracco S, Ferrando ML, Saluzzo F, Rimoldi SG, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Comandatore F. Cultivation and sequencing-free protocol for Serratia marcescens detection and typing. iScience 2024; 27:109402. [PMID: 38510115 PMCID: PMC10952028 DOI: 10.1016/j.isci.2024.109402] [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: 09/25/2023] [Revised: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Serratia marcescens is an opportunistic pathogen that survives in inhospitable environments causing large outbreaks, particularly in neonatal intensive care units (NICUs). Genomic studies revealed that most S. marcescens nosocomial infections are caused by a specific clone (here "Infectious clone"). Whole genome sequencing (WGS) is the only portable method able to identify this clone, but it requires days to obtain results. We present a cultivation-free hypervariable-locus melting typing (HLMT) protocol for the fast detection and typing of S. marcescens, with 100% detection capability on mixed samples and a limit of detection that can reach the 10 genome copies. The protocol was able to identify the S. marcescens infectious clone with 97% specificity and 96% sensitivity when compared to WGS, yielding typing results portable among laboratories. The protocol is a cost and time saving method for S. marcescens detection and typing for large environmental/clinical surveillance screenings, also in low-middle income countries.
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Affiliation(s)
- Alessandro Alvaro
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Biosciences and Pediatric Clinical Research Center "Romeo Ed Enrica Invernizzi", University of Milan, 20133 Milan, Italy
| | - Aurora Piazza
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia 27100, Italy
| | - Stella Papaleo
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Matteo Perini
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Ajay Ratan Pasala
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Biochemistry, Microbiology and Immunology Department, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Innovation, Canadian Blood Services, Ottawa, ON K1G 4J5, Canada
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Tiago Nardi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Riccardo Nodari
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Lodovico Sterzi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Cristina Pagani
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, 20157 Milan, Italy
| | - Cristina Merla
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100 Pavia, Italy
| | - Daniele Castelli
- Microbiology Unit, Fondazione IRCCS San Gerardo, 20900 Monza, Italy
| | - Emanuela Olivieri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 27100 Pavia, Italy
| | - Silvia Bracco
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Maria Laura Ferrando
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sara Giordana Rimoldi
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, 20157 Milan, Italy
| | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100 Pavia, Italy
| | | | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 27100 Pavia, Italy
| | - Claudio Farina
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Paediatrics, Children’s Hospital "V. Buzzi", 20154 Milano, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
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2
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Fakhri O, Hartley CA, Devlin JM, Browning GF, Noormohammadi AH, Lee SW. Development and application of high-resolution melting analysis for the classification of infectious laryngotracheitis virus strains and detection of recombinant progeny. Arch Virol 2018; 164:427-438. [PMID: 30421085 PMCID: PMC6373279 DOI: 10.1007/s00705-018-4086-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022]
Abstract
Live attenuated vaccines against infectious laryngotracheitis virus (ILTV) are widely used in the poultry industry to control disease and help prevent economic losses. Molecular epidemiological studies of currently circulating strains of ILTV within poultry flocks in Australia have demonstrated the presence of highly virulent viruses generated by genomic recombination events between vaccine strains. In this study, high-resolution melting (HRM) analysis was used to develop a tool to classify ILTV isolates and to investigate ILTV recombination. The assay was applied to plaque-purified progeny viruses generated after co-infection of chicken embryo kidney (CEK) monolayers with the A20 and Serva ILT vaccine strains and also to viruses isolated from field samples. The results showed that the HRM analysis is a suitable tool for the classification of ILTV isolates and can be used to detect recombination between ILTV vaccine strains in vitro. This method can be used to classify a broad range of ILTV strains to facilitate the classification and genotyping of ILTV and help to further understand recombination in these viruses.
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Affiliation(s)
- Omid Fakhri
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, Australia
| | - Sang-Won Lee
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
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3
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Angione SL, Croote D, Leung JW, Mermel LA, Tripathi A. Single fluorophore melting curve analysis for detection of hypervirulent Clostridium difficile. J Med Microbiol 2015; 65:62-70. [PMID: 26516039 DOI: 10.1099/jmm.0.000199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study demonstrates a novel detection assay able to identify and subtype strains of Clostridium difficile. Primers carefully designed for melting curve analysis amplify DNA from three C. difficile genes, tcdB, tcdC and cdtB, during quantitative (q)PCR. The tcdB gene allows for confirmation of organism presence, whilst the tcdC and cdtB genes allow for differentiation of virulence status, as deletions in the tcdC gene and the concurrent presence of the cdtB gene, which produces binary toxin, are associated with hypervirulence. Following qPCR, subtyping is then achieved by automated, inline melting curve analysis using only a single intercalating dye and verified by microchip electrophoresis. This assay represents a novel means of distinguishing between toxigenic and hypervirulent C. difficile strains NAP1/027/BI and 078 ribotype, which are highly prevalent hypervirulent strains in humans. This methodology can help rapidly detect and identify C. difficile strains that impose a significant health and economic burden in hospitals and other healthcare settings.
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Affiliation(s)
- Stephanie L Angione
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Derek Croote
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Joshua W Leung
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Leonard A Mermel
- Division of Infectious Diseases, Department of Medicine, Rhode Island Hospital, , Providence, RI, USA.,Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
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Mercante JW, Winchell JM. Current and emerging Legionella diagnostics for laboratory and outbreak investigations. Clin Microbiol Rev 2015; 28:95-133. [PMID: 25567224 PMCID: PMC4284297 DOI: 10.1128/cmr.00029-14] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Legionnaires' disease (LD) is an often severe and potentially fatal form of bacterial pneumonia caused by an extensive list of Legionella species. These ubiquitous freshwater and soil inhabitants cause human respiratory disease when amplified in man-made water or cooling systems and their aerosols expose a susceptible population. Treatment of sporadic cases and rapid control of LD outbreaks benefit from swift diagnosis in concert with discriminatory bacterial typing for immediate epidemiological responses. Traditional culture and serology were instrumental in describing disease incidence early in its history; currently, diagnosis of LD relies almost solely on the urinary antigen test, which captures only the dominant species and serogroup, Legionella pneumophila serogroup 1 (Lp1). This has created a diagnostic "blind spot" for LD caused by non-Lp1 strains. This review focuses on historic, current, and emerging technologies that hold promise for increasing LD diagnostic efficiency and detection rates as part of a coherent testing regimen. The importance of cooperation between epidemiologists and laboratorians for a rapid outbreak response is also illustrated in field investigations conducted by the CDC with state and local authorities. Finally, challenges facing health care professionals, building managers, and the public health community in combating LD are highlighted, and potential solutions are discussed.
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Affiliation(s)
- Jeffrey W Mercante
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Monteiro ADA, Pires RN, Persson S, Rodrigues Filho EM, Pasqualotto AC. A search for Clostridium difficile ribotypes 027 and 078 in Brazil. Braz J Infect Dis 2014; 18:672-4. [PMID: 25307680 PMCID: PMC9425211 DOI: 10.1016/j.bjid.2014.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/21/2014] [Indexed: 11/29/2022] Open
Abstract
Toxigenic strains of Clostridium difficile may be disseminating. Here we prospectively screened patients with nosocomial diarrhoea in two hospitals in Brazil. To identify C. difficile polymerase chain reaction ribotypes 027/078 strains, we used high resolution melting and multiplex polymerase chain reaction. Among 116 screened patients, 11 were positive for C. difficile. The polymerase chain reaction ribotypes 027/078 strains were not identified in this study.
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Affiliation(s)
| | - Renata Neto Pires
- PPG Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil; Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, RS, Brazil
| | | | | | - Alessandro Comarú Pasqualotto
- PPG Patologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil; Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, RS, Brazil.
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6
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Suin V, Nazé F, Francart A, Lamoral S, De Craeye S, Kalai M, Van Gucht S. A two-step lyssavirus real-time polymerase chain reaction using degenerate primers with superior sensitivity to the fluorescent antigen test. BIOMED RESEARCH INTERNATIONAL 2014; 2014:256175. [PMID: 24822188 PMCID: PMC4009295 DOI: 10.1155/2014/256175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/15/2014] [Accepted: 03/15/2014] [Indexed: 12/25/2022]
Abstract
A generic two-step lyssavirus real-time reverse transcriptase polymerase chain reaction (qRT-PCR), based on a nested PCR strategy, was validated for the detection of different lyssavirus species. Primers with 17 to 30% of degenerate bases were used in both consecutive steps. The assay could accurately detect RABV, LBV, MOKV, DUVV, EBLV-1, EBLV-2, and ABLV. In silico sequence alignment showed a functional match with the remaining lyssavirus species. The diagnostic specificity was 100% and the sensitivity proved to be superior to that of the fluorescent antigen test. The limit of detection was ≤ 1 50% tissue culture infectious dose. The related vesicular stomatitis virus was not recognized, confirming the selectivity for lyssaviruses. The assay was applied to follow the evolution of rabies virus infection in the brain of mice from 0 to 10 days after intranasal inoculation. The obtained RNA curve corresponded well with the curves obtained by a one-step monospecific RABV-qRT-PCR, the fluorescent antigen test, and virus titration. Despite the presence of degenerate bases, the assay proved to be highly sensitive, specific, and reproducible.
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Affiliation(s)
- Vanessa Suin
- National Reference Centre of Rabies, Viral Diseases, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Engeland Street 642, 1180 Brussels, Belgium
| | - Florence Nazé
- National Reference Centre of Rabies, Viral Diseases, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Engeland Street 642, 1180 Brussels, Belgium
| | - Aurélie Francart
- National Reference Centre of Rabies, Viral Diseases, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Engeland Street 642, 1180 Brussels, Belgium
| | - Sophie Lamoral
- National Reference Centre of Rabies, Viral Diseases, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Engeland Street 642, 1180 Brussels, Belgium
| | - Stéphane De Craeye
- Toxoplasma Laboratory, Food-borne Pathogens, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Engeland Street 642, 1180 Brussels, Belgium
| | - Michael Kalai
- National Reference Centre of Rabies, Viral Diseases, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Engeland Street 642, 1180 Brussels, Belgium
| | - Steven Van Gucht
- National Reference Centre of Rabies, Viral Diseases, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Engeland Street 642, 1180 Brussels, Belgium
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Gürtler V, Grando D. Reprint of New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes. METHODS IN MICROBIOLOGY 2013; 95:425-40. [PMID: 24050948 DOI: 10.1016/j.mimet.2013.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/24/2022]
Abstract
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This has increased awareness for the need to track outbreaks and PCR-ribotyping has found widespread use to elucidate epidemiologically linked isolates. PCR-ribotyping uses conserved regions of the 16S rRNA gene and 23S rRNA gene as primer binding sites to produce varying PCR products due to the intergenic spacer (ITS1) regions of the multiple operons. With the explosion of whole genome sequence data it became possible to analyse the start of the 23S rRNA gene for a more accurate selection of regions closer to the end of the ITS1. However the following questions must still be asked: (i) Does the chromosomal organisation of the rrn operon vary between C. difficile strains? and (ii) just how conserved are the primer binding regions? Eight published C. difficile genomes have been aligned to produce a detailed database of indels of the ITS1's from the rrn operon sets. An iPad Filemaker Go App has been constructed and named RiboTyping (RT). It contains detail such as sequences, ribotypes, strain numbers, GenBank numbers and genome position numbers. Access to various levels of the database is provided so that details can be printed. There are three main regions of the rrn operon that have been analysed by the database and related to each other by strain, ribotype and operon: (1) 16S gene (2) ITS1 indels (3) 23S gene. This has enabled direct intra- and inter-genomic comparisons at the strain, ribotype and operon (allele) levels in each of the three genomic regions. This is the first time that such an analysis has been done. By using the RT App with search criteria it will be possible to select probe combinations for specific strains/ribotypes/rrn operons for experiments to do with diagnostics, typing and recombination of operons. Many more incomplete C. difficile whole genome sequencing projects are recorded in GenBank as underway and the rrn operon information from these can also be added to the RT App when available. The RT App will help simplify probe selection because of the complexity of the ITS1 in C. difficile even in a single genome and because other allele-specific regions (16S and 23S genes) of variability can be relationally compared to design extra probes to increase sensitivity.
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Affiliation(s)
- Volker Gürtler
- School of Applied Sciences, Building 223, Level 1, Bundoora Campus RMIT University, PO Box 71, Bundoora 3083, Australia.
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8
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Pallis A, Jazayeri J, Ward P, Dimovski K, Svobodova S. Rapid detection of Clostridium difficile toxins from stool samples using real-time multiplex PCR. J Med Microbiol 2013; 62:1350-1356. [DOI: 10.1099/jmm.0.058339-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In this study, a total of 650 stool samples were tested to show that our method is capable of detecting four Clostridium difficile genes; tcdA, tcdB, encoding toxin A (TcdA) and toxin B (TcdB), and the binary toxin C. difficile transferase genes (cdtA and/or cdtB) encoding CDT toxin. Besides detecting the targeted C. difficile genes, our method can be used to detect the presence of any inhibitory components in the PCR. This assay, combined with a selective culture medium, such as the chromID™ C. difficile, can be applied directly for screening C. difficile-associated disease. The PCR-based assay developed here is rapid (4 h per 21 stool samples) and accurate in diagnosing C. difficile infection, 100 % assay sensitivity and negative predictive value (NPV) were obtained. However, the assay specificity of 99.1 % and positive predictive value (PPV) of 94.9 % were slightly lower than the optimal value of 100 %. The assay protocol outlined here can be used as a rapid screening tool to assist infection control units and in managing infected patients by reducing the number of patients requiring isolation and extended hospitalization. Rapid detection can prevent unnecessary antibiotic therapy and potentially reduce the spread of infection by emerging hypervirulent C. difficile strains.
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Affiliation(s)
- Ann Pallis
- Molecular Diagnostic and Microbiology Laboratory, Austin Pathology, Melbourne, VIC 3084, Australia
| | - Jalal Jazayeri
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Peter Ward
- Molecular Diagnostic and Microbiology Laboratory, Austin Pathology, Melbourne, VIC 3084, Australia
| | | | - Suzanne Svobodova
- Molecular Diagnostic and Microbiology Laboratory, Austin Pathology, Melbourne, VIC 3084, Australia
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9
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Gürtler V, Grando D. New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes. J Microbiol Methods 2013; 93:257-72. [PMID: 23545446 DOI: 10.1016/j.mimet.2013.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This has increased awareness for the need to track outbreaks and PCR-ribotyping has found widespread use to elucidate epidemiologically linked isolates. PCR-ribotyping uses conserved regions of the 16S rRNA gene and 23S rRNA gene as primer binding sites to produce varying PCR products due to the intergenic spacer (ITS1) regions of the multiple operons. With the explosion of whole genome sequence data it became possible to analyse the start of the 23S rRNA gene for a more accurate selection of regions closer to the end of the ITS1. However the following questions must still be asked: (i) Does the chromosomal organisation of the rrn operon vary between C. difficile strains? and (ii) just how conserved are the primer binding regions? Eight published C. difficile genomes have been aligned to produce a detailed database of indels of the ITS1's from the rrn operon sets. An iPad Filemaker Go App has been constructed and named RiboTyping (RT). It contains detail such as sequences, ribotypes, strain numbers, GenBank numbers and genome position numbers. Access to various levels of the database is provided so that details can be printed. There are three main regions of the rrn operon that have been analysed by the database and related to each other by strain, ribotype and operon: (1) 16S gene (2) ITS1 indels (3) 23S gene. This has enabled direct intra- and inter-genomic comparisons at the strain, ribotype and operon (allele) levels in each of the three genomic regions. This is the first time that such an analysis has been done. By using the RT App with search criteria it will be possible to select probe combinations for specific strains/ribotypes/rrn operons for experiments to do with diagnostics, typing and recombination of operons. Many more incomplete C. difficile whole genome sequencing projects are recorded in GenBank as underway and the rrn operon information from these can also be added to the RT App when available. The RT App will help simplify probe selection because of the complexity of the ITS1 in C. difficile even in a single genome and because other allele-specific regions (16S and 23S genes) of variability can be relationally compared to design extra probes to increase sensitivity.
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Affiliation(s)
- Volker Gürtler
- School of Applied Sciences, Building 223, Level 1, Bundoora Campus RMIT University, PO Box 71, Bundoora 3083, Australia.
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Chen JHK, Cheng VCC, Chan JFW, She KKK, Yan MK, Yau MCY, Kwan GSW, Yam WC, Yuen KY. The use of high-resolution melting analysis for rapid spa typing on methicillin-resistant Staphylococcus aureus clinical isolates. J Microbiol Methods 2012; 92:99-102. [PMID: 23154043 DOI: 10.1016/j.mimet.2012.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/05/2012] [Accepted: 11/06/2012] [Indexed: 11/29/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has been endemic in Hong Kong for three decades. This study evaluated the practical use of high-resolution melting (HRM) real-time PCR analysis on MRSA staphylococcal Protein A (spa) typing on local MRSA isolates. Among 55 clinical MRSA isolates collected in 2011, 12 different spa types were observed by the conventional PCR-sequencing method including the locally predominant spa type t1081 and two locally predominant community acquired MRSA spa types t019 and t437. By using the HRM method, it could differentiate all 12 spa genotypes by distinct melting curves and HRM difference plot analysis. These two methods demonstrated 100% concordance whereas the HRM method required only 3h of turnaround time and one-fifth of reagent cost compared to the conventional method. Our study confirmed that the cost effective and rapid HRM typing approach is practically useful for MRSA community transmission monitoring and nosocomial outbreak control in Hong Kong.
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Affiliation(s)
- Jonathan Hon-Kwan Chen
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
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Global phylogeny of Shigella sonnei strains from limited single nucleotide polymorphisms (SNPs) and development of a rapid and cost-effective SNP-typing scheme for strain identification by high-resolution melting analysis. J Clin Microbiol 2012; 51:303-5. [PMID: 23115259 DOI: 10.1128/jcm.02238-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The current Shigella sonnei pandemic involves geographically associated, multidrug-resistant clones. This study has demonstrated that S. sonnei phylogeny can be accurately defined with limited single nucleotide polymorphisms (SNPs). By typing 6 informative SNPs using a high-resolution melting (HRM) assay, major S. sonnei lineages/sublineages can be identified as defined by whole-genome variation.
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