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Georghiou SB, Penn-Nicholson A, de Vos M, Macé A, Syrmis MW, Jacob K, Mape A, Parmar H, Cao Y, Coulter C, Ruhwald M, Pandey SK, Schumacher SG, Denkinger CM. Analytical performance of the Xpert MTB/XDR® assay for tuberculosis and expanded resistance detection. Diagn Microbiol Infect Dis 2021; 101:115397. [PMID: 34130215 DOI: 10.1016/j.diagmicrobio.2021.115397] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/15/2021] [Accepted: 04/10/2021] [Indexed: 11/16/2022]
Abstract
In a manufacturer-independent laboratory validation study, the Xpert MTB/XDR® assay demonstrated equivalent limit of detection to Xpert MTB/RIF®, detected 100% of tested resistance mutations and showed some utility for resistance detection in strain mixtures. The Xpert MTB/XDR assay is a reliable, sensitive assay for tuberculosis and expanded resistance detection.
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Affiliation(s)
| | | | | | | | - Melanie W Syrmis
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia; The University of Queensland Centre for Clinical Research, University of Queensland, Queensland, Australia
| | - Kevin Jacob
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Alyanna Mape
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Heta Parmar
- New Jersey Medical School, Rutgers University, New Jersey, USA
| | - Yuan Cao
- New Jersey Medical School, Rutgers University, New Jersey, USA
| | - Chris Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | | | - Sushil K Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | | | - Claudia M Denkinger
- FIND, Geneva, Switzerland; Division of Tropical Medicine, Center of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
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Zowawi HM, Syrmis MW, Kidd TJ, Balkhy HH, Walsh TR, Al Johani SM, Al Jindan RY, Alfaresi M, Ibrahim E, Al-Jardani A, Al Salman J, Dashti AA, Sidjabat HE, Baz O, Trembizki E, Whiley DM, Paterson DL. Identification of carbapenem-resistant Pseudomonas aeruginosa in selected hospitals of the Gulf Cooperation Council States: dominance of high-risk clones in the region. J Med Microbiol 2018; 67:846-853. [PMID: 29664716 DOI: 10.1099/jmm.0.000730] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE The molecular epidemiology and resistance mechanisms of carbapenem-resistant Pseudomonas aeruginosa (CRPA) were determined in hospitals in the countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, the United Arab Emirates, Oman, Qatar, Bahrain and Kuwait. METHODOLOGY Isolates were screened for common carbapenem-resistance genes by PCR. Relatedness between isolates was assessed using previously described genotyping methods: an informative-single nucleotide polymorphism MassARRAY iPLEX assay (iPLEX20SNP) and the enterobacterial repetitive intergenic consensus (ERIC)-PCR assay, with selected isolates being subjected to multilocus sequence typing (MLST). Ninety-five non-repetitive isolates that were found to be resistant to carbapenems were subjected to further investigation.Results/Key findings. The most prevalent carbapenemase-encoding gene, blaVIM-type, was found in 37/95 (39 %) isolates, while only 1 isolate (from UAE) was found to have blaIMP-type. None of the CRPA were found to have blaNDM-type or blaKPC-type. We found a total of 14 sequence type (ST) clusters, with 4 of these clusters being observed in more than 1 country. Several clusters belonged to the previously recognized internationally disseminated high-risk clones ST357, ST235, ST111, ST233 and ST654. We also found the less predominant ST316, ST308 and ST823 clones, and novel MLST types (ST2010, ST2011, ST2012 and ST2013), in our collection. CONCLUSION Overall our data show that 'high-risk' CRPA clones are now detected in the region and highlight the need for strategies to limit further spread of such organisms, including enhanced surveillance, infection control precautions and further promotion of antibiotic stewardship programmes.
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Affiliation(s)
- Hosam M Zowawi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.,King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | | | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Hanan H Balkhy
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | - Timothy R Walsh
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.,Department of Medical Microbiology and Infectious Diseases, School of Medicine, Cardiff University, Heath Park, Cardiff, UK
| | - Sameera M Al Johani
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Microbiology, Department of Pathology and Lab Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Reem Y Al Jindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mubarak Alfaresi
- Pathology and Laboratory Medicine Department at Sheikh Khalifa General Hospital, Umm Al Quwain, UAE.,College of Medicine, University of Sharjah, UAE
| | - Emad Ibrahim
- Clinical Microbiology Department, Hamad Medical Corporation, Doha, Qatar
| | - Amina Al-Jardani
- Medical Microbiology Department, The Royal Hospital, Muscat, Oman
| | - Jameela Al Salman
- Samlaniya Medical Complex, Infectious Diseases Unit, Manama, Bahrain
| | - Ali A Dashti
- Medical Laboratory Department, Faculty of Allied Health Sciences, Health Science Center, Kuwait University, Kuwait City, Kuwait
| | - Hanna E Sidjabat
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - Omar Baz
- King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - Ella Trembizki
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - David M Whiley
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.,Pathology Queensland, Brisbane, Queensland 4029, Australia
| | - David L Paterson
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
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3
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Syrmis MW, Pandey S, Tolson C, Carter R, Congdon J, Sloots T, Coulter C, Whiley D. Identification of Mycobacterium abscessus complex and M. abscessus subsp. massiliense culture isolates by real-time assays. J Med Microbiol 2015; 64:790-794. [PMID: 25976000 DOI: 10.1099/jmm.0.000085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Melanie W Syrmis
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Queensland, Australia.,Queensland Children's Medical Research Institute, Queensland, Australia.,University of Queensland, Queensland, Australia
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Carla Tolson
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Robyn Carter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Jake Congdon
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - Theo Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Queensland, Australia.,Queensland Children's Medical Research Institute, Queensland, Australia.,University of Queensland, Queensland, Australia
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Queensland, Australia
| | - David Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Health Services, Queensland, Australia.,Queensland Children's Medical Research Institute, Queensland, Australia.,University of Queensland, Queensland, Australia
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4
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Syrmis MW, Kidd TJ, Moser RJ, Ramsay KA, Gibson KM, Anuj S, Bell SC, Wainwright CE, Grimwood K, Nissen M, Sloots TP, Whiley DM. A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis. BMC Infect Dis 2014; 14:307. [PMID: 24902856 PMCID: PMC4053291 DOI: 10.1186/1471-2334-14-307] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 05/28/2014] [Indexed: 12/26/2022] Open
Abstract
Background Molecular typing is integral for identifying Pseudomonas aeruginosa strains that may be shared between patients with cystic fibrosis (CF). We conducted a side-by-side comparison of two P. aeruginosa genotyping methods utilising informative-single nucleotide polymorphism (SNP) methods; one targeting 10 P. aeruginosa SNPs and using real-time polymerase chain reaction technology (HRM10SNP) and the other targeting 20 SNPs and based on the Sequenom MassARRAY platform (iPLEX20SNP). Methods An in-silico analysis of the 20 SNPs used for the iPLEX20SNP method was initially conducted using sequence type (ST) data on the P. aeruginosa PubMLST website. A total of 506 clinical isolates collected from patients attending 11 CF centres throughout Australia were then tested by both the HRM10SNP and iPLEX20SNP assays. Type-ability and discriminatory power of the methods, as well as their ability to identify commonly shared P. aeruginosa strains, were compared. Results The in-silico analyses showed that the 1401 STs available on the PubMLST website could be divided into 927 different 20-SNP profiles (D-value = 0.999), and that most STs of national or international importance in CF could be distinguished either individually or as belonging to closely related single- or double-locus variant groups. When applied to the 506 clinical isolates, the iPLEX20SNP provided better discrimination over the HRM10SNP method with 147 different 20-SNP and 92 different 10-SNP profiles observed, respectively. For detecting the three most commonly shared Australian P. aeruginosa strains AUST-01, AUST-02 and AUST-06, the two methods were in agreement for 80/81 (98.8%), 48/49 (97.8%) and 11/12 (91.7%) isolates, respectively. Conclusions The iPLEX20SNP is a superior new method for broader SNP-based MLST-style investigations of P. aeruginosa. However, because of convenience and availability, the HRM10SNP method remains better suited for clinical microbiology laboratories that only utilise real-time PCR technology and where the main interest is detection of the most highly-prevalent P. aeruginosa CF strains within Australian clinics.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - David M Whiley
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Queensland 4029, Australia.
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Syrmis MW, Moser RJ, Kidd TJ, Hunt P, Ramsay KA, Bell SC, Wainwright CE, Grimwood K, Nissen MD, Sloots TP, Whiley DM. High-throughput single-nucleotide polymorphism-based typing of shared Pseudomonas aeruginosa strains in cystic fibrosis patients using the Sequenom iPLEX platform. J Med Microbiol 2013; 62:734-740. [PMID: 23412772 DOI: 10.1099/jmm.0.055905-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shared strains of Pseudomonas aeruginosa are now well recognized in people with cystic fibrosis (CF), and suitable P. aeruginosa laboratory typing tools are pivotal to understanding their clinical significance and guiding infection control policies in CF clinics. We therefore compared a single-nucleotide polymorphism (SNP)-based typing method using Sequenom iPLEX matrix-assisted laser desorption ionization with time-of-flight mass spectrometry (MALDI-TOF MS) with typing methods used routinely by our laboratory. We analysed 617 P. aeruginosa isolates that included 561 isolates from CF patients collected between 2001 and 2009 in two Brisbane CF clinics and typed previously by enterobacterial repetitive intergenic consensus (ERIC)-PCR, as well as 56 isolates from non-CF patients analysed previously by multilocus sequence typing (MLST). The isolates were tested using a P. aeruginosa Sequenom iPLEX MALDI-TOF (PA iPLEX) method comprising two multiplex reactions, a 13-plex and an 8-plex, to characterize 20 SNPs from the P. aeruginosa housekeeping genes acsA, aroE, guaA, mutL, nuoD, ppsA and trpE. These 20 SNPs were employed previously in a real-time format involving 20 separate assays in our laboratory. The SNP analysis revealed 121 different SNP profiles for the 561 CF isolates. Overall, there was at least 96% agreement between the ERIC-PCR and SNP analyses for all predominant shared strains among patients attending our CF clinics: AUST-01, AUST-02 and AUST-06. For the less frequently encountered shared strain AUST-07, 6/25 (24%) ERIC-PCR profiles were misidentified initially as AUST-02 or as unique, illustrating the difficulty of gel-based analyses. SNP results for the 56 non-CF isolates were consistent with previous MLST data. Thus, the PA iPLEX format provides an attractive high-throughput alternative to ERIC-PCR for large-scale investigations of shared P. aeruginosa strains.
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Affiliation(s)
- Melanie W Syrmis
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Ralf J Moser
- Sequenom Inc., Sequenom Asia Pacific, Herston, Queensland, Australia
| | - Timothy J Kidd
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Priscilla Hunt
- Sequenom Inc., Sequenom Asia Pacific, Herston, Queensland, Australia
| | - Kay A Ramsay
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Queensland, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Queensland Children's Respiratory Centre, Royal Children's Hospital, Brisbane, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia
| | - Keith Grimwood
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Michael D Nissen
- Microbiology Division, Pathology Queensland Central Laboratory, Herston, Queensland, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Theo P Sloots
- Microbiology Division, Pathology Queensland Central Laboratory, Herston, Queensland, Australia.,Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - David M Whiley
- Queensland Children's Medical Research Institute, Royal Children's Hospital, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Brisbane, Queensland, Australia
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Syrmis MW, Moser RJ, Whiley DM, Vaska V, Coombs GW, Nissen MD, Sloots TP, Nimmo GR. Comparison of a multiplexed MassARRAY system with real-time allele-specific PCR technology for genotyping of methicillin-resistant Staphylococcus aureus. Clin Microbiol Infect 2011; 17:1804-10. [PMID: 21595795 DOI: 10.1111/j.1469-0691.2011.03521.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Sequenom MassARRAY iPLEX single-nucleotide polymorphism (SNP) typing platform uses matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled with single-base extension PCR for high-throughput multiplex SNP detection. In this study, we investigated the use of iPLEX MassARRAY technology for methicillin-resistant Staphylococcus aureus (MRSA) genotyping. A 16-plex MassARRAY iPLEX GOLD assay (MRSA-iPLEX) was developed that targets a set of informative SNPs and binary genes for MRSA characterization. The method was evaluated with 147 MRSA isolates, and the results were compared with those of an established SYBR Green-based real-time PCR system utilizing the same SNP-binary markers. A total of 2352 markers belonging to 44 SNP-binary profiles were analysed by both real-time PCR and MRSA-iPLEX. With real-time PCR as the reference standard, MRSA-iPLEX correctly assigned 2298 of the 2352 (97.7%) markers. Sequence variation in the MRSA-iPLEX primer targets accounted for the majority of MRSA-iPLEX erroneous results, highlighting the importance of primer target selection. MRSA-iPLEX provided optimal throughput for MRSA genotyping, and was, on a reagent basis, more cost-effective than the real-time PCR methods. The 16-plex MRSA-iPLEX is a suitable alternative to SYBR Green-based real-time PCR typing of major sequence types and clonal complexes of MRSA.
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Affiliation(s)
- M W Syrmis
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Brisbane, Australia
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7
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Anuj SN, Whiley DM, Kidd TJ, Ramsay KA, Bell SC, Syrmis MW, Grimwood K, Wainwright CE, Nissen MD, Sloots TP. Rapid single-nucleotide polymorphism-based identification of clonal Pseudomonas aeruginosa isolates from patients with cystic fibrosis by the use of real-time PCR and high-resolution melting curve analysis. Clin Microbiol Infect 2011; 17:1403-8. [PMID: 21129101 DOI: 10.1111/j.1469-0691.2010.03439.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa genotyping relies mainly upon DNA fingerprinting methods, which can be subjective, expensive and time-consuming. The detection of at least three different clonal P. aeruginosa strains in patients attending two cystic fibrosis (CF) centres in a single Australian city prompted the design of a non-gel-based PCR method to enable clinical microbiology laboratories to readily identify these clonal strains. We designed a detection method utilizing heat-denatured P. aeruginosa isolates and a ten-single-nucleotide polymorphism (SNP) profile. Strain differences were detected by SYBR Green-based real-time PCR and high-resolution melting curve analysis (HRM10SNP assay). Overall, 106 P. aeruginosa sputum isolates collected from 74 patients with CF, as well as five reference strains, were analysed with the HRM10SNP assay, and the results were compared with those obtained by pulsed-field gel electrophoresis (PFGE). The HRM10SNP assay accurately identified all 45 isolates as members of one of the three major clonal strains characterized by PFGE in two Brisbane CF centres (Australian epidemic strain-1, Australian epidemic strain-2 and P42) from 61 other P. aeruginosa strains from Australian CF patients and two representative overseas epidemic strain isolates. The HRM10SNP method is simple, is relatively inexpensive and can be completed in <3 h. In our setting, it could be made easily available for clinical microbiology laboratories to screen for local P. aeruginosa strains and to guide infection control policies. Further studies are needed to determine whether the HRM10SNP assay can also be modified to detect additional clonal strains that are prevalent in other CF centres.
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Affiliation(s)
- S N Anuj
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Qld, Australia.
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O'Carroll MR, Syrmis MW, Wainwright CE, Greer RM, Mitchell P, Coulter C, Sloots TP, Nissen MD, Bell SC. Clonal strains of Pseudomonas aeruginosa in paediatric and adult cystic fibrosis units. Eur Respir J 2005; 24:101-6. [PMID: 15293611 DOI: 10.1183/09031936.04.00122903] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Despite recent reports of clonal strains of Pseudomonas aeruginosa in cystic fibrosis (CF) units, the need for routine microbiological surveillance remains contentious. Sputum was collected prospectively from productive patients attending the regional paediatric and adult CF units in Brisbane, Australia. All P. aeruginosa isolates were typed using pulsed-field gel electrophoresis. Spirometry, anthropometrics, hospitalisations and antibiotic sensitivity data were recorded. The first 100 sputum samples (first 50 patients at each clinic) harboured 163 isolates of P. aeruginosa. A total of 39 patients shared a common strain (pulsotype 2), 20 patients shared a strain with at least one other patient and 41 patients harboured unique strains. Eight patients shared a strain identical to a previously reported Australian transmissible strain (pulsotype 1). Compared with the unique strain group, patients harbouring pulsotype 2 were younger and had poorer lung function. Treatment requirements were similar in these two groups, as were the rates of multiresistance. In conclusion, 59% of patients harboured a clonal strain, supporting the need for routine microbiological surveillance. In contrast to previously described clonal strains, the dominant pulsotype was indistinguishable from nonclonal strains with respect to both colonial morphology and multiresistance. The clinical significance of clonal strains remains uncertain and requires longitudinal study.
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Affiliation(s)
- M R O'Carroll
- Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Chermside, Australia
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Punch G, Syrmis MW, Rose BR, Harbour C, Bye PTP, Nissen MD, Elkins MR, Sloots TP. Method for detection of respiratory viruses in the sputa of patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2005; 24:54-7. [PMID: 15616837 PMCID: PMC7088139 DOI: 10.1007/s10096-004-1273-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since the role of respiratory viruses in lung exacerbations of patients with cystic fibrosis has been hampered by the difficulty of detecting viruses in viscous sputum specimens, a multiplex reverse transcriptase PCR (RT-PCR) assay combined with colorimetric amplicon detection was tested for the identification of seven common respiratory viruses in the sputa of cystic fibrosis patients. Of 52 sputa from 38 patients, 12 (23%) samples from 12 patients were positive for a respiratory virus (4 for influenza B, 3 for parainfluenza 1, 3 for influenza A and 2 for respiratory syncytial virus). These results suggest that the RT-PCR method carried out on sputum may provide a convenient means of investigating the role of virus infection in lung exacerbations of cystic fibrosis patients.
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Affiliation(s)
- G Punch
- Department of Infectious Diseases and Immunology, University of Sydney, Parramatta Road, Camperdown, New South Wales 2006, Australia
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10
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Syrmis MW, O'Carroll MR, Sloots TP, Coulter C, Wainwright CE, Bell SC, Nissen MD. Rapid genotyping of Pseudomonas aeruginosa isolates harboured by adult and paediatric patients with cystic fibrosis using repetitive-element-based PCR assays. J Med Microbiol 2004; 53:1089-1096. [PMID: 15496385 DOI: 10.1099/jmm.0.45611-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, the suitability of two repetitive-element-based PCR (rep-PCR) assays, enterobacterial repetitive intergenic consensus (ERIC)-PCR and BOX-PCR, to rapidly characterize Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis (CF) was examined. ERIC-PCR utilizes paired sequence-specific primers and BOX-PCR a single primer that target highly conserved repetitive elements in the P. aeruginosa genome. Using these rep-PCR assays, 163 P. aeruginosa isolates cultured from sputa collected from 50 patients attending an adult CF clinic and 50 children attending a paediatric CF clinic were typed. The results of the rep-PCR assays were compared to the results of PFGE. All three assays revealed the presence of six major clonal groups shared by multiple patients attending either of the CF clinics, with the dominant clonal group infecting 38 % of all patients. This dominant clonal group was not related to the dominant clonal group detected in Sydney or Melbourne (pulsotype 1), nor was it related to the dominant groups detected in the UK. In all, PFGE and rep-PCR identified 58 distinct clonal groups, with only three of these shared between the two clinics. The results of this study showed that both ERIC-PCR and BOX-PCR are rapid, highly discriminatory and reproducible assays that proved to be powerful surveillance screening tools for the typing of clinical P. aeruginosa isolates recovered from patients with CF.
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Affiliation(s)
- Melanie W Syrmis
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Mark R O'Carroll
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Theo P Sloots
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Chris Coulter
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Scott C Bell
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Michael D Nissen
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
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Whiley DM, Crisante ME, Syrmis MW, Mackay IM, Sloots TP. Detection of Neisseria Meningitidis in clinical samples by a duplex real-time PCR targeting the porA and ctrA genes. ACTA ACUST UNITED AC 2004; 7:141-5. [PMID: 15068383 DOI: 10.1007/bf03260030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND In recent years PCR has proven to be a highly sensitive and specific method for the diagnosis of infections caused by Neisseria meningitidis. STUDY DESIGN We developed and evaluated a N. meningitidis LightCycler real-time duplex PCR (NM-LCdPCR) capable of simultaneously detecting and distinguishing between two separate genes on the N. meningitidis genome. METHODS The NM-LCdPCR was developed on the LightCycler platform (Roche Diagnostics, Castle Hill, NSW, Australia) and comprised two primer pairs and two hybridization probe sets, enabling the detection of both the porA and ctrA genes within the same reaction mix. To distinguish between the fluorescence emitted by each hybridization probe set, each downstream probe was labeled with a different fluorophore (either LC-Red640 or LC-Red705). The results obtained by the NM-LCdPCR were then compared with the results obtained by a mono-specific LightCycler assay targeting the porA gene only (porA-LCPCR). PATIENTS One-hundred and forty-eight clinical samples from patients with suspected meningococcal infection were evaluated. RESULTS The results of the NM-LCdPCR and porA-LCPCR gave 100% agreement; N. meningitidis DNA was detected in 25 samples whereas 123 samples were negative by both assays. The breakdown of the NM-LCdPCR results show that both genes were detected in 26 of the 28 positive samples. DISCUSSION By targeting two separate N. meningitidis genes, the NM-LCdPCR has the potential to prevent the false-positive results which may arise from sequence variation. In addition, the ability to detect and discriminate between the two different N. meningitidis genes within the same reaction mix offers a rapid means for confirming the presence of N. meningitidis DNA in clinical samples, thereby reducing the need for subsequent confirmatory assays to be performed. CONCLUSIONS The sensitivity and specificity of the NM-LCdPCR assay, combined with its ability to detect and discriminate both the N. meningitidis porA and ctrA genes, make it suitable for the diagnosis of N. meningitidis infections in the routine clinical laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston, and Clinical Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
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Whiley DM, Mackay IM, Syrmis MW, Witt MJ, Sloots TP. Detection and differentiation of herpes simplex virus types 1 and 2 by a duplex LightCycler PCR that incorporates an internal control PCR reaction. J Clin Virol 2004; 30:32-8. [PMID: 15072751 DOI: 10.1016/j.jcv.2003.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2003] [Revised: 08/12/2003] [Accepted: 08/15/2003] [Indexed: 11/27/2022]
Abstract
BACKGROUND In recent years polymerase chain reaction (PCR) has proven to be a highly sensitive and specific method for the diagnosis of herpes simplex virus (HSV) infections. The advent of real-time HSV PCR protocols now enables rapid result turnaround times with minimal hands-on time. OBJECTIVES In this study, we developed a real-time duplex PCR assay (HSVgD-dPCR) comprising of HSV and internal control PCR reactions. STUDY DESIGN Using the LightCycler, the HSVgD-dPCR targeted the HSV glycoprotein D gene and HSV typing was performed by melting curve analysis. The internal control PCR reaction targeted sequences of the DNA of the human endogenous retrovirus (ERV-3). In total, 300 swab specimens, from patients with suspected HSV infection, were tested by the HSVgD-dPCR assay. The results were then compared to the results obtained by another HSV LightCycler assay, which utilized published primer and probe sequences targeting the HSV DNA polymerase gene (Dpol-HSV-LCPCR). RESULTS Overall, 91 (30.3%) specimens were positive and 204 (68.0%) specimens were negative for HSV by both LightCycler assays. In addition, four (1.3%) specimens were positive by Dpol-HSV-LCPCR and negative by HSVgD-dPCR, whereas one (0.3%) specimen was positive by HSVgD-dPCR and negative by Dpol-HSV-LCPCR. The presence of HSV in these five specimens was confirmed by conventional PCR. Melting curve analysis by the HSVgD-dPCR assay enabled all HSV positive specimens to be typed, whereas sequence variation prevented three HSV positive specimens from being typed by the Dpol-HSV-LCPCR. Using the ERV-3 PCR, 5% specimens were found to contain inhibitory substances. CONCLUSIONS By developing the HSVgD-dPCR we have enhanced the diagnostic utility of real-time detection of HSV by incorporating an internal control reaction and by accurately typing a greater proportion of HSV positive specimens.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Queensland 4029, Australia
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Whiley DM, LeCornec GM, Baddeley A, Savill J, Syrmis MW, Mackay IM, Siebert DJ, Burns D, Nissen M, Sloots TP. Detection and differentiation of Plasmodium species by polymerase chain reaction and colorimetric detection in blood samples of patients with suspected malaria. Diagn Microbiol Infect Dis 2004; 49:25-9. [PMID: 15135496 DOI: 10.1016/j.diagmicrobio.2003.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 10/24/2003] [Indexed: 11/20/2022]
Abstract
Polymerase chain reaction (PCR) is now recognized as a sensitive and specific method for detecting Plasmodium species in blood. In this study, we tested 279 blood samples, from patients with suspected malaria, by a PCR assay utilizing species-specific colorimetric detection, and compared the results to light microscopy. Overall, both assays were in agreement for 270 of the 279 specimens. P. vivax was detected in 131 (47.0%) specimens, P. falciparum in 64 (22.9%) specimens, P. ovale in 6 (2.1%) specimens, and P. malariae in 5 (1.8%) specimens. Both P. falciparum and P. vivax were detected in a further 10 (3.6%) specimens, and 54 (19.3%) specimens were negative by both assays. In the remaining nine specimens, microscopy either failed to detect the parasite or incorrectly identified the species present. In summary, the sensitivity, specificity and simplicity of the PCR assay makes it particularly suitable for use in a diagnostic laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Clinical Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
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Syrmis MW, Whiley DM, Thomas M, Mackay IM, Williamson J, Siebert DJ, Nissen MD, Sloots TP. A sensitive, specific, and cost-effective multiplex reverse transcriptase-PCR assay for the detection of seven common respiratory viruses in respiratory samples. J Mol Diagn 2004; 6:125-31. [PMID: 15096568 PMCID: PMC1867476 DOI: 10.1016/s1525-1578(10)60500-4] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2004] [Indexed: 10/18/2022] Open
Abstract
Cell culture and direct fluorescent antibody (DFA) assays have been traditionally used for the laboratory diagnosis of respiratory viral infections. Multiplex reverse transcriptase polymerase chain reaction (m-RT-PCR) is a sensitive, specific, and rapid method for detecting several DNA and RNA viruses in a single specimen. We developed a m-RT-PCR assay that utilizes multiple virus-specific primer pairs in a single reaction mix combined with an enzyme-linked amplicon hybridization assay (ELAHA) using virus-specific probes targeting unique gene sequences for each virus. Using this m-RT-PCR-ELAHA, we examined the presence of seven respiratory viruses in 598 nasopharyngeal aspirate (NPA) samples from patients with suspected respiratory infection. The specificity of each assay was 100%. The sensitivity of the DFA was 79.7% and the combined DFA/culture amplified-DFA (CA-DFA) was 88.6% when compared to the m-RT-PCR-ELAHA. Of the 598 NPA specimens screened by m-RT-PCR-ELAHA, 3% were positive for adenovirus (ADV), 2% for influenza A (Flu A) virus, 0.3% for influenza B (Flu B) virus, 1% for parainfluenza type 1 virus (PIV1), 1% for parainfluenza type 2 virus (PIV2), 5.5% for parainfluenza type 3 virus (PIV3), and 21% for respiratory syncytial virus (RSV). The enhanced sensitivity, specificity, rapid result turnaround time and reduced expense of the m-RT-PCR-ELAHA compared to DFA and CA-DFA, suggests that this assay would be a significant improvement over traditional assays for the detection of respiratory viruses in a clinical laboratory.
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Affiliation(s)
- Melanie W Syrmis
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, Australia
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Whiley DM, Arden KE, Mackay IM, Syrmis MW, Sloots TP. Simultaneous detection and differentiation of human polyomaviruses JC and BK by a rapid and sensitive PCR-ELAHA assay and a survey of the JCV subtypes within an Australian population. J Med Virol 2004; 72:467-72. [PMID: 14748071 DOI: 10.1002/jmv.20005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human polyomaviruses JCV and BKV can cause several clinical manifestations in immunocompromised hosts, including progressive multifocal leukoencephalopathy (PML) and haemorrhagic cystitis. Molecular detection by polymerase chain reaction (PCR) is recognised as a sensitive and specific method for detecting human polyomaviruses in clinical samples. In this study, we developed a PCR assay using a single primer pair to amplify a segment of the VP1 gene of JCV and BKV. An enzyme linked amplicon hybridisation assay (ELAHA) using species-specific biotinylated oligonucleotide probes was used to differentiate between JCV and BKV. This assay (VP1-PCR-ELAHA) was evaluated and compared to a PCR assay targeting the human polyomavirus T antigen gene (pol-PCR). DNA sequencing was used to confirm the polyomavirus species identified by the VP1-PCR-ELAHA and to determine the subtype of each JCV isolate. A total of 297 urine specimens were tested and human polyomavirus was detected in 105 specimens (35.4%) by both PCR assays. The differentiation of JCV and BKV by the VP1-PCR-ELAHA showed good agreement with the results of DNA sequencing. Further, DNA sequencing of the JCV positive specimens showed the most prevalent JCV subtype in our cohort was 2a (27%) followed by 1b (20%), 1a (15%), 2c (14%), 4 (14%) and 2b (10%). The results of this study show that the VP1-PCR-ELAHA is a sensitive, specific and rapid method for detecting and differentiating human polyomaviruses JC and BK and is highly suitable for routine use in the clinical laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, Australia
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Whiley DM, Syrmis MW, Mackay IM, Sloots TP. Preliminary Comparison of Three LightCycler PCR Assays for the Detection of Herpes Simplex Virus in Swab Specimens. Eur J Clin Microbiol Infect Dis 2003; 22:764-7. [PMID: 14605937 DOI: 10.1007/s10096-003-1031-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Three Herpes Simplex Virus LightCycler polymerase chain reaction assays were compared for the detection of herpes simplex virus in 48 swab specimens. The assays comprised of one in-house assay and two commercial kits: the Artus HSV LC RealArt PCR kit and the Roche LightCycler HSV 1/2 Detection kit. On the whole, the three assays had comparable sensitivities. However, differentiation of herpes simplex virus types 1 and 2 by melting curve analysis was problematic in all assays. Overall, the results highlight the limitations of typing herpes simplex virus by melting curve analysis.
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Affiliation(s)
- D M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston Road, 4029 Herston, Queensland, Australia
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Mackay IM, Jacob KC, Woolhouse D, Waller K, Syrmis MW, Whiley DM, Siebert DJ, Nissen M, Sloots TP. Molecular assays for detection of human metapneumovirus. J Clin Microbiol 2003; 41:100-5. [PMID: 12517833 PMCID: PMC149567 DOI: 10.1128/jcm.41.1.100-105.2003] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recent description of the respiratory pathogen human metapneumovirus (hMPV) has highlighted a deficiency in current diagnostic techniques for viral agents associated with acute lower respiratory tract infections. We describe two novel approaches to the detection of viral RNA by use of reverse transcriptase PCR (RT-PCR). The PCR products were identified after capture onto a solid-phase medium by hybridization with a sequence-specific, biotinylated oligonucleotide probe. The assay was applied to the screening of 329 nasopharyngeal aspirates sampled from patients suffering from respiratory tract disease. These samples were negative for other common microbial causes of respiratory tract disease. We were able to detect hMPV sequences in 32 (9.7%) samples collected from Australian patients during 2001. To further reduce result turnaround times we designed a fluorogenic TaqMan oligoprobe and combined it with the existing primers for use on the LightCycler platform. The real-time RT-PCR proved to be highly reproducible and detected hMPV in an additional 6 out of 62 samples (9.6%) tested during the comparison of the two diagnostic approaches. We found the real-time RT-PCR to be the test of choice for future investigation of samples for hMPV due to its speed, reproducibility, specificity, and sensitivity.
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Affiliation(s)
- Ian M Mackay
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
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Whiley DM, Syrmis MW, Mackay IM, Sloots TP. Detection of human respiratory syncytial virus in respiratory samples by LightCycler reverse transcriptase PCR. J Clin Microbiol 2002; 40:4418-22. [PMID: 12454129 PMCID: PMC154614 DOI: 10.1128/jcm.40.12.4418-4422.2002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory diagnosis of human respiratory syncytial virus (hRSV) infections has traditionally been performed by virus isolation in cell culture and the direct fluorescent-antibody assay (DFA). Reverse transcriptase PCR (RT-PCR) is now recognized as a sensitive and specific alternative for detection of hRSV in respiratory samples. Using the LightCycler instrument, we developed a rapid RT-PCR assay for the detection of hRSV (the LC-RT-PCR) with a pair of hybridization probes that target the hRSV L gene. In the present study, 190 nasopharyngeal aspirate samples from patients with clinically recognized respiratory tract infections were examined for hRSV. The results were then compared to the results obtained with a testing algorithm that combined DFA and a culture-augmented DFA (CA-DFA) assay developed in our laboratory. hRSV was detected in 77 (41%) specimens by LC-RT-PCR and in 75 (39%) specimens by the combination of DFA and CA-DFA. All specimens that were positive by the DFA and CA-DFA testing algorithm were positive by the LC-RT-PCR. The presence of hRSV RNA in the two additional LC-RT-PCR-positive specimens was confirmed by a conventional RT-PCR method that targets the hRSV N gene. The sensitivity of LC-RT-PCR was 50 PFU/ml; and this, together with its high specificity and rapid turnaround time, makes the LC-RT-PCR suitable for the detection of hRSV in clinical specimens.
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Affiliation(s)
- David M. Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
| | - Melanie W. Syrmis
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
| | - Ian M. Mackay
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
| | - Theo P. Sloots
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
- Corresponding author. Mailing address: Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston Rd., Herston, Queensland 4029, Australia. Phone: 61-7-3636 8833. Fax: 61-7-36361401. E-mail:
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