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Trembizki E, Smith H, Lahra MM, Chen M, Donovan B, Fairley CK, Guy R, Kaldor J, Regan D, Ward J, Nissen MD, Sloots TP, Whiley DM. High-throughput informative single nucleotide polymorphism-based typing of Neisseria gonorrhoeae using the Sequenom MassARRAY iPLEX platform. J Antimicrob Chemother 2014; 69:1526-32. [DOI: 10.1093/jac/dkt544] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Tozer SJ, Lambert SB, Strong CL, Field HE, Sloots TP, Nissen MD. Potential Animal and Environmental Sources of Q Fever Infection for Humans in Queensland. Zoonoses Public Health 2013; 61:105-12. [DOI: 10.1111/zph.12051] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Indexed: 11/30/2022]
Affiliation(s)
- S. J. Tozer
- Queensland Paediatric Infectious Diseases Laboratory; Queensland Children's Medical Research Institute; Children's Health Queensland Hospitals and Health Service ; The University of Queensland; Brisbane Qld Australia
| | - S. B. Lambert
- Queensland Children's Medical Research Institute; Children's Health Queensland Hospitals and Health Service; The University of Queensland; Brisbane Qld Australia
- Immunisation Program, Communicable Diseases Branch; Queensland Health; Brisbane Qld Australia
| | - C. L. Strong
- Atmospheric Environment Research Centre; Griffith University; Brisbane Qld Australia
| | - H. E. Field
- Queensland Department of Agriculture, Fisheries & Forestry; Queensland Centre for Emerging Infectious Diseases; Biosecurity; Brisbane Qld Australia
| | - T. P. Sloots
- Queensland Paediatric Infectious Diseases Laboratory; Queensland Children's Medical Research Institute; Children's Health Queensland Hospitals and Health Service ; The University of Queensland; Brisbane Qld Australia
| | - M. D. Nissen
- Queensland Paediatric Infectious Diseases Laboratory; Queensland Children's Medical Research Institute; Children's Health Queensland Hospitals and Health Service ; The University of Queensland; Brisbane Qld Australia
- Microbiology Division; Pathology Queensland Central Laboratory; Queensland Health; Brisbane Qld Australia
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Goire N, Lahra MM, Ohnishi M, Hogan T, Liminios AE, Nissen MD, Sloots TP, Whiley DM. Polymerase chain reaction-based screening for the ceftriaxone-resistant Neisseria gonorrhoeae F89 strain. ACTA ACUST UNITED AC 2013; 18:20444. [PMID: 23594520 DOI: 10.2807/1560-7917.es2013.18.14.20444] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Emergence and spread of Neisseria gonorrhoeae resistant to extended spectrum cephalosporins is a major problem threatening treatment of gonorrhoea and is further highlighted by the recent report of a second ceftriaxone-resistant N. gonorrhoeae strain (F89) in Europe, initially observed in France and subsequently identified in Spain. N. gonorrhoeae antimicrobial resistance (AMR) surveillance has acquired new importance and molecular tools have the potential to enhance bacterial culture-based methods. In this study, we established a polymerase chain reaction (PCR) protocol for direct detection of the F89 strain. A key component of this screening protocol was the development of a hybridisation probe-based melting curve analysis assay (mosaic501-hybPCR) to detect the presence of an A501P substitution on the N. gonorrhoeae mosaic penicillin binding protein 2 (PBP2) sequence, an important characteristic of the F89 strain. The mosaic501-hybPCR was evaluated using plasmid-derived positive controls (n=3) and characterised gonococcal (n=33) and non-gonococcal (n=58) isolates. The protocol was then applied to 159 clinical specimens from Sydney, Australia, collected during the first half of the year 2012 that were N. gonorrhoeae PCR-positive. Overall, the results indicate that the PCR-based protocol is suitable for direct detection of the N. gonorrhoeae F89 strain in non-cultured clinical samples. It therefore provides an additional tool to aid investigations into the potential spread of F89 strain throughout Europe and elsewhere.
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Affiliation(s)
- N Goire
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, The University of Queensland, Queensland, Australia
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Whiley DM, Limnios A, Moon NJ, Gehrig N, Goire N, Hogan T, Lam A, Jacob K, Lambert SB, Nissen MD, Sloots TP. False-negative results using Neisseria gonorrhoeae porA pseudogene PCR - a clinical gonococcal isolate with an N. meningitidis porA sequence, Australia, March 2011. Euro Surveill 2011; 16:19874. [PMID: 21632019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
The gonococcal porA pseudogene is a popular target for in-house Neisseria gonorrhoeae PCR methods. With this study we present two novel findings: the first case of an N. gonorrhoeae porA pseudogene PCR false-negative result caused by sequence variation, and in the same organism, the first description of a clinical N. gonorrhoeae strain harbouring an N. meningitidis porA sequence.
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Affiliation(s)
- D M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children s Health Services, Australia.
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Whiley DM, Limnios A, Moon NJ, Gehrig N, Goire N, Hogan T, Lam A, Jacob K, Lambert SB, Nissen MD, Sloots TP. False-negative results using Neisseria gonorrhoeae porA pseudogene PCR - a clinical gonococcal isolate with an N. meningitidis porA sequence, Australia, March 2011. Euro Surveill 2011. [DOI: 10.2807/ese.16.21.19874-en] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gonococcal porA pseudogene is a popular target for in-house Neisseria gonorrhoeae PCR methods. With this study we present two novel findings: the first case of an N. gonorrhoeae porA pseudogene PCR false-negative result caused by sequence variation, and in the same organism, the first description of a clinical N. gonorrhoeae strain harbouring an N. meningitidis porA sequence.
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Affiliation(s)
- D M Whiley
- Clinical Medical Virology Centre, Sir Albert Sakzewski Virus Research Centre, The University of Queensland, Queensland, Australia
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - A Limnios
- World Health Organization Collaborating Centre for Sexually Transmitted Diseases, Sydney, Microbiology Department, South Eastern Area Laboratory Services, The Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - N J Moon
- Microbiology Department, Hunter Area Pathology Service, Division of Pathology North, Newcastle, New South Wales, Australia
| | - N Gehrig
- Microbiology Department, Hunter Area Pathology Service, Division of Pathology North, Newcastle, New South Wales, Australia
| | - N Goire
- Clinical Medical Virology Centre, Sir Albert Sakzewski Virus Research Centre, The University of Queensland, Queensland, Australia
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - T Hogan
- World Health Organization Collaborating Centre for Sexually Transmitted Diseases, Sydney, Microbiology Department, South Eastern Area Laboratory Services, The Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - A Lam
- World Health Organization Collaborating Centre for Sexually Transmitted Diseases, Sydney, Microbiology Department, South Eastern Area Laboratory Services, The Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - K Jacob
- Clinical Medical Virology Centre, Sir Albert Sakzewski Virus Research Centre, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
| | - S B Lambert
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
- Clinical Medical Virology Centre, Sir Albert Sakzewski Virus Research Centre, The University of Queensland, Queensland, Australia
| | - M D Nissen
- Microbiology Department, Hunter Area Pathology Service, Division of Pathology North, Newcastle, New South Wales, Australia
- Clinical Medical Virology Centre, Sir Albert Sakzewski Virus Research Centre, The University of Queensland, Queensland, Australia
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - T P Sloots
- Microbiology Department, Hunter Area Pathology Service, Division of Pathology North, Newcastle, New South Wales, Australia
- Clinical Medical Virology Centre, Sir Albert Sakzewski Virus Research Centre, The University of Queensland, Queensland, Australia
- Queensland Children’s Medical Research Institute, The University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, 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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Ferguson PE, Gilroy NM, Sloots TP, Nissen MD, Dwyer DE, Sorrell TC. Evaluation of a clinical scoring system and directed laboratory testing for respiratory virus infection in hematopoietic stem cell transplant recipients. Transpl Infect Dis 2011; 13:448-55. [PMID: 21501357 PMCID: PMC7169734 DOI: 10.1111/j.1399-3062.2011.00631.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
P.E. Ferguson, N.M. Gilroy, T.P. Sloots, M.D. Nissen, D.E. Dwyer, T.C. Sorrell. Evaluation of a clinical scoring system and directed laboratory testing for respiratory virus infection in hematopoietic stem cell transplant recipients.
Transpl Infect Dis 2011: 13: 448–455. xx: 000–000. All rights reserved Abstract: A simple clinical screening (CS) tool for respiratory virus (RV) infection was introduced and evaluated in a single hematology ward, as part of a strategy to reduce nosocomial RV infection. Up to 6 clinical symptoms or signs were scored and a predefined threshold score of ≥2 prompted paired nose/throat swab (NTS) collection for RV testing. The criterion standard for RV infection was positive immunofluorescence (IF) or polymerase chain reaction (PCR) for 7 and 15 viruses, respectively. The tool was shown to be most beneficial at excluding infection at a threshold score of 1 (negative predictive value [NPV] 89%, [95% confidence interval 78–96%], sensitivity 85% [70–94%], specificity 35% [27–43%]), compared with a score of 2 (NPV 85% [76–91%], sensitivity 63% [46–77%], specificity 57% [48–65%]) at a prevalence of 22%. The tool's ability to diagnose infection was limited (positive predictive value 27% and 29% at thresholds 1 and 2). The sensitivity of IF compared with PCR was 45% for the 7 viruses common to both, and 23% for the extended virus panel detected by PCR. An algorithm incorporating CS, paired NTS collection at a threshold of 1 symptom or sign, and sensitive testing including PCR can guide infection control measures in hospitalized hematopoietic stem cell transplant recipients.
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Affiliation(s)
- P E Ferguson
- Centre for Infectious Diseases and Microbiology, and NHMRC Clinical Centre for Research Excellence in Infection, Bioethics and Haematological Malignancies, Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia.
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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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Wainwright CE, France MW, O'Rourke P, Anuj S, Kidd TJ, Nissen MD, Sloots TP, Coulter C, Ristovski Z, Hargreaves M, Rose BR, Harbour C, Bell SC, Fennelly KP. Cough-generated aerosols of Pseudomonas aeruginosa and other Gram-negative bacteria from patients with cystic fibrosis. Thorax 2009; 64:926-31. [PMID: 19574243 PMCID: PMC2764123 DOI: 10.1136/thx.2008.112466] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is the most common bacterial pathogen in patients with cystic fibrosis (CF). Current infection control guidelines aim to prevent transmission via contact and respiratory droplet routes and do not consider the possibility of airborne transmission. It was hypothesised that subjects with CF produce viable respirable bacterial aerosols with coughing. METHODS A cross-sectional study was undertaken of 15 children and 13 adults with CF, 26 chronically infected with P aeruginosa. A cough aerosol sampling system enabled fractioning of respiratory particles of different sizes and culture of viable Gram-negative non-fermentative bacteria. Cough aerosols were collected during 5 min of voluntary coughing and during a sputum induction procedure when tolerated. Standardised quantitative culture and genotyping techniques were used. RESULTS P aeruginosa was isolated in cough aerosols of 25 subjects (89%), 22 of whom produced sputum samples. P aeruginosa from sputum and paired cough aerosols were indistinguishable by molecular typing. In four cases the same genotype was isolated from ambient room air. Approximately 70% of viable aerosols collected during voluntary coughing were of particles <or=3.3 microm aerodynamic diameter. P aeruginosa, Burkholderia cenocepacia, Stenotrophomonas maltophilia and Achromobacter xylosoxidans were cultivated from respiratory particles in this size range. Positive room air samples were associated with high total counts in cough aerosols (p = 0.003). The magnitude of cough aerosols was associated with higher forced expiratory volume in 1 s (r = 0.45, p = 0.02) and higher quantitative sputum culture results (r = 0.58, p = 0.008). CONCLUSION During coughing, patients with CF produce viable aerosols of P aeruginosa and other Gram-negative bacteria of respirable size range, suggesting the potential for airborne transmission.
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Affiliation(s)
- C E Wainwright
- Department of Respiratory Medicine, Royal Children's Hospital and Health Service District, Brisbane, Australia.
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Greer RM, McErlean P, Arden KE, Faux CE, Nitsche A, Lambert SB, Nissen MD, Sloots TP, Mackay IM. Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections? J Clin Virol 2009; 45:10-5. [PMID: 19376742 PMCID: PMC7185458 DOI: 10.1016/j.jcv.2009.03.008] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 03/11/2009] [Accepted: 03/13/2009] [Indexed: 10/31/2022]
Abstract
BACKGROUND Human rhinoviruses (HRVs) are often concurrently detected with other viruses found in the respiratory tract because of the high total number of HRV infections occurring throughout the year. This feature has previously relegated HRVs to being considered passengers in acute respiratory infections. HRVs remain poorly characterized and are seldom included as a target in diagnostic panels despite their pathogenic potential, infection-associated healthcare expenditure and relatively unmoderated elicitation of an antiviral state. OBJECTIVES To test the hypothesis that respiratory viruses are proportionately more or less likely to co-occur, particularly the HRVs. STUDY DESIGN Retrospective PCR-based analyses of 1247 specimens for 17 viruses, including HRV strains, identified 131 specimens containing two or more targets. We investigated the proportions of co-detections and compared the proportion of upper vs. lower respiratory tract presentations in the HRV positive group. Both univariate contingency table and multivariate logistic regression analyses were conducted to identify trends of association among the viruses present in co-detections. RESULTS Many of the co-detections occurred in patterns. In particular, HRV detection was associated with a reduced probability of detecting human adenoviruses, coronaviruses, bocavirus, metapneumovirus, respiratory syncytial virus, parainfluenza virus, influenza A virus, and the polyomaviruses KIPyV and WUPyV (p < or = 0.05). No single HRV species nor cluster of particular strains predominated. CONCLUSIONS HRVs were proportionately under-represented among viral co-detections. For some period, HRVs may render the host less likely to be infected by other viruses.
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Affiliation(s)
- R M Greer
- School of Veterinary Science, University of Queensland, St Lucia, Queensland, Australia
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Bialasiewicz S, Whiley DM, Buhrer-Skinner M, Bautista C, Barker K, Aitken S, Gordon R, Muller R, Lambert SB, Debattista J, Nissen MD, Sloots TP. A novel gel-based method for self-collection and ambient temperature postal transport of urine for PCR detection of Chlamydia trachomatis. Sex Transm Infect 2008; 85:102-5. [PMID: 19004866 DOI: 10.1136/sti.2008.032607] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES The aim of this study was to develop a novel urine transport method to be used in self-collection-based screening for Chlamydia trachomatis. The method needed to be suitable for C trachomatis PCR detection, be economical and suitable for transport by standard envelope mailing. METHODS An anhydrous gel composed of super-absorbent polymer and buffering agent was used to desiccate urine into a dry granulous state, which could subsequently be reconstituted upon arrival at a laboratory. DNA was then extracted from the reconstituted solution using the Roche MagNA Pure protocol for the detection of C trachomatis by PCR. Collections of urine specimens from three populations with widely differing chlamydia prevalence (100%,n = 56; 47%, n = 70; 3%, n = 97) were used. We determined the gel method's impact on C trachomatis PCR sensitivity and specificity using neat and gel-processed urine specimens. An equine herpes virus PCR was used to test for assay inhibition. RESULTS Overall, the sensitivity of the gel-based method ranged from 94.6-100% compared with neat urine, with a specificity of 100%. No PCR inhibition or decrease in analytical sensitivity was observed using the gel-processed extracts. CONCLUSIONS The gel-based method was found to be suitable for the detection of C trachomatis by PCR. In addition, its ease of use, effectiveness at ambient temperature and low cost makes it well-suited for self-collection kits used in population-based C trachomatis screening, particularly for geographically and socially isolated individuals.
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Affiliation(s)
- S Bialasiewicz
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, University of Queensland, Clinical Medical Virology Centre, Queensland, Australia.
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Whiley DM, Lambert SB, Bialasiewicz S, Goire N, Nissen MD, Sloots TP. False-negative results in nucleic acid amplification tests-do we need to routinely use two genetic targets in all assays to overcome problems caused by sequence variation? Crit Rev Microbiol 2008; 34:71-6. [PMID: 18568861 DOI: 10.1080/10408410801960913] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nucleic acid amplification tests (NAATs) have numerous advantages over traditional diagnostic techniques and so are now widely used by diagnostic laboratories for routine detection of infectious agents. However, there is some concern over the increasing numbers of reports of NAAT false-negative results caused by sequence variation. Highly conserved NAAT target sequences have been reported for many organisms, yet sequence-related problems continue to be observed in commercial and in-house assays targeting a broad range of microbial pathogens. In light of these ongoing problems, it may be time to consider the use of two genetic targets in NAAT methods to reduce the potential for sequence-related false-negative results.
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Affiliation(s)
- D M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service Distric, Queensland, Australia.
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Bialasiewicz S, Whiley DM, Lambert SB, Jacob K, Bletchly C, Wang D, Nissen MD, Sloots TP. Presence of the newly discovered human polyomaviruses KI and WU in Australian patients with acute respiratory tract infection. J Clin Virol 2008; 41:63-8. [PMID: 18083616 PMCID: PMC7108439 DOI: 10.1016/j.jcv.2007.11.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 11/01/2007] [Indexed: 11/10/2022]
Abstract
Background Currently, the role of the novel human polyomaviruses, KI (KIV) and WU (WUV) as agents of human disease remains uncertain. Objectives We sought to determine the prevalence of these viruses and their rate of co-detection with other viral respiratory pathogens, in an Australian population. Study design Polymerase chain reaction assays previously described were used to examine the presence of KIV and WUV in 2866 respiratory specimens collected from January to December 2003 from Australian patients with acute respiratory infections. Results KIV and WUV were present in our population with an annual prevalence of 2.6% and 4.5%, respectively. There was no apparent seasonal variation for KIV, but a predominance of infection was detected during late winter to early summer for WUV. The level of co-infection of KIV or WUV with other respiratory viruses was 74.7% and 79.7%, respectively. Both viruses were absent from urine and blood specimens collected from a variety of patient sources. Conclusions KIV and WUV circulate annually in the Australian population. Although there is a strong association with the respiratory tract, more comprehensive studies are required to prove these viruses are agents causing respiratory disease.
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Affiliation(s)
- S Bialasiewicz
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston Road, Herston, Queensland 4029, Australia
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Abstract
The recent advances in molecular technology have enabled the detection of several new viral agents in specimens collected from the human respiratory tract. Human metapneumovirus was first described in 2001, and is a significant respiratory pathogen, particularly of children. Following the identification of severe acute respiratory syndrome (SARS) associated coronavirus, two other newly detected coronaviruses, NL63 and HKU1, have been linked to respiratory disease in humans. However, identifying a new virus as the causative agent of a specific disease is difficult, and ideally would involve satisfying Koch's postulates. The recently described human bocavirus and polyomaviruses KI and WU have been detected in samples collected from humans with acute respiratory infection, but as yet, have not been conclusively proven to be agents of human disease. We review the new viral agents that have been detected in respiratory samples since 2001, and examine their contribution as agents of human disease.
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Affiliation(s)
- T P Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, 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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Affiliation(s)
- M D Nissen
- Department of Clinical Microbiology, Westmead Hospital, New South Wales, Australia.
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18
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Emery RW, Emery AM, Flavin TF, Nissen MD, Mooney MR, Arom KV. Revascularization using angioplasty and minimally invasive techniques documented by thermal imaging. Ann Thorac Surg 1996; 62:591-3. [PMID: 8694640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Minimally invasive direct coronary artery bypass grafting offers mortality and morbidity advantages to selected patients. To broaden indications for such, an appropriate and combined disciplinary approach using angioplasty and minimally invasive direct coronary artery bypass grafting is described in a patient requiring reoperative grafting. Documentation of patency of new left internal mammary artery-to-left anterior descending artery anastomoses performed without the use of cardiopulmonary bypass was obtained intraoperatively using a Thermal Imaging Camera.
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Affiliation(s)
- R W Emery
- Cardiac Surgical Associates, Minneapolis, Minnesota 55407, USA
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19
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Gayes JM, Emery RW, Nissen MD. Anesthetic considerations for patients undergoing minimally invasive coronary artery bypass surgery: mini-sternotomy and mini-thoracotomy approaches. J Cardiothorac Vasc Anesth 1996; 10:531-5. [PMID: 8776652 DOI: 10.1016/s1053-0770(05)80019-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J M Gayes
- Department of Anesthesiology, Abbott Northwestern Hospital, Minneapolis, MN 55407, USA
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Abstract
Myoclonic encephalopathy of infancy (MEI) is a unique cause of acute ataxia in infants and is a rare presentation of neuroblastoma. Five cases presenting to a tertiary referral children's hospital during a 10 year period are reviewed. Two cases were associated with a neuroblastoma. All children were treated with intramuscular injections of adrenocorticotropic hormone, with symptomatic improvement. One child died from an opportunistic infection following chemotherapy for neuroblastoma. The four survivors have mild to moderate clinical and intellectual deficits. Investigation and continuing observation for occult neural crest tumours is emphasized for all cases of MEI, though no underlying cause was found in 60% of children in this study.
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Affiliation(s)
- M D Nissen
- Department of Neurology, Royal Children's Hospital, Herston, Queensland, Australia
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21
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Affiliation(s)
- J M Gayes
- Department of Anesthesiology, Abbott Northwestern Hospital, Minneapolis, MN 55407
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