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Obande GA, Banga Singh KK. Current and Future Perspectives on Isothermal Nucleic Acid Amplification Technologies for Diagnosing Infections. Infect Drug Resist 2020; 13:455-483. [PMID: 32104017 PMCID: PMC7024801 DOI: 10.2147/idr.s217571] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
Nucleic acid amplification technology (NAAT) has assumed a critical position in disease diagnosis in recent times and contributed significantly to healthcare. Application of these methods has resulted in a more sensitive, accurate and rapid diagnosis of infectious diseases than older traditional methods like culture-based identification. NAAT such as the polymerase chain reaction (PCR) is widely applied but seldom available to resource-limited settings. Isothermal amplification (IA) methods provide a rapid, sensitive, specific, simpler and less expensive procedure for detecting nucleic acid from samples. However, not all of these IA techniques find regular applications in infectious diseases diagnosis. Disease diagnosis and treatment could be improved, and the rapidly increasing problem of antimicrobial resistance reduced, with improvement, adaptation, and application of isothermal amplification methods in clinical settings, especially in developing countries. This review centres on some isothermal techniques that have found documented applications in infectious diseases diagnosis, highlighting their principles, development, strengths, setbacks and imminent potentials for use at points of care.
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Affiliation(s)
- Godwin Attah Obande
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Microbiology, Faculty of Science, Federal University Lafia, Lafia, Nasarawa State, Nigeria
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
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Göçmen JS, Cağlayan O, Azap A. An Easy-to-Use, Rapid and Inexpensive Method to Determine Methicillin Resistance In Staphylococcus aureus. JOURNAL OF CLINICAL AND EXPERIMENTAL INVESTIGATIONS 2016. [DOI: 10.5799/jcei.328616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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3
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Liu Y, Zhang J, Ji Y. PCR-based Approaches for the Detection of Clinical Methicillin-resistant Staphylococcus aureus. Open Microbiol J 2016; 10:45-56. [PMID: 27335617 PMCID: PMC4899539 DOI: 10.2174/1874285801610010045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus is an important pathogen that can cause a variety of infections, including superficial and systematic infections, in humans and animals. The persistent emergence of multidrug resistant S. aureus, particularly methicillin-resistant S. aureus, has caused dramatically economic burden and concerns in the public health due to limited options of treatment of MRSA infections. In order to make a correct choice of treatment for physicians and understand the prevalence of MRSA, it is extremely critical to precisely and timely diagnose the pathogen that induces a specific infection of patients and to reveal the antibiotic resistant profile of the pathogen. In this review, we outlined different PCR-based approaches that have been successfully utilized for the rapid detection of S. aureus, including MRSA and MSSA, directly from various clinical specimens. The sensitivity and specificity of detections were pointed out. Both advantages and disadvantages of listed approaches were discussed. Importantly, an alternative approach is necessary to further confirm the detection results from the molecular diagnostic assays.
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Affiliation(s)
- Ying Liu
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, China; Department of Veterinary Biomedical Science, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
| | - Jiang Zhang
- Shanghai Vocational College of Agriculture and Forestry, Shanghai, China
| | - Yinduo Ji
- Department of Veterinary Biomedical Science, College of Veterinary Medicine, University of Minnesota, Saint Paul, United States
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4
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Molecular Detection and Identification of Methicillin‐Resistant
Staphylococcus aureus. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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te Witt R, van Belkum A, van Leeuwen WB. Molecular diagnostics and genotyping of MRSA: an update. Expert Rev Mol Diagn 2010; 10:375-80. [PMID: 20465491 DOI: 10.1586/erm.10.34] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Pasanen T, Korkeila M, Mero S, Tarkka E, Piiparinen H, Vuopio-Varkila J, Vaara M, Tissari P. A selective broth enrichment combined with real-time nuc-mecA-PCR in the exclusion of MRSA. APMIS 2010; 118:74-80. [PMID: 20041874 DOI: 10.1111/j.1600-0463.2009.02562.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We analyzed the performance of a selective enrichment broth combined with Taqman-based real-time duplex nuc-mecA-PCR to expedite the screening of methicillin-resistant Staphylococcus aureus (MRSA). We found the broth to be able to select MRSA strains (oxacillin MIC range 4-256 microg/ml) from MSSA strains. A total of 31 MRSA strains were found from 1250 clinical samples screened. The nuc-mecA-PCR was positive from all enrichment broths containing MRSA. From the remaining 1219 samples negative for MRSA on culture/subculture, 138 samples were nuc+/mecA+ in PCR. The sensitivity of the test was 93.5%, specificity 88.6%, positive predictive value 17.3%, and negative predictive value 99.8% as compared to culture. Thus, with this method, the negative MRSA results can be reliably reported within 24-48 h from sampling. The method is a practical additional alternative to those already described for the same purpose.
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Affiliation(s)
- Tanja Pasanen
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
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Molecular Diagnostics and Comparative Genomics in Clinical Microbiology. MOLECULAR DIAGNOSTICS 2010. [PMCID: PMC7150202 DOI: 10.1016/b978-0-12-374537-8.00030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Initially, the availability of molecular diagnostics was considered a panacea, but replacement of conventional tests for detection and identification of microorganisms by molecular procedures eventually gathered momentum. This chapter describes current state-of-the-art molecular diagnostics and comparative genomics in medical microbiology to provide an understanding of infectious disease over the coming years. Nucleic acid-based tests are being introduced with increasing speed into routine clinical microbiology laboratories. Some of the problems remaining to be solved prior to general acceptance of nucleic acid-mediated detection and identification of microbial pathogens are reviewed. Historic objections are slowly being taken apart, and an accelerated introduction of molecular diagnostics is being pursued in many cases. Clear improvement in clinical testing is achieved by introducing molecular tests. Therefore, swift introduction of such tests into clinical practice is important to be pursued. Several PCR tests show increased sensitivity, excellent specificity, and cost effectiveness highlighting the success of the novel applications in the field of bacterial infections. Finally, some of the problems remaining to be solved prior to general acceptation of nucleic acid-mediated detection and identification of microbial pathogens are also reviewed.
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Naikare H, Ramachandran A, Goad D, Clarke J, Clarke C. CE-based detection of methicillin-resistant Staphylococcus aureus. Electrophoresis 2009; 30:472-8. [PMID: 19156761 DOI: 10.1002/elps.200800360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Rapid and sensitive detection of methicillin-resistant Staphylococcus aureus is crucial for effective treatment and control of clinical infections caused by this bacterium. The goal of this study is to develop a CE-based detection method for multiplexed identification of a femA sequence specific for S. aureus and a unique mecA sequence encoding methicillin resistance. Blood samples spiked with known concentrations of bacteria were used for testing. Crude cell lysates were prepared by treating the spiked blood samples with DNazol Direct reagent and used as the template for isothermal amplification of mecA and femA genes. The amplified gene products then underwent a cycling probe reaction (CPR)-based assay to generate a short fluorophore-labeled oligonucleotide for detection in a CZE-LIF system. The assay enables a gene-specific fluorophore-labeled DNA-RNA-DNA chimeric probe to hybridize with complementary target in the presence of RNase H enzyme. The RNase H enzyme specifically cleaves probe RNA residues of the duplex, releasing a fluorophore fragment for detection and the target for recycling and hybridization with another chimeric probe. Intact and cleaved probe fragments were separated and detected using a CZE-LIF system. The limit of detection for isothermal amplification and CPR-CZE-LIF was approximately 10(4) colony-forming units of bacteria/mL of blood. This method accurately detects methicillin-resistant S. aureus within 3 h.
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Affiliation(s)
- Hemant Naikare
- Texas Veterinary Medical Diagnostic Laboratory, Amarillo, TX 19106, USA.
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Khorvash F, Mostafavizadeh K, Mobasherizadeh S. Frequency of mecA gene and borderline oxacillin resistant Staphylococcus aureus in nosocomial acquired methicillin resistance Staphylococcus aureus infections. Pak J Biol Sci 2008; 11:1282-1285. [PMID: 18819540 DOI: 10.3923/pjbs.2008.1282.1285] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The aim of the study was to determine the frequency and type of MRSA strains and antibiotic susceptibility in Al-Zahra Hospital, Isfahan, Iran. In an analytic descriptive survey in 2005 and early 2006, patients admitted to the hospital who contracted S. aureus nosocomial infections were enrolled in the study. All isolates were identified by the conventional laboratory tests. Minimal Inhibitory Concentration (MIC) of oxacillin on isolated bacteria was determined by E-Test method. According to Clinical and Laboratory Standard Institute (CLSI) criteria all strains with MIC of > or = 4 microg for oxacillin were identified as MRSA. Intrinsic high level resistance (mecA positive) and borderline oxacillin resistant Staphylococcus aureus (BORSA) were detected by amoxicillin-clavulanate E-test strips. Strains with MIC of > or = 4 microg for oxacillin and > or = 8 microg for amoxicillin-clavulanate were identified as mecA positive MRSA. Other staphylococcus with MIC > or = 4 microg for oxacillin and < or = 4 for amoxicillin-clavulanate were identified as mecA negative MRSA (BORSA). MIC of vancomycin also was determined on isolated bacteria. Data were analyzed by SPSS version 13 and Who net version 5. Out of 134 Staphylococcus aureus samples which were isolated from nosocomial infections 90 (67.2%) were MRSA. Sixty seven out of 90 (74.5%) MRSA were mecA positive and 23 out of 90 (25.5%) were mecA negative (BORSA). Although most of the MRSA strains were isolated from surgical site infections, there were no statistically significant differences between types of Staphylococcus aureus growing from variant sites of infections. Only one (1.49) of the mecA positive MRSA had reduced susceptibility to vancomycin but all of the mecA-negative MRSA (BORSA) were sensitive to it. Because one fourth of our staphylococcus strains are mecA negative BORSA and there is no alternative for vancomycin against mecA positive MRSA and Enterococcus spp. in our hospital, vancomycin should be reserved only for life threatening infections due to these organisms. Thus MRSA typing should be done to choose appropriate antibiotic for optimal treatment of MRSA infections.
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Affiliation(s)
- F Khorvash
- Isfahan University of Medical Sciences, Hezar Jerib Street, Isfahan, Iran
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Savelkoul PHM, Melles DC, Buffing N, Gorkink R, Simons G, van Belkum A. High density whole genome fingerprinting of methicillin-resistant and -susceptible strains of Staphylococcus aureus in search of phenotype-specific molecular determinants. J Microbiol Methods 2007; 71:44-54. [PMID: 17854930 DOI: 10.1016/j.mimet.2007.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 07/24/2007] [Indexed: 10/23/2022]
Abstract
AFLP is a selective restriction fragment amplification method generating DNA fingerprints for microbial isolates. We present high-throughput AFLP (htAFLP) to characterize molecular markers associated with bacterial phenotypes. Methicillin-resistant and -susceptible isolates of Staphylococcus aureus have been used for this model study in conjunction with the available S. aureus genome sequences. This facilitates the calculation of theoretical AFLP fingerprints, comparison of these fingerprints with genuine experimental fingerprints, and the subsequent identification of polymorphic AFLP markers without sequence analysis. Analysis of 46 MRSA and 46 MSSA strains by 39 different AFLP reactions generated more than 2500 fragments per strain and an overall number of 6180 scorable markers within all strains. We successfully identify MRSA specific markers and elaborate on the general applicability of the htAFLP approach. This method can be applied to any microbial species for which at least one full-genome sequence is available.
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Affiliation(s)
- Paul H M Savelkoul
- VU University Medical Center, Department of Medical Microbiology & Infection Control, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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11
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Abstract
Staphylococci are among the leading causes of nosocomial infections. Increasing insusceptibility to beta-lactams and the glycopeptides complicates treatment of these infections. This review examines the current status and future perspectives for the therapy of infections caused by Staphylococcus aureus and coagulase-negative staphylococci.
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Affiliation(s)
- A L Casey
- Department of Clinical Microbiology and Infection Control, University Hospital Birmingham NHS Foundation Trust, The Queen Elizabeth Hospital, Edgbaston, Birmingham B15 2TH, UK
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12
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Wharam SD, Hall MJ, Wilson WH. Detection of virus mRNA within infected host cells using an isothermal nucleic acid amplification assay: marine cyanophage gene expression within Synechococcus sp. Virol J 2007; 4:52. [PMID: 17553149 PMCID: PMC1904187 DOI: 10.1186/1743-422x-4-52] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 06/06/2007] [Indexed: 11/14/2022] Open
Abstract
Background Signal-Mediated Amplification of RNA Technology (SMART) is an isothermal nucleic acid amplification technology, developed for the detection of specific target sequences, either RNA (for expression) or DNA. Cyanophages are viruses that infect cyanobacteria. Marine cyanophages are ubiquitous in the surface layers of the ocean where they infect members of the globally important genus Synechococcus. Results Here we report that the SMART assay allowed us to differentiate between infected and non-infected host cultures. Expression of the cyanophage strain S-PM2 portal vertex gene (g20) was detected from infected host Synechococcus sp. WH7803 cells. Using the SMART assay, we demonstrated that g20 mRNA peaked 240 – 360 minutes post-infection, allowing us to characterise this as a mid to late transcript. g20 DNA was also detected, peaking 10 hours post-infection, coinciding with the onset of host lysis. Conclusion The SMART assay is based on isothermal nucleic acid amplification, allowing the detection of specific sequences of DNA or RNA. It was shown to be suitable for differentiating between virus-infected and non-infected host cultures and for the detection of virus gene expression: the first reported use of this technology for such applications.
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Affiliation(s)
- Susan D Wharam
- Bigelow Laboratory for Ocean Sciences, 180 McKown Point, West Boothbay Harbor, Maine 04575, USA
- Cytocell Ltd., Banbury Business Park, Adderbury, OX17 3SN, UK
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Matthew J Hall
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
| | - William H Wilson
- Bigelow Laboratory for Ocean Sciences, 180 McKown Point, West Boothbay Harbor, Maine 04575, USA
- Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK
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13
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Jury F, Al-Mahrous M, Apostolou M, Sandiford S, Fox A, Ollier W, Upton M. Rapid cost-effective subtyping of meticillin-resistant Staphylococcus aureus by denaturing HPLC. J Med Microbiol 2006; 55:1053-1060. [PMID: 16849725 DOI: 10.1099/jmm.0.46409-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The importance of meticillin-resistant Staphylococcus aureus (MRSA) in hospital-acquired infection is widely acknowledged. The UK government has stated that MRSA bloodstream infection rates will have to be halved by 2008. Such radical improvements will require advances on several fronts. Screening for MRSA in high-risk patients on arrival at hospital allows isolation of carriers and reduces transmission to staff and other patients. Concurrent subtyping of MRSA could also inform outbreak investigations and long-term epidemiological studies. The variability within the staphylococcal protein A, or spaA, gene-repeat region can be used as a marker of short- and long-term genetic variation. A novel application is described of denaturing HPLC (DHPLC) for rapid, inexpensive characterization of spaA gene amplification products, without the need for DNA sequence determination. The method allowed rapid and precise sizing of spaA gene-repeat regions from 99 S. aureus strains and was combined with heteroduplex analysis, using reference PCR products, to indicate the spa type of the test isolate. The method allowed subtyping of strains in less than 5 h from receipt of a primary isolation plate. When applied to an outbreak that occurred during this study, the authors were able to demonstrate relatedness of the isolates more than 5 days before results were received from a reference laboratory. If combined with direct amplification from swabs, DHPLC analysis of spaA gene variation could prove extremely valuable in outbreak investigation and MRSA surveillance.
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Affiliation(s)
- F Jury
- Centre for Integrated Genomic Medical Research, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
| | - M Al-Mahrous
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - M Apostolou
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - S Sandiford
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - A Fox
- Health Protection Agency (HPA) North West Laboratory, Manchester Medical Microbiology Partnership, Clinical Sciences Building 2, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
| | - W Ollier
- Centre for Integrated Genomic Medical Research, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
| | - M Upton
- Division of Laboratory and Regenerative Medicine, Faculty of Medical and Human Sciences, University of Manchester, Clinical Sciences Building 1, Manchester Royal Infirmary, Oxford Road, Manchester M13 9WL, UK
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Brown DFJ, Edwards DI, Hawkey PM, Morrison D, Ridgway GL, Towner KJ, Wren MWD. Guidelines for the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA). J Antimicrob Chemother 2005; 56:1000-18. [PMID: 16293678 DOI: 10.1093/jac/dki372] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
These evidence-based guidelines have been produced after a literature review of the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA). We have considered the detection of MRSA in screening samples and the detection of reduced susceptibility to glycopeptides in S. aureus. Recommendations are given for the identification of S. aureus and for suitable methods of susceptibility testing and screening for MRSA and for S. aureus with reduced susceptibility to glycopeptides. These guidelines indicate what tests should be used but not when the tests are applicable, as aspects of this are dealt with in guidelines on control of MRSA. There are currently several developments in screening media and molecular methods. It is likely that some of our recommendations will require modification as the new methods become available.
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Affiliation(s)
- Derek F J Brown
- Health Protection Agency, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QW, UK
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15
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Metan G, Zarakolu P, Unal S. Rapid detection of antibacterial resistance in emerging Gram-positive cocci. J Hosp Infect 2005; 61:93-9. [PMID: 16009459 DOI: 10.1016/j.jhin.2005.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Accepted: 02/28/2005] [Indexed: 01/07/2023]
Abstract
Effective infection control efforts obviously depend on the performance of the laboratory to detect emerging resistant pathogens accurately and confirm resistance patterns by additional methods to conventional or automated systems. Conventional methods still remain the predominant approaches for detection and identification of bacteria and resistance patterns. However, the estimated time for conventional tests to detect resistance is at least 24-48 h for methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and other epidemiologically important pathogens. Most of the tests used for rapid detection require bacterial growth in culture. There is an important clinical need for rapid detection of bacteria directly from patient samples. Rapid methods based on immunological or molecular technologies have contributed significantly. Molecular assays for several resistance markers are reliable, such as for mecA in staphylococci and vanA in enterococci. However, for other resistance markers, there is a lack of field testing. Cost-effectiveness of rapid detection of antibacterial resistance is another concern. Molecular assays would be useful for tertiary hospitals considering the investment costs and requirement of expert laboratory staff. For smaller centres, rapid tests based on immunological techniques may be a better choice.
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Affiliation(s)
- G Metan
- Section of Infectious Diseases, Department of Medicine, Hacettepe University School of Medicine, 06100 Ankara, Turkey
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Woodford N, Sundsfjord A. Molecular detection of antibiotic resistance: when and where? J Antimicrob Chemother 2005; 56:259-61. [PMID: 15967769 DOI: 10.1093/jac/dki195] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance is a key issue affecting public health, and diagnostic bacteriology laboratories are essential for prompt recognition of resistant isolates. Determination of susceptibility or resistance using phenotypic tests is a 'gold standard' against which newer technologies are compared in terms of performance, cost and ease of use. Molecular methods for detecting resistance are myriad, and are used widely in academia and in reference laboratories, but gaining a significant foothold in diagnostic laboratories is proving more difficult. However, if used widely in a diagnostic setting, these techniques would impact more directly on patient care and would be valuable infection control tools, e.g. by rapidly confirming patients colonized by resistant bacteria. The cost of molecular assays may be considered prohibitive, and this is compounded by the daunting variety of proprietary platforms available; most diagnostic laboratories would prefer to invest their capital and to train their staff in a single versatile technology. In a market that has no clear leader, many laboratories are understandably reluctant to gamble on making the correct choice. If molecular detection of resistance is to achieve wide acceptance, manufacturers must broaden the repertoires of their technologies, develop more off-the-shelf applications with in-built quality control, and make them suitable for laboratory personnel with no specialist expertise in molecular biology.
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Affiliation(s)
- Neil Woodford
- Antibiotic Resistance Monitoring and Reference Laboratory, Centre for Infections, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK.
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17
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Levi K, Towner KJ. Rapid detection of methicillin-resistant Staphylococcus aureus from screening enrichment broths by real-time PCR. Eur J Clin Microbiol Infect Dis 2005; 24:423-7. [PMID: 15926061 DOI: 10.1007/s10096-005-1336-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The aim of this study was to evaluate real-time PCR (LightCycler) kits for the detection of methicillin-resistant Staphylococcus aureus in enrichment broth using 200 sets of patient screening swab samples. One hundred sets were processed using a lysostaphin/lysozyme extraction method and a further 100 were tested using a column extraction kit. The PCR kits with lysostaphin/lysozyme lysis showed 95.7% sensitivity, 90.8% specificity, and negative and positive predictive values of 98.6% and 75.9%, respectively, compared with 88%, 95.9%, 84.6% and 95.9%, respectively, with the column extraction kit.
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Affiliation(s)
- K Levi
- Department of Microbiology, Molecular Diagnostics and Typing Unit, University Hospital, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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18
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Huletsky A, Lebel P, Picard FJ, Bernier M, Gagnon M, Boucher N, Bergeron MG. Identification of methicillin-resistant Staphylococcus aureus carriage in less than 1 hour during a hospital surveillance program. Clin Infect Dis 2005; 40:976-81. [PMID: 15824989 DOI: 10.1086/428579] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Accepted: 11/22/2004] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) has spread worldwide and is responsible for significant morbidity, mortality, and health care costs. Control strategies to limit the emergence and spread of this organism rely on rapid and sensitive tests for detection of MRSA carriage. However, the standard surveillance culture method for detecting MRSA is labor intensive and time-consuming (2-3 days per procedure). There is thus a need for a rapid and accurate method to screen for MRSA carriage. METHODS We recently developed an easy-to-use real-time polymerase chain reaction (PCR) assay suitable for specific detection of MRSA in nasal specimens in <1 h. We studied the efficacy of our new PCR assay in routine screening for nasal MRSA carriage during a hospital surveillance program. A total of 331 nasal specimens obtained from 162 patients at risk for colonization were tested by both the standard mannitol agar culture method and our PCR assay. RESULTS The PCR assay detected MRSA in all 81 samples that were culture positive for MRSA. The PCR assay detected 4 additional MRSA-positive specimens, for a specificity of 98.4%, a positive predictive value of 95.3%, and a sensitivity and negative predictive value of 100%. CONCLUSIONS This novel PCR assay allows reliable identification of MRSA carriers in <1 h. This test should facilitate the efficacy of MRSA surveillance programs.
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Affiliation(s)
- Ann Huletsky
- Centre de Recherche en Infectiologie, Universite Laval, Sainte-Foy, Canada
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19
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Paule SM, Pasquariello AC, Hacek DM, Fisher AG, Thomson RB, Kaul KL, Peterson LR. Direct detection of Staphylococcus aureus from adult and neonate nasal swab specimens using real-time polymerase chain reaction. J Mol Diagn 2005; 6:191-6. [PMID: 15269294 PMCID: PMC1876277 DOI: 10.1016/s1525-1578(10)60509-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nasal carriage of Staphylococcus aureus is considered a source of subsequent infection in health care settings. Utilization of real-time polymerase chain reaction (PCR) for detection of S. aureus has the potential to dramatically affect infection control practice by rapidly identifying S. aureus-colonized patients. We developed and validated the use of real-time PCR for detection of S. aureus colonization in two patient populations. Paired nasal swabs were collected from 299 neonates and from 151 adult patients at Evanston Hospital. One swab was used for culture and the other placed into a bacterial lysis solution containing achromopeptidase. The DNA liberated was used as the template for real-time PCR with primers for the femA gene. SYBR Green was used for amplicon detection. In the neonatal population the sensitivity, specificity, predictive value positive and predictive value negative for culture and PCR was 92% versus 96%, 100% versus 100%, 100% versus 100%, and 98% versus 99%, respectively. In the adults the results were 90% versus 100%, 100% versus 98%, 100% versus 96%, and 95% versus 100%, respectively. Real-time PCR was able to detect S. aureus in 2 hours compared to 1 to 4 days for culture and provided sensitivity equal to or greater than culture.
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Affiliation(s)
- Suzanne M Paule
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Evanston Northwestern Healthcare, 2650 Ridge Avenue, Evanston, IL 60201, USA.
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Diekema DJ, Dodgson KJ, Sigurdardottir B, Pfaller MA. Rapid detection of antimicrobial-resistant organism carriage: an unmet clinical need. J Clin Microbiol 2004; 42:2879-83. [PMID: 15243032 PMCID: PMC446269 DOI: 10.1128/jcm.42.7.2879-2883.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Daniel J Diekema
- Department of Internal Medicine, Division of Medical Microbiology, C 606 GH, 200 Hawkins Dr., Iowa City, IA 52242, USA.
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