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Xiao Y, Leung EKY. Over-the-Counter and Direct-to-Consumer Testing for Group A Streptococcus. Clin Biochem 2022; 117:34-38. [DOI: 10.1016/j.clinbiochem.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 11/03/2022]
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Dubois C, Smeesters PR, Refes Y, Levy C, Bidet P, Cohen R, Chalumeau M, Toubiana J, Cohen JF. Diagnostic accuracy of rapid nucleic acid tests for group A streptococcal pharyngitis: systematic review and meta-analysis. Clin Microbiol Infect 2021; 27:1736-1745. [PMID: 33964409 DOI: 10.1016/j.cmi.2021.04.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acute pharyngitis is one of the most common conditions in outpatient settings and an important source of inappropriate antibiotic prescribing. Rapid antigen detection tests (RADTs) offer diagnosis of group A streptococcus at the point of care but have limited sensitivity. Rapid nucleic acid tests (RNATs) are now available; a systematic review of their accuracy is lacking. OBJECTIVES To evaluate the accuracy of RNATs in patients with pharyngitis; to explore test-level and study-level factors that could explain variability in accuracy; and to compare the accuracy of RNATs with that of RADTs. DATA SOURCES MEDLINE, Embase, Web of Science (1990-2020). STUDY ELIGIBILITY CRITERIA Cross-sectional studies and randomized trials. PARTICIPANTS Patients with pharyngitis. INDEX TEST/S AND REFERENCE STANDARDS RNAT commercial kits compared with throat culture. METHODS We assessed risk of bias and applicability using QUADAS-2. We performed meta-analysis of sensitivity and specificity using the bivariate random-effects model. Variability was explored by subgroup analyses and meta-regression. RESULTS We included 38 studies (46 test evaluations; 17 411 test results). RNATs were most often performed in a laboratory. The overall methodological quality of primary studies was uncertain because of incomplete reporting. RNATs had a summary sensitivity of 97.5% (95% CI 96.2%-98.3%) and a summary specificity of 95.1% (95% CI 93.6%-96.3%). There was low variability in estimates across studies. Variability in sensitivity and specificity was partially explained by test type (p < 0.05 for both). Sensitivity analyses limited to studies with low risk of bias showed robust accuracy estimates. RNATs were more sensitive than RADTs (13 studies; 96.8% versus 82.3%, p 0.004); there was no difference in specificity (p 0.92). CONCLUSIONS The high diagnostic accuracy of RNATs may allow their use as stand-alone tests to diagnose group A streptococcus pharyngitis. Based on direct comparisons, RNATs have greater sensitivity than RADTs and equal specificity. Further studies should evaluate RNATs in point-of-care settings.
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Affiliation(s)
- Constance Dubois
- Université de Paris, Centre of Research in Epidemiology and Statistics (CRESS), INSERM, Paris, France
| | - Pierre R Smeesters
- Academic Children Hospital Queen Fabiola, Université libre de Bruxelles, Department of Paediatrics, Brussels, Belgium; Molecular Bacteriology Laboratory, Université libre de Bruxelles, Brussels, Belgium
| | | | - Corinne Levy
- Association Clinique et Thérapeutique Infantile du Val-de-Marne, ACTIV, Créteil, France
| | - Philippe Bidet
- Robert Debré Hospital, APHP, Université de Paris, Department of Microbiology, Paris, France
| | - Robert Cohen
- Association Clinique et Thérapeutique Infantile du Val-de-Marne, ACTIV, Créteil, France
| | - Martin Chalumeau
- Université de Paris, Centre of Research in Epidemiology and Statistics (CRESS), INSERM, Paris, France; Necker-Enfants malades Hospital, APHP, Université de Paris, Department of General Paediatrics and Paediatric Infectious Diseases, Paris, France
| | - Julie Toubiana
- Necker-Enfants malades Hospital, APHP, Université de Paris, Department of General Paediatrics and Paediatric Infectious Diseases, Paris, France; Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Jérémie F Cohen
- Université de Paris, Centre of Research in Epidemiology and Statistics (CRESS), INSERM, Paris, France; Necker-Enfants malades Hospital, APHP, Université de Paris, Department of General Paediatrics and Paediatric Infectious Diseases, Paris, France.
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Dodd M, Adolphe A, Parada A, Brett M, Culbreath K, Mercier RC. Clinical Impact of a Rapid Streptococcal Antigen Test on Antibiotic Use in Adult Patients. Diagn Microbiol Infect Dis 2018; 91:339-344. [PMID: 29731388 DOI: 10.1016/j.diagmicrobio.2018.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Adult pharyngitis is rarely attributable to group A streptococci. Utilization of a rapid streptococcal antigen test (RADT) may improve appropriate prescribing for bacterial pharyngitis. METHODS Clinic 1 performed RADTs with subsequent Group A DNA probe test (GADNA) from November 2014-March 2015 and November 2015-March 2016 while Clinic 2 was the control clinic, then implemented the RADT with a GADNA from November 2015-March 2016. All GADNA results were obtained for each clinic from October 2013-March 2016. RESULTS At Clinic 1, 22.2% versus 8.5% of patients received inappropriately prescribed antibiotics for a GADNA or RADT result, respectively (p=0.048). For Clinic 2, 51.1% compared to 21.4% of patients were inappropriately prescribed antibiotic for a GADNA or RADT result, respectively (p=0.038). Overall, the total GADNA without RADT testing or RADTs with subsequent GADNA testing, 41.6% versus 11% of patients were inappropriately prescribed antibiotics, respectively (p=<0.0001). CONCLUSION Utilizing the RADT prevented unnecessary prescribing of antibiotics in adults.
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Affiliation(s)
- Monique Dodd
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America; TriCore Reference Laboratories, Albuquerque, New Mexico, United States of America
| | - Allen Adolphe
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Alisha Parada
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Meghan Brett
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Karissa Culbreath
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America; TriCore Reference Laboratories, Albuquerque, New Mexico, United States of America
| | - Renée-Claude Mercier
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America.
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Evaluation of Simplexa Group A Strep Direct Kit Compared to Hologic Group A Streptococcal Direct Assay for Detection of Group A Streptococcus in Throat Swabs. J Clin Microbiol 2018; 56:JCM.01666-17. [PMID: 29305544 DOI: 10.1128/jcm.01666-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/21/2017] [Indexed: 11/20/2022] Open
Abstract
Diagnosis of bacterial pharyngitis is confirmed by detection of group A Streptococcus (GAS) in patient throat samples. Testing of throat samples has historically relied on culture, but new molecular methods allow much faster test turnaround time (i.e., same day versus 48 to 72 h for culture). Our laboratory uses the Hologic GAS Direct (GASD) assay for screening more than 125,000 throat samples per year. Simplexa GAS Direct is a new real-time quantitative PCR (qPCR) assay that does not require initial DNA extraction. Performance of Simplexa qPCR was compared to GASD. A total of 289 throat swabs were collected from patients attending ambulatory clinics in Calgary, Alberta, Canada. A total of 60 (20.8%) of the samples were initially GAS positive by either method: 54 by both methods, 4 by Simplex qPCR alone, and 2 by GASD alone. An in-house PCR using a unique GAS primer set was used to resolve the 6 discrepant results. Overall, GASD compared to Simplexa qPCR had a sensitivity, specificity, positive predictive value, and negative predictive value of 93.1% versus 100%, 100% versus 100%, 100% versus 100%, and 98.31% versus 100%, respectively. Implementation of Simplexa qPCR in our laboratory setting would cost more but allow the high sample volume to be reported in half the time and save 0.62 medical laboratory technician (MLT) full-time equivalent (FTE). In comparison to culture, the implementation of Simplexa qPCR would save 2.79 medical laboratory assistant (MLA) FTE plus 0.94 MLT FTE. Simplexa qPCR has improved performance and diagnostic efficiency in a high-volume laboratory compared to GASD for GAS detection in throat swabs.
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Cohen JF, Bertille N, Cohen R, Chalumeau M. Rapid antigen detection test for group A streptococcus in children with pharyngitis. Cochrane Database Syst Rev 2016; 7:CD010502. [PMID: 27374000 PMCID: PMC6457926 DOI: 10.1002/14651858.cd010502.pub2] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Group A streptococcus (GAS) accounts for 20% to 40% of cases of pharyngitis in children; the remaining cases are caused by viruses. Compared with throat culture, rapid antigen detection tests (RADTs) offer diagnosis at the point of care (within five to 10 minutes). OBJECTIVES To determine the diagnostic accuracy of RADTs for diagnosing GAS in children with pharyngitis. To assess the relative diagnostic accuracy of the two major types of RADTs (enzyme immunoassays (EIA) and optical immunoassays (OIA)) by indirect and direct comparison. SEARCH METHODS We searched CENTRAL, MEDLINE, EMBASE, Web of Science, CDSR, DARE, MEDION and TRIP (January 1980 to July 2015). We also conducted related citations tracking via PubMed, handsearched reference lists of included studies and relevant review articles, and screened all articles citing included studies via Google Scholar. SELECTION CRITERIA We included studies that compared RADT for GAS pharyngitis with throat culture on a blood agar plate in a microbiology laboratory in children seen in ambulatory care. DATA COLLECTION AND ANALYSIS Two review authors independently screened titles and abstracts for relevance, assessed full texts for inclusion, and carried out data extraction and quality assessment using the QUADAS-2 tool. We used bivariate meta-analysis to estimate summary sensitivity and specificity, and to investigate heterogeneity across studies. We compared the accuracy of EIA and OIA tests using indirect and direct evidence. MAIN RESULTS We included 98 unique studies in the review (116 test evaluations; 101,121 participants). The overall methodological quality of included studies was poor, mainly because many studies were at high risk of bias regarding patient selection and the reference standard used (in 73% and 43% of test evaluations, respectively). In studies in which all participants underwent both RADT and throat culture (105 test evaluations; 58,244 participants; median prevalence of participants with GAS was 29.5%), RADT had a summary sensitivity of 85.6%; 95% confidence interval (CI) 83.3 to 87.6 and a summary specificity of 95.4%; 95% CI 94.5 to 96.2. There was substantial heterogeneity in sensitivity across studies; specificity was more stable. There was no evidence of a trade-off between sensitivity and specificity. Heterogeneity in accuracy was not explained by study-level characteristics such as whether an enrichment broth was used before plating, mean age and clinical severity of participants, and GAS prevalence. The sensitivity of EIA and OIA tests was comparable (summary sensitivity 85.4% versus 86.2%). Sensitivity analyses showed that summary estimates of sensitivity and specificity were stable in low risk of bias studies. AUTHORS' CONCLUSIONS In a population of 1000 children with a GAS prevalence of 30%, 43 patients with GAS will be missed. Whether or not RADT can be used as a stand-alone test to rule out GAS will depend mainly on the epidemiological context. The sensitivity of EIA and OIA tests seems comparable. RADT specificity is sufficiently high to ensure against unnecessary use of antibiotics. Based on these results, we would expect that amongst 100 children with strep throat, 86 would be correctly detected with the rapid test while 14 would be missed and not receive antibiotic treatment.
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Affiliation(s)
- Jérémie F Cohen
- Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Inserm UMR1153, Paris Descartes UniversityObstetrical, Perinatal and Pediatric Epidemiology Research Team (EPOPé)ParisFrance
- Necker Hospital, AP‐HP and Paris Descartes UniversityDepartment of PediatricsParisFrance
| | - Nathalie Bertille
- Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Inserm UMR1153, Paris Descartes UniversityObstetrical, Perinatal and Pediatric Epidemiology Research Team (EPOPé)ParisFrance
| | - Robert Cohen
- Association Clinique et Thérapeutique Infantile du Val‐de‐Marne (ACTIV)27 Rue InkermannSaint‐Maur‐des‐FossésFrance
- Centre Hospitalier Intercommunal de Créteil (CHIC)Department of Microbiology40 avenue de VerdunCréteilFrance94010
| | - Martin Chalumeau
- Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Inserm UMR1153, Paris Descartes UniversityObstetrical, Perinatal and Pediatric Epidemiology Research Team (EPOPé)ParisFrance
- Necker Hospital, AP‐HP and Paris Descartes UniversityDepartment of PediatricsParisFrance
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Tabb MM, Batterman HJ. The Simplexa™ Group A Strep Direct Assay: a sample-to-answer molecular assay for the diagnosis of group A streptococcal pharyngitis. Expert Rev Mol Diagn 2016; 16:269-76. [DOI: 10.1586/14737159.2016.1133297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Evaluation of the Lyra Direct Strep Assay To Detect Group A Streptococcus and Group C and G Beta-Hemolytic Streptococcus from Pharyngeal Specimens. J Clin Microbiol 2015; 54:175-7. [PMID: 26491174 DOI: 10.1128/jcm.02405-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/13/2015] [Indexed: 11/20/2022] Open
Abstract
The Lyra Direct strep assay was compared to culture for its ability to detect Streptococcus group A and β-hemolytic groups C/G using rapid antigen-negative pharyngeal specimens (n = 161). The Lyra assay correctly detected all β-hemolytic streptococci (group A, n = 19; group C/G, n = 5). In batch mode, the Lyra assay reduced intralaboratory turnaround time by 60% (18.1 h versus 45.0 h) but increased hands-on time by 96% (3 min 16 s versus 1 min 40 s per specimen).
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Molecular and clinical diagnosis of group A streptococcal pharyngitis in children. J Clin Microbiol 2014; 52:3884-9. [PMID: 25143573 DOI: 10.1128/jcm.01489-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Group A Streptococcus (GAS) pharyngitis is a very common condition causing significant morbidity in children. Accurate diagnosis followed by appropriate antimicrobial therapy is recommended to prevent postinfectious sequelae. Diagnosis of GAS pharyngitis by a rapid antigen detection test (RADT) or culture in the absence of discriminating clinical findings remains challenging. Validation of new sensitive rapid diagnostic tests is therefore a priority. The performance of a loop-mediated isothermal amplification (LAMP) assay (illumigene assay) for the diagnosis of GAS pharyngitis was compared with that of a RADT and standard culture in 361 pediatric throat swab samples. Discrepant results were resolved using an alternate molecular assay. Test results were correlated with clinical presentations in patients positive by either method. The closest estimate of the true prevalence of GAS pharyngitis was 19.7% (71/361 samples). The illumigene assay alone detected 70/71 GAS-positive samples; RADT and culture detected 35/71 and 55/71 samples, respectively. RADT followed by culture confirmation of RADT-negative specimens detected 58/71 cases. The illumigene assay increased identification among children eligible for testing by American College of Physicians (ACP)/American Academy of Family Physicians (AAFP) criteria from 31 to 39 positive cases, five of which were false positives. Analysis of clinical data in GAS-positive patients indicated that a significantly greater proportion of children with McIsaac scores of ≥ 4 tested positive by the illumigene assay versus RADT and culture. Overall, the illumigene assay was much more sensitive and was similarly specific for GAS detection, compared to culture alone, RADT alone, or the ACP/AAFP RADT/culture algorithm. Combining high sensitivity with rapidly available results, the illumigene GAS assay is an appropriate alternative to culture for the laboratory diagnosis of GAS pharyngitis in patients for whom testing is clinically indicated.
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Leung AKC, Newman R, Kumar A, Davies HD. Rapid antigen detection testing in diagnosing group A β-hemolytic streptococcal pharyngitis. Expert Rev Mol Diagn 2014; 6:761-6. [PMID: 17009909 DOI: 10.1586/14737159.6.5.761] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Group A beta-hemolytic streptococcus (GABHS) is the most common bacterial cause of acute pharyngitis. Clinical criteria alone are not reliable enough to diagnose GABHS pharyngitis. Microbiological-testing is required for correct diagnosis. Although a throat swab culture remains the gold standard for documenting the presence of GABHS, a significant disadvantage of the culture is the delayed time of 1-2 days to obtain results. Most rapid antigen detection tests can provide results in less than 15 min. Rapid identification and treatment of patients with GABHS pharyngitis can reduce the risk of the spread of disease, may shorten the duration of symptoms, decrease the incidence of suppurative complications, decrease the amount of time lost from school/work, decrease the inappropriate use of antibiotics, reduce patient/parent dissatisfaction and alleviate the need for costly follow-up visits. All rapid antigen detection tests involve extraction of the group-specific carbohydrate antigen from the GABHS cell wall and identification of the antigen by an immunological reaction. There are numerous rapid antigen detection testing methods, namely latex agglutination, enzyme immunoassay, optical immunoassay, chemiluminescent DNA probes and PCR methods. Most of the rapid antigen detection tests that are currently in use have an excellent specificity of greater than 95% and a sensitivity of greater than or equal to 90%. Owing to the high specificity of the rapid antigen detection tests, a positive rapid antigen detection test is accepted as adequate for the diagnosis of GABHS pharyngitis. Conversely, confirmation of a negative antigen detection test with a throat culture result is necessary, unless the physician has ascertained in his/her practice that the sensitivity of the rapid antigen test used is comparable with that of a throat culture.
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Affiliation(s)
- Alexander K C Leung
- University of Calgary and the Alberta Children's Hospital, Department of Pediatrics, Calgary, Alberta, Canada.
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Nakhoul GN, Hickner J. Management of adults with acute streptococcal pharyngitis: minimal value for backup strep testing and overuse of antibiotics. J Gen Intern Med 2013; 28:830-4. [PMID: 23054930 PMCID: PMC3663957 DOI: 10.1007/s11606-012-2245-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/10/2012] [Accepted: 09/24/2012] [Indexed: 11/30/2022]
Abstract
BACKGROUND Rapid antigen detection tests (RADT) are commonly used to guide appropriate antibiotic treatment of group A beta-hemolytic streptococcal (GABHS) pharyngitis. In adults, there is controversy about the need for routine backup testing of negative RADT. OBJECTIVE Estimate the costs and benefits in adults of routine backup testing by DNA Gen-probe of negative RADT (Acceava). DESIGN Observational follow-up study. PARTICIPANTS All patients aged 18 years and older visiting a Cleveland Clinic generalist physician in 2009 and 2010 with a visit diagnosis of acute pharyngitis (ICD codes 462, 034.0). MAIN MEASURES The patients were identified using the Cleveland Clinic Epic Clarity database. We determined the proportion of false negative RADT, antibiotic prescription patterns and rate of serious suppurative complications within 30 days of the office visit. KEY RESULTS Of 25,130 patients with acute pharyngitis, 19% had no testing and 81% were tested. Of the 15,555 patients that had a negative RADT and follow-up DNA probe, 6% had a positive DNA probe. Of the 953 patients who had a negative RADT and a positive DNA strep probe, 48% received an antibiotic prescription at the time of the visit and 51% received an antibiotic prescription after an average of 2.3 days. Only one patient with a negative RADT and no follow-up DNA probe developed a peritonsillar abscess. Overall, of the 15,555 DNA probes performed, management was altered in only 3% of the patients at a total cost of $1,757,715. Fifty-six percent received an antibiotic while only 19.5% had a confirmed strep throat diagnosis. CONCLUSIONS The false negative rate of Acceava RADT for the diagnosis of GABHS pharyngitis was 6%. We question the benefit of routine DNA probe backup testing in adults because of its substantial cost, an average delay in antibiotic prescribing of over 2 days, and because suppurative complications are very uncommon. We found a high rate of inappropriate antibiotic prescribing.
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Affiliation(s)
- Georges N Nakhoul
- Cleveland Clinic Foundation, Internal Medicine Residency Office 9500 Euclid Avenue, Cleveland, OH 44195, USA.
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Multicenter clinical evaluation of the illumigene group A Streptococcus DNA amplification assay for detection of group A Streptococcus from pharyngeal swabs. J Clin Microbiol 2013; 51:1474-7. [PMID: 23447639 DOI: 10.1128/jcm.00176-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute pharyngitis is a nonspecific symptom that can result from a number of viral or bacterial infections. For most etiologies, symptoms are self-limited and resolve without lasting effects; however, pharyngitis resulting from infection with Streptococcus pyogenes (a group A Streptococcus [GAS]) can be associated with serious sequelae, including acute rheumatic fever and acute glomerulonephritis. Rapid accurate detection of GAS in pharyngeal specimens from individuals suffering from pharyngitis aids in the management and selection of antibiotic therapy for these patients. A total of 796 pharyngeal swabs were collected at three separate clinical centers. Each specimen was analyzed using the illumigene group A strep DNA amplification assay (Meridian Bioscience Inc., Cincinnati, OH). To confirm GAS identification, the results were compared to those from direct and extracted culture methods using Gram staining and a GAS-specific latex agglutination test. Discrepant results were resolved using an alternative nucleic acid amplification test. The prevalence of culture-detected GAS in this study was 12.8% (102/796 specimens). The illumigene assay detected GAS in 74/74 direct culture-positive specimens (100% sensitivity) and 100/102 extracted culture-positive specimens (98.0% sensitivity). GAS was detected by the illumigene assay in an additional 42 specimens that were direct culture negative (94.2% specificity) and 16 specimens that were extracted culture negative (97.7% specificity). Discrepant analysis using an alternative molecular assay detected GAS nucleic acid in 13/16 (81.3%) false-positive specimens and 1/2 false-negative specimens, resulting in a final sensitivity of 99.0% and a specificity of 99.6% for the detection of GAS in pharyngeal swabs using the illumigene assay.
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DNA Probes for Culture Confirmation and Direct Detection of Bacterial and Fungal Infections: a Review of Current Technologies and Assays. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch2] [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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Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG. Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 2004; 42:3686-95. [PMID: 15297518 PMCID: PMC497632 DOI: 10.1128/jcm.42.8.3686-3695.2004] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 761-bp portion of the tuf gene (encoding the elongation factor Tu) from 28 clinically relevant streptococcal species was obtained by sequencing amplicons generated using broad-range PCR primers. These tuf sequences were used to select Streptococcus-specific PCR primers and to perform phylogenetic analysis. The specificity of the PCR assay was verified using 102 different bacterial species, including the 28 streptococcal species. Genomic DNA purified from all streptococcal species was efficiently detected, whereas there was no amplification with DNA from 72 of the 74 nonstreptococcal bacterial species tested. There was cross-amplification with DNAs from Enterococcus durans and Lactococcus lactis. However, the 15 to 31% nucleotide sequence divergence in the 761-bp tuf portion of these two species compared to any streptococcal tuf sequence provides ample sequence divergence to allow the development of internal probes specific to streptococci. The Streptococcus-specific assay was highly sensitive for all 28 streptococcal species tested (i.e., detection limit of 1 to 10 genome copies per PCR). The tuf sequence data was also used to perform extensive phylogenetic analysis, which was generally in agreement with phylogeny determined on the basis of 16S rRNA gene data. However, the tuf gene provided a better discrimination at the streptococcal species level that should be particularly useful for the identification of very closely related species. In conclusion, tuf appears more suitable than the 16S ribosomal RNA gene for the development of diagnostic assays for the detection and identification of streptococcal species because of its higher level of species-specific genetic divergence.
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Affiliation(s)
- François J Picard
- Centre de Recherche en Infectiologie de l'Université Laval, Centre Hospitalier Universitaire de Québec, Pavillon CHUL, 2705 Boul. Laurier, Ste-Foy, Québec, Canada G1V 4G2
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Gerber MA, Shulman ST. Rapid diagnosis of pharyngitis caused by group A streptococci. Clin Microbiol Rev 2004; 17:571-80, table of contents. [PMID: 15258094 PMCID: PMC452552 DOI: 10.1128/cmr.17.3.571-580.2004] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although commercial rapid antigen detection tests (RADTs) are more expensive than blood agar plate (BAP) cultures, the advantage they offer is the speed with which they provide results. Rapid identification and consequent prompt treatment of patients with pharyngitis due to group A beta-hemolytic streptococci (GABHS) can reduce the risk of spread of GABHS, can allow patients to return to school or work sooner, and may reduce the acute morbidity of this illness. In most studies, RADTs have been compared with BAP cultures as the criterion standard. However, these comparisons are complicated by the fact that there is no universally accepted procedure for performing a BAP culture. The great majority of the RADTs that are currently available have a high specificity (i.e., 95% or greater) and a sensitivity of between 70 and 90% compared with BAP cultures. Few published studies have compared the performance of various RADTs to each other or examined the performance of various RADTs in the office setting. There is also relatively little published information about how physicians in practice actually use RADTs, but the available information suggests that many physicians do not follow recommended guidelines. While the development of easy-to-perform RADTs for the diagnosis of GABHS pharyngitis has altered clinical practice substantially, only limited data about cost-effectiveness are currently available.
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Affiliation(s)
- Michael A Gerber
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MC5019, Cincinnati, OH 45229-3039, USA.
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Bourbeau PP, Heiter BJ. Use of swabs without transport media for the Gen-Probe Group A Strep Direct Test. J Clin Microbiol 2004; 42:3207-11. [PMID: 15243083 PMCID: PMC446290 DOI: 10.1128/jcm.42.7.3207-3211.2004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For several years we used rayon or Dacron swabs with liquid transport media for collection and transport of throat swab specimens for testing with the Gen-Probe Group A Strep Direct Test (GASDT). A report of favorable results with a Dacron swab without any transport media for GASDT by another laboratory prompted us to compare detection of group A streptococci (GAS) with and without transport media (referred to as "wet" and "dry" swabs, respectively). Phase one of this study used swabs seeded with GAS. Initially, six recent clinical isolates of GAS were inoculated onto wet and dry swabs and stored at room temperature (RT). After 1, 2, and 3 days of storage, colony counting and GASDT were performed with the swabs. The results, expressed as the mean percentage of the results at zero time, were as follows: for GASDT with wet swabs at 1, 2, and 3 days, 62, 51, and 56%, respectively; for GASDT with dry swabs at 1, 2, and 3 days, 105, 80, and 85%, respectively; for colony counts with wet swabs at 1, 2, and 3 days, 52, 26, and 13%, respectively; for colony counts with dry swabs at 1, 2, and 3 days, 10, 0, and 0%, respectively. An additional six strains of GAS were tested in a similar manner, except that extracts of pharyngeal flora (PF) were added to the inocula. The results obtained with extracts of PF were comparable to those obtained with GAS alone. We also compared the performance of GASDT with wet and dry swabs stored at RT and 4 degrees C. Ten strains of GAS were inoculated onto wet and dry swabs, and GASDT was performed each day for 9 days. The GASDT results for swabs on day 9, expressed as the mean percentage of the results obtained at zero time, were as follows: dry swab and 4 degrees C, 59%; wet swab and 4 degrees C, 31%; dry swab and RT, 33%; and wet swab and RT, 19%. In phase two of this study we conducted a clinical evaluation to determine whether the differences observed with seeded specimens would also be evident with patient specimens. We used a single dry Dacron swab paired with a single rayon Bacti-Swab with liquid Stuart transport medium for the clinical evaluation. Specimens were collected from 1,005 outpatients, plated onto a Strep Selective Agar plate, and then tested within 30 min by GASDT. If culture of GAS from the same swab is used to define a true-positive test result, the sensitivities and specificities were as follows: GASDT with wet swabs, 86.2 and 98.5%, respectively; GASDT with dry swabs, 90.7 and 98.1%, respectively. However, the use of culture as the "gold standard" may understate the actual performance characteristics of GASDT, particularly for the dry swabs. In conclusion, for GASDT the use of swabs without transport media may be preferable to the use of swabs with transport media.
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Affiliation(s)
- Paul P Bourbeau
- Division of Laboratory Medicine, Geisinger Medical Center, Danville, PA 17822-0131, USA.
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Bourbeau PP. Role of the microbiology laboratory in diagnosis and management of pharyngitis. J Clin Microbiol 2003; 41:3467-72. [PMID: 12904340 PMCID: PMC179871 DOI: 10.1128/jcm.41.8.3467-3472.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Paul P Bourbeau
- Division of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania 17822-0131, USA.
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Bourbeau PP, Heiter BJ. Evaluation of Copan swabs with liquid transport media for use in the Gen-Probe Group A Strep Direct Test. J Clin Microbiol 2003; 41:2686-9. [PMID: 12791905 PMCID: PMC156473 DOI: 10.1128/jcm.41.6.2686-2689.2003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gen-Probe Group A Streptococcus Direct Test (GASDT), which detects the presence or absence of group A streptococci directly from pharyngeal specimens, utilizes a specific relative light unit (RLU) cutoff of 4,500 to differentiate between positive and negative test results. In response to a report by a manufacturer that the background RLU values for the Copan rayon swabs with liquid media were higher than the RLU values typically observed with Culturette swabs, we tested multiple lots of Copan rayon swabs with liquid media and determined that the swabs are unacceptable for routine use in the GASDT. The high background RLU values for the Copan rayon swabs appear to be a direct result of the gamma irradiation used to sterilize the swabs. We also performed a comparative clinical evaluation of Copan Dacron swabs with liquid media and Culturette swabs for use in the GASDT. Overall, there was 97.5% agreement between the results obtained with the Copan Dacron swabs and those obtained with the Culturette swabs. Compared to Culturette swabs, the Copan Dacron swabs had a sensitivity and a specificity of 97 and 98%, respectively. Copan Dacron swabs with liquid media are an acceptable alternative to the swabs currently qualified for use with the GASDT, but Copan rayon swabs with liquid transport media should not be used in the GASDT.
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Affiliation(s)
- Paul P Bourbeau
- Division of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania 17822, USA.
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19
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Schmuziger N, Schneider S, Frei R. [Reliability and general practice value of 2 rapid Streptococcus A tests]. HNO 2003; 51:806-12. [PMID: 14523534 DOI: 10.1007/s00106-003-0816-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Rapid streptococcal-A-antigen detection assays have good specificity (over 90 percent) but moderate sensitivity (between 80 and 90 percent), when the tests are compared with a standard throat culture. Contradictory results have been found for one of the more recent tests, the optical immune assay Strep A OIA MAX, while for 6 years, we have been using the immune assay Strep A Plus. Results of the optical immunoassay and the conventional immune assay Strep A Plus were compared in 65 patients with acute pharyngitis. A standard culture was used as reference and confirmed by enhanced broth culturing and nucleic acid hybridization assay (Gen-Probe) when the two detection assays produced contradictory results. While both assays were equally sensitive (78.3%), Strep A OIA MAX and Strep A Plus had a similar specificity of 95.2% and 100%, respectively. Four and nine steps were required for Strep A Plus and for Strep A OIA MAX test procedures, respectively with results being available in 4-5 min and in 9-10 min, respectively. We conclude that both rapid immunoassays have a similar reliability while the handling of the Strep A Plus is much simpler than the handling of the Strep A OIA MAX. Neither rapid immunoassays are sensitive enough to eliminate the need for backup cultures.
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Affiliation(s)
- N Schmuziger
- HNO-Universitätsklinik, Kantonspital Basel, Germany.
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Uhl JR, Adamson SC, Vetter EA, Schleck CD, Harmsen WS, Iverson LK, Santrach PJ, Henry NK, Cockerill FR. Comparison of LightCycler PCR, rapid antigen immunoassay, and culture for detection of group A streptococci from throat swabs. J Clin Microbiol 2003; 41:242-9. [PMID: 12517855 PMCID: PMC149598 DOI: 10.1128/jcm.41.1.242-249.2003] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared the performance characteristics of a real-time PCR method, the LightCycler Strep-A assay (Roche Applied Science, Indianapolis, Ind.), to those of a rapid antigen immunoassay, the Directigen 1-2-3 Group A Strep Test kit (BD Diagnostic Systems, Sparks, Md.), and a standard culture method for detection of group A streptococci (GAS) from 384 throat swabs. The LightCycler PCR produced more positive results (n = 58) than either culture (n = 55) or the Directigen immunoassay (n = 31). The results of the LightCycler PCR and the Directigen method were independently compared to the results of the accepted "gold standard," bacterial culture. The sensitivities, specificities, and positive and negative predictive values for this comparison were as follows: for the Directigen method, 55, 99, 97, and 93%, respectively; for the LightCycler PCR, 93, 98, 88, and 99%, respectively. In no case was a throat swab positive by both the LightCycler PCR and the Directigen method but negative by culture. The medical histories of patients whose throat swabs were negative by culture but positive by either the LightCycler PCR (n = 7) or the Directigen method (n = 1) were reviewed. All of these patients had signs or symptoms compatible with GAS disease, and therefore, all of these discordant positive results (along with positive results by either the Directigen method or the LightCycler PCR that agreed with the culture results) were counted as true positives for statistical analysis. For this analysis, the LightCycler PCR detected more true-positive results than the culture method (58 versus 55 swabs); however, this difference was not statistically significant (P = 0.5465). In contrast, statistically significantly more true-positive results occurred by culture than by the Directigen method (55 versus 31 swabs; P < 0.0001) and by the LightCycler PCR than by the Directigen method (58 versus 31 swabs; P < 0.0001). The LightCycler PCR is a suitable stand-alone method for the detection of GAS from throat swabs. Additionally, this method requires less than half the personnel time and the procedure can be completed in considerably less time ( approximately 1 h) than our standard approach (up to 2 days) for detection of GAS in throat swabs (i.e., testing by the Directigen method with negative results verified by culture).
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Affiliation(s)
- J R Uhl
- Division of Clinical Microbiology, Mayo Clinic and Foundation, Rochester, Minnesota 55905, USA
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21
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Chapin KC, Blake P, Wilson CD. Performance characteristics and utilization of rapid antigen test, DNA probe, and culture for detection of group a streptococci in an acute care clinic. J Clin Microbiol 2002; 40:4207-10. [PMID: 12409399 PMCID: PMC139657 DOI: 10.1128/jcm.40.11.4207-4210.2002] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Group A streptococcus (GAS) antigen testing has become a routine point-of-care (POC) test in acute care settings. Concern about performance parameters (PP) of these tests as well as inappropriate antibiotic use has resulted in various recommendations regarding diagnosis of GAS. There were two objectives in this study. The first was to evaluate the rapid GAS antigen test presently in use (Thermo BioStar, Boulder, Colo.) and the GAS Direct probe test (Gen-Probe, San Diego, Calif.) compared to culture. The second was to define the optimal use of these technologies in a large acute care pediatric clinic. A total of 520 consecutive pediatric patients presenting with symptoms of pharyngitis at any of three Lahey Clinic acute care facilities were evaluated. Pharyngeal specimens were collected using a double-swab collection device (Copan, Corona, Calif.). One swab was used for the antigen test, the second was used for the probe test, and the pledget was placed in the collection device for culture on 5% sheep blood agar, incubated for 48 h anaerobically, and subsequently placed in Todd-Hewitt broth. After discrepant analysis, sensitivity, specificity, and positive and negative predictive values were as follows: 94.8, 100, 100, and 96.9% for the probe test and 86.1, 97.1, 93.7, and 93.4% for the antigen test, respectively. Sensitivity using an enhanced culture technique was 99.4% (163 of 164). False-positive (FP) antigen results were often seen from patients previously diagnosed and/or treated for GAS. No FP results were seen with the probe test. Colony counts for the false-negative (FN) antigen tests were higher than those for the FN probe tests. Compared to culture and DNA probe, the rapid antigen test (RAT) offered a result at the time of the patient's visit, with acceptable PP when prevalence of disease is high. Follow-up testing with the RAT of GAS patients who previously tested as positive should be avoided due to increased FP results. The probe test was comparable to culture in performance. Results indicate the probe test can be used as the primary test or as a backup to negative antigen tests. The probe test offers the advantage over culture of same-day reporting of a final result but, in contrast to a POC test, necessitates follow-up communication to the patient. Preliminary data show the specificity of the probe test to be greater than that of the RAT for patients previously diagnosed with GAS.
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Affiliation(s)
- Kimberle C Chapin
- Department of Laboratory Medicine. Department of Pediatrics, Lahey Clinic Medical Center, Burlington, Massachusetts 01805, USA.
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Abstract
Molecular testing methods have the potential to replace many conventional microbiology laboratory assays. Recent refinements in technology have resulted in more user-friendly testing platforms. These platforms are automated and have lowered risks for contamination, decreased costs, and are faster than older platforms. The success of these technologies depends on their successful application to patient care. Quality issues include appropriate specimens for analysis, performance characteristics of different analytical methods, optimal specimen processing, the effects of PCR inhibitors, and false-positive results caused by contaminating nucleic acids. Quality control guidelines for molecular microbiologic diagnostic assays are in their infancy and require further development. Additionally, the problem of "too much" sensitivity (brought on by the extreme sensitivity of these techniques coupled with the potential presence of small numbers of pathogenic organisms in asymptomatic individuals) should be considered. Potential problems when monitoring therapy (because molecular detection techniques do not generally have the ability to determine whether an organism is dead or alive) can also occur. Cost-effective test use, pathogen- or disease-targeted algorithms, and standardized methods will be necessary for the true value of these technologies to be realized. This is especially important, because, unlike traditional culture methods, most molecular microbiology methods are pathogen-specific. Clinicians familiar with the reasons why "pan-culture" (i.e., requesting all culture possibilities at once) is inadvisable should not use the same irrational approach when requesting molecular tests. The clinical usefulness of molecular testing will be maximized as targeted algorithms are developed and an understanding of molecular test ordering patterns is realized. Laboratory technicians and physicians must continue to apply and combine theories of traditional microbiology, clinical chemistry, and general medicine to the understanding and application of molecular diagnostics.
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Affiliation(s)
- D Wolk
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
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Whelen AC, Persing DH. The role of nucleic acid amplification and detection in the clinical microbiology laboratory. Annu Rev Microbiol 1996; 50:349-73. [PMID: 8905084 DOI: 10.1146/annurev.micro.50.1.349] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Clinical microbiology is in the midst of a new era. Methodology that is based on nucleic acid detection has slowly appeared in the diagnostic laboratory, and is revolutionizing our ability to assist physicians in the diagnosis and management of patients suffering from infectious diseases. Much like the introduction of immunoassays built around hybridoma technology in the 1980s, considerable doubt and promise exist hand in hand in the 1990s. Conventional testing that is technically straight forward, informative, and timely will always be a part of clinical microbiology; however, considerable room for improvement exists with organisms/diseases for which laboratory methods are limited. Nucleic acid methodology will have its greatest and long-awaited impact in this arena.
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Affiliation(s)
- A C Whelen
- Microbiology Service, Brooke Army Medical Center, Fort Sam Houston, San Antonio, Texas 78234, USA
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Heelan JS, Wilbur S, Depetris G, Letourneau C. Rapid antigen testing for group A Streptococcus by DNA probe. Diagn Microbiol Infect Dis 1996; 24:65-9. [PMID: 9147910 DOI: 10.1016/0732-8893(95)00275-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Gen-probe group A Streptococcus direct test (GASD), a nucleic acid probe assay for detecting GAS from throat swabs, has recently been developed. The test uses an acridium ester-labeled DNA probe which is complementary to the rRNA of Streptococcus pyogenes. In this study, 318 single culturette throat swabs were tested by this method using culture as a "gold standard." After plating onto trypticase soy agar plates with 5% sheep blood, swabs were stored at 4 degrees C for no more than 72 h before the probe assay was performed. Our patient population consisted of symptomatic outpatients seen in the Memorial Hospital Emergency Department and in the Family Care Center. After discrepancy testing, sensitivity, specificity, and positive and negative predictive values were 91.4%, 97%, 91.4%, and 97%. The GASD is a rapid, easy-to-perform method for batch screening for streptococcal pharyngitis.
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Affiliation(s)
- J S Heelan
- Department of Pathology, Memorial Hospital of Rhode Island, Pawtucket, USA
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Dale JC, Vetter EA, Contezac JM, Iverson LK, Wollan PC, Cockerill FR. Evaluation of two rapid antigen assays, BioStar Strep A OIA and Pacific Biotech CARDS O.S., and culture for detection of group A streptococci in throat swabs. J Clin Microbiol 1994; 32:2698-701. [PMID: 7852559 PMCID: PMC264145 DOI: 10.1128/jcm.32.11.2698-2701.1994] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Two rapid methods, BioStar Strep A OIA (OIA; BioStar, Inc., Boulder, Colo.), an optical immunoassay, and CARDS O.S. (O.S.; Pacific Biotech, Inc., San Diego, Calif.), a color immunochromographic assay, and two culture methods, one with 5% sheep blood agar (SBA) and one with Todd-Hewitt broth (TH; Remel, Lenexa, Kans.), were evaluated for use in the detection of Streptococcus pyogenes from pharnygeal swabs. Seven hundred forty-six double swabs (Culturette II) were processed, with OIA and SBA culture performed on one swab and O.S. and SBA culture performed on the other swab. The pledget from the Culturette II was incubated overnight in TH and was subcultured onto SBA for an additional 48 h in ambient air. All beta-hemolytic streptococci from culture were tested by a direct fluorescent-antibody test (Difco Laboratories, Detroit, Mich.). Specimens with discordant fluorescent-antibody test and rapid test results were also tested by using the Streptex latex agglutination reagent (Murex Diagnostics Limited, Dartford, England). The results obtained by all testing methods were compared with a combined test result ("gold standard"), which was defined as any positive culture detected by the SBA or TH culture methods and confirmed by Streptex latex agglutination or, in the case of negative results by both culture methods, a concomitant positive result by OIA and O.S. antigen testing. Sensitivity and specificity results for each of the methods were as follows, respectively: OIA, 81.0 and 97.5%; O.S., 74.4 and 99.0%; SBA culture, 92.3 and 98.3%; and TH culture, 86.4 and 100%. Both OIA and O.S. are suitable screening methods for detecting S. pyogenes directly from throat swabs but are of insufficient sensitivity to eliminate the need for backup cultures for specimens with negative OIA and O.S. results.
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Affiliation(s)
- J C Dale
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905
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