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Santos CGD, Sabidó M, Leturiondo AL, Ferreira CDO, da Cruz TP, Benzaken AS. Development, validation and testing costs of an in-house real-time PCR assay for the detection of Chlamydia trachomatis. J Med Microbiol 2017; 66:312-317. [PMID: 28141509 DOI: 10.1099/jmm.0.000443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To improve the screening of Chlamydia trachomatis(C. trachomatis) in Brazil, an accurate and affordable method is needed. The objective of this study was to develop and assess the performance and costs of a new in-house real-time PCR (qPCR) assay for the diagnosis of C. trachomatis infection. METHODOLOGY Asymptomatic women aged 14-25 years who attended primary health services in Manaus, Brazil, were screened for C. trachomatis using the Digene Hybrid Capture II CT-ID (HCII CT-ID) DNA test. A subset of cervical specimens were tested using an in-house qPCR and a commercial qPCR, ArtusC. trachomatis Plus RG PCR 96 CE (Artus qPCR) kit, as a reference test. A primer/probe based on the sequence of cryptic plasmid (CP) was designed. An economic evaluation was conducted from the provider's perspective. RESULTS The primers were considered specific for C. trachomatis because they did not amplify any product from non-sexually transmitted bacterial species tested. Overall, 292 specimens were tested by both the commercial kit (Artus qPCR) and the in-house qPCR. Of those, one resulted in no amplification and was excluded from the analysis. The sensitivity, specificity, and positive and negative predictive values of the in-house qPCR were 99.5 % [95 % confidence interval (CI): 97.1-100], 95.1 % (95 % CI: 89-98.4), 97.4 % (95 % CI: 94-99.1) and 99.0 % (95 % CI: 94.5-100), respectively. The cost per case of C. trachomatis was £0.44 ($0.55) for HCII CT-ID, £1.16 ($1.45) for Artus qPCR and £1.06 ($1.33) for in-house qPCR. CONCLUSION We have standardized an in-house qPCR to detect cervical C. trachomatis targeting CP. The in-house qPCR showed excellent accuracy and was more affordable than the commercial qPCR kit.
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Affiliation(s)
- Camila Gurgel Dos Santos
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil.,Fundação Alfredo da Matta, Manaus, Amazonas, Brazil
| | - Meritxell Sabidó
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil.,TransLab, Departament of Medical Sciences, Universitat de Girona, Catalunya, Spain.,CIBER de Epidemiologia y Salud Pública, CIBERESP, Spain
| | | | | | | | - Adele Schwartz Benzaken
- Fundação Alfredo da Matta, Manaus, Amazonas, Brazil.,Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil.,Departamento de IST, Aids e Hepatites Virais, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Brazil
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Neves D, Sabidó M, Bôtto-Menezes C, Benzaken NS, Jardim L, Ferreira C, Leturiondo A, Santos CGD, Benzaken AS. Evaluation of screening for Chlamydia trachomatis among young women in primary health care services in Manaus, Amazonas State, Brazil. CAD SAUDE PUBLICA 2016; 32:e00101015. [PMID: 27783757 DOI: 10.1590/0102-311x00101015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 01/05/2016] [Indexed: 11/22/2022] Open
Abstract
Screening for Chlamydia trachomatis is not routinely offered to young asymptomatic women in Brazil. This study evaluated the performance, usefulness, and operational suitability of the Digene Hybrid Capture II (HCII) CT-ID DNA-test as an opportunistic screening tool to detect C. trachomatis in the public health system in Manaus, Amazonas State. Women aged 14-25 years who attended primary health care services were interviewed and one cervical specimen was collected during cytological screening. The HCII CT test was evaluated for its ability to detect the presence of C. trachomatis and against real-time PCR (q-PCR) in a subset of samples. Operational performance was assessed through interviews with providers and patients. Overall, 1,187 women were screened, and 1,169 had a HCII CT-ID test result (292 of these were also tested by q-PCR). Of those, 13.1% (n = 153) were positive. The sensitivity, specificity, positive and negative predictive values of HCII CT were 72.3% (95%CI: 65.4-78.6), 91.3% (95%CI: 84.1-95.9), 93.8% (95%CI: 88.5-97.1), and 64.4% (95%CI: 56.0-72.1), respectively. Sample collection caused discomfort in 19.7% of women. Among health professionals (n = 52), the main barriers reported included positive cases who did not return for results (56.4%), unwillingness to screen without an appointment (45.1%), and increase in their workload (38.8%). HCII CT-ID identified a high proportion of C. trachomatis cases among young women in Manaus. However, its moderate sensitivity limits its use as an opportunistic screening tool in primary health care settings in Manaus. Screening was well accepted although the barriers we identified, especially among health professionals, challenge screening detection and treatment efforts.
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Affiliation(s)
- Dária Neves
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Brasil
| | - Meritxell Sabidó
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Brasil
| | - Camila Bôtto-Menezes
- Programa de Pós-graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Brasil
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Gibson J, Young S, Leng B, Zreik R, Rao A. Molecular diagnostic testing of cytology specimens: current applications and future considerations. J Am Soc Cytopathol 2014; 3:280-294. [PMID: 31051718 DOI: 10.1016/j.jasc.2014.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/12/2014] [Accepted: 08/12/2014] [Indexed: 06/09/2023]
Abstract
Molecular mechanisms of pathogenesis continue to be discovered, accelerating significant expansion of the spectrum of clinically useful molecular diagnostic tests and their incorporation into patient care algorithms. Currently, molecular assays facilitate identification of infectious processes, detection of specific constitutional and somatically acquired pathogenic mutations, guidance of therapy selection, and monitoring of treatment response and disease progression. The correlation of genomic test results with clinical, morphologic, and immunophenotypic findings has defined the practice of "precision medicine" with wide-reaching implications for health care. As novel promising techniques such as microarrays and next-generation sequencing are adopted by health care providers, new practice standards are being developed for incorporation into practice. Cytology specimens are good sources of high-quality nucleic acids. Although sometimes limited in quantity, in many cases such specimens are well suited for molecular diagnostic testing, which is capable of maximizing the number of tests from small amounts of sample. The pathologist continues to serve as a central resource for diagnostic testing and consultation regarding appropriate use of molecular tests. Understanding current methodologies, clinical utility of currently available nucleic acid tests, validation requirements for test implementation, quality assurance metrics, and future technology trends is essential to the practice of contemporary molecular pathology.
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Affiliation(s)
- Jane Gibson
- Department of Clinical Sciences, University of Central Florida College of Medicine, 6850 Lake Nona Boulevard, Orlando, Florida.
| | - Stephen Young
- Tricore Reference Laboratories, University of New Mexico, Albuquerque, New Mexico
| | - Bing Leng
- Department of Pathology, Scott & White Healthcare and Texas A&M Health Science Center College of Medicine, Temple, Texas
| | - Riyam Zreik
- Department of Pathology, Scott & White Healthcare and Texas A&M Health Science Center College of Medicine, Temple, Texas
| | - Arundhati Rao
- Department of Pathology, Scott & White Healthcare and Texas A&M Health Science Center College of Medicine, Temple, Texas
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Levi AW, Beckman D, Hui P, Schofield K, Harigopal M, Chhieng DC. Comparing two methods of detection for Chlamydia trachomatis in liquid-based Papanicolaou tests. Am J Clin Pathol 2012; 138:236-40. [PMID: 22904135 DOI: 10.1309/ajcp2b7xqtcnamjp] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
This study compared the performance of Chlamydia trachomatis testing using 2 methods: the BD ProbeTec Chlamydia trachomatis Q(x) Amplified DNA Assay (CTQ) on the BD Viper System with XTR technology (CTQ assay) and the Hybrid Capture (HC) 2 assay. A total of 1,054 Surepath and ThinPrep specimens were tested for C trachomatis nucleic acids using the CTQ assay and the HC2 assay. For positive and discrepant C trachomatis test results, confirmatory test for C trachomatis was performed using a reverse transcriptase-polymerase chain reaction. Of 1,054 liquid-based gynecologic cytology samples tested for C trachomatis using both assays, 1,041 tested negative on both. In 6 (0.57%) samples, findings were discordant. The CTQ assay and the HC2 assay had sensitivity rates of 100% and 66.7%, respectively, with comparable specificity (99.9%). The positive predictive values were 92.3% and 88.9% with the CTQ and HC2 assays, respectively. In this study, the CTQ assay was found to be more sensitive than the HC2 assay in detecting chlamydial infection; the CTQ assay also demonstrated a higher positive predictive value.
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Affiliation(s)
| | | | - Pei Hui
- Department of Pathology, Yale University, New Haven, CT
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Singh A, Arutyunov D, Szymanski CM, Evoy S. Bacteriophage based probes for pathogen detection. Analyst 2012; 137:3405-21. [PMID: 22724121 DOI: 10.1039/c2an35371g] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid and specific detection of pathogenic bacteria is important for the proper treatment, containment and prevention of human, animal and plant diseases. Identifying unique biological probes to achieve a high degree of specificity and minimize false positives has therefore garnered much interest in recent years. Bacteriophages are obligate intracellular parasites that subvert bacterial cell resources for their own multiplication and production of disseminative new virions, which repeat the cycle by binding specifically to the host surface receptors and injecting genetic material into the bacterial cells. The precision of host recognition in phages is imparted by the receptor binding proteins (RBPs) that are often located in the tail-spike or tail fiber protein assemblies of the virions. Phage host recognition specificity has been traditionally exploited for bacterial typing using laborious and time consuming bacterial growth assays. At the same time this feature makes phage virions or RBPs an excellent choice for the development of probes capable of selectively capturing bacteria on solid surfaces with subsequent quick and automatic detection of the binding event. This review focuses on the description of pathogen detection approaches based on immobilized phage virions as well as pure recombinant RBPs. Specific advantages of RBP-based molecular probes are also discussed.
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Affiliation(s)
- Amit Singh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4, Canada.
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Performance of the cobas CT/NG test compared to the Aptima AC2 and Viper CTQ/GCQ assays for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. J Clin Microbiol 2012; 50:2244-9. [PMID: 22518864 DOI: 10.1128/jcm.06481-11] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The next-generation amplification test for Chlamydia trachomatis and Neisseria gonorrhoeae (Roche cobas 4800), a fully automated system, was compared head to head, using female samples, to Gen-Probe Aptima Combo 2 and BD ProbeTec using Viper. Endocervical swabs, female urine, and endocervical samples in liquid-based cytology medium were run on at least two of three platforms. A total of 4,316 samples were evaluated, and 281 chlamydial and 69 gonococcal infections were identified. Estimates of sensitivity and specificity were obtained relative to the patient infection standard (PIS) and using latent class analysis (LCA). Chlamydia sensitivity estimates ranged from 86.9 to 95.6% using PIS and 97.6 to 98% using LCA. Specificity was ≥ 99.6% for all sample types. Sensitivity ranged from 95.6 to 100% using PIS and 96.9 to 100% using LCA for the detection of gonococcal infections. Specificity for gonococcal infections was ≥ 99.8%. cobas 4800 performance was equivalent to the comparator assays (all P values, >0.05), and the fully automated system provides high laboratory efficiency.
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Procop GW. Molecular diagnostics for the detection and characterization of microbial pathogens. Clin Infect Dis 2007; 45 Suppl 2:S99-S111. [PMID: 17683022 DOI: 10.1086/519259] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
New and advanced methods of molecular diagnostics are changing the way we practice clinical microbiology, which affects the practice of medicine. Signal amplification and real-time nucleic acid amplification technologies offer a sensitive and specific result with a more rapid turnaround time than has ever before been possible. Numerous methods of postamplification analysis afford the simultaneous detection and differentiation of numerous microbial pathogens, their mechanisms of resistance, and the construction of disease-specific assays. The technical feasibility of these assays has already been demonstrated. How these new, often more expensive tests will be incorporated into routine practice and the impact they will have on patient care remain to be determined. One of the most attractive uses for such techniques is to achieve a more rapid characterization of the infectious agent so that a narrower-spectrum antimicrobial agent may be used, which should have an impact on resistance patterns.
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Affiliation(s)
- Gary W Procop
- Department of Pathology, Jackson Memorial Hospital and University of Miami Miller School of Medicine, Miami, Florida 33136, USA.
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Marshall R, Chernesky M, Jang D, Hook EW, Cartwright CP, Howell-Adams B, Ho S, Welk J, Lai-Zhang J, Brashear J, Diedrich B, Otis K, Webb E, Robinson J, Yu H. Characteristics of the m2000 automated sample preparation and multiplex real-time PCR system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. J Clin Microbiol 2007; 45:747-51. [PMID: 17202273 PMCID: PMC1829145 DOI: 10.1128/jcm.01956-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay.
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Affiliation(s)
- R Marshall
- Abbott Molecular Inc., Des Plaines, IL 60018, USA
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Taha NSA, Focchi J, Ribalta JCL, Castelo A, Lorincz A, Dôres GB. Universal Collection Medium (UCM)® is as suitable as the Standard Transport Medium (STM)® for Hybrid Capture II® (HC-2) assay. J Clin Virol 2006; 36:32-5. [PMID: 16483839 DOI: 10.1016/j.jcv.2005.12.011] [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] [Received: 06/03/2005] [Revised: 12/06/2005] [Accepted: 12/12/2005] [Indexed: 11/20/2022]
Abstract
BACKGROUND Collection of cervical-vaginal material in liquid media enables simultaneous evaluation of both oncologic cytology and molecular tests for the detection of Human papillomavirus (HPV), Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG). Universal Collection Medium (UCM) has been developed to fulfill this objective. OBJECTIVES To compare Hybrid Capture II (HC-2) to diagnose HPV, NG and CT in specimens collected in UCM and in the current Digene Standard Transport Medium (STM). STUDY DESIGN The study was cross-sectional. Three collections of endocervical and ectocervical material were performed in each of 893 women referred for colposcopy in the following order: (1) to prepare a conventional Pap smear slide using the accompanying brush of the STM kit and with Ayre spatula; (2) for HC-2 test and liquid-based cytology using a 1 ml UCM vial as transport medium; material was collected with another similar brush; (3) for HC-2 test using a 1 ml STM vial as transport medium; material was collected with the same brush that we used in the procedure no. (1) (conventional Pap smear). HC-2 results from samples taken from STM and UCM media were compared by using simple linear regression analysis and Kappa statistic. RESULTS AND CONCLUSIONS HC-2 results from the two media were highly correlated: high-risk HPV (kappa=0.92; r(2)=0.92), low-risk HPV (kappa=0.85; r(2)=0.86) and NG/CT (kappa=0.96; r(2)=0.81). Despite being obtained from a second specimen, the UCM HC-2 results were equivalent to those obtained with the standard medium STM and the UCM medium.
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Affiliation(s)
- Nabiha Saadi Abrahão Taha
- Department of Gynecology, Federal University of São Paulo-Escola Paulista de Medicina (UNIFESP-EPM), Rua Borges Lagoa, 1231 CJ 62, CEP 04038-034, São Paulo (SP), Brazil.
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Mothershed EA, Whitney AM. Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory. Clin Chim Acta 2006; 363:206-20. [PMID: 16139259 DOI: 10.1016/j.cccn.2005.05.050] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 05/25/2005] [Accepted: 05/26/2005] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in nucleic acid-based methods to detect bacteria offer increased sensitivity and specificity over traditional microbiological techniques. The potential benefit of nucleic acid-based testing to the clinical laboratory is reduced time to diagnosis, high throughput, and accurate and reliable results. METHODS Several PCR and hybridization tests are commercially available for specific organism detection. Furthermore, hundreds of nucleic acid-based bacterial detection tests have been published in the literature and could be adapted for use in the clinical setting. Contamination potential, lack of standardization or validation for some assays, complex interpretation of results, and increased cost are possible limitations of these tests, however, and must be carefully considered before implementing them in the clinical laboratory. CONCLUSIONS A major area of advancement in nucleic acid-based assay development has been for specific and broad-range detection of bacterial pathogens.
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Affiliation(s)
- Elizabeth A Mothershed
- Meningitis and Special Pathogens Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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