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Nolte FS. Molecular Microbiology. PRINCIPLES AND APPLICATIONS OF MOLECULAR DIAGNOSTICS 2018. [PMCID: PMC7150357 DOI: 10.1016/b978-0-12-816061-9.00005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background Nucleic acid (NA) amplification techniques are now commonly used to diagnose and manage patients with infectious diseases. The growth in the number of Food and Drug Administration–approved test kits and analyte-specific reagents has facilitated the use of this technology in clinical laboratories. Technological advances in NA amplification techniques, automation, NA sequencing, and multiplex analysis have reinvigorated the field and created new opportunities for growth. Simple, sample-in, answer-out molecular test systems are now widely available that can be deployed in a variety of laboratory and clinical settings. Molecular microbiology remains the leading area in molecular pathology in terms of both the numbers of tests performed and clinical relevance. NA-based tests have reduced the dependency of the clinical microbiology laboratory on more traditional antigen detection and culture methods and created new opportunities for the laboratory to impact patient care. Content This chapter reviews NA testing as it applies to specific pathogens or infectious disease syndromes, with a focus on those diseases for which NA testing is now considered the standard of care and highlights the unique challenges and opportunities that these tests present for clinical laboratories.
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[Expression of gamma interferon during HPV and Chlamydia trachomatis infection in cervical samples]. Enferm Infecc Microbiol Clin 2014; 33:105-9. [PMID: 25541008 DOI: 10.1016/j.eimc.2014.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/27/2014] [Accepted: 05/29/2014] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The aim of this study was to mesure the expression of gamma interferon in HPV and Chlamydia trachomatis infection in squamous intraepithelial lesions. METHOD Samples from 100 patients diagnosed by colposcopy with or without squamous intraepithelial lesions were used in the present study. Each patient was found to be infected by HPV and C.trachomatis. Relative gamma interferon mRNA expression was assessed using a real-time reverse transcriptase PCR assay (RT-PCR). RESULTS The relative units of expression of gamma interferon mRNA were 13, 1.8 and 0.3, for HPV and C.trachomatis co-infection, or HPV or C.trachomatis infection, respectively. CONCLUSION HPV and C.trachomatis could overstimulate the expression of gamma interferon.
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Khader SN, Schlesinger K, Grossman J, Henry RI, Suhrland M, Fox AS. APTIMA assay on SurePath liquid-based cervical samples compared to endocervical swab samples facilitated by a real time database. Cytojournal 2010; 7:11. [PMID: 20806073 PMCID: PMC2924530 DOI: 10.4103/1742-6413.65057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 02/09/2010] [Indexed: 11/21/2022] Open
Abstract
Background: Liquid-based cytology (LBC) cervical samples are increasingly being used to test for pathogens, including: HPV, Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) using nucleic acid amplification tests. Several reports have shown the accuracy of such testing on ThinPrep (TP) LBC samples. Fewer studies have evaluated SurePath (SP) LBC samples, which utilize a different specimen preservative. This study was undertaken to assess the performance of the Aptima Combo 2 Assay (AC2) for CT and GC on SP versus endocervical swab samples in our laboratory. Materials and Methods: The live pathology database of Montefiore Medical Center was searched for patients with AC2 endocervical swab specimens and SP Paps taken the same day. SP samples from CT-and/or GC-positive endocervical swab patients and randomly selected negative patients were studied. In each case, 1.5 ml of the residual SP vial sample, which was in SP preservative and stored at room temperature, was transferred within seven days of collection to APTIMA specimen transfer tubes without any sample or patient identifiers. Blind testing with the AC2 assay was performed on the Tigris DTS System (Gen-probe, San Diego, CA). Finalized SP results were compared with the previously reported endocervical swab results for the entire group and separately for patients 25 years and younger and patients over 25 years. Results: SP specimens from 300 patients were tested. This included 181 swab CT-positive, 12 swab GC-positive, 7 CT and GC positive and 100 randomly selected swab CT and GC negative patients. Using the endocervical swab results as the patient’s infection status, AC2 assay of the SP samples showed: CT sensitivity 89.3%, CT specificity 100.0%; GC sensitivity and specificity 100.0%. CT sensitivity for patients 25 years or younger was 93.1%, versus 80.7% for patients over 25 years, a statistically significant difference (P = 0.02). Conclusions: Our results show that AC2 assay of 1.5 ml SP samples transferred to APTIMA specimen transfer medium within seven days is sufficiently sensitive and specific to be used to screen for CT and GC. CT sensitivity may be somewhat reduced in samples from patients over 25 years. SP specimens retained in the original SP fixative for longer time intervals also may have decreased sensitivity, due to deterioration of RNA, but this was not assessed in this study. The ability to tap the live pathology database is a valuable tool that can useful to conduct clinical studies without a costly prospective clinical trial.
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Affiliation(s)
- Samer N Khader
- Division of Cytopathology, Department of Pathology, Montefiore Medical Center, The University Hospital for the Albert Einstein College of Medicine, Bronx, NY, USA
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Epidemiology of HPV in HIV-positive and HIV-negative fertile women in Cameroon, West Africa. Infect Dis Obstet Gynecol 2010; 2009:810596. [PMID: 20169094 PMCID: PMC2821770 DOI: 10.1155/2009/810596] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 12/14/2009] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND HPV types vary by country and HIV status. There are no data on the prevalent HPV genotypes from Cameroon. METHODS We conducted a cross-sectional, observational study on 65 Cameroonian women. Samples were sent for HPV genotyping and Thin Prep analyses. RESULTS 41 out of 61 samples tested (67.2%) had HPV subtypes detected. The most common high risk types encountered were: 45 (24.6%) and 58 (21.5%). HIV-positive women were more likely to test positive for any HPV (P = .014), have more than one HPV subtype (P = .003), and to test positive for the high risk subtypes (P = .007). Of those with high risk HPV, HIV-positive women were more likely to have Thin Prep abnormalities than HIV-negative women (P = .013). CONCLUSIONS Oncogenic HPV subtypes 45 and 58 were more prevalent than those subtypes carried in the quadrivalent vaccine. Further studies are needed to assess whether the current vaccine will be effective in this region.
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Sevestre H, Mention J, Lefebvre JF, Eb F, Hamdad F. Assessment of Chlamydia trachomatis infection by Cobas Amplicor PCR and in-house LightCycler assays using PreservCyt and 2-SP media in voluntary legal abortions. J Med Microbiol 2009; 58:59-64. [PMID: 19074653 DOI: 10.1099/jmm.0.000737-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chlamydial infection of the upper genital tract after abortion is well recognized, but routine screening for infection before termination is rare, and few centres are aware of the prevalence of post-abortion complications in their patient population. Knowledge of the patient population is the best guide for developing screening strategies. The aim of this study was to determine the prevalence of chlamydial infection in patients presenting for legal termination of pregnancy, and to assess the presence of Chlamydia trachomatis by PCR on specimens collected in either PreservCyt (ThinPrep) or 2-sucrose phosphate (2-SP) transport medium. Two hundred and eleven single, sexually active women, aged 15-26 years, attending the Gynaecology and Obstetric Hospital, Amiens, France, for surgical termination of pregnancy were enrolled in this study from June 2002 to June 2003. C. trachomatis detection using a Cobas Amplicor PCR test (Roche Diagnostics) targeting a 207 bp segment of the common cryptic plasmid and a quantitative LightCycler real-time PCR (LC-PCR) (Roche Diagnostics) targeting a 123 bp fragment within the highly conserved constant domain 3 of the single-chromosome-copy ompA gene were performed on endocervical swabs in 2-SP, and on specimens collected using a cytobrush and placed in PreservCyt medium. The in-house LC-PCR was used as a chromosomal diagnosis method and to determine the load of C. trachomatis. This method was able to detect the mutant Swedish variant with a deletion of 377 bp in the target area in the cryptic plasmid, which is the region targeted by the Cobas Amplicor PCR test. C. trachomatis was detected in 19/211 patients (9 %) by both PCR methods. Among the 19 infected women, C. trachomatis was detected by the Cobas Amplicor PCR in 16 specimens in PreservCyt (7.6 %) and in 12 endocervical swabs in 2-SP (5.7 %). Specimens from only nine women were PCR-positive in both PreservCyt and 2-SP media by this method. Cobas Amplicor PCR revealed that 10.9 and 2.3 % of the PreservCyt and 2-SP samples, respectively, contained inhibitors. The same 19 infected women were LC-PCR positive in both PreservCyt and 2-SP samples. No additional infected women were found by this last method; thus, it was concluded that none of the samples contained the new variant of C. trachomatis. The load in each sample varied from 10(2) to 10(7) copies ml(-1).
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Affiliation(s)
- Henri Sevestre
- Laboratoire d'Anatomo-Pathologie, Centre Hospitalo-Universitaire d'Amiens, Amiens, France
| | - Jacques Mention
- Centre de Gynécologie-Obstétrique, Centre Hospitalo-Universitaire d'Amiens, Amiens, France
| | - Jean-François Lefebvre
- Centre de Ressources Régionales en Biologie Moléculaire, Université de Picardie Jules Verne, Amiens, France
| | - François Eb
- Service de Bactériologie, Centre Hospitalo-Universitaire d'Amiens, Amiens, France
| | - Farida Hamdad
- Service de Bactériologie, Centre Hospitalo-Universitaire d'Amiens, Amiens, France
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Chernesky M, Freund GG, Hook E, Leone P, D'Ascoli P, Martens M. Detection of Chlamydia trachomatis and Neisseria gonorrhoeae infections in North American women by testing SurePath liquid-based Pap specimens in APTIMA assays. J Clin Microbiol 2007; 45:2434-8. [PMID: 17581931 PMCID: PMC1951209 DOI: 10.1128/jcm.00013-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The APTIMA COMBO 2 assay, which detects and amplifies rRNA from Chlamydia trachomatis and/or Neisseria gonorrhoeae, is approved for use on ThinPrep liquid-based Pap test specimens. The objective was to determine the clinical utility of the APTIMA assays (APTIMA COMBO 2 assay, APTIMA CT assay for Chlamydia trachomatis, and APTIMA GC assay for Neisseria gonorrhoeae) for screening women during their annual Pap exam, using SurePath liquid-based Pap test specimens. Two cervical samples were collected from 1,615 females attending six clinical sites in North America. A cervical broom sample was processed for cytology, with the residuum aliquoted into an APTIMA specimen transfer kit tube. The second cervical swab sample was put into APTIMA specimen transport medium, and both samples were tested with each APTIMA assay on a direct sampling system. Using a subject-infected status that utilized cervical-swab specimen results from two APTIMA assays, the prevalence was 7.9% for Chlamydia trachomatis and 2.5% for N. gonorrhoeae. For the liquid-based Pap samples, the sensitivities, specificities, positive predictive values, and negative predictive values for Chlamydia trachomatis detection were 85.2%, 99.5%, 93.2%, and 98.7%, respectively, for the APTIMA COMBO 2 assay and 89.1%, 98.7%, 85.7%, and 99.1%, respectively, for the APTIMA CT assay. For N. gonorrhoeae detection, the values were 92.5%, 100%, 100%, and 99.8%, respectively, for the APTIMA COMBO 2 assay and 92.5%, 99.9%, 97.4%, and 99.8%, respectively, for the APTIMA GC assay. The high predictive values support the use of the assays with SurePath liquid-based Pap specimens processed with the APTIMA specimen transfer kit.
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Affiliation(s)
- Max Chernesky
- St. Joseph's Healthcare/McMaster University, Hamilton, Ontario, Canada.
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Chernesky M, Jang D, Portillo E, Chong S, Smieja M, Luinstra K, Petrich A, Macritchie C, Ewert R, Hayhoe B, Sarabia A, Thompson F. Abilities of APTIMA, AMPLICOR, and ProbeTec assays to detect Chlamydia trachomatis and Neisseria gonorrhoeae in PreservCyt ThinPrep Liquid-based Pap samples. J Clin Microbiol 2007; 45:2355-8. [PMID: 17537943 PMCID: PMC1951221 DOI: 10.1128/jcm.00405-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infections with Chlamydia trachomatis and Neisseria gonorrhoeae are often asymptomatic. Liquid-based Pap (L-Pap) screening may provide samples for testing by commercial assays. Women attending a health clinic or a street youth clinic had a PreservCyt ThinPrep sample and a cervical swab (CS) collected. The L-Pap sample was tested for cytopathology; then 1 ml was transferred to an L-Pap specimen transfer tube for testing by the Gen-Probe APTIMA assays (APTIMA Combo 2 [AC2], APTIMA C. trachomatis [ACT], and APTIMA N. gonorrhoeae [AGC]). The residual L-Pap sample was tested for C. trachomatis and N. gonorrhoeae using Roche AMPLICOR (AMP) and Becton Dickinson ProbeTec (PT). The CS was tested by AC2. A patient was considered infected if two specimens were positive or if a single specimen was positive in two tests. The prevalence of infection was 10% (29/290) for C. trachomatis and 2.4% (7/290) for N. gonorrhoeae. Most of the positive patients had specimens that were reactive in all assays (20/29 for C. trachomatis; 6/7 for N. gonorrhoeae). Four patients had double infections. The sensitivities and specificities of the various tests for the specimens tested were as follows. For C. trachomatis on L-Pap, sensitivity and specificity were 100 and 98.1%, respectively, for ACT, 93.1 and 98.8% for AC2, 86.2 and 91.2% for AMP, and 72.4 and 92.7% for PT. For N. gonorrhoeae on L-Pap, sensitivity and specificity were 100% for both AGC and AC2, 85.7 and 100% for AMP, and 85.7 and 100% for PT. For AC2 with CSs, sensitivity and specificity were 93.1 and 98.5%, respectively, for C. trachomatis, and both were 100% for N. gonorrhoeae. There were significant differences in sensitivity and specificity (P < 0.001). The APTIMA assays were more sensitive and specific than AMP or PT for detecting women's C. trachomatis and/or N. gonorrhoeae infections by testing ThinPrep samples.
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Affiliation(s)
- M Chernesky
- St. Joseph's Healthcare/McMaster University, Toronto, Ontario, Canada.
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Clarke HE, Kado-Fong H, Maggs DJ. Effects of temperature and time in transit on polymerase chain reaction detection of feline herpesvirus DNA. J Vet Diagn Invest 2006; 18:388-91. [PMID: 16921880 DOI: 10.1177/104063870601800412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The purpose of this study was to report methods currently recommended by commercial laboratories for collecting, shipping, and processing of samples for feline herpesvirus type 1 (FHV-1) testing using polymerase chain reaction (PCR) and to determine the effect of temperature and time on the ability of 1 PCR method to detect FHV-1 DNA in experimental and clinical samples. Eleven laboratories offering FHV-1 PCR were surveyed. There was notable variation in sample types and shipping conditions recommended and PCR protocols used by these laboratories. Subsequently, using a single PCR method, FHV-1 DNA was detected in samples exposed to various temperatures within the laboratory. Finally, FHV-1 PCR was performed on paired clinical samples collected from 25 cats and shipped at ambient temperatures via US Postal Service (USPS) or with an ice pack via a courier. Samples sent by USPS were exposed to significantly longer transit time and arrived at significantly higher temperature than did samples sent by courier. Despite this, all sample pairs yielded concordant results when tested for FHV-1 DNA using this PCR method. Although it may not be necessary for samples collected for detection of FHV-1 DNA using this PCR method to be shipped under the most expedient or temperature-controlled conditions, this should be verified for a variety of PCR assays and sample types.
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Affiliation(s)
- Heather E Clarke
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
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Ghanem KG, Koumans EH, Johnson RE, Sawyer MK, Papp JR, Unger ER, Black CM, Markowitz LE. Effect of specimen order on Chlamydia trachomatis and Neisseria gonorrhoeae test performance and adequacy of Papanicolaou smear. J Pediatr Adolesc Gynecol 2006; 19:23-30. [PMID: 16472725 DOI: 10.1016/j.jpag.2005.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
STUDY OBJECTIVE To evaluate the effect of specimen collection order on the performance of diagnostic tests for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC), and the specimen adequacy of ThinPrep Papanicolaou (Pap) smears. DESIGN Prospective cohort study. SETTING Public adolescent clinic. POPULATION 313 women. INTERVENTIONS The order of five cervical testing specimens was randomized for (1) ligase chain reaction (LCR) and (2) polymerase chain reaction (PCR) for both CT and GC; (3) transcription-mediated amplification (TMA) for CT; (4) culture for CT; and (5) cytology and LCR for GC and CT performed on ThinPrep Pap specimens. For CT and GC, a reference standard was based on three different tests performed on separate specimens. Generalized estimating equations were used to account for repeated measures. MAIN OUTCOME MEASURE Sensitivity and specificity of diagnostic tests. RESULTS The proportion of inadequate Pap smears was independent of specimen order. As a group, nucleic acid amplification test (NAAT) sensitivity and specificity for GC and CT were similar in the first two (early) and last three (late) swabs. Although point estimates for sensitivity were higher in the early swabs compared to the late swabs for GC LCR (13% difference), GC PCR (13%), and CT TMA (10%), these differences were not statistically significant. Their clinical significance warrants further investigation. CONCLUSIONS In clinical settings where both Pap smears and STI testing are performed in adolescents, clinical considerations can influence the order of specimen collection, since neither Pap specimen adequacy nor test performance of NAAT for CT and GC were significantly associated with swab order.
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Affiliation(s)
- Khalil G Ghanem
- Johns Hopkins University School of Medicine, Bayview Medical Center, 4940 Eastern Avenue B3 North, Baltimore, MD 21224, USA.
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Hawthorne CM, Farber PJ, Bibbo M. Chlamydia/gonorrhea combo and HR HPV DNA testing in liquid-based pap. Diagn Cytopathol 2005; 33:177-80. [PMID: 16078250 DOI: 10.1002/dc.20325] [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: 01/28/2023]
Abstract
Residual material from liquid-based pap (LBP) test has been used for molecular testing of Human Papilloma Virus (HR HPV) DNA. LBP test specimens (1,025) were evaluated to determine how often residual material was insufficient to perform microbiological testing. The specimens were tested for Chlamydia trachomatis and Neisseria gonorrhea (CCGT) alone and in combination with HR HPV(CCGT + HR HPV), using PCR method and HYBRID CAPTURE 2, respectively. A minimum volume of 5 ml (CCGT: 0.5-1 ml, HPV: 4 ml) of residual material is required for both the tests. The residual material was measured at >5 ml, < or =5 ml, and 0.5 ml volumes and documented. Results were tabulated. The insufficient rate for cases submitted for CCGT was 0.2% and 7.6% for HR HPV, with a detection rate of 40.9% for HR HPV. Utilizing residual material from LBP test for microbiological testing, as well as DNA testing for HR HPV is a convenient, cost-effective means to enhance patient care.
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Affiliation(s)
- Clementine M Hawthorne
- Cytology Laboratory, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania 19107, USA.
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Garbar C, Mascaux C, Fontaine V. Efficiency of an inexpensive liquid-based cytology performed by cytocentrifugations: a comparative study using the histology as reference standard. Cytojournal 2005; 2:15. [PMID: 16164754 PMCID: PMC1262738 DOI: 10.1186/1742-6413-2-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 09/15/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although liquid-based cytology (LBC) is now recommended for cervical cancer screening, it requires expensive automated devices and materials. To evaluate the efficiency of inexpensive LBC methods relying on an inexpensive fixative liquid, Easyfix, we compared the results obtained by the liquid-based cytology (LBC) diagnoses performed by cytocentrifugations (Papspin and Turbitec) with those obtained by histology. Furthermore, we evaluated the efficiency of the fixative liquid, Easyfix, to preserve HPV DNA in the collected samples. METHOD 266 LBC were compared with 174 colposcopies and 91 Loop Electrosurgical Excision Procedure (LEEP). Among the LBC, 51 were performed using the Papspin system and 215 were performed using the Turbitec system. To control the quality of the preservation liquid, Easyfix, we correlated the results of HCII assays with those of HPV PCR. RESULTS For Papspin and Turbitec systems, the sensitivities were respectively 82.6% (95% CI: 61.2-95.0%, p < 0.001) and 75.0% (95% CI: 64.4-89.8%, p < 0.001) and the specificities were 92.6% (95%CI: 76.5-99.1%, p < 0.001) and 96.2% (95% CI: 91.3-98.7%, p < 0.001). We find no statistical difference between the results of the both systems (p = ns). The sensitivity of the HCII was 86.4% (95% IC: 77.4-92.8%, p < 0.001) and the specificity was 39.4% (95% CI: 31.2-48.1%, p < 0.001). The comparison between HCII and HPV-PCR shows a good correlation: the kappa was 0.89. CONCLUSION LBC performed by cytocentrifugations are inexpensive, reduce inadequate smears, show excellent efficiency and allow HPV detection by molecular biology.
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Affiliation(s)
- Christian Garbar
- Department of Pathology, CHU de Charleroi (Université Libre de Bruxelles), 1 Boulevard Zoé Drion, 6000 Charleroi, Belgium
| | - Corinne Mascaux
- Department of Pathology, CHU de Charleroi (Université Libre de Bruxelles), 1 Boulevard Zoé Drion, 6000 Charleroi, Belgium
| | - Véronique Fontaine
- Department of Pathology, CHU de Charleroi (Université Libre de Bruxelles), 1 Boulevard Zoé Drion, 6000 Charleroi, Belgium
- Laboratory of Molecular Virology, Pasteur Institute, 642 rue Engeland, 1180 Brussels, Belgium
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Abstract
Chlamydia trachomatis and Neisseria gonorrhoeae are the two most prevalent bacterial sexually transmitted infections reported in the United States. The purpose of this article is to review the various tests available for diagnosing C. trachomatis and N. gonorrhoeae. The nucleic acid amplification tests are preferred owing to their high sensitivity and specificity and use on specimens obtained noninvasively. Non-amplified non-culture tests, such as the DNA probe test, remain a choice for settings in which nucleic acid amplification tests are not available or affordable. Culture is recommended for use on conjunctival, oropharyngeal, and rectal specimens and in cases of suspected abuse. In addition, for gonorrhea, culture is recommended when screening in populations with a low prevalence of infection. Point-of-care tests are limited by low sensitivity and should be used for only populations unlikely to return for follow-up.
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Affiliation(s)
- Elyse Olshen
- Division of Adolescent/Young Adult Medicine, Children's Hosital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Keegan H, Boland C, Malkin A, Griffin M, Ryan F, Lambkin H. Comparison of DNA extraction from cervical cells collected in PreservCyt solution for the amplification of Chlamydia trachomatis. Cytopathology 2005; 16:82-7. [PMID: 15787650 DOI: 10.1111/j.1365-2303.2005.00239.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE The aim of this study was to compare and evaluate three methods of DNA extraction for the amplification of Chlamydia trachomatis in uterine cervical samples collected in PreservCyt solution. ThinPrep is the trade name for the slide preparation. METHODS Thirty-eight samples collected in LCx buffer medium, which were identified as C. trachomatis infected by ligase chain reaction (LCR), were selected for this study. DNA from the PreservCyt samples was extracted by three methods: (i) QIAamp kit, (ii) boiling in Tris-EDTA buffer with Chelex purification, and (iii) Proteinase K digestion with Chelex purification. Sample DNA was tested for the presence of C. trachomatis by PCR using cryptic plasmid research (CTP) primers and major outer membrane protein research momp gene (MOMP) primers. Real-time (LightCycler) PCR for relative C. trachomatis quantification following DNA extraction was performed using primers (Hsp 60) for the 60 kDa heat-shock protein hsp60 gene. RESULTS Amplification using CTP primers was the most successful with each of the extraction protocols. Boiling in buffer was the least successful extraction method. QIAamp was the best extraction method, yielding the most positives with both the CTP and MOMP primers. Proteinase K-Chelex extraction gave similar sensitivity to QIAamp extraction with CTP primers but lower for MOMP primers. CONCLUSIONS The DNA extraction method must be carefully selected to ensure that larger PCR amplicons can be successfully produced by PCR and to ensure high sensitivity of detection of C. trachomatis. In this study it was found that the QIAamp extraction method followed by PCR with the CTP primers was the most successful for amplification of C. trachomatis DNA.
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Affiliation(s)
- H Keegan
- Molecular Biomedical Research, School of Biological Sciences, Dublin Institute of Technology, Dublin, Ireland
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Hinrikson HP, Hurst SF, De Aguirre L, Morrison CJ. Molecular methods for the identification ofAspergillusspecies. Med Mycol 2005; 43 Suppl 1:S129-37. [PMID: 16110805 DOI: 10.1080/13693780500064722] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Invasive aspergillosis (IA) is a leading cause of morbidity and mortality in immunocompromised hosts. In some institutions, species of Aspergillus less susceptible to amphotericin B than Aspergillus fumigatus are becoming more common, making an accurate identification of species important. However, species identification has traditionally relied on macroscopic colony characteristics and microscopic morphology, which may require several days of culture. Additional sub-culturing on specialized media may be required to induce conidia formation; in some cases conidia may never form, confounding identification. Therefore, rapid, nucleic acid-based methods that identify species of Aspergillus independent of morphology are now being developed to augment or replace phenotypic identification methods. The most successful methods to date have employed polymerase chain reaction (PCR) amplification of target sequences within the ribosomal RNA gene complex, including the 28S ribosomal subunit (D1-D2 region) and the internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions). We therefore developed a PCR-based assay to differentiate medically important species of Aspergillus from one another, and from other opportunistic moulds and yeasts, by employing universal, pan-fungal primers directed to conserved ribosomal genes and species-specific DNA probes directed to the highly variable ITS2 region. Amplicons were then detected in a simple, colorimetric enzyme immunoassay format (PCR-EIA). DNA sequencing of the ITS1 and ITS2 regions and of the D1-D2 region was also conducted for the differentiation of species by comparative GenBank sequence analysis. The PCR-EIA method was found to be rapid, sensitive, and specific for the identification and differentiation of the most medically important species of Aspergillus. In addition, methods to identify species of Aspergillus by comparative GenBank sequence analysis were found to be more reliable using the ITS1 and ITS2 regions than the D1-D2 region.
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Affiliation(s)
- H P Hinrikson
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop G-11, Atlanta, GA 30333, USA
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Aslan DL, Gulbahce HE, Stelow EB, Setty S, Brown CA, McGlennen RC, Pambuccian SE. The diagnosis ofTrichomonas vaginalis in liquid-based Pap tests: Correlation with PCR. Diagn Cytopathol 2005; 32:341-4. [PMID: 15880709 DOI: 10.1002/dc.20256] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The conventional Papanicolaou smear (CPS) is not considered accurate for the diagnosis of Trichomonas vaginalis (T. vaginalis), and women noted to carry the organism on CPS are recommended to undergo confirmatory testing. Liquid-based preparations have been shown to facilitate the diagnosis of squamous lesions and may also facilitate the diagnosis of T. vaginalis. We used polymerase chain reaction (PCR) to investigate the accuracy of the diagnosis of T. vaginalis by the liquid-based Pap test (LBP). LBP with the diagnosis of T. vaginalis from a 12-mo period were identified. Residual samples from these cases were subjected to PCR for T. vaginalis as were the residual samples of a control group of 195 LBP (including 103 inflammatory LBP and 69 cases of atypical squamous cells) in which T. vaginalis was not diagnosed cytologically. PCR confirmed the presence of T. vaginalis in 50 of 51 (98%) LBP and identified 2 additional cases. Morphologic identification of T. vaginalis on LBP is highly accurate and should not require confirmatory testing.
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Affiliation(s)
- Deniz L Aslan
- Department of Pathology and Laboratory Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Hopwood J, Mallinson H, Hodgson E, Hull L. Liquid based cytology: examination of its potential in a chlamydia screening programme. Sex Transm Infect 2004; 80:371-3. [PMID: 15459404 PMCID: PMC1744897 DOI: 10.1136/sti.2003.008359] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVE To assess the feasibility of testing for chlamydia directly on a single liquid based specimen (ThinPrep test) collected for cervical screening. METHOD Cervical smears were taken using a Cervex spatula and rinsed in the liquid based cytology collection vial. Following this, the conventional sample for chlamydia testing was taken from the endocervix using an Abbott Collection kit. Cytological specimens were prepared using an automated slide processor. Residual cellular material and the conventional samples were sent to the laboratory where both were tested for chlamydia by ligase chain reaction (LCR). The manufacturer's protocol for LCR urine testing was modified to substitute 1 ml of PreservCyt suspension. RESULTS 581 women had both swab and cytology suspension tested for Chlamydia trachomatis with LCR. There were 19 concordant positive and 562 concordant negative reports. The stability of chlamydia in the cytology suspension was maintained for at least 5 months. CONCLUSION The findings lead us to conclude that samples collected for liquid based cytology using the ThinPrep test collection vial provide a potential platform for chlamydia screening, though the study established several issues to be addressed to make this a practical proposition.
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Affiliation(s)
- J Hopwood
- Chlamydia Office, St Catherine's Hospital, Birkenhead CH42 0LQ, UK.
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Koumans EH, Black CM, Markowitz LE, Unger E, Pierce A, Sawyer MK, Papp JR. Comparison of methods for detection of Chlamydia trachomatis and Neisseria gonorrhoeae using commercially available nucleic acid amplification tests and a liquid pap smear medium. J Clin Microbiol 2003; 41:1507-11. [PMID: 12682137 PMCID: PMC153886 DOI: 10.1128/jcm.41.4.1507-1511.2003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2002] [Revised: 12/14/2002] [Accepted: 12/28/2002] [Indexed: 11/20/2022] Open
Abstract
Annual screening for Chlamydia trachomatis infection is currently recommended for sexually active women 15 to 25 years old and for women older than 25 if they have a new or multiple sex partners and have not used condoms during the previous 3 months. Annual screening for cervical abnormalities using the Pap smear has achieved a substantial reduction in morbidity and mortality from cervical cancer. Screening for Neisseria gonorrhoeae infection has likely contributed significantly to the reduction in the rates of gonococcal infection. The introduction of liquid Pap smear methods using exfoliated cervical cells presents an opportunity to screen for these three conditions using one specimen. We evaluated the preservation of C. trachomatis and Neisseria gonorrhoeae DNAs from ThinPrep liquid media (PreservCyt; Cytyc Corp., Boxborough, Mass.); tested the feasibility of using a clinical specimen of this medium for the detection of cytologic abnormalities, C. trachomatis, and N. gonorrhoeae; evaluated the agreement between ligase chain reaction (LCR) performed on PreservCyt and LCR performed on a cervical specimen; and compared the performance of LCR performed on PreservCyt to those of LCR performed on a cervical specimen, culture, PCR performed on a cervical specimen, on urine, and on a vaginal specimen (a multiple-site infection status standard), and transcription-mediated amplification (for C. trachomatis only) from 255 sexually active adolescent women. The agreement between LCR performed on PreservCyt and LCR from a cervical swab in LCx transport medium was high (for C. trachomatis, agreement = 0.97 and kappa = 0.92; for N. gonorrhoeae, agreement = 0.99 and kappa = 0.96). Test performances were similar for LCR-urine, LCR-cervix, and LCR-ThinPrep, with sensitivities from 93 to 99% for C. trachomatis and 81 to 83% for N. gonorrhoeae and specificities from 95.5 to 99% for C. trachomatis and 99.1 to 99.6% for N. gonorrhoeae using a PCR-based multiple-site infection status standard. This is the first study to examine the agreement between liquid cytologic media and multiple nucleic acid amplification tests for the detection of C. trachomatis and N. gonorrhoeae from patient samples. Cytologic fluid shows promise for simultaneous screening for cytologic abnormalities and sexually transmitted infections.
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Affiliation(s)
- Emilia H Koumans
- Centers for Disease Control and Prevention. Department of Pediatrics, Emory University, Atlanta, Georgia, USA.
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