Validation of Roche COBAS Amplicor Assay for Detection of
            <i>Chlamydia trachomatis</i>
            in Rectal and Pharyngeal Specimens by an
            <i>omp1</i>
            PCR Assay

Lister, Nichole A.; Tabrizi, Sepehr N.; Fairley, Christopher K; Garland, Suzanne M.

doi:10.1128/jcm.42.1.239-241.2004

Cited by 41 publications

(25 citation statements)

References 20 publications

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“…The high failure rate may be due to a lower sensitivity of the omp1 nested PCR because only a single-copy of the gene target, omp1, is present. In contrast, the COBAS AMPLICOR assay exhibited a higher sensitivity for targeting cryptic plasmid that is present as approximately 10 copies (Lister et al, 2004a;Mahony et al, 1993). Other studies also reported that positive genital samples identified using the COBAS or ligase chain reaction (LCR) assay could not be amplified by omp1 PCR (Pedersen et al, 2000;Vincelette et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

Genotyping of Chlamydia trachomatis from clinical specimens in Taiwan

Hsu

Tsai

Chen

et al. 2006

Journal of Medical Microbiology

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This study was conducted to determine the prevalence and distribution of Chlamydia trachomatis genotypes in Taiwan. Urine and endocervical-swab samples were collected from two hospitals located in northern and southern Taiwan. The genotypes of a total of 145 samples positive for C. trachomatis were analysed by sequencing the omp1 gene and this was successful in 102 samples. Nine different C. trachomatis genotypes were identified. Genotype E was the most prevalent (22 %), followed by D and Da (19 %), F (16 %), J (15 %), K (11 %), G (11 %), H (6 %) and Ba (2 %). There was a geographical difference in the prevalence of genotype H (P<0?018) between northern and southern Taiwan. Sequence mutation analysis by BLAST searching against GenBank reference sequences identified 12 genetic variants from a total of 102 omp1 gene sequences. INTRODUCTIONChlamydia trachomatis infection is the most prevalent sexually transmitted bacterial disease. It is estimated that 89 million cases occur annually worldwide (Gaydos et al., 2004). Because in 50 % of men and 80 % of women infected individuals are asymptomatic, the actual number of reported cases represents only a fraction of the infected population (Gaydos et al., 2004). Currently 19 human serovars and related variants (A, B/Ba, C, D/Da, E, F, G, Ga, H, I/Ia, J, K, L1, L2, L2a and L3) have been identified by using polyclonal and monoclonal antibodies against the major outer-membrane protein (MOMP) (Grayston & Wang, 1975;Ngandjio et al., 2004;Pedersen et al., 2000;Suchland & Stamm, 1991;Wang et al., 1985;Yuan et al., 1989). Based on the pathogenic potential, serovars A, B, Ba and C are commonly associated with trachoma. Serovars D to K are commonly associated with urogenital infections, such as urethritis, epididymitis, cervicitis, salpingitis, pelvic inflammatory disease and ectopic pregnancy; serovars L1 to L3 are commonly associated with lymphogranuloma venereum (Yuan et al., 1989). Furthermore, suggestions have been made that the infections with C. trachomatis serovars G, I and D are associated with cervical squamous cell carcinoma, and chronic infections with serotype K in women have been recognized as a cause of infertility (Anttila et al., 2001;Koskela et al., 2000;Marrazzo & Stamm, 1998;Morre et al., 2000).Serological typing methods have a limitation in that newly emerging types may be missed and culturing of clinical isolate is usually required (Eckert et al., 2000;Suchland & Stamm, 1991). Compared to serotyping, the genotyping methods are more sensitive and specific for C. trachomatis serovar identification (Molano et al., 2004). Many studies have shown the feasibility of deducing the serotypes of C. trachomatis clinical isolates using PCR-based RFLP or sequencing of the amplified omp1 gene that encodes the MOMP, the main surface antigen of C. trachomatis (Ikehata et al., 2000; Lysén et al., 2004;Ngandjio et al., 2003Ngandjio et al., , 2004Singh et al., 2003). The omp1 gene exhibits extensive DNA sequence variation in four discrete regions, termed variable segments (VS1-4...

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Section: Discussionmentioning

confidence: 99%

Genotyping of Chlamydia trachomatis from clinical specimens in Taiwan

Hsu

Tsai

Chen

et al. 2006

Journal of Medical Microbiology

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“…DNA extraction and omp1-specific PCR were performed as described previously (20,21). Three omp1-specific PCRs were used: PCR VD1-4 with primers P1 and OMP2 to amplify a region of the gene containing all four variable domains (17), nested PCR VD1/2 with primers P1 and CT6 (5) to amplify a region containing VD1 and VD2, and nested PCR VD3/4 with primers CT6 (sense) and OMP2 to amplify a region containing VD3 and VD4.…”

Section: Methodsmentioning

confidence: 99%

Variability of theChlamydia trachomatis omp1Gene Detected in Samples from Men Tested in Male-Only Saunas in Melbourne, Australia

Lister¹,

Tabrizi

Fairley³

et al. 2004

J Clin Microbiol

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C. trachomatis serovars can be differentiated by sequencing the omp1 gene, which codes for the major outer membrane protein (MOMP) (1, 5, 8, 15-17, 25, 31). Preliminary evidence suggests that MOMP is a porin that assembles as ␤ barrels containing conserved domains (CDs) of transmembrane ␤ strands and periplasmic loops and four variable domains (VDs) located on the outer loops (14, 28). Serovars exhibit MOMP sequence heterogeneity that is mainly localized to the VDs (27, 36). Variability in the MOMP sequence is presumably a result of host selection and bacterial adaptation (3,4,19), although recent analysis of nucleotide and amino acid substitutions for omp1 and MOMP, respectively, showed a lack of evolutionary pattern with respect to disease or tissue tropism (29). The findings from studies of the clinical manifestations of disease and the association of those manifestations with specific serovars (2,7,12,17,23,26,34), geographic clustering (5, 8, 11), and the amount of variation within genotypes and the changes in the frequencies of the genotypes circulating over time (16,17,25,30,35) have been mixed. Other studies have highlighted the importance of MOMP diversity in strains isolated from sex workers, whose sexual network was described as a core group creating selective immune pressure on circulating strains (3, 4). Overall, of the serovars usually associated with urogenital infection (serovars D to K), serovars D, E, and F are the most common (1,5,8,11,12,15,17,23,30,31).The aims of the present study were to characterize the C. trachomatis strains detected in samples collected during a sauna screening program (20) by sequencing the omp1 gene and determining the corresponding serovars. Determination of the serovars and the omp1 variability of the C. trachomatis strains detected in these samples may give insight into the C. trachomatis strains circulating among MSM who frequent saunas. MATERIALS AND METHODSClinical samples. A sample of 47 C. trachomatis-positive specimens collected from 39 men who participated in a screening program in male-only saunas in Melbourne, Victoria, Australia (20), was used. These 47 samples comprised 34 anal swab specimens, 10 urine samples, and 3 throat swab specimens. Two anal swab specimens were collected from each of five men, and two urine samples were collected from each of two men; i.e., the samples were collected at the initial consultation in the sauna and repeat samples were then collected (for confirmation before antibiotic treatment). C. trachomatis was detected at two anatomical sites in one man: from an anal swab specimen and a urine sample.Isolation of DNA and omp1-specific PCR. DNA extraction and omp1-specific PCR were performed as described previously (20,21). Three omp1-specific PCRs were used: PCR VD1-4 with primers P1 and OMP2 to amplify a region of the gene containing all four variable domains (17), nested PCR VD1/2 with primers P1 and CT6 (5) to amplify a region containing VD1 and VD2, and nested PCR VD3/4 with primers CT6 (sense) and OMP2 to amplify a region con...

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“…These approaches are, in particular, important for detection from the rectum and oropharynx, which is crucial particularly in population groups of men who have sex with men (20) or with history of oral and/or anal sex. Currently, extragenital specimens are not licensed for use by the FDA; however, several studies have conducted an evaluation and shown appropriate sensitivity with these types of samples using the available commercial NAATs (21)(22)(23)(24)(25)(26)(27)(28). Nevertheless, most studies evaluating the sensitivity and specificity of the gonococcal and chlamydial NAATs utilize clinical samples whereby the gold standard for confirmation of N. gonorrhoeae is a consensus NAAT gold standard (22).…”

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confidence: 99%