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Sepehr N Tabrizi

Publications and source records attributed to Sepehr N Tabrizi.

17 recordsLinked to original sources
PubMed2026

A droplet digital PCR assay targeting 16 human papillomavirus genotypes.

Background. Cervical screening with high-precision assays such as human papillomavirus (HPV) DNA testing is essential for the detection and treatment of precancerous lesions. HPV genotypes have different oncogenic potential and require different clinical management, illustrating the importance of extended genotyping. HPV quantification has demonstrated clinical relevance in both diagnosis and treatment. Objective. To develop a droplet digital PCR assay for the detection and quantification of 16 HPV genotypes, with comparison to a commercial test and validation on clinical samples. Methods. Primers and probes were designed to target the E6 region of 16 HPV genotypes: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68, 73 and 82. Each target was evaluated to assess performance and reliability using synthetic DNA constructs, quantified international reference standards and clinical screening samples (n=303) genotyped using the Seegene Anyplex II HR HPV Detection assay. Results. Each assay demonstrated high target specificity, without cross-reactivity observed among the HPV genotypes selected. Using international molecular standards, the assay reliably detected high-risk genotypes across serial dilutions, with detection down to the level of one international unit or genome equivalent per microlitre. When applied to clinical samples with and without a histological diagnosis of cervical intraepithelial neoplasia 2 or worse (CIN2+), the assay reliably detected key HPV genotypes, with the exception of 7 of 234 (3%) of HPV-positive samples, all of which exhibited very low viral load. Conclusion. Although previous studies have described digital PCR methods targeting HPV E6, they have typically focused on a limited number of genotypes. This study expands upon existing methodology by introducing a sensitive and specific method for detection and quantification of 16 high-risk and potentially high-risk HPV genotypes.

PCR↗
PubMed2006

Human papillomavirus genotyping using a modified linear array detection protocol.

A standardized PCR-based linear array genotyping assay has been developed (Roche Molecular Systems) allowing the concurrent typing of 37 human papillomavirus (HPV) types. A component of this assay, the PCR amplicon detection protocol, requires the use of a shaking water-bath incubator for amplicon/probe hybridization and subsequent stringent washing, which many laboratories may find cumbersome or simply not possess. In this study, the utility of a dry-air incubator in substitution of the recommended shaking water-bath for use in this assay was confirmed. DNA was extracted by AmpliLute method from 150 PreservCyt specimens collected from patients undergoing ablation treatment for histologically confirmed cervical abnormality. The DNA was amplified by PCR and amplicons detected by both standard and modified protocols, varying only by the method of incubation for DNA hybridization and stringent washing. Identical HPV-type profiles were generated in 149/150 (99.3%) of the specimens tested by both protocols, representing a near perfect level of concordance (kappa = 0.98). It was proposed that this modification would markedly simplify the detection process, reduce setup time and eliminate the potential for water spillover, thereby allowing more laboratories to adopt this method subsequent to in-house validation.

Cervix Uteri↗
PubMed2006

Prevalence and typing of human papilloma virus (HPV) among female sex workers and outpatient women in southern Thailand.

BACKGROUND: Thai sex workers (SW) have high rates of sexually transmitted infections (STIs); however, detection and treatment is often complicated by accessibility to sensitive and accurate diagnostic tests. Self-sampling of women combined with molecular amplification techniques could help in accurate diagnosis, treatment and follow-up of such women. Detection of persistent high-risk human papilloma virus (HPV) in such populations could also be beneficial in identifying women who may need more frequent follow-up for cervical cytology screening. The current study aimed to examine the prevalence of HPV in this population and compare this with the lower-risk outpatient women (OPW) in Thailand. METHODS: Four hundred and thirty OPW and 524 Thai SW were sampled by a self-administered tampon collection. Cells were extracted from tampons and, subsequently, women underwent routine vaginal examination for detection of other STIs. Detection of HPV was performed by polymerase chain reaction (PCR) using the L1 consensus primers, followed by L1 consensus probe using an in-house PCR-enzyme-linked immunosorbent assay (ELISA). All positive samples were typed using PCR-ELISA and type-specific oligonucleotide probes. RESULTS: Overall, HPV was detected in 20/430 (4.6%) and 120/524 (22.9%) in OPW and SW respectively. Over 98% of samples produced a beta-globin signal, indicating adequately collected samples. Human papilloma virus typing probes detected HPV16 or 18 in 14% and 26% of the positive samples from OPW and SW respectively. HPV31, 33, 35 or 39 were detected in 19% and 12% and HPV45, 51 or 52 in 9.5% and 4% of positive OPW and SW patients respectively. Low risk HPV6 or 11 were detected in 1% and 4.9% of OPW and SW respectively. CONCLUSION: There was a significantly higher HPV prevalence in Thai SW than OPW, with the majority (21%) of positive samples containing the oncogenic HPV16 or 18 DNA. The results indicate that PCR could serve as a rapid and easy method for identification of women who require more frequent screening for cervical cancer.

Adolescent↗
PubMed2006

Prevalence of Gardnerella vaginalis and Atopobium vaginae in virginal women.

OBJECTIVES: The objectives of this study was to determine the prevalence of Gardnerella vaginalis and Atopobium vaginae in virginal women and to establish if nonpenetrative sexual activity is associated with these organisms. GOAL: The goal of this study was to assess prevalence of G. vaginalis and A. vaginae in virginal women. STUDY DESIGN: Forty-four virginal female patients self-collected tampon specimens, which were tested for G. vaginalis and A. vaginae by polymerase chain reaction, and provided either brief or detailed information regarding sexual practices by self-administered questionnaire. RESULTS: Twenty women (45%) had G. vaginalis and 3 (7%) A. vaginae detected. Among the 27 who provided detailed information, 12 (46%) had G. vaginalis and none had A. vaginae detected. G. vaginalis was significantly more likely to be detected in those who had participated in oral sex (odds ratio = 22; 95% confidence interval = 2.2-222) and hand-genital contact without penetration (P = 0.02), but not genital-genital contact. CONCLUSION: This study shows that nonpenetrative intimate sexual contact is associated with carriage of G. vaginalis in virginal women.

Actinobacteria↗
PubMed2006

Detection of Candida species by PCR in self-collected vaginal swabs of women after taking antibiotics.

Women undergoing antibiotic treatment can develop vulvovaginal candidiasis. This study evaluated polymerase chain reaction (PCR) for the detection of Candida species in comparison with the conventional laboratory culture methods in samples from women with and without symptoms of postantibiotic candidiasis. The self-collected vaginal swabs from 90 women, with no recent symptoms of vulvovaginal candidiasis (VVC), who were prescribed antibiotics for non-genital infection were evaluated 8 days after completion of antibiotics and/or at the time of developing symptoms of VVC. Broad-spectrum fungal PCR was performed on extracted DNA from each sample. Overall PCR detected four additional Canidida albicans, three Candida parapsilosis and one Candida tropicalis when compared with culture. All but one case additionally detected by PCR were found in patients with no VVC symptoms. PCR, although more sensitive than conventional culture methods, in this small number of cases, has not been able to detect Candida species in significantly more patients with symptoms suggestive of candidiasis. The results of this study may indicate that other agents including other yeast species may be responsible for symptoms of postantibiotic vulvovaginitis.

Anti-Bacterial Agents↗
PubMed2006

Assessment of MagNA pure LC extraction system for detection of human papillomavirus (HPV) DNA in PreservCyt samples by the Roche AMPLICOR and LINEAR ARRAY HPV tests.

Roche Molecular Systems recently released two PCR-based assays, AMPLICOR and LINEAR ARRAY (LA), for the detection and genotyping, respectively, of human papillomaviruses (HPVs). The manual specimen processing method recommended for use with both assays, AmpliLute, can be time-consuming and labor-intensive and is open to potential specimen cross-contamination. We evaluated the Roche MagNA Pure LC (MP) as an alternative for specimen processing prior to use with either assay. DNA was extracted from cervical brushings, collected in PreservCyt media, by AmpliLute and MP using DNA-I and Total Nucleic Acid (TNA) kits, from 150 patients with histologically confirmed cervical abnormalities. DNA was amplified and detected by AMPLICOR and the LA HPV test. Concordances of 96.5% (139 of 144) (kappa=0.93) and 95.1% (135 of 142) (kappa=0.90) were generated by AMPLICOR when we compared DNA extracts from AmpliLute to MP DNA-I and TNA, respectively. The HPV genotype profiles were identical in 78.7 and 74.7% of samples between AmpliLute and DNA-I or TNA, respectively. To improve LA concordance, all 150 specimens were extracted by MP DNA-I protocol after the centrifugation of 1-ml PreservCyt samples. This modified approach improved HPV genotype concordance levels between AmpliLute and MP DNA-I to 88.0% (P=0.043) without affecting AMPLICOR sensitivity. Laboratories that have an automated MP extraction system would find this procedure more feasible and easier to handle than the recommended manual extraction method and could substitute such extractions for AMPLICOR and LA HPV tests once internally validated.

Cervix Uteri↗
PubMed2006

Azithromycin failure in Mycoplasma genitalium urethritis.

We report significant failure rates (28%, 95% confidence interval 15%-45%) after administering 1 g azithromycin to men with Mycoplasma genitalium-positive nongonococcal urethritis. In vitro evidence supported reduced susceptibility of M. genitalium to macrolides. Moxifloxacin administration resulted in rapid symptom resolution and eradication of infection in all cases. These findings have implications for management of urethritis.

Adult↗
PubMed2005

Etiologies of nongonococcal urethritis: bacteria, viruses, and the association with orogenital exposure.

BACKGROUND: The purpose of the present study was to determine pathogens and behaviors associated with nongonococcal urethritis (NGU) and the usefulness of the urethral smear in predicting the presence of pathogens. METHODS: We conducted a case-control study of men with and without symptoms of NGU. Sexual practices were measured by questionnaire. First-stream urine was tested for Chlamydia trachomatis, Mycoplasma genitalium, Ureaplasma parvum, U. urealyticum, herpes simplex virus (HSV)-1, HSV-2, adenoviruses, and Gardnerella vaginalis by polymerase chain reaction. RESULTS: C. trachomatis (20%), M. genitalium (9%), adenoviruses (4%), and HSV-1 (2%) were more common in cases with NGU (n = 329) after age and sexual risk were adjusted for (P< or =.01); U. urealyticum, U. parvum, and G. vaginalis were not. Infection with adenoviruses or HSV-1 was associated with distinct clinical features, oral sex, and male partners, whereas infection with M. genitalium or C. trachomatis was associated with unprotected vaginal sex. Oral sex was associated with NGU in which no pathogen was detected (P < or = .001). Fewer than 5 polymorphonuclear leukocytes (PMNLs) per high-power field (HPF) on urethral smear were present in 32%, 37%, 38%, and 44% of cases with C. trachomatis, M. genitalium, adenoviruses, and HSV, respectively. CONCLUSION: We identified adenoviruses and HSV-1 as significant causes of NGU with distinct clinical and behavioral characteristics and highlighted the association between insertive oral sex and NGU. A urethral PMNL count of > or =5 PMNLs/HPF is not sufficiently sensitive to exclude pathogens in men with urethral symptoms.

Adenovirus Infections, Human↗
PubMed2005

Evaluation of opa-based real-time PCR for detection of Neisseria gonorrhoeae.

OBJECTIVES: Detection of Neisseria gonorrhoeae by commercial and in-house-based assays has been hampered by false-positive and false-negative results. The current study describes a sensitive and specific real-time 5'-nuclease PCR assay targeting a 90-bp region of the multicopy opa gene. GOAL: To evaluate the sensitivity and specificity of this assay in detection of gonococcus. STUDY: Sensitivity and specificity were determined by testing a panel of 173 microorganisms. In addition, 135 clinical samples previously evaluated by 4 nucleic acid amplification methods were also tested. RESULTS: A sensitivity of 1 copy per reaction was achieved. Positive results were only obtained for N gonorrhoeae strains including 20 cppB-negative strains. Overall, 134 of 135 clinical sample results agreed with the consensus nucleic amplification methods. CONCLUSION: This study demonstrates opa-based target can be used as an accurate and rapid PCR assay for the detection of N gonorrhoeae in clinical specimens.

Bacterial Outer Membrane Proteins↗
PubMed2005

Comprehensive clinical care on-site in men-only saunas: confidential STI/HIV screening outreach clinic.

During 2001 and 2002 an anonymous outreach-screening programme in Melbourne, Australia, offered testing for gonorrhoea and chlamydia on-site at men-only saunas. Modifications were made to this screening programme to offer a comprehensive testing clinic for sexually transmissible infections (STIs), including HIV. The comprehensive clinic was evaluated after one year of operation, and comparisons were made with the earlier anonymous screening programme. The comprehensive outreach clinic made contact with fewer men (n = 557), however, men tested had a higher prevalence of gonorrhoea and chlamydia (17%), and all men tested positive for STIs/HIV were followed up. The findings and comparisons outlined in this paper may be used for different communities to decide what screening programme model best suits their individual situation: anonymous programme with fewer tests offered, confidential and comprehensive STI/HIV testing programme, or both. On the basis of our evaluation, we have opted to continue the comprehensive STI/HIV testing programme in local men-only saunas.

Adult↗
PubMed2005

Evaluation of a modified reverse line blot assay for detection and typing of human papillomavirus.

Detection and typing of human papillomaviruses (HPVs) are requested by clinicians with growing frequency as part of the overall management of patients. A new method using consensus L1 amplification and a reverse line blot hybridization detection method has been described for broad spectrum HPV genotype identification. This method involves hybridization at 53 degrees C in a shaking water bath, which many laboratories might find cumbersome. We describe a modified hybridization step, using a dry-air incubator, that simplifies the detection protocol. Overall, comparable results were obtained by the modified, more easily performed protocol, indicating that laboratories might validate and use this modified method.

Female↗
PubMed2004

Diagnosis of sexually transmitted infections (STI) using self-collected non-invasive specimens.

Paramount in control of transmission of sexually transmitted infections (STIs) is their prompt recognition and appropriate treatment. In countries where definitive diagnoses are difficult, a 'syndromic approach' to management of STIs is recommended and practiced, yet many STIs have common symptoms or are asymptomatic and therefore go undetected and untreated. This is of particular concern with the recognition that HIV transmission is increased with co-existent STIs: the attributable risk for each STI varying with the prevalence within a particular population. Hence, HIV public health prevention approaches must include STI preventative strategies to be effective. Even then, microbiological screening is incorporated into STI control strategies; lack of access to appropriate services (especially in rural and remote areas), reluctance of at-risk populations to attend for treatment, fear of invasive genital examinations, and lower sensitivities of conventional diagnostic assays reduces the effectiveness of such programmes. Therefore, accurate, cost-effective, reliable diagnostic assays (preferably those which can be used in the field) are needed to impact on the incidence of the various STIs, as well as HIV. With the advent of molecular technologies, including target and signal amplification methods, diagnoses of STIs have been revolutionised and allow the use of non or minimally invasive sampling techniques, some of which are self-collected by the patient, e.g. first-void urine, cervico-vaginal lavage, low vaginal swabs, and tampons. Most studies evaluating such self-sampling with molecular diagnostic techniques have demonstrated an equivalent or superior detection of STIs as compared to conventional sampling and detection methods. These sampling methods can also be used to determine prevalence of STIs in various populations, but particularly those with difficult access to medical care. In this article, the utility of self-sampling collection devices for detection of various STIs, particularly in women, is reviewed as one step towards formulating appropriate strategies in control of STIs, and which are especially suited for remote areas.

Adult↗
PubMed2004

Characterization of Chlamydia trachomatis omp1 genotypes detected in eye swab samples from remote Australian communities.

Chlamydia trachomatis conjunctival samples collected over a 6-month period from individuals with clinical signs of trachoma and located in remote communities in the Australian Northern Territory were differentially characterized according to serovar and variants. The rationale was to gain an understanding of the epidemiology of an apparent increased prevalence of acute trachoma in areas thought to be less conducive to this disease. Characterization was performed through sequencing of a region of the omp1 gene spanning the four variable domains and encoding the major outer membrane protein. Nucleotide and deduced amino acid sequences were genotyped by using a BLAST similarity search and were examined by phylogenetic analyses to illustrate evolutionary relationships between the clinical and GenBank reference strains. The predominant genotype identified corresponded to that of serovar C (87.1%), followed by the genotype corresponding to serovar Ba (12.9%). All nucleotide and amino acid sequences exhibited minor levels of variation with respect to GenBank reference sequences. The omp1 nucleotide sequences of the clinical samples best aligned with those of the conjunctival C. trachomatis reference strains C/TW-3/OT and Ba/Apache-2. All clinical samples (of serovar C) exhibited four or five nucleotide changes compared with C/TW-3/OT, while all serovar Ba samples had one or two nucleotide differences from Ba/Apache-2. Phylogenetic analyses revealed close relationships between these Northern Territory chlamydial samples and the respective reference strains, although the high proportion of sequence variants suggests an evolutionarily distinct C. trachomatis population causing eye infections in Australia. Given that such genotypic information has gone unreported, these findings provide knowledge and a foundation for trachoma-associated C. trachomatis variants circulating in the Northern Territory.

Adolescent↗
PubMed2004

Variability of the Chlamydia trachomatis omp1 gene detected in samples from men tested in male-only saunas in Melbourne, Australia.

A recent screening program in Melbourne, Victoria, Australia, has shown that Chlamydia trachomatis is an important infection among men who frequent male-only saunas. To evaluate the C. trachomatis isolates circulating in local saunas, the C. trachomatis-positive samples collected during the program underwent amplification and sequencing of the omp1 gene, and the corresponding serovars were deduced. Forty-seven C. trachomatis-positive samples collected (from October 2001 to September 2002) from 39 men were evaluated. The deduced serovars found, in descending order of prevalence, were D, G, and J; and serovars B, E, F, and H were each found in single samples. The seven different serovars identified in the study sample indicate that local saunas are a reservoir of multiple C. trachomatis strains, possibly maintained by the introduction of new patrons or regular patrons who have been exposed to C. trachomatis elsewhere. No significant genetic variants were found, as most variable positions were silent and were detected only in single samples.

Anal Canal↗
PubMed2002

Infectious diseases. 6: Sexually transmitted infections: new diagnostic approaches and treatments.

1. Commercially available nucleic acid amplification assays (eg, polymerase or ligase chain reaction) are now the "gold standard" tests for genital chlamydial infection and also have a role in screening for gonococcal infection. 2. Single-dose oral antibiotics are available for treatment of Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis infections. 3. Strains of N. gonorrhoeae in urban Australia are often penicillin resistant, while strains from South East Asia and those in homosexually active men may show high-level resistance to quinolones. 4. Imiquimod, a novel immune-response modifier, is now available for effective, safe, self-administered treatment of genital warts. 5. The Pap smear remains the cornerstone of screening for precursor lesions of cervical cancer, but human papillomavirus genotyping may have a role in clinical decision-making for women with equivocal or early precancerous lesions. 6. Treatment of primary genital herpes changes the clinical course, and long-term suppressive therapy is effective for those with multiple recurrences. New technologies have made diagnosis and screening easier for patients and clinicians

Adolescent↗
PubMed2002

Evaluation of self-collected samples in contrast to practitioner-collected samples for detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis by polymerase chain reaction among women living in remote areas.

BACKGROUND: Self-collected samples have been shown to be an acceptable and sensitive method for the detection by polymerase chain reaction (PCR) of sexually transmitted infections (STIs) among women. GOAL The goal of the study was to compare self-collected sampling methods to conventional practitioner endocervical sampling for the PCR detection of Chlamydia trachomatis and Neisseria gonorrhoeae to compare two self-collected sampling methods for the detection of T vaginalis by PCR. STUDY DESIGN: Women (n = 318) from urban and remote areas of central Australia participated in the study when attending their health clinic for a check-up. They each provided a FVU sample, self-collected vaginal swab specimen, and tampon specimen. This was followed by a clinical examination by a practitioner, with collection of endocervical and high vaginal swabs for testing by conventional microscopy and culture for N gonorrhoeae and T vaginalis, respectively. The FVU, self-collected vaginal swab, tampon, and endocervical swab specimens were tested by Roche Cobas Amplicor for C trachomatis and N gonorrhoeae. The self-collected vaginal swab and tampon specimens were also tested by an in-house PCR method for the detection of T vaginalis. RESULTS: In toto, C trachomatis was detected by PCR in 11.5%, N gonorrhoeae in 11.8%, and T vaginalis in 24.6%. Molecular diagnostics for N gonorrhoeae and T vaginalis were significantly more sensitive than traditional assays with microscopy and culture. For the detection of C trachomatis by PCR, tampons were the most sensitive (100.0%) and urine the least sensitive (72.7%) specimens ( = 0.01). For the detection of by PCR, the self-collected tampon was the most sensitive specimen, followed by the endocervical swab, self-collected swab, and urine specimen, with sensitivities of 97.2%, 92.6%, 71.9%, and 31.2%, respectively. For detection of N gonorrhoeae, statistically significant differences were detected for urine versus tampon ( < 0.0001), endocervical swab ( < 0.001), and self-collected swab ( = 0.01) and for self-collected swab versus tampon ( = 0.01). Subsequent data collection showed that sensitivity of urine PCR for detection of N gonorrhoeae improved with freezing of urine specimens and shorter transport time. Tampons were also more sensitive than self-collected swabs for detection of T vaginalis (sensitivity of 100% versus 87.7%). CONCLUSION: Self-collected specimens offer women in remote communities an acceptable and sensitive alternative method of testing for STIs. The low sensitivity of N gonorrhoeae PCR of urine specimens may reflect poor transport and storage conditions, which we have shown can be improved by freezing urine specimens and reducing transport delays.

Animals↗