RNA amplification by nucleic acid sequence-based amplification with an internal standard enables reliable detection of Chlamydia trachomatis in cervical scrapings and urine samples

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.

A critical review of point-of-care diagnostic technologies to combat viral pandemics

The COVID-19 global pandemic of 2019-2020 pointedly revealed the lack of diagnostic solutions that are able to keep pace with the rapid spread of the virus. Despite the promise of decades of lab-on-a-chip research, no commercial products were available to deliver rapid results or enable testing in the field at the onset of the pandemic. In this critical review, we assess the current state of progress on the development of point-of-care technologies for the diagnosis of viral diseases that cause pandemics. While many previous reviews have reported on progress in various lab-on-a-chip technologies, here we address the literature from the perspective of the testing needs of a rapidly expanding pandemic. First, we recommend a set of requirements to heed when designing point-of-care diagnostic technologies to address the testing needs of a pandemic. We then review the current state of assay technologies with a focus on isothermal amplification and lateral-flow immunoassays. Though there is much progress on assay development, we argue that the largest roadblock to deployment exists in sample preparation. We summarize current approaches to automate sample preparation and discuss both the progress and shortcomings of these developments. Finally, we provide our recommendations to the field of specific challenges to address in order to prepare for the next pandemic.

Longitudinal association of gonorrhea and bacterial vaginosis with repeat chlamydia diagnoses among U.S. Army women: a retrospective cohort analysis

BACKGROUND

Historically, sexually transmitted infections have affected the health of the U.S. military. To determine whether gonorrhea, bacterial vaginosis, genital herpes, and trichomoniasis are predictors of repeat chlamydia diagnoses among U.S. Army women, medical data reported into the Defense Medical Surveillance System during the 2006-2012 period were analyzed.

METHODS

For all inpatient and outpatient medical records, the first and second International Classification of Diseases, version 9 (ICD-9) diagnostic positions were reviewed for each chlamydia case to determine the occurrence of repeat diagnoses. The Andersen-Gill regression model, an extension of the Cox model for multiple failure-time data, was used to study associations between predictors and repeat chlamydia diagnoses.

RESULTS

Among 28,201 women with a first chlamydia diagnosis, 5145 (18.2%), 1163 (4.1%), 267 (0.9%), and 88 (0.3%) had one, two, three, and four or more repeat diagnoses, respectively. Overall, the incidence of repeat chlamydia was 8.31 cases per 100 person-years, with a median follow-up time of 3.39 years. Gonorrhea (hazard ratio (HR) = 1.58, 95% CI: 1.44-1.73) and bacterial vaginosis (HR = 1.40, 95% CI: 1.09-1.79) were significant predictors for repeat chlamydia. These estimated hazard ratios were attenuated, but remained significant, after controlling for age, race/ethnicity, marital status, and military rank. No significant association was found for genital herpes (HR = 1.13, 95% CI: 0.55-2.29) and trichomoniasis (HR = 1.43, 95% CI: 0.43-4.68).

CONCLUSIONS

This large cohort study suggests that gonorrhea and bacterial vaginosis were associated with repeat chlamydia diagnoses among U.S. Army women. These findings can be used in formulating new interventions to prevent repeat chlamydia diagnoses.

HCV Detection, Discrimination, and Genotyping Technologies

According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.

Does the Hazard of Chlamydia Increase with the Number of Gonorrhea Diagnoses? A Large Population-Based Study Among U.S. Army Women

BACKGROUND

In the U.S. military, chlamydia and gonorrhea are common sexually transmitted infections, especially among female service members. The aim of this study was to determine whether the number of gonorrhea diagnoses sustained an increased hazard of chlamydia among military women.

METHODS

This population-based study involved an analysis of all female gonorrhea cases in the U.S. Army reported in the Defense Medical Surveillance System between 2006 and 2012. The effect of the number of gonorrhea diagnoses on the hazard of chlamydia was analyzed using the Prentice-Williams-Peterson gap-time model.

RESULTS

Among 3,618 women with gonorrhea diagnosis, 702 (19.4%) had a subsequent chlamydia diagnosis yielding a rate of 6.06 (95% CI = 5.63-6.53) cases per 100 person-years. Compared to women with one gonorrhea diagnosis, the hazard ratio of chlamydia for women with two gonorrhea diagnoses was 5.09 (95% CI = 4.42-5.86) and for women with three gonorrhea diagnoses was 6.53 (95% CI = 3.93-10.83). The median time to chlamydia diagnosis decreased from 2.39 to 0.67 years for women with two to three gonorrhea diagnoses.

CONCLUSIONS

The hazard of chlamydia increased significantly with the number of gonorrhea diagnoses and the median time to chlamydia diagnosis decreased with an increasing number of gonorrhea diagnoses among U.S. Army women.

Sexual inactivity and occurrence of STIs in relation to weight status in women: Two large population-based studies

The aim of this study was to examine sexual inactivity and occurrence of selected sexually transmitted infections in relation to body mass index. We used data from two large Danish population-based cross-sectional studies conducted in 1991-1995 (HPV study: 6869 women, aged 22-32 years) and in 2004-2005 (Liva study: 19,484 women, aged 18-45 years). Data were collected using a structured interview and measured weight, height, high-risk human papillomavirus DNA, Chlamydia DNA for the HPV study and a structured questionnaire for the Liva study. Overweight and obese women were more likely to have had no lifetime sexual partner or no sexual partner in the last year, e.g., obese women had a threefold (95 percent CI: 1.95-5.04) odds ratio of having had no sexual partner in the last year compared to normal weight women. Additionally, overweight and obese women had a lower likelihood of genital warts and high-risk human papillomavirus infection. A similar tendency was found for self-reported Chlamydia, but not with presence of Chlamydia DNA. If higher likelihood of no lifetime or recent sexual partners among overweight and obese women reflects unmet sexual needs, it could give rise to concern because quality of sexual life is associated with general quality of life.

Risk Factors for Incident and Redetected Chlamydia trachomatis Infection in Women: Results of a Population-Based Cohort Study

OBJECTIVES

To investigate risk factors for incident and redetected Chlamydia trachomatis (CT) infection in women, including the role of high-risk human papillomavirus (HPV).

METHODS

In this population-based, prospective cohort study conducted in Copenhagen, Denmark, 10,729 women aged 20 to 29 years were tested for CT and HPV DNA and provided information on sexual and health behavior at baseline. Of these, 7998 (74.5%) participated in a follow-up visit 2 years later with identical data collection. We used logistic regression to investigate risk factors for incident and redetected CT infection at follow-up.

RESULTS

Among CT DNA negative women at baseline (n = 7529), 106 (1.4%) were CT DNA positive at follow-up (incident infection). Increasing number of sexual partners during follow-up (odds ratio [OR], 1.07 per partner; 95% confidence interval (CI), 1.02-1.11), low educational level (OR, 1.69; 95% CI, 1.11-2.56; for basic education vs. high school or higher), and high-risk HPV positivity at baseline (OR, 1.66; 95% CI, 1.06-2.58) were risk factors for incident infection, whereas older age (OR, 0.86 per year increase; 95% CI, 0.80-0.93) and condom use (OR, 0.60; 95% CI, 0.38-0.94) were associated with reduced risk. Among CT DNA positive women at baseline (n = 469), 108 (23.0%) tested positive at follow-up (redetected infection). We found no statistically significant associations between age, educational level, sexual behavior, smoking, or high-risk HPV status and the risk for redetected CT.

CONCLUSION

Young age, low educational level, high number of sexual partners, failure to use condoms, and high-risk HPV positivity are associated with increased risk for incident CT infection. These findings may guide the development of targeted CT prevention strategies, including screening and information campaigns.

Repeat infection with Neisseria gonorrhoeae among active duty U.S. Army personnel: a population-based case-series study

Little information is known on the rate of repeat gonorrhea infection among U.S. military personnel. We analyzed all gonorrhea cases reported to the Defense Medical Surveillance System during 2006–2012 to determine the rate of repeat infection. During the seven-year study period, 17,602 active duty U.S. Army personnel with a first incident gonorrhea infection were reported. Among the 4987 women with a first gonorrhea infection, 14.4% had at least one repeat infection. Among the 12,615 men with a first gonorrhea infection, 13.7% had at least one repeat infection. Overall, the rate of repeat gonorrhea infection was 44.5 and 48.9 per 1000 person-years for women and men, respectively. Service members aged 17–19 years (hazard ratio [HR] for women = 1.51; HR for men = 1.71), African-American personnel (HR for women = 1.26; HR for men = 2.17), junior enlisted personnel (HR for women = 2.64; HR for men = 1.37), and those with one year or less of service (HR for women = 1.23; HR for men = 1.37) were at higher risk of repeat infection. The findings from this study highlight the need to develop targeted prevention initiatives including education, counseling, and retesting to prevent gonorrhea reinfections among U.S. Army personnel.

Bacterial vaginosis in pregnant adolescents: proinflammatory cytokine and bacterial sialidase profile. Cross-sectional study

CONTEXT AND OBJECTIVE

Bacterial vaginosis occurs frequently in pregnancy and increases susceptibility to sexually transmitted infections (STI). Considering that adolescents are disproportionally affected by STI, the aim of this study was to evaluate the cervicovaginal levels of interleukin (IL)-1 beta, IL-6, IL-8 and bacterial sialidase in pregnant adolescents with bacterial vaginosis.

DESIGN AND SETTING

Cross-sectional study at mother and child referral units in Belém, Pará, Brazil.

METHODS

Vaginal samples from 168 pregnant adolescents enrolled were tested for trichomoniasis and candidiasis. Their vaginal microbiota was classified according to the Nugent criteria (1991) as normal, intermediate or bacterial vaginosis. Cervical infection due to Chlamydia trachomatisand Neisseria gonorrhoeae was also assessed. Cytokine and sialidase levels were measured, respectively, using enzyme-linked immunosorbent assays and MUAN conversion in cervicovaginal lavages. Forty-eight adolescents (28.6%) were excluded because they tested positive for some of the infections investigated. The remaining 120 adolescents were grouped according to vaginal flora type: normal (n = 68) or bacterial vaginosis (n = 52). Their cytokine and sialidase levels were compared between the groups using the Mann-Whitney test (P < 0.05).

RESULTS

The pregnant adolescents with bacterial vaginosis had higher levels of IL-1 beta, IL-6 and IL-8 (P < 0.05). Sialidase was solely detected in 35 adolescents (67.2%) with bacterial vaginosis.

CONCLUSIONS

Not only IL-1 beta and sialidase levels, but also IL-6 and IL-8 levels are higher in pregnant adolescents with bacterial vaginosis, thus indicating that this condition elicits a more pronounced inflammatory response in this population, which potentially increases vulnerability to STI acquisition.

Chlamydia trachomatis and risk of cervical intraepithelial neoplasia grade 3 or worse in women with persistent human papillomavirus infection: a cohort study

OBJECTIVES

Some studies suggest that Chlamydia trachomatis (CT) enhances cervical carcinogenesis; however, a possible confounding effect of persistent human papillomavirus (HPV) infection was not addressed. We examined the potential role of CT infection in the development of subsequent cervical intraepithelial neoplasia grade 3 or worse (CIN3+) in women with prevalent HPV infection and in a subgroup of women with persistent HPV infection.

METHODS

Participants in this population-based cohort study underwent a structured interview, including history of CT infection, and subsequently cervical exfoliated cells were obtained for HPV DNA and CT DNA testing. Women with high-risk HPV DNA infection and no prevalent cervical disease constituted the overall study population (n=1390). A subgroup of women with persistent HPV infection (n=320) was also identified. All women were passively followed for development of cervical lesions in the national Pathology Data Bank. HRs and 95% CIs for CIN3+ during follow-up (up to 19 years) were estimated in an accelerated failure time model.

RESULTS

Women who reported more than one CT infection had a statistically significantly increased risk of CIN3+ (high-risk HPV-positive, HR=2.51, 95% CI 1.44 to 4.37) (persistent HPV infection, HR=3.65, 95% CI 1.53 to 8.70). We found no association between CT DNA and subsequent risk of CIN3+ among women who were HPV-positive or had a persistent HPV infection at baseline.

CONCLUSIONS

Repeated CT infections increased the risk of CIN3+ among women with prevalent as well as persistent high-risk HPV infection.

Isothermal nucleic acid amplification technologies for point-of-care diagnostics: a critical review

Nucleic Acid Testing (NAT) promises rapid, sensitive and specific diagnosis of infectious, inherited and genetic disease. The next generation of diagnostic devices will interrogate the genetic determinants of such conditions at the point-of-care, affording clinicians prompt reliable diagnosis from which to guide more effective treatment. The complex biochemical nature of clinical samples, the low abundance of nucleic acid targets in the majority of clinical samples and existing biosensor technology indicate that some form of nucleic acid amplification will be required to obtain clinically relevant sensitivities from the small samples used in point-of-care testing (POCT). This publication provides an overview and thorough review of existing technologies for nucleic acid amplification. The different methods are compared and their suitability for POCT adaptation are discussed. Current commercial products employing isothermal amplification strategies are also investigated. In conclusion we identify the factors impeding the integration of the methods discussed in fully automated, sample-to-answer POCT devices.

Epidemiology of Chlamydia trachomatis infection in women and the cost-effectiveness of screening

BACKGROUND

The majority of Chlamydia trachomatis infections in women are asymptomatic, but may give rise to pelvic inflammatory disease (PID) and tubal infertility. Screening programmes aim at reducing morbidity in individuals by early detection and treatment, and at decreasing the overall prevalence of infection in the population. A number of modelling studies have tried to calculate the threshold prevalence of chlamydia lower genital tract infection above which screening becomes cost-effective. There is considerable debate over the exact complication rates after chlamydia infections, and more precise estimates of PID and tubal infertility are needed, for instance to be inserted in economic models.

METHODS

With reference to key studies and systematic reviews, an overview is provided focusing on the epidemiology of chlamydia infection and the risk-estimates of its late complications.

RESULTS

In the literature, the generally assumed risk of developing PID after lower genital tract chlamydia infection varies considerably, and is up to 30%. For developing tubal infertility after PID the risks are 10-20%. This implies that the risk of test-positive women of developing tubal infertility would range between 0.1 and 6%. We included chlamydia IgG antibody testing in a model and estimated a risk of tubal infertility up to 4.6%.

CONCLUSION

The risk of developing late complications after chlamydia lower genital tract infection appears low. High quality RCTs dealing with the transition from cervicitis to infertility are needed to broaden the evidence. In screening programmes, chlamydia antibody testing, as an intermediate marker for potential adverse sequelae, might enable more precise estimates.

Internal control for nucleic acid testing based on the use of purified Bacillus atrophaeus subsp. globigii spores

Commonly used internal controls (ICs) to monitor the efficiency of nucleic acid testing (NAT) assays do not allow verification of nucleic acid extraction efficiency. Since microbial cells are often difficult to lyse, it is important to ensure that nucleic acids are efficiently extracted from any target organism. For this purpose, we developed a cellular IC based on the use of nonpathogenic Bacillus spores. Purified Bacillus atrophaeus subsp. globigii (referred to hereafter as simply B. atrophaeus) spores were added to vaginal and anal samples, which were then subjected to rapid DNA extraction and subsequent PCR amplification. The proof of concept of this cellular IC was made through the use of both manual and automated DNA extraction methods, using vaginal or anal samples spiked with B. atrophaeus spores, combined with a multiplex real-time PCR assay for the specific detection of group B streptococci (GBS) and B. atrophaeus. The performance of the cellular IC was compared to that of a standard IC plasmid added to PCRs. Approximately 500 B. atrophaeus spores per PCR was found to be optimal since this did not interfere significantly with GBS detection for either DNA extraction method and yielded reproducible amplification and/or detection of B. atrophaeus genomic DNA serving as an IC template. Performance of the cellular IC was comparable to that of the standard IC. This novel IC system using nonpathogenic and hard-to-lyse B. atrophaeus spores allowed validation of both the DNA extraction procedure and the amplification and detection process. Use of a spore-based control also provides a universal control for microbial cell lysis.

Conjunctival chlamydial 16S ribosomal RNA expression in trachoma: is chlamydial metabolic activity required for disease to develop?

BACKGROUND

Nucleic acid amplification testing frequently detects conjunctival Chlamydia trachomatis infection in subjects without clinical signs of trachoma. It is unclear whether such subjects are actually infected. We measured chlamydial 16S ribosomal RNA (rRNA) expression, a marker of chlamydial metabolic activity, in comparison with the quantitation of a chlamydial DNA target in subjects exposed to trachoma.

METHODS

Subjects from 2 Gambian villages where trachoma was endemic were examined. Conjunctival samples were tested for the presence of C. trachomatis DNA using a quantitative real-time polymerase chain reaction (PCR) assay for the omp1 gene and for the expression of C. trachomatis 16S rRNA using a 1-step, real-time reverse-transcriptase PCR assay.

RESULTS

A total of 248 people were examined. The prevalence of clinically active trachoma was 16.9%. C. trachomatis was detected in 19.8% and 6.8% of subjects by the omp1 and 16S rRNA assays, respectively. For subjects with positive results for both tests, the number of copies of 16S rRNA was approximately 100-fold greater than the number of copies of the omp1 gene. In samples from subjects in whom the omp1 gene was detected in the absence of 16S rRNA, typically only a few copies of omp1 were present. The expression of 16S rRNA was strongly associated with the presence of clinical signs of active trachoma.

CONCLUSIONS

The use of 16S rRNA expression for the detection of chlamydial metabolic activity appears to usefully discriminate established infections from the inoculation of the conjunctiva with dead or subviable organisms, which probably occurs frequently in settings in which trachoma is endemic. The data support conclusions from primate challenge studies that live Chlamydiae species or antigens derived from them are needed to provoke the clinical signs of disease.

Real-time nucleic acid sequence-based amplification assay for detection of hepatitis A virus

A nucleic acid sequence-based amplification (NASBA) assay in combination with a molecular beacon was developed for the real-time detection and quantification of hepatitis A virus (HAV). A 202-bp, highly conserved 5' noncoding region of HAV was targeted. The sensitivity of the real-time NASBA assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, with only HAV positively identified. When combined with immunomagnetic separation, the NASBA assay successfully detected as few as 10 PFU from seeded lake water samples. Due to its isothermal nature, its speed, and its similar sensitivity compared to the real-time RT-PCR assay, this newly reported real-time NASBA method will have broad applications for the rapid detection of HAV in contaminated food or water.

Development and use of an internal positive control for detection of Bordetella pertussis by PCR

An internal control of amplification was constructed by recombinant PCR to detect PCR inhibitors. This exogenous DNA was included in the reaction mixture and coamplified with the target gene. This detection was successfully applied to the diagnosis of whooping cough by amplification of a fragment of Bordetella pertussis IS481.

Multiparametric duplex real-time nucleic acid sequence-based amplification assay for mRNA profiling

Nucleic acid sequence-based amplification (NASBA) is a sensitive isothermal transcription-based amplification method. We have developed real-time NASBA assays to detect mRNA coding for the estrogen receptor α (ESR1) and the progesterone receptor (PGR) in breast tumors by means of duplex reactions using cyclophilin B (PPIB) as the normalizing gene. Both the ESR1/PPIB and PGR/PPIB duplex NASBA assays are highly sensitive, specific, and reproducible. Quantification is determined using external standard calibration curves and the ratio between the number of target and housekeeping gene mRNA copies. Amplification of the target gene in the duplex NASBA assay was disrupted when this latter was mixed with a large amount of the housekeeping PPIB gene, suggesting that it is preferable for the normalizing gene chosen to have an expression level comparable to the target gene. Sensitivity and robustness of the duplex NASBA assays were assessed in breast cancer cell lines. Such a rapid and easy-to-use multiparametric duplex real-time NASBA assay could also advantageously be set up for other mRNA profiling applications.

Chlamydia trachomatis serovar E isolates from patients with different clinical manifestations have similar courses of infection in a murine model: host factors as major determinants of C trachomatis mediated pathogenesis

BACKGROUND

Some investigators have proposed an association between certain Chlamydia trachomatis serovars and the clinical course of infection in humans. A recent study of over 1100 patients with culture confirmed and serotyped C trachomatis urogenital infection detected no such association.

AIMS

To corroborate these results using a murine model of female genital tract infection.

METHODS

Various parameters of infection were assessed in mice intravaginally infected with human genital isolates of C trachomatis serovar E from four cases with either a clear symptomatic or asymptomatic clinical course in both the patient and their partner.

RESULTS

No differences were seen among the strains in the incidence or duration of infection, polymorphonuclear granulocyte responses, or upper genital tract progression.

CONCLUSIONS

An investigation to determine the correlation between the clinical manifestations of different isolates of C trachomatis serovar E in humans and certain parameters of microbial pathogenesis in a mouse model failed to reveal an association between the measured parameters and the tendency of serovar E to produce symptomatic versus asymptomatic infections in humans. These findings suggest that differences in the clinical course of infection in humans seen with these strains may be more related to host factors than to genetic variation among strains.

Prevalence and determinants of Chlamydia trachomatis infections in women from Bogota, Colombia

OBJECTIVES

Chlamydia trachomatis infection in the cervix and uterus has been hypothesised to be a co-factor for cervical cancer. We performed a cross sectional study in Bogota, Colombia, where cervical cancer rates are high, to determine the prevalence and determinants of C trachomatis infection, and in particular its association with human papillomavirus (HPV).

METHODS

1829 low income sexually active women were interviewed and tested for C trachomatis, using an endogenous plasmid PCR-EIA, and for 37 HPV types, using a general primer GP5+/6+ mediated PCR-EIA.

RESULTS

The overall prevalence of C trachomatis was 5.0%, and it did not differ substantially between women with normal (5.0%) and those with abnormal (5.2%) cervical cytology. Women infected with any HPV type (15.1%) had a slightly increased risk of being simultaneously infected with C trachomatis (adjusted OR 1.3, 95% CI: 0.8 to 2.4). This association was stronger when multiple HPV infections (adjusted OR 2.5, 95% CI: 1.1 to 5.9) were present. No other lifestyle or reproductive characteristics were clearly associated with risk of C trachomatis infection.

CONCLUSIONS

HPV infected women, particularly women with multiple HPV infections, are at increased risk of being infected with C trachomatis.

Evaluation of the NucliSens Basic Kit assay for detection of Norwalk virus RNA in stool specimens

Norwalk-like viruses (NLVs) are a genetically diverse group of human caliciviruses that are the most common cause of epidemic gastroenteritis and are detected typically in stool by reverse transcription (RT)-PCR or electron microscopy (EM). The application of a rapid nucleic acid sequence-based amplification (NASBA) assay for the detection of NLV RNA in stool is described using the NucliSens Basic Kit. Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate. When compared directly with RT-PCR on a dilution series of NV stool filtrate, the NucliSens Basic Kit assay was equally sensitive. Cross-reactivity studies with a representative panel of other enteric pathogens were negative. When applied to 15 stool specimens from NV-challenged volunteers, the NASBA Basic Kit application for NV detection yielded 100% sensitivity, 50% specificity, and 67% concordance, using RT-PCR as the 'gold standard'. Despite the specificity of the NASBA primer/probe sequences for NV, other representatives from both NLV genogroups I and II could be detected by the Basic Kit assay in outbreak stool specimens, although the results were inconsistent. Our results suggest that the NucliSens Basic Kit assay provides a rapid and sensitive alternative to RT-PCR for detecting NV RNA in stool specimens. However, improvements in test specificity and primer design will be needed before the assay can be used routinely in the clinical setting.

Low grade squamous intra-epithelial lesions and human papillomavirus infection in Colombian women

Low grade squamous intra-epithelial lesions could be considered as a manifestation of human papillomavirus exposition, however the discrepancy between rates of infection with human papillomavirus and development of low grade squamous intra-epithelial lesions is notable. Here we report a cross-sectional three-armed case-control study in the Colombian population, to compare the risk factors of women with low grade squamous intra-epithelial lesions with that of human papillomavirus DNA-negative and positive women with normal cytology.

The natural course of asymptomatic Chlamydia trachomatis infections: 45% clearance and no development of clinical PID after one-year follow-up

The natural course of asymptomatic Chlamydia trachomatis infections in women was studied during one year in a cohort based nested case-control study. Healthy women (n = 744, from four company health services in Amsterdam) with a medical check-up prior to job engagement were included. C. trachomatis-positive women (n = 30, cases) and a randomly selected control group of C. trachomatis-negative women (n = 186, controls) were followed for one year. Urine specimens (at one, six and 12 months) were analysed for the presence of C. trachomatis-DNA and the C. trachomatis-serovars, and questionnaires were filled in. The C. trachomatis prevalence and natural course in relation to demographic and sexual characteristics after one, six and 12 months were studied. The main outcome measures were 1) the prevalence of C. trachomatis using urine specimens; 2) self-reported complaints; 3) clinical symptoms reported to the coordinating physicians. The prevalence of asymptomatic C. trachomatis infections was 4% and there was no correlation with demographic and sexual characteristics. The person/year clearance rate was 44.7% per year. None of the C. trachomatis-positive women developed clinical symptoms or used C. trachomatis specific antibiotic treatment. Women with or without an asymptomatic infection had the same number of self-reported urogenital complaints during follow-up. In persisting infections twice as many C. trachomatis-serovar E infections were detected as compared to clearing infections. Our findings showed that almost half of the asymptomatic C. trachomatis infections in women cleared during one year of follow-up and none developed clinical pelvic inflammatory disease (PID), which is a much lower figure than previously suggested. Therefore these data are important for cost effectiveness calculations in screening programmes for asymptomatic C. trachomatis infections.

Prevalence and persistence of asymptomatic Chlamydia trachomatis infections in urine specimens from Danish male military recruits

Danish male military recruits (n = 388) were included in a follow-up study to investigate the prevalence and persistence of asymptomatic Chlamydia trachomatis infections. Urine specimens were collected at enrolment and after approximately six months. C. trachomatis was detected by polymerase chain reaction (Amplicor, Roche). Questionnaires were filled out concerning sexual behaviour and clinical symptoms. The prevalence of asymptomatic C. trachomatis in Danish male military recruits was 4.6% (18 out of 388). From five C. trachomatis-positive men no follow-up sample was obtained. From the remaining 13 C. trachomatis-positive men four (31%) were treated for C. trachomatis between the two visits (outside the study protocol). Of the remaining nine men, one cleared the infection and eight men (89%) had a persistent infection. The number of lifetime sexual partners was associated with the presence of C. trachomatis at enrolment. Although based on small numbers, this follow-up study shows, in contrast to women with asymptomatic C. trachomatis infections, a high percentage of C. trachomatis persistence in asymptomatically infected males.

Development of real-time NASBA assays with molecular beacon detection to quantify mRNA coding for HHV-8 lytic and latent genes

BACKGROUND

Human herpesvirus-8 (HHV-8) is linked to the pathogenesis of Kaposi's sarcoma (KS), and the HHV-8 DNA load in peripheral blood mononuclear cells (PBMC) is associated with the clinical stage of KS. To examine the expression of HHV-8 in PBMC, four HHV-8 mRNA specific NASBA assays were developed

METHODS

We have developed four quantitative nucleic acid sequence-based amplification assays (NASBA-QT) specifically to detect mRNA coding for ORF 73 (latency-associated nuclear antigen, LANA), vGCR (a membrane receptor), vBcl-2 (a viral inhibitor of apoptosis) and vIL-6 (a viral growth factor). The NASBA technique amplifies nucleic acids without thermocycling and mRNA can be amplified in a dsDNA background. A molecular beacon is used during amplification to enable real-time detection of the product. The assays were tested on PBMC samples of two AIDS-KS patients from the Amsterdam Cohort.

RESULTS

For all four assays, the limit of detection (LOD) of 50 molecules and the limit of quantification (LOQ) of 100 molecules were determined using in vitro transcribed RNA. The linear dynamic range was 50 to 10(7) molecules of HHV-8 mRNA. We found HHV-8 mRNA expression in 9 out of the 10 tested samples.

CONCLUSION

These real-time NASBA assays with beacon detection provide tools for further study of HHV-8 expression in patient material.

Detection of Mycoplasma pneumoniae in spiked clinical samples by nucleic acid sequence-based amplification

Isothermal nucleic acid sequence-based amplification (NASBA) was applied to the detection of Mycoplasma pneumoniae. M. pneumoniae RNA prepared from a plasmid construct was used to assess the sensitivity of the assay, and an internal control for the detection of inhibitors was constructed. The sensitivity of the NASBA assay was 10 molecules of wild-type M. pneumoniae RNA generated in vitro and 5 color-changing units (CCU) of M. pneumoniae. An appropriate specimen preparation procedure was developed: after protease treatment of the respiratory specimens, guanidine thiocyanate lysis solution (4.7 M guanidine thiocyanate [Sigma-Aldrich NV], 46 mM Tris-HCl [Merck, Darmstadt, Germany], 20 mM EDTA [Sigma-Aldrich NV], 1.2% [wt/vol] Triton X-100 [Sigma-Aldrich NV], pH 6.2.) was added. With spiked throats, nasopharyngeal aspirates, bronchoalveolar lavage specimens, and sputum specimens, the sensitivity of the NASBA assay in the presence of the internal control was 2 x 10(4) molecules of in vitro-generated RNA or 5 CCU of M. pneumoniae. The sensitivity of the NASBA assay was comparable to that of a PCR targeted to the P1 adhesin gene. Fifteen clinical specimens positive for M. pneumoniae by PCR were also positive by NASBA. These results indicate that the sensitivity of detection of M. pneumoniae in spiked respiratory samples by NASBA is high. Together with the use of the internal control, the assay merits evaluation as a diagnostic tool.

Comparison of three commercially available peptide-based immunoglobulin G (IgG) and IgA assays to microimmunofluorescence assay for detection of Chlamydia trachomatis antibodies

Three commercially available, peptide-based enzyme-linked immunosorbent assay (ELISA) systems (Chlamydia trachomatis IgG and IgA EIA [CT-EIA; Labsystems OY, Helsinki, Finland], SeroCT IgG and IgA [SeroCT; Savyon Diagnostics Ltd., Ashdod, Israel], and Chlamydia trachomatis IgG and IgA pELISA [CT pELISA; Medac, Wedel, Germany]) were evaluated for the detection of serum immunoglobulin G (IgG) and IgA antibodies specific for Chlamydia trachomatis and compared to the "gold standard" assay, the microimmunofluorescence (MIF) assay. Serological responses were analyzed in 149 women aged 20 to 30 years. Cervical swabs obtained from these women were examined for C. trachomatis by PCR, and 43 were found to be positive. The overall seroprevalence rates detected by CT-EIA, SeroCT, CT pELISA, and the MIF assay were 42, 42, 35, and 39%, respectively, for IgG and 7, 7, 3, and 7%, respectively, for IgA. The IgG seroprevalence rates for the PCR-positive women were two to three times higher than those for the PCR-negative women, i.e., 72 versus 29%, 72 versus 29%, 47 versus 26%, and 74 versus 25% for CT-EIA, SeroCT, CT pELISA, and the MIF assay, respectively. After discrepancy analysis, the sensitivity, specificity, positive predictive value, and negative predictive value were calculated for the IgG assays; for CT-EIA they were 84.7, 98.6, 98.4, and 86.7%, respectively; for CT pELISA they were 71.4, 97.3, 96.2, and 78.3%, respectively; for SeroCT they were 84.7, 98.6, 98.4, and 86.3%, respectively; and for the MIF assay they were 79.2, 83.1, 98.3, and 83.1%, respectively. In conclusion, these peptide-based ELISA systems for the serological detection of C. trachomatis infection performed as well as the MIF assay. Since these tests are less time-consuming, less expensive, and easier to perform than the MIF assay, they might be useful in the serodiagnosis of chlamydial infection.

Characteristics and applications of nucleic acid sequence-based amplification (NASBA)

Nucleic acid sequence-based amplification (NASBA) is a sensitive, isothermal, transcription-based amplification system specifically designed for the detection of RNA targets. In some NASBA systems, DNA is also amplified though very inefficiently and only in the absence of the corresponding RNA target or in case of an excess (>1,000-fold) of target DNA over RNA. As NASBA is primer-dependent and amplicon detection is based on probe binding, primer and probe design rules are included. An overview of various target nucleic acids that have been amplified successfully using NASBA is presented. For the isolation of nucleic acids prior to NASBA, the "Boom" method, based on the denaturing properties of guanidine isothiocyanate and binding of nucleic acid to silica particles, is preferred. Currently, electro-chemiluminescence (ECL) is recommended for the detection of the amplicon at the end of amplification. In the near future, molecular beacons will be introduced enabling "real-time detection," i.e., amplicon detection during amplification. Quantitative HIV-1 NASBA and detection of up to 48 samples can then be performed in only 90 min.

Quantitative competitive NASBA for measuring mRNA expression levels of the immediate early 1, late pp67, and immune evasion genes US3, US6 and US11 in cells infected with human cytomegalovirus

Different cell types were infected with human cytomegalovirus (HCMV) and RNA expression dynamics were analyzed by quantitative NASBA assays for IE1 (UL123), pp67 (UL65) and the immune evasion genes (US3, US6 and US11). The quantitative NASBA assays gave reproducible quantification in the range of 10(3)-10(6) RNA copies for IE1 and pp67 RNA, from 3x10(3) to 1x10(6) RNA copies for US6 and US11 RNA, and from 1x10(4) to 1x10(6) RNA copies for US3 RNA. SMC, HAEC and HUVEC cells infected with an, in endothelial cells, propagated HCMV strain (VHL/E) showed similar RNA expression dynamics for the analyzed genes. Expression of all genes studied was observed within the first 4 h post-infection. The first gene for which expression could be detected was IE1, followed by US3, US11, pp67 and US6. Fibroblasts infected with HCMV strain AD169 showed a different RNA expression pattern for US3. Translation of the mRNA studied was demonstrated by detection of the proteins 48 h post-infection by immunofluorescence.

Detection of dengue viral RNA using a nucleic acid sequence-based amplification assay

Faster techniques are needed for the early diagnosis of dengue fever and dengue hemorrhagic fever during the acute viremic phase of infection. An isothermal nucleic acid sequence-based amplification (NASBA) assay was optimized to amplify viral RNA of all four dengue virus serotypes by a set of universal primers and to type the amplified products by serotype-specific capture probes. The NASBA assay involved the use of silica to extract viral nucleic acid, which was amplified without thermocycling. The amplified product was detected by a probe-hybridization method that utilized electrochemiluminescence. Using normal human plasma spiked with dengue viruses, the NASBA assay had a detection threshold of 1 to 10 PFU/ml. The sensitivity and specificity of the assay were determined by testing 67 dengue virus-positive and 21 dengue virus-negative human serum or plasma samples. The "gold standard" used for comparison and evaluation was the mosquito C6/36 cell culture assay followed by an immunofluorescent assay. Viral infectivity titers in test samples were also determined by a direct plaque assay in Vero cells. The NASBA assay was able to detect dengue viral RNA in the clinical samples at plaque titers below 25 PFU/ml (the detection limit of the plaque assay). Of the 67 samples found positive by the C6/36 assay, 66 were found positive by the NASBA assay, for a sensitivity of 98.5%. The NASBA assay had a specificity of 100% based on the negative test results for the 21 normal human serum or plasma samples. These results indicate that the NASBA assay is a promising assay for the early diagnosis of dengue infections.

Evaluation of the NucliSens Basic Kit for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in genital tract specimens using nucleic acid sequence-based amplification of 16S rRNA

We evaluated a new RNA amplification and detection kit, the NucliSens Basic Kit (Organon Teknika), for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in genitourinary specimens. The Basic Kit provides an open platform for RNA amplification and detection and contains isolation reagents for nucleic acid extraction, nucleic acid sequence-based amplification (NASBA) reagents (enzymes and buffers), and a generic ruthenium-labeled probe for electrochemiluminescent (ECL) detection of amplified product. Using freshly purified and titrated stocks of C. trachomatis and N. gonorrhoeae and in vitro-generated RNA transcripts for sensitivity determinations, the Basic Kit detected 1 inclusion-forming unit of C. trachomatis, 1 CFU of N. gonorrhoeae, and 100 RNA molecules of 16S rRNA for both bacteria. The clinical performance of the Basic Kit was evaluated by testing a total of 250 specimens for N. gonorrhoeae by culture and NASBA and a total of 96 specimens for C. trachomatis by PCR and NASBA. The Basic Kit detected 139 of 142 N. gonorrhoeae culture-positive specimens and gave a negative result for 73 of 74 culture-negative specimens, for a sensitivity and specificity of 97.9 and 98.7%, respectively. For C. trachomatis, the Basic Kit detected 24 of 24 PCR-positive specimens and gave a negative result for 71 of 72 PCR-negative specimens, for a sensitivity and specificity of 100 and 98.6%, respectively. The Basic Kit also detected specimens containing both N. gonorrhoeae and C. trachomatis, using a multiplex NASBA assay using primers for both bacteria. The NucliSens Basic Kit offers a versatile platform for the development of sensitive RNA detection assays for sexually transmitted diseases.

Detection of antimicrobial-treated Chlamydia trachomatis with Amplicor PCR test kit

A polymerase chain reaction (PCR) method for the detection of Chlamydia trachomatis has been developed and is now available in the clinical setting. However, one of the major problems with this method is possible false-positive detection posttreatment. Nonviable C. trachomatis was established by in-vitro exposure to an antimicrobial agent, and we tried to detect the nonviable cells (NVCs) of C. trachomatis by PCR with variant primer sets. C. trachomatis strains (D/UW-3/Cx) were cultured in a medium containing the antimicrobial agent, at 8 x MIC (minimal inhibitory concentration) 15 to 20 h postinfection. Amplicor and two sets of PCR primers were used to detect the DNA of NVCs. Serial passages of NVCs were done five times. All samples were positive on Amplicor, and all except the fourth passage were positive for the two sets of primers. Although the PCR test appears to be valuable, NVCs may possibly be detected by this method, and this may be clinically responsible for the false detection of C. trachomatis after appropriate antimicrobial chemotherapy.

Analysis of genetic heterogeneity in Chlamydia trachomatis clinical isolates of serovars D, E, and F by amplified fragment length polymorphism

Amplified fragment length polymorphism (AFLP) fingerprinting of clinical isolates of Chlamydia trachomatis serovars D, E, and F showed a low percentage of genetic heterogeneity, but clear differences were found. Isolates from index patients and partners had identical AFLP patterns and AFLP markers. Characterization of these AFLP markers could give more insight into the differences in virulence and clinical course of C. trachomatis infections.

Urogenital Chlamydia trachomatis serovars in men and women with a symptomatic or asymptomatic infection: an association with clinical manifestations?

To determine whether certain Chlamydia trachomatis serovars are preferentially associated with a symptomatic or an asymptomatic course of infection, C. trachomatis serovar distributions were analyzed in symptomatically and asymptomatically infected persons. Furthermore, a possible association between C. trachomatis serovars and specific clinical symptoms was investigated. C. trachomatis-positive urine specimens from 219 asymptomatically infected men and women were obtained from population-based screening programs in Amsterdam. Two hundred twenty-one C. trachomatis-positive cervical and urethral swabs from symptomatically and asymptomatically infected men and women were obtained from several hospital-based departments. Serovars were determined using PCR-based genotyping, i.e., restriction fragment length polymorphism analysis of the nested-PCR-amplified omp1 gene. The most prevalent C. trachomatis serovars, D, E, and F, showed no association with either a symptomatic or asymptomatic course of infection. The most prominent differences found were (i) the association of serovar Ga with symptoms in men (P = 0.0027), specifically, dysuria (P < 0.0001), and (ii) detection of serovar Ia more often in asymptomatically infected people (men and women) (P = 0.035). Furthermore, in women, serovar K was associated with vaginal discharge (P = 0.002) and serovar variants were found only in women (P = 0.045).

Determination of Chlamydia trachomatis prevalence in an asymptomatic screening population: performances of the LCx and COBAS Amplicor tests with urine specimens

This study determined the performances of the LCx (Abbott) and COBAS Amplicor (Roche) tests with urine specimens for the detection of Chlamydia trachomatis in an asymptomatic screening population. Randomly selected women and men (age range, 15 to 40 years) registered in 20 general practices in Amsterdam, The Netherlands, were invited to participate in this study. Urine specimens (n = 2, 906; 1,138 specimens from men and 1,717 specimens from women) were tested for C. trachomatis by the COBAS Amplicor (Roche) and LCx (Abbott) tests. Samples which were positive by only one assay were subjected to discrepant analyses by a third assay (in-house plasmid PCR). By the LCx assay C. trachomatis DNA was detected in urine specimens from 46 of 1,717 women and 29 of 1,138 men, while the COBAS Amplicor detected C. trachomatis DNA in 52 and 35 specimens, respectively. When comparing the LCx and COBAS Amplicor tests, 32 test results (20 for women and 12 for men) were discrepant. After discrepant analyses the following sensitivities, specificities, and positive predictive values were found for the LCx and COBAS Amplicor tests: 78.6 versus 98.8%, 99.7 versus 99.9%, and 88.0 versus 95.4%, respectively. No prominent differences were found between men and women with regard to the test performances. After discrepant analyses the overall prevalences of C. trachomatis in women and men were 3.0 and 2.8%, respectively. For both women and men the prevalence in the younger age groups was higher than that in the older age groups. In conclusion, the COBAS Amplicor tests shows better diagnostic characteristics than the LCx assay for the detection of C. trachomatis in urine specimens from an asymptomatic screening population. In this asymptomatic population the overall prevalence of C. trachomatis was 2.9%.

Expression of Epstein-Barr virus (EBV) transcripts encoding homologues to important human proteins in diverse EBV associated diseases

AIMS

To examine the expression of Epstein-Barr virus (EBV) transcripts encoding proteins homologous to important human proteins in diverse EBV associated diseases. The proteins were: BHRF1 (homologous to Bcl-2), BDLF2 (homologous to cyclin B1), BARF1 (homologous to intercellular cell adhesion molecule 1 (ICAM-1)), and BCRF1 (viral IL-10 (vIL-10), homologous to human IL-10 (hIL-10)).

METHODS

Six cases of oral hairy leukoplakia, seven of Hodgkin's disease, eight of T cell non-Hodgkin's lymphoma, and nine of nasopharyngeal carcinoma were examined at the mRNA level using either the reverse transcriptase polymerase chain reaction (RT-PCR) or nucleic acid sequence based amplification (NASBA). Different primer sets allowed the differentiation by RT-PCR of the latent (Cp/Wp driven) and lytic (Hp driven) transcripts of BHRF1. A specific NASBA reaction was developed for the detection of vIL-10 and BDLF2 transcripts and this was tested initially on cell lines and later on clinical samples.

RESULTS

vIL-10 and BDLF2 were expressed almost exclusively in oral hairy leukoplakia, whereas BARF1 transcripts were present in all cases of nasopharyngeal carcinoma, with weak expression in one oral hairy leukoplakia and isolated cases of lymphoid malignancy. Both BHRF1 transcripts were detected across the range of tissues tested, but strong expression of lytic BHRF1 transcripts was seen only in oral hairy leukoplakia.

CONCLUSIONS

vIL-10 and BDLF2 transcripts are expressed during productive EBV infection and are unlikely to be important in the pathogenesis of EBV associated malignancies. BARF1 appears to be expressed preferentially during viral latency and is more closely associated with malignant rather than benign epithelial proliferations. The alternative transcripts derived from the BHRF1 open reading frame may have very different roles during latent or productive infection.

Mailed, home-obtained urine specimens: a reliable screening approach for detecting asymptomatic Chlamydia trachomatis infections

The use of mailed, home-obtained urine specimens could facilitate screening programs for the detection of asymptomatic Chlamydia trachomatis infections. Since transport time could have an adverse effect on the sensitivity of C. trachomatis detection by PCR, the influence of DNA degradation on amplification was monitored over the course of 1 week. Therefore, urine specimens were aliquoted on the day of collection or arrival. Two groups of urine specimens were investigated. Group I contains first-void C. trachomatis-positive and -negative urine samples. DNA degradation was monitored in group I samples for 7 days at room temperature (RT) and at 4 degrees C by amplifying different lengths of the human beta-globin gene and the C. trachomatis plasmid target. DNA degradation was observed only for the larger human beta-globin fragments at days 5 to 7 at RT. In contrast, at 4 degrees C all targets could be amplified. Urine specimens were also frozen and thawed before aliquoting to mimic freezing during transport. This resulted in a lower sensitivity for the detection of C. trachomatis after thawing and 3 to 4 days at RT. In addition, mailed, home-obtained C. trachomatis-positive urine specimens (group II) were analyzed for 7 days after arrival by two commercially available C. trachomatis detection systems (PCR and ligase chain reaction [LCR]). The C. trachomatis plasmid target in mailed, home-obtained urine specimens could be amplified by both PCR and LCR after 1 week of storage and/or transport at RT. In conclusion, our findings indicate that mailed, home-obtained urine specimens are suitable for the sensitive detection of asymptomatic C. trachomatis infections by amplification methods, even if the transport time is up to 1 week at RT. These findings support the feasibility and validity of screening programs based on mailed, home-obtained urine specimens. Larger studies should be initiated to confirm our results.

Multicenter evaluation of the fully automated COBAS AMPLICOR PCR test for detection of Chlamydia trachomatis in urogenital specimens

The fully automated COBAS AMPLICOR CT/NG test for the detection of Chlamydia trachomatis was evaluated in a multicenter trial. Test performance was evaluated for 2,014 endocervical swab and 1,278 urine specimens obtained from women and for 373 urethral swab and 254 urine specimens obtained from men. Culture served as the reference test. Culture-negative, COBAS AMPLICOR-positive specimens that tested positive in a confirmatory PCR test for an alternative target sequence within the C. trachomatis major outer membrane protein gene were resolved as true positives. The overall prevalence of chlamydia was 4.3% in cervical swabs and 11.0% in urethral swabs from men. When the results for each specimen type were considered separately, the resolved sensitivities were 96.5% (83 of 86) for endocervical swab specimens, 95.1% (39 of 41) for urine specimens from women, 100.0% (41 of 41) for urethral swab specimens from men, and 94.4% (17 of 18) for urine specimens from men; the resolved specificities were 99.4% (1,912 of 1,924) for endocervical swab specimens, 99.8% (1,204 of 1,207) for urine specimens from women, 98. 5% (325 of 330) for urethral swab specimens from men, and 100.0% (236 of 236) for urine specimens from men. For the subset of patients from whom both swab and urine specimens were collected, the combined results for both specimen types were used to identify all infected patients. Using these combined reslts as criteria, the resolved sensitivities for the COBAS AMPLICOR test were 82.6% (38 of 46) for endocervical swab specimens, 84.4% (38 of 45) for urine specimens from women, 84.2% (16 of 19) for urethral swab specimens from men, and 89.5% (17 of 19) for urine specimens from men. In comparison, the sensitivity of culture was only 56.5% (26 of 46) for endocervical specimens and 63.2% (12 of 19) for urethral specimens from men. The internal control provided in the COBAS AMPLICOR test revealed that 2.9% of specimens were inhibitory when they were initially tested. Nevertheless, valid results were obtained for 99. 1% of specimens because 68.7% of the inhibitory specimens were not inhibitory when a second aliquot of the original sample was tested. Two additional COBAS AMPLICOR-positive specimens were detected by retesting inhibitory specimens. The COBAS AMPLICOR CT/NG test for the detection of C. trachomatis exhibited equally high sensitivities and specificities with both urogenital swab and urine specimens and, thus, is well-suited for use in screening.

Nucleic acid sequence-based amplification, a new method for analysis of spliced and unspliced Epstein-Barr virus latent transcripts, and its comparison with reverse transcriptase PCR

Nucleic acid sequence-based amplification (NASBA) assays were developed for direct detection of Epstein-Barr virus (EBV) transcripts encoding EBV nuclear antigen 1 (EBNA1), latent membrane proteins (LMP) 1 and 2, and BamHIA rightward frame 1 (BARF1) and for the noncoding EBV early RNA 1 (EBER1). The sensitivities of all NASBAs were at least 100 copies of specific in vitro-generated RNA. Furthermore, 1 EBV-positive JY cell in a background of 50,000 EBV-negative Ramos cells (the relative sensitivity) was detected by using the EBNA1, LMP1, and LMP2 NASBA assays. The relative sensitivity of the EBER1 NASBA was 100 EBV-positive cells, which was probably related to the loss of small RNA molecules during the isolation. The BARF1 and LMP2 NASBAs were evaluated on clinical material. BARF1 expression was found in 6 of 7 nasopharyngeal carcinomas (NPC) but in 0 of 22 Hodgkin's disease (HD) cases, whereas LMP2 expression was found in 7 of 7 NPCs and in 17 of 22 HD cases. For detection of EBNA1 transcripts in HLs (n = 12) and T- and B-cell non-Hodgkin's lymphomas (n = 3 and n = 2, respectively), NASBA was compared with reverse transcriptase (RT) PCR. Two samples were positive only with NASBA, and two other samples were positive only with RT-PCR; for all other samples, the RT-PCR and NASBA results were in agreement. We conclude that NASBA is suitable for sensitive and specific detection of the above-mentioned EBV transcripts, regardless of their splicing patterns and the presence of EBV DNA. The EBNA1, LMP2, and BARF1 NASBAs developed in this study proved to be reliable assays for detection of the corresponding transcripts in EBV-positive clinical material.

Genotyping of Chlamydia trachomatis in urine specimens will facilitate large epidemiological studies

The serovars of Chlamydia trachomatis-positive urine specimens (n = 81; as detected by PCR and ligase chain reaction) were successfully analyzed in 94% of cases by omp1 PCR-based RFLP analysis. The use of urine specimens and this simple and sensitive typing method will greatly facilitate epidemiological studies of C. trachomatis serovar distribution in asymptomatic C. trachomatis infections in both females and males.

Monitoring of Chlamydia trachomatis infections after antibiotic treatment using RNA detection by nucleic acid sequence based amplification

AIM

To investigate the value of RNA detection by nucleic acid sequence based amplification (NASBA) for the monitoring of Chlamydia trachomatis infections after antibiotic treatment.

METHODS

Cervical smears (n = 97) and urine specimens (n = 61) from 25 C trachomatis positive female patients were analysed for the presence of C trachomatis 16S ribosomal RNA (rRNA) by NASBA and C trachomatis plasmid DNA by the polymerase chain reaction (PCR) before and up to five weeks after antibiotic treatment.

RESULTS

Chlamydia trachomatis RNA was found in all cervical smears taken before antibiotic treatment (n = 24) and in two smears taken one week after antibiotic treatment; no C trachomatis RNA was detected after two weeks or more. In contrast, C trachomatis DNA was found in all such specimens before treatment, and 21 of 25, six of 21, and five of 20 smears were found to be positive at one, two, and three weeks after treatment, respectively. After four weeks, only one of six smears was positive, and this smear had been negative in the two preceding weeks. Of the 61 urine samples investigated, C trachomatis DNA and C trachomatis RNA were found in all before treatment (n = 15), whereas one week after treatment four of 15 were C trachomatis DNA positive and C trachomatis RNA was detected in one sample only.

CONCLUSIONS

These data show that RNA detection by NASBA can be used successfully to monitor C trachomatis infections after antibiotic treatment. Furthermore, it might be possible to use urine specimens as a test of cure because neither C. trachomatis DNA or RNA could be detected two weeks or more after treatment.

Diagnostic value of monitoring human cytomegalovirus late pp67 mRNA expression in renal-allograft recipients by nucleic acid sequence-based amplification

The diagnostic value of monitoring human cytomegalovirus (HCMV) late pp67 mRNA expression by nucleic acid sequence-based amplification (NASBA) after renal-allograft transplantation was evaluated. RNAs were isolated from 489 whole-blood specimens of 42 patients for the specific amplification of the late pp67 (UL65) mRNA. NASBA results were compared to results from the pp65 antigenemia assay, virus isolation by cell culture, and serology. The sensitivity value for NASBA proved to be higher than that for the antigenemia assay (50 versus 35%) for the detection of HCMV infection, while the sensitivity values of cell culture and NASBA were comparable (54 and 50%, respectively). NASBA detected the onset of HCMV infection simultaneously with cell culture and the antigenemia assay. Both the antigenemia assay and NASBA are very specific (100%) and highly predictive (100%) for the onset of HCMV infection. Antiviral therapy with ganciclovir resulted in negative results for cell culture, the antigenemia assay, and NASBA. In conclusion, monitoring HCMV pp67 mRNA expression by NASBA is a highly specific method for the detection of HCMV infection in renal-allograft recipients and is more sensitive than the antigenemia assay. Furthermore, NASBA can be used to monitor the progression of HCMV infections and the effect of antiviral therapy on viral activity.