Pooling of urine samples for screening for Neisseria gonorrhoeae by ligase chain reaction: accuracy and application

Pool testing with dilution effects and heterogeneous priors

The Dorfman pooled testing scheme is a process in which individual specimens (e.g., blood, urine, swabs, etc.) are pooled and tested together; if the merged sample tests positive for infection, then each specimen from the pool is tested individually. Through this procedure, laboratories can reduce the expected number of tests required to screen the population, as individual tests are only carried out when the pooled test detects an infection. Several different partitions of the population can be used to form the pools. In this study, we analyze the performance of ordered partitions, those in which subjects with similar probability of infection are pooled together. We derive sufficient conditions under which ordered partitions outperform other types of partitions in terms of minimizing the expected number of tests, the expected number of false negatives, and the expected number of false positive classifications. These sufficient conditions can be easily verified in practical applications once the dilution effect has been estimated. We also propose a measure of equity and present conditions under which this measure is maximized by ordered partitions.

Sample pooling: burden or solution?

BACKGROUND

Pool-testing strategies combine samples from multiple people and test them as a group. A pool-testing approach may shorten the screening time and increase the test rate during times of limited test availability and inadequate reporting speed. Pool testing has been effectively used for a wide variety of infectious disease screening settings. Historically, it originated from serological testing in syphilis. During the current coronavirus disease 2019 (COVID-19) pandemic, pool testing is considered across the globe to inform opening strategies and to monitor infection rates after the implementation of interventions.

AIMS

This narrative review aims to provide a comprehensive overview of the global efforts to implement pool testing, specifically for COVID-19 screening.

SOURCES

Data were retrieved from a detailed search for peer-reviewed articles and preprint reports using Medline/PubMed, medRxiv, Web of Science, and Google up to 21st March 2021, using search terms "pool testing", "viral", "serum", "SARS-CoV-2" and "COVID-19".

CONTENT

This review summarizes the history and theory of pool testing. We identified numerous peer-reviewed articles that describe specific details and practical implementation of pool testing. Successful examples as well as limitations of pool testing, in general and specifically related to the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and antibodies, are reviewed. While promising, significant operational, pre-analytical, logistical, and economic challenges need to be overcome to advance pool testing.

IMPLICATIONS

The theory of pool testing is well understood and numerous successful examples from the past are available. Operationalization of pool testing requires sophisticated processes that can be adapted to the local medical circumstances. Special attention needs to be paid to sample collection, sample pooling, and strategies to avoid re-sampling.

Active Surveillance of Asymptomatic, Presymptomatic, and Oligosymptomatic SARS-CoV-2-Infected Individuals in Communities Inhabiting Closed or Semi-closed Institutions

Background: The high COVID-19 dissemination rate demands active surveillance to identify asymptomatic, presymptomatic, and oligosymptomatic (APO) SARS-CoV-2-infected individuals. This is of special importance in communities inhabiting closed or semi-closed institutions such as residential care homes, prisons, neuropsychiatric hospitals, etc., where risk people are in close contact. Thus, a pooling approach-where samples are mixed and tested as single pools-is an attractive strategy to rapidly detect APO-infected in these epidemiological scenarios. Materials and Methods: This study was done at different pandemic periods between May 28 and August 31 2020 in 153 closed or semi-closed institutions in the Province of Buenos Aires (Argentina). We setup pooling strategy in two stages: first a pool-testing followed by selective individual-testing according to pool results. Samples included in negative pools were presumed as negative, while samples from positive pools were re-tested individually for positives identification. Results: Sensitivity in 5-sample or 10-sample pools was adequate since only 2 Ct values were increased with regard to single tests on average. Concordance between 5-sample or 10-sample pools and individual-testing was 100% in the Ct ≤ 36. We tested 4,936 APO clinical samples in 822 pools, requiring 86-50% fewer tests in low-to-moderate prevalence settings compared to individual testing. Conclusions: By this strategy we detected three COVID-19 outbreaks at early stages in these institutions, helping to their containment and increasing the likelihood of saving lives in such places where risk groups are concentrated.

Pooling RT-qPCR testing for SARS-CoV-2 in 1000 individuals of healthy and infection-suspected patients

Severe acute respiratory coronavirus 2 (SARS-CoV-2) testing reagents are expected to become scarce worldwide. However, little is known regarding whether pooling of samples accurately detects SARS-CoV-2. To validate the feasibility of pooling samples, serial dilution analysis and spike-in experiments were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2-positive and -negative patients. Furthermore, we studied 1000 individuals, 667 of whom were “healthy” individuals (195 healthcare workers and 472 hospitalized patients with disorders other than COVID-19 infection), and 333 infection-suspected patients with cough and fever. Serial dilution analysis showed a limit of detection of around 10–100 viral genome copies according to the protocol of the National Institute of Infectious Diseases, Japan. Spike-in experiments demonstrated that RT-qPCR detected positive signals in pooled samples with SARS-CoV-2-negative and -positive patients at 5-, 10-, 20-fold dilutions. By screening with this pooling strategy, by the end of April 2020 there were 12 SARS-CoV-2-positive patients in 333 infection-suspected patients (3.6%) and zero in 667 “healthy” controls. We obtained these results with a total of 538 runs using the pooling strategy, compared with 1000 standard runs. In a prospective study, we successfully detected SARS-CoV-2 using 10- to 20-fold diluted samples of nasopharyngeal swabs from eighteen COVID-19 patients with wide ranges of viral load. Pooling sample is feasible for conserving test reagents and detecting SARS-CoV-2 in clinical settings. This strategy will help us to research the prevalence infected individuals and provide infected-status information to prevent the spread of the virus and nosocomial transmission.

A Population-Specific Optimized GeneXpert Pooling Algorithm for Chlamydia trachomatis and Neisseria gonorrhoeae To Reduce Cost of Molecular Sexually Transmitted Infection Screening in Resource-Limited Settings

The sexually transmitted infections (STIs) chlamydia (CT) and gonorrhea (NG) are often asymptomatic in women and undetected by syndromic management, leading to complications such as pelvic inflammatory disease, infertility, and ectopic pregnancy. Molecular testing, such as the GeneXpert CT/NG assay, is highly sensitive, but cost restraints preclude implementation of these technologies in resource-limited settings. Pooled testing is one strategy to reduce the cost per sample, but the extent of savings depends on disease prevalence. The current study describes a pooling strategy based on identification of sociodemographic and laboratory factors associated with CT/NG prevalence in a high-risk cohort of Zambian female sex workers and single mothers conducted from 2016 to 2019. Factors associated with testing positive for CT/NG via logistic regression modeling included city, younger age, lower education, long-acting reversible contraception usage, Trichomonas vaginalis infection, bacterial vaginosis, and incident syphilis infection. Based on these factors, the study population was stratified into high-, intermediate-, and low-prevalence subgroups and tested accordingly-individually, pools of 3, or pools of 4, respectively. The cost per sample was reduced from $18 to as low as $9.43 in the low-prevalence subgroup. The checklist tool and pooling approach described can be used in a variety of treatment algorithms to lower the cost per sample and increase access to molecular STI screening. This is particularly valuable in resource-limited settings to detect and treat asymptomatic CT/NG infections missed by traditional syndromic management.

Pooling of urine samples for molecular detection of Chlamydia trachomatis, Neisseria gonorrhoeae and Mycoplasma genitalium as a screening strategy among young adults in Catalonia

INTRODUCTION

Bacterial sexually transmitted infections (STIs) have an important impact on reproductive health, highlighting the increase in Chlamydia trachomatis infection rates among young people. To reduce the costs of STI detection, the pooling strategy is beneficial for high-throughput tests in low-prevalence populations using non-invasive samples.

OBJECTIVES

(1) To describe the performance of a 7-STI PCR assay using the pooling of three urine samples to detect C. trachomatis, Neisseria gonorrhoeae and Mycoplasma genitalium; (2) to estimate the cost saving of the pooling strategy; (3) to describe the prevalence, risk factors and coinfections of C. trachomatis, N. gonorrhoeae and M. genitalium in young people ≤25 years in Catalonia.

METHODS

cross-sectional prevalence study conducted in 2016 among young people ≤25 years of age seen in sexual and reproductive health centres throughout Catalonia from pools of three urine samples. A standardized questionnaire was used to collect clinical-epidemiological and behavioural variables.

RESULTS

1032 young people were tested. The prevalence of C. trachomatis, N. gonorrhoeae and M. genitalium was 8.5%, 0.6% and 3.5%, respectively. The pooling strategy provided a 33% savings in reagent costs.

CONCLUSIONS

The pooling strategy implemented for epidemiological studies in our context provides a savings that has an impact on the viability of STI detection programmes. In the same way, this study shows that C. trachomatis prevalence continues to increase in this population and, for the first time in Catalonia, the prevalence of M. genitalium in young people is shown.

Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications

Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.

Sexually Transmitted Diseases and Managed Care: An Inquiry and Review of Issues Affecting Service Delivery

To understand the potential role of managed care organizations (MCOs) in prevention and control of sexually transmitted diseases (STDs), we conducted a systematic review of articles on STDs and managed care and sought qualitative information from MCOs on STD-related activities. The review focused on prevention, risk assessment, patient education, counseling, screening, and costs of care, but revealed relatively few published articles. Barriers to STD service delivery included competing priorities, lack of time or supporting organizational structures, and differing mandates of health departments and MCOs. Facilitators included collaboration between health departments and MCOs, regulatory and performance incentives, buy-in from key stakeholders, availability of infrastructure to support data collection, and inclusion of chlamydia screening in the Health Employer Data and Information Set to monitor plan performance. Because of the shift of STD service delivery from the public to private sector, incentives need to maximize interest and cooperation of patients, clinicians, and MCOs in STD prevention.

Estimating the Total Annual Direct Cost of Providing Sexually Transmitted Infection and HIV Testing and Counseling for Men Who Have Sex With Men in the United States

BACKGROUND

The Centers for Disease Control and Prevention recommends annual sexually transmitted infection (STI) and HIV testing and counseling for men who have sex with men (MSM) in the United States. We estimated the annual total direct medical cost of providing recommended STI and HIV testing and counseling services for MSM in the United States.

METHODS

We included costs for 9 STI (including anatomic site-specific) tests recommended by the Centers for Disease Control and Prevention (HIV, syphilis, gonorrhea, chlamydia, hepatitis B viral infection, and herpes simplex virus type 2), office visits, and counseling. We included nongenital tests for MSM with exposure at nongenital sites. All cost data were obtained from the 2012 MarketScan outpatient claims database. Men were defined as MSM if they had a male sex partner within the last 12 months, which was estimated at 2.9% (2.6%-3.2%) of the male population in a 2012 study. All costs were updated to 2014 US dollars.

RESULTS

The estimated average costs were as follows: HIV ($18 [$9-$27]), hepatitis B viral infection ($23 [$12-$35]), syphilis ($8 [$4-$11]), gonorrhea and chlamydia ($45 [$22-$67]) per anatomic site), herpes simplex virus type 2 ($27 [$14-$41]), office visit ($100 [$50-$149]), and counseling ($29 [$15-$44]). We estimated that the total annual direct cost of a universal STI and HIV testing and counseling program was $1.1 billion ($473 million-$1.7 billion) for all MSM and $756 (range, $338-$1.2 billion) when excluding office visit cost.

CONCLUSIONS

These estimates provide the potential costs associated with universal STI and HIV testing and counseling for MSM in the United States. This information may be useful in future cost and/or cost-effectiveness analyses that can be used to evaluate STI and HIV prevention efforts.

Case-control data analysis for randomly pooled biomarkers

Pooled study designs, where individual biospecimens are combined prior to measurement via a laboratory assay, can reduce lab costs while maintaining statistical efficiency. Analysis of the resulting pooled measurements, however, often requires specialized techniques. Existing methods can effectively estimate the relation between a binary outcome and a continuous pooled exposure when pools are matched on disease status. When pools are of mixed disease status, however, the existing methods may not be applicable. By exploiting characteristics of the gamma distribution, we propose a flexible method for estimating odds ratios from pooled measurements of mixed and matched status. We use simulation studies to compare consistency and efficiency of risk effect estimates from our proposed methods to existing methods. We then demonstrate the efficacy of our method applied to an analysis of pregnancy outcomes and pooled cytokine concentrations. Our proposed approach contributes to the toolkit of available methods for analyzing odds ratios of a pooled exposure, without restricting pools to be matched on a specific outcome.

Cost savings and increased efficiency using a stratified specimen pooling strategy for Chlamydia trachomatis and Neisseria gonorrhoeae

Idaho Chlamydia trachomatis-Neisseria gonorrhoeae specimens from July 2009 were pooled by stratified specimen pooling, an approach that removes high-risk specimens from the pooling population and pools low-risk specimens to maximize pooling efficiency. This approach reduced pool positivity rates by 8%, repeated tests by 9%, and saved 47.4% in direct costs.

Informative Retesting

In situations where individuals are screened for an infectious disease or other binary characteristic and where resources for testing are limited, group testing can offer substantial benefits. Group testing, where subjects are tested in groups (pools) initially, has been successfully applied to problems in blood bank screening, public health, drug discovery, genetics, and many other areas. In these applications, often the goal is to identify each individual as positive or negative using initial group tests and subsequent retests of individuals within positive groups. Many group testing identification procedures have been proposed; however, the vast majority of them fail to incorporate heterogeneity among the individuals being screened. In this paper, we present a new approach to identify positive individuals when covariate information is available on each. This covariate information is used to structure how retesting is implemented within positive groups; therefore, we call this new approach "informative retesting." We derive closed-form expressions and implementation algorithms for the probability mass functions for the number of tests needed to decode positive groups. These informative retesting procedures are illustrated through a number of examples and are applied to chlamydia and gonorrhea testing in Nebraska for the Infertility Prevention Project. Overall, our work shows compelling evidence that informative retesting can dramatically decrease the number of tests while providing accuracy similar to established non-informative retesting procedures.

Logistic regression analysis of biomarker data subject to pooling and dichotomization

There is growing interest in pooling specimens across subjects in epidemiologic studies, especially those involving biomarkers. This paper is concerned with regression analysis of epidemiologic data where a binary exposure is subject to pooling and the pooled measurement is dichotomized to indicate either that no subjects in the pool are exposed or that some are exposed, without revealing further information about the exposed subjects in the latter case. The pooling process may be stratified on the disease status (a binary outcome) and possibly other variables but is otherwise assumed random. We propose methods for estimating parameters in a prospective logistic regression model and illustrate these with data from a population-based case-control study of colorectal cancer. Simulation results show that the proposed methods perform reasonably well in realistic settings and that pooling can lead to sizable gains in cost efficiency. We make recommendations with regard to the choice of design for pooled epidemiologic studies.

Informative Dorfman screening

Since the early 1940s, group testing (pooled testing) has been used to reduce costs in a variety of applications, including infectious disease screening, drug discovery, and genetics. In such applications, the goal is often to classify individuals as positive or negative using initial group testing results and the subsequent process of decoding of positive pools. Many decoding algorithms have been proposed, but most fail to acknowledge, and to further exploit, the heterogeneous nature of the individuals being screened. In this article, we use individuals' risk probabilities to formulate new informative decoding algorithms that implement Dorfman retesting in a heterogeneous population. We introduce the concept of "thresholding" to classify individuals as "high" or "low risk," so that separate, risk-specific algorithms may be used, while simultaneously identifying pool sizes that minimize the expected number of tests. When compared to competing algorithms which treat the population as homogeneous, we show that significant gains in testing efficiency can be realized with virtually no loss in screening accuracy. An important additional benefit is that our new procedures are easy to implement. We apply our methods to chlamydia and gonorrhea data collected recently in Nebraska as part of the Infertility Prevention Project.

Group testing regression models with fixed and random effects

Group testing, where subjects are tested in pools rather than individually, has a long history of successful application in infectious disease screening. In this article, we develop group testing regression models to include covariate effects that are best regarded as random. We present approaches to fit mixed effects models using maximum likelihood, investigate likelihood ratio and score tests for variance components, and evaluate small sample performance using simulation. We illustrate our methods using chlamydia and gonorrhea data collected by the state of Nebraska as part of the Infertility Prevention Project.

Global goodness-of-fit tests for group testing regression models

In a variety of biomedical applications, particularly those involving screening for infectious diseases, testing individuals (e.g. blood/urine samples, etc.) in pools has become a standard method of data collection. This experimental design, known as group testing (or pooled testing), can provide a large reduction in testing costs and can offer nearly the same precision as individual testing. To account for covariate information on individual subjects, regression models for group testing data have been proposed recently. However, there are currently no tools available to check the adequacy of these models. In this paper, we present various global goodness-of-fit tests for regression models with group testing data. We use simulation to examine the small-sample size and power properties of the tests for different pool composition strategies. We illustrate our methods using two infectious disease data sets, one from an HIV study in Kenya and one from the Infertility Prevention Project.

Comparison of Group Testing Algorithms for Case Identification in the Presence of Test Error

We derive and compare the operating characteristics of hierarchical and square array-based testing algorithms for case identification in the presence of testing error. The operating characteristics investigated include efficiency (i.e., expected number of tests per specimen) and error rates (i.e., sensitivity, specificity, positive and negative predictive values, per-family error rate, and per-comparison error rate). The methodology is illustrated by comparing different pooling algorithms for the detection of individuals recently infected with HIV in North Carolina and Malawi.

Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge

Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.

Nucleic acid amplification tests for gonorrhea and chlamydia: practice and applications

Nucleic acid amplification tests (NAATs), which are highly sensitive and specific, have provided the ability to use alternative sam-ple types for the diagnosis of sexually transmitted infections (STIs). Self-collected genital specimens, such as urine or even vaginal swabs, can now be accurately used to diagnose gonorrhea or chlamydia infections. In many cases, use of these sample types can decrease the necessity for a clinician to perform a pelvic examination on women or to collect a urethral swab from men, thus extending the diagnostic capability for detecting these infections to nonclinic screening venues. As most chlamydia infections and many gonorrhea infections are asymptomatic, the use of NAATs for self-collected samples greatly increases the types and numbers of patients that can be screened outside of clinic settings. Self-sampling also allows clinicians to easily screen patients in the clinic for STIs who are not presenting for pelvic or urogenital examinations. The application of NAATs to self-collected specimens has the potential to augment public health programs designed to control the epidemic of STIs in the community.

Utility of pooled urine specimens for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in men attending public sexually transmitted infection clinics in Mumbai, India, by PCR

Pooling urogenital specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by nucleic acid amplification tests is an attractive alternative to individual testing. As pooling can reduce the costs of testing as well as labor, it has been advocated for use in resource-poor settings. However, it has neither been widely adopted nor evaluated for use in developing countries. We evaluated the practical use of pooling first-catch urine (FCU) specimens for the detection of C. trachomatis and N. gonorrhoeae from 690 men in Mumbai, India, by PCR. FCU, urethral smears, and swabs were collected from men seen at two sexually transmitted infection (STI) clinics. All laboratory testing was done at the Lokmanya Tilak General Hospital. Gram stain smears and culture isolation for N. gonorrhoeae were performed. Each FCU was tested individually and in pools using the Roche Amplicor PCR for C. trachomatis and N. gonorrhoeae with an internal control for inhibition. Specimen pools consisted of aliquots from five consecutively processed FCUs combined into an amplification tube. An optical density reading of > or =0.20 indicated a pool for which subsequent testing of individual samples was required. Prevalence by PCR on single specimens was 2.2% (15/690) for C. trachomatis and 5.4% (37/690) for N. gonorrhoeae. Compared to individual FCU results, pooling for C. trachomatis and N. gonorrhoeae had an overall sensitivity of 96.1% (50/52). Specificity was 96.5% (83/86) in that three pools required single testing that failed to identify a positive specimen. Pooling missed two positive specimens, decreased the inhibition rate, and saved 50.3% of reagent costs. In this resource-limited setting, the use of pooling to detect C. trachomatis and N. gonorrhoeae by PCR proved to be a simple, accurate, and cost-effective procedure compared to individual testing.

Urine nucleic acid amplification tests for the diagnosis of sexually transmitted infections in clinical practice

PURPOSE OF REVIEW

With the advent of highly sensitive and specific nucleic acid amplification assays, this report will demonstrate that self-collected genital specimens, such as urine or even vaginal swabs can be accurately used to diagnose sexually transmitted infections.

RECENT FINDINGS

Use of self collected samples can eliminate the necessity of a clinician to perform a pelvic examination for women or collect a urethral swab for men, thus extending the diagnostic capability for sexually transmitted infections to non-clinic screening venues. As many sexually transmitted infections are asymptomatic, this ability to use self-sampling greatly increases the numbers of patients that can be screened, and has the potential to augment public health programs designed to control the epidemic of sexually transmitted infections in the community. Patient collected samples are highly acceptable, highly accurate, and are becoming widely used. Self-sampling also allows clinicians to easily screen patients in the clinic, who are not presenting for pelvic or urogenital examinations, for sexually transmitted infections.

SUMMARY

Highly accurate molecular tests and easily obtained self-collected urogenital samples represent the ideal combination for obtaining the public health goal of decreasing the sexually transmitted infection epidemic among sexually active persons in the United States today.

[Up to date in sexually transmitted infections: epidemiology, diagnostic approaches and treatments]

In the last years, there have been important advances in sexually transmitted infections such as genome sequencing of Treponema pallidum, Chlamydia trachomatis or Mycoplasma genitalium; the new taxonomic position of Calymmatobacterium granulomatis; commercial diagnostic systems based on nucleic acid amplification; the emergence of quinolone resistance in Neisseria gonorrhoeae; new therapeutic approaches in vulvovaginal candidiasis that include boric acid; the demonstration that valacyclovir reduces the risk of transmission of genital herpes or the availability of immune-response modifier in the treatment of genital warts, and that are questions in the goal of this review. Viral hepatitis and HIV were no reviewed by space reasons.

Cost-effectiveness of universal screening for chlamydia and gonorrhea in US jails

Universal screening for the sexually transmitted diseases (STDs) of chlamydia and gonorrhea on intake in jails has been proposed as the most effective strategy to decrease morbidity in inmates and to reduce transmission risk in communities after release. Most inmates come from a population that is at elevated risk for STDs and has limited access to health care. However, limited resources and competing priorities force decision makers to consider the cost of screening programs in comparison to other needs. The costs and cost-effectiveness of universal screening in correctional settings have not been documented. We estimated the incremental cost-effectiveness of universal urine-based screening for chlamydia and gonorrhea among inmates on intake in US jails compared to the commonly used practice of presumptive treatment of symptomatic inmates without laboratory testing. Decision analysis models were developed to estimate the cost-effectiveness of screening alternatives and were applied to hypothetical cohorts of male and female inmates. For women, universal screening for chlamydia only was cost-saving to the health care system, averting more health care costs than were incurred in screening and treatment. However, for men universal chlamydia screening cost $4,856 more per case treated than presumptive treatment. Universal screening for both chlamydia and gonorrhea infection cost the health care system $3,690 more per case of pelvic inflammatory disease averted for women and $650 more per case of infection treated for men compared to universal screening for chlamydia only. Jails with a high prevalence of chlamydia and gonorrhea represent an operationally feasible and cost-effective setting to universally test and treat women at high risk for STDs and with limited access to care elsewhere.

The Use of Urine and Self-obtained Vaginal Swabs for the Diagnosis of Sexually Transmitted Diseases

Studies have reported that self-collected specimens, such as urine or vaginal swabs, can be successfully used to diagnose sexually transmitted infections when they are used with nucleic acid amplification assays. This eliminates the necessity for a clinician-performed pelvic examination for women, or a urethral swab for men, for sample collection. These nucleic acid amplification assays used with self-collected specimens are highly sensitive and specific, and their use may be extended to broad nonclinic screening venues, where their use can augment public health programs designed to control the epidemic of sexually transmitted diseases.

Chlamydia, gonorrhea, and HIV-1 prevalence among five populations of women in the Czech and Slovak Republics

BACKGROUND

Five populations at risk for sexually transmitted diseases (STDs) in the Czech and Slovak Republics were sampled.

GOAL

To estimate prevalence of Chlamydia trachomatis, Neisseria gonorrhoeae, and HIV-1 infections.

STUDY DESIGN

Urine specimens were collected serially from women at a Prague prenatal clinic (n = 134), a Prague dermatovenerealogy clinic (n = 91), sex workers from northern and central Bohemia (n = 35), students from a northern Bohemian school (n = 217), and Gypsies from Jarovnice, Slovakia (n = 128). These specimens were tested for chlamydia and gonorrhea using a ligase chain reaction pooling algorithm, and for HIV using an enzyme immunoassay confirmed by Western blot.

RESULTS

The prevalence of chlamydia was 2.2% (95% CI, 0.4-6.4) in the prenatal clinic, 5.5% (95% CI, 1.8-12.4) in the STD clinic, 22.9% (95% CI, 10.4-40.1) among street sex workers, 8.2% (95% CI, 3.6-15.6) among sexually active female high school students, and 3.9% (95% CI, 1.3-8.9) among Gypsy women. Gonorrhea was found in only two populations: 2.2% (95% CI, 0.3-7.7) in the STD clinic, and 2.9% (95% CI, 0.1-14.9) among sex workers. No HIV-1 infection was detected.

CONCLUSIONS

Urine screening was an efficient and accurate method for identifying groups at risk for STDs in the Czech Republic and Slovakia because sample collection was fast and noninvasive, and potential participation bias was reduced by high acceptability.

Feasibility of pooling sera for HIV-1 viral RNA to diagnose acute primary HIV-1 infection and estimate HIV incidence

OBJECTIVE

To develop a pooling method for detection of viral RNA for diagnosis of acute HIV infection and estimation of HIV-1 incidence.

METHODS

Sera from 700 consecutive seronegative patients attending sexually transmitted disease clinics in Pune, India, were screened individually for p24 antigen, and pooled into seven pools of 100 for detection of HIV-1 RNA by reverse transcriptase-polymerase chain reaction. HIV-1 incidence was calculated by the traditional cohort method, the p24 antigen method, and a multistage pooling method in which RNA-positive pools were re-analyzed in smaller pools.

RESULTS

Sera from 700 individuals were grouped into seven pools of 100, of which four were positive. These four positive pools were subdivided into eight pools of 50, of which seven were positive. The seven positive pools were subdivided into 35 pools of 10, of which 10 were positive. Based on the 10 RNA-positive pools, the point estimate of HIV-1 incidence was 19.9% per year [95% confidence interval (CI), 7.3-31.8%]. Of the 700 samples analyzed for p24 antigen, eight were positive, resulting in a point estimate of incidence of 18.5%/year (8.0-36.5%). In contrast, the incidence rate based on the traditional cohort method of follow-up was lower at 9.4%/year (4.8-16.4%) due to a low follow-up rate. Testing of individual samples from the 10 RNA-positive pools identified 10 individuals with acute primary HIV-1.

CONCLUSION

The multistage pooling method for detection of HIV-1 RNA was more sensitive than the p24 antigen method, and was five-fold less expensive than the p24 antigen assays. Pooling samples for RNA detection was effective in estimating current incidence rates with cost savings that would be practical for use in developing countries.

The Use of Molecular Techniques for the Diagnosis and Epidemiologic Study of Sexually Transmitted Infections

Molecular diagnostic tests are more sensitive and, in many cases, more specific than conventional laboratory methods for the detection of sexually transmitted infections. Here, we review recently developed molecular methods for the diagnosis and subtyping of the most common sexually transmitted infections: infections caused by Chlamydia trachomatis, Neisseria gonorrhoeae, human papillomavirus, Trichomonas vaginalis, and the agents of genital ulcer disease (Haemophilus ducreyi, herpes simplex virus, Treponema pallidum, and Calymmatobacterium granulomatis). We also provide an overview of the laboratory diagnostic tests and clinical specimens to use when infection with these agents is suspected.