Evaluation of Multiplex-Based Antibody Testing for Use in Large-Scale Surveillance for Yaws: a Comparative Study.
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ABSTRACT:
SUBMITTER: Cooley GM
PROVIDER: S-EPMC4844712 | biostudies-literature | 2016 May
REPOSITORIES: biostudies-literature
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Project description:BackgroundYaws is a non-venereal treponemal infection caused by Treponema pallidum subspecies pertenue. The disease is targeted by WHO for eradication by 2020. Rapid diagnostic tests (RDTs) are envisaged for confirmation of clinical cases during treatment campaigns and for certification of the interruption of transmission. Yaws testing requires both treponemal (trep) and non-treponemal (non-trep) assays for diagnosis of current infection. We evaluate a sequential testing strategy (using a treponemal RDT before a trep/non-trep RDT) in terms of cost and cost-effectiveness, relative to a single-assay combined testing strategy (using the trep/non-trep RDT alone), for two use cases: individual diagnosis and community surveillance.MethodsWe use cohort decision analysis to examine the diagnostic and cost outcomes. We estimate cost and cost-effectiveness of the alternative testing strategies at different levels of prevalence of past/current infection and current infection under each use case. We take the perspective of the global yaws eradication programme. We calculate the total number of correct diagnoses for each strategy over a range of plausible prevalences. We employ probabilistic sensitivity analysis (PSA) to account for uncertainty and report 95% intervals.ResultsAt current prices of the treponemal and trep/non-trep RDTs, the sequential strategy is cost-saving for individual diagnosis at prevalence of past/current infection less than 85% (81-90); it is cost-saving for surveillance at less than 100%. The threshold price of the trep/non-trep RDT (below which the sequential strategy would no longer be cost-saving) is US$ 1.08 (1.02-1.14) for individual diagnosis at high prevalence of past/current infection (51%) and US$ 0.54 (0.52-0.56) for community surveillance at low prevalence (15%).DiscussionWe find that the sequential strategy is cost-saving for both diagnosis and surveillance in most relevant settings. In the absence of evidence assessing relative performance (sensitivity and specificity), cost-effectiveness is uncertain. However, the conditions under which the combined test only strategy might be more cost-effective than the sequential strategy are limited. A cheaper trep/non-trep RDT is needed, costing no more than US$ 0.50-1.00, depending on the use case. Our results will help enhance the cost-effectiveness of yaws programmes in the 13 countries known to be currently endemic. It will also inform efforts in the much larger group of 71 countries with a history of yaws, many of which will have to undertake surveillance to confirm the interruption of transmission.
| S-EPMC5658197 | biostudies-literature
Project description:BackgroundRapid COVID-19 testing platforms can identify infected individuals at the point of care (POC), allowing immediate isolation of infected individuals and reducing the risk of transmission. While lab-based nucleic acid amplification testing (NAAT) is often considered the gold standard to detect SARS-CoV-2 in the community, results typically take 2-7 days to return, rendering POC testing a critical diagnostic tool for infection control. The National Football League (NFL) and NFL Players Association deployed a new POC testing strategy using a newly available reverse transcriptase polymerase chain reaction (RT-PCR) rapid test during the 2020 season, and evaluated diagnostic effectiveness compared to other available devices using real-world population surveillance data.MethodsRT-PCR POC test results were compared to NAAT results from same-day samples by calculation of positive and negative concordance. Sensitivity analyses were performed for three subgroups: (1) individuals symptomatic at time of positive test; (2) individuals tested during the pilot phase of rollout; and (3) individuals tested daily.ResultsAmong 4989 same-day POC/NAAT pairs, 4957 (99.4%) were concordant, with 93.1% positive concordance and 99.6% negative concordance. Based on adjudicated case status, the false negative rate was 0.2% and false positive rate was 2.9%. In 43 instances, the immediate turnaround of results by POC allowed isolation of infected individuals 1 day sooner than lab-based testing. Positive/negative concordance in sensitivity analyses were relatively stable.ConclusionRT-PCR POC testing provided timely results that were highly concordant with lab-based NAAT in population surveillance. Expanded use of effective RT-PCR POC can enable rapid isolation of infected individuals and reduce COVID-19 infection in the community.
| S-EPMC9088538 | biostudies-literature
Project description:Yaws is a non-venereal treponemal infection caused by Treponema pallidum ssp. pertenue. The WHO has launched a worldwide control programme, which aims to eradicate yaws by 2020. The development of a rapid diagnostic test (RDT) for serological diagnosis in the isolated communities affected by yaws is a key requirement for the successful implementation of the WHO strategy. We conducted a study to evaluate the utility of the DPP test in screening for yaws, utilizing samples collected as part of a community prevalence survey conducted in the Solomon Islands. 415 serum samples were tested using both traditional syphilis serology (TPPA and quantitative RPR) and the Chembio DPP Syphilis Screen and Confirm RDT. We calculated the sensitivity and specificity of the RDT as compared to gold standard serology. The sensitivity of the RDT against TPPA was 58.5% and the specificity was 97.6%. The sensitivity of the RDT against RPR was 41.7% and the specificity was 95.2%. The sensitivity of the DPP was strongly related to the RPR titre with a sensitivity of 92.0% for an RPR titre of >1/16. Wider access to DPP testing would improve our understanding of worldwide yaws case reporting and the test may play a key role in assessing patients presenting with yaws like lesions in a post-mass drug administration (MDA) setting.
| S-EPMC4161315 | biostudies-literature
Project description:Measuring antimalarial antibodies can estimate transmission in a population. To compare outputs, standardized laboratory testing is required. Here we describe the in-country establishment and quality control (QC) of a multiplex bead assay (MBA) for three sero-surveys in Haiti. Total IgG data against 21 antigens were collected for 32,758 participants. Titration curves of hyperimmune sera were included on assay plates, assay signals underwent 5-parameter regression, and inspection of the median and interquartile range (IQR) for the y-inflection point was used to determine assay precision. The medians and IQRs were similar for Surveys 1 and 2 for most antigens, while the IQRs increased for some antigens in Survey 3. Levey-Jennings charts for selected antigens provided a pass/fail criterion for each assay plate and, of 387 assay plates, 13 (3.4%) were repeated. Individual samples failed if IgG binding to the generic glutathione-S-transferase protein was observed, with 659 (2.0%) samples failing. An additional 455 (1.4%) observations failed due to low bead numbers (<20/analyte). The final dataset included 609,438 anti-malaria IgG data points from 32,099 participants; 96.6% of all potential data points if no QC failures had occurred. The MBA can be deployed with high-throughput data collection and low inter-plate variability while ensuring data quality.
| S-EPMC6981173 | biostudies-literature
Project description:Multiple testing of correlations arises in many applications including gene coexpression network analysis and brain connectivity analysis. In this paper, we consider large scale simultaneous testing for correlations in both the one-sample and two-sample settings. New multiple testing procedures are proposed and a bootstrap method is introduced for estimating the proportion of the nulls falsely rejected among all the true nulls. The properties of the proposed procedures are investigated both theoretically and numerically. It is shown that the procedures asymptotically control the overall false discovery rate and false discovery proportion at the nominal level. Simulation results show that the methods perform well numerically in terms of both the size and power of the test and it significantly outperforms two alternative methods. The two-sample procedure is also illustrated by an analysis of a prostate cancer dataset for the detection of changes in coexpression patterns between gene expression levels.
| S-EPMC4894362 | biostudies-literature
Project description:BackgroundSewage surveillance, by detecting SARS-CoV-2 virus circulation at the community level, has the potential to supplement individual surveillance for COVID-19. However, to date, there have been no reports about the large-scale implementation and validation of sewage surveillance for public health action.ObjectiveHere, we developed a standardized approach for SARS-CoV-2 detection in sewage and applied it prospectively to supplement public health interventions.MethodsWe analyzed 1,169 sewage samples collected at 492 sites from December 2020 to March 2021. Forty-seven of 492 sites tested positive, 44 (94%) of them had traceable sources of viral signals in the corresponding sewershed, either from previously unsuspected but subsequently confirmed patients or recently convalescent patients or from both patient groups.ResultsSewage surveillance had a sensitivity of 54%, a specificity of 95%, a positive predictive value of 53%, and a negative predictive value of 95% for identifying a previously unsuspected patient within a sewershed. Sewage surveillance in Hong Kong provided a basis for the statutory public health action to detect silent COVID-19 transmission.DiscussionConsidering the epidemiological data together with the sewage testing results, compulsory testing was conducted for individual residents at 27 positive sewage sites and uncovered total of 62 previously unsuspected patients, demonstrating the value of sewage surveillance in uncovering previously unsuspected patients in the community. Our study suggests that sewage surveillance could be a powerful management tool for the control of COVID-19. https://doi.org/10.1289/EHP9966.
| S-EPMC9097955 | biostudies-literature
Project description:PurposeThe objective of this work was to examine whether offers of multiplex genetic testing increase health-care utilization among healthy patients aged 25-40 years. The identification of genetic variants associated with common disease is accelerating rapidly. "Multiplex tests" that give individuals feedback on large panels of genetic variants have proliferated. Availability of these test results may prompt consumers to use more health-care services.MethodsA total of 1,599 continuously insured adults aged 25-40 years were surveyed and offered a multiplex genetic susceptibility test for eight common health conditions. Health-care utilization from automated records was compared in 12-month pre- and posttest periods among persons who completed a baseline survey only (68.7%), those who visited a study website but opted not to test (17.8%), and those who chose the multiplex genetic susceptibility test (13.6%).ResultsIn the pretest period, persons choosing genetic testing used an average of 1.02 physician visits per quarter as compared with 0.93 and 0.82 for the baseline-only and Web-only groups, respectively (P < 0.05). There were no statistically significant differences by group in the pretest use of any common medical tests or procedures associated with four common health conditions. When changes in physician and medical test/procedure use in the posttest period were compared among the groups, no statistically significant differences were observed for any utilization category.ConclusionsPersons offered and completing multiplex genetic susceptibility testing used more physician visits before testing, but testing was not associated with subsequent changes in use. This study supports the supposition that multiplex genetic testing offers can be provided directly to the patients in such a way that use of health services is not inappropriately increased.
| S-EPMC3424345 | biostudies-literature
Project description:BackgroundMedium density DNA microchips that carry a collection of probes for a broad spectrum of pathogens, have the potential to be powerful tools for simultaneous species identification, detection of virulence factors and antimicrobial resistance determinants. However, their widespread use in microbiological diagnostics is limited by the problem of low pathogen numbers in clinical specimens revealing relatively low amounts of pathogen DNA.ResultsTo increase the detection power of a fluorescence-based prototype-microarray designed to identify pathogenic microorganisms involved in sepsis, we propose a large scale multiplex PCR (LSplex PCR) for amplification of several dozens of gene-segments of 9 pathogenic species. This protocol employs a large set of primer pairs, potentially able to amplify 800 different gene segments that correspond to the capture probes spotted on the microarray. The LSplex protocol is shown to selectively amplify only the gene segments corresponding to the specific pathogen present in the analyte. Application of LSplex increases the microarray detection of target templates by a factor of 100 to 1000.ConclusionOur data provide a proof of principle for the improvement of detection of pathogen DNA by microarray hybridization by using LSplex PCR.
| S-EPMC2631447 | biostudies-literature
Project description:Large-scale SARS-CoV-2 molecular testing coupled with whole genome sequencing in the diagnostic laboratories is instrumental for real-time genomic surveillance. The extensive genomic, laboratory, and clinical data provide a valuable resource for understanding cases of reinfection versus prolonged RNA shedding and protracted infections. In this study, data from a total of 22,292 clinical specimens, positive by SARS-CoV-2 molecular diagnosis at Johns Hopkins clinical virology laboratory between March 11th 2020 to September 23rd 2021, were used to identify patients with two or more positive results. A total of 3,650 samples collected from 1,529 patients who had between 2 and 20 positive results were identified in a time frame that extended up to 403 days from the first positive. Cycle threshold values (Ct) were available for 1,622 samples, the median of which was over 30 by 11 days after the first positive. Extended recovery of infectious virus on cell culture was notable for up to 70 days after the first positive in immunocompromised patients. Whole genome sequencing data generated as a part of our SARS-CoV-2 genomic surveillance was available for 1,027 samples from patients that had multiple positive tests. Positive samples collected more than 10 days after initial positive with high quality sequences (coverage >90% and mean depth >100), were more likely to be from unvaccinated, or immunosuppressed patients. Reinfections with viral variants of concern were found in 3 patients more than 130 days from prior infections with a different viral clade. In 75 patients that had 2 or more high quality sequences, the acquisition of more substitutions or deletions was associated with lack of vaccination and longer time between the recovered viruses. Our study highlights the value of integrating genomic, laboratory, and clinical data for understanding the biology of SARS-CoV-2 as well as for setting a precedent for future epidemics and pandemics.
| S-EPMC9035932 | biostudies-literature
Project description:BackgroundFemale sex workers (FSW) and men having sex with men (MSM) in Kenya have high rates of HIV infection. Following a 2015 WHO recommendation, Kenya initiated national scale-up of pre-exposure prophylaxis (PrEP) for all persons at high-risk. Concerns have been raised about PrEP users' potential changes in sexual behaviors such adopting condomless sex and multiple partners as a result of perceived reduction in HIV risk, a phenomenon known as risk compensation. Increased condomless sex may lead to unintended pregnancies and sexually transmitted infections and has been described in research contexts but not in the programmatic setting. This study looks at changes in condom use among FSW and MSM on PrEP through a national a scale-up program.MethodsRoutine program data collected between February 2017 and December 2019 were used to assess changes in condom use during the first three months of PrEP in 80 health facilities supported by a scale-up project, Jilinde. The primary outcome was self-reported condom use. Analyses were conducted separately for FSW and for MSM. Log-Binomial Regression with Generalized Estimating Equations was used to compare the incidence proportion ("risk") of consistent condom use at the month 1, and month 3 visits relative to the initiation visit.ResultsAt initiation, 69% of FSW and 65% of MSM reported consistent condom use. At month 3, this rose to 87% for FSW and 91% for MSM. MSM were 24% more likely to report consistent condom use at month 1 (Relative Risk [RR], 1.24, 95% Confidence Interval [CI], 1.18-1.30) and 40% more likely at month 3 (RR, 1.40, 95% CI, 1.33-1.47) compared to at initiation. FSW were 15% more likely to report consistent condom use at the month one visit (RR, 1.15, 95% CI, 1.13-1.17) and 27% more likely to report condom use on the month 3 visit (RR 1.27, 95% CI, 1.24-1.29).ConclusionCondom use increased substantially among both FSW and MSM. This may be because oral PrEP was provided as part of a combination prevention strategy that included counseling and condoms but could also be due to the low retention rates among those who initiated.
| S-EPMC8842980 | biostudies-literature