Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

Background: Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR).Methods/Principal Findings: The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm.Conclusions/Significance: Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production.This work received financial support from the Ministry of Science and Technology of Argentina [PICT 2011-0207 to AGS] and the National Scientific and Technical Research Council in Argentina (CONICET) [PIP 112 2011-010-0974 to AGS]. Work related to evaluation of biological samples was partially sponsored by the Pan-American Health Organization (PAHO) [Small Grants Program PAHO-TDR]; the Drugs and Neglected Diseases Initiative (DNDi, Geneva, Switzerland), Wellcome Trust (London, United Kingdom), SANOFI-AVENTIS (Buenos Aires, Argentina) and the National Council for Science and Technology in Mexico (CONACYT) [FONSEC 161405 to JMR]

Estimated performance for all index tests (RDTs).

BackgroundChagas disease (CD), caused by the parasite Trypanosoma cruzi, is the most important endemic anthropozoonosis in Argentina. Since 2010, the World Health Organization has highlighted the urgent need to validate diagnostic systems that allow rapid detection of T. cruzi, infection in primary healthcare centers. Serological rapid diagnostic tests (RDTs) for T. cruzi, infection could be used to improve case management, as RDTs do not require specialized laboratories or highly trained staff to use them. We aimed to generate unbiased performance data of RDTs in Argentina, to evaluate their usefulness for improving T. cruzi, diagnosis rates.Methods and principal findingsThis is a retrospective, laboratory-based, diagnostic evaluation study to estimate the clinical sensitivity/specificity of four commercially available RDTs for T. cruzi, using the Chagas disease diagnostic algorithm currently used in Argentina as the reference standard. In total, 400 serum samples were tested, 200 from individuals with chronic T. cruzi infection and 200 from individuals not infected with T. cruzi. All results were registered as the agreement of at least two operators who were blinded to the reference standard results. The sensitivity estimates ranged from 92.5–100% (95% confidence interval (CI) lower bound 87.9–98.2%); for specificity, the range was 76–96% (95% CI lower bound 69.5–92.3%). Most RDTs evaluated showed performances comparable with the reference standard method, showing almost perfect concordance (Kappa 0.76–0.92).ConclusionsOur study demonstrates that, under controlled laboratory conditions, commercially available RDTs for CD have a performance comparable to the Argentinian diagnostic algorithm, which is based on laboratory-based serological tests. For the next stage of our work, the RDTs will be evaluated in real-world settings.</div

Excel spreadsheet containing reference test results.

Excel spreadsheet containing reference test results.</p

Three-way analysis (significant differences in sensitivity and specificity between two methods, in a paired fashion versus the reference algorithm).

Three-way analysis (significant differences in sensitivity and specificity between two methods, in a paired fashion versus the reference algorithm).</p

Number of positive/negative samples needed for a range of estimated sensitivities/specificities.

Number of positive/negative samples needed for a range of estimated sensitivities/specificities.</p

Usability scores of the RDTs evaluated by four operators.

Usability scores of the RDTs evaluated by four operators.</p

Flowchart depicting study design in conformity with the Standards for Reporting of Diagnostic Accuracy Studies (STARD) guidelines.

Flowchart depicting study design in conformity with the Standards for Reporting of Diagnostic Accuracy Studies (STARD) guidelines.</p

Images of each index test verified with the WHO anti-<i>Trypanosoma cruzi</i> I and II antibody reference panel (NIBSC).

a) WL Check Chagas, positive control result; b) WL Check Chagas, negative control result; c) Chagas Rapid First Response, positive control result d) Chagas Rapid First Response, negative control result; e) ACCU-TELL Chagas Cassette, positive control result; f) ACCU-TELL Chagas Cassette, negative control result; g) SD Chagas Ab Rapid, positive control result; h) SD Chagas Ab Rapid, negative control result. (TIF)</p

Manufacturer’s details for the rapid diagnostic tests evaluated.

Manufacturer’s details for the rapid diagnostic tests evaluated.</p