Evaluation of five automated and one manual method for Toxoplasma and human DNA extraction from artificially spiked amniotic fluid

Systematic Review and Meta-Analysis of Congenital Toxoplasmosis Diagnosis: Advances and Challenges

Objective

To understand how congenital toxoplasmosis (CT) diagnosis has evolved over the years, we performed a systematic review and meta-analysis to summarize the kind of analysis that has been employed for CT diagnosis.

Methods

PubMed and Lilacs databases were used in order to access the kind of analysis that has been employed for CT diagnosis in several samples. Our search combined the following combining terms: "congenital toxoplasmosis" or "gestational toxoplasmosis" and "diagnosis" and "blood," "serum," "amniotic fluid," "placenta," or "colostrum." We extracted data on true positive, true negative, false positive, and false negative to generate pooled sensitivity, specificity, and diagnostic odds ratio (DOR). Random-effects models using MetaDTA were used for analysis.

Results

Sixty-five articles were included in the study aiming for comparisons (75.4%), diagnosis performance (52.3%), diagnosis improvement (32.3%), or to distinguish acute/chronic infection phases (36.9%). Amniotic fluid (AF) and placenta were used in 36.9% and 10.8% of articles, respectively, targeting parasites and/or T. gondii DNA. Blood was used in 86% of articles for enzymatic assays. Colostrum was used in one article to search for antibodies. In meta-analysis, PCR in AF showed the best performance for CT diagnosis based on the highest summary sensitivity (85.1%) and specificity (99.7%) added to lower magnitude heterogeneity.

Conclusion

Most of the assays being researched to diagnose CT are basically the same traditional approaches available for clinical purposes. The range in diagnostic performance and the challenges imposed by CT diagnosis indicate the need to better explore pregnancy samples in search of new possibilities for diagnostic tools. Exploring immunological markers and using bioinformatics tools and T. gondii recombinant antigens should address the research needed for a new generation of diagnostic tools to face these challenges.

Congenital toxoplasmosis among hospitalized infants in Poland in the years 2007-2021: study based on the national hospital registry

Congenital toxoplasmosis (CT) is a rare entity and it may pose a life-threatening risk for the newborns. The aim of the study was to evaluate the incidence and other selected factors of CT in Poland. Our study is a population-based study on CT patients in 2007-2021. The study was based on 1504 hospitalization records of first-time diagnosis of CT in newborns. In the study group, we observed 763 males (50.7%) and 741 females (49.3%). The mean and median age was 31 days and 10 days, respectively. Based on the hospital registry, the mean annual CT incidence was estimated to be 2.6 per 10,000 live births (95% CI 2.0-3.2 per 10,000 live births). The incidence of CT cases fluctuated over the years 2007-2021, with the highest incidence in 2010 and the lowest one in 2014. There were no statistically significant differences between the incidence of CT in relation to sex or place of residence. The periodic fluctuations in the number of cases of congenital toxoplasmosis indicates the need to develop effective prevention programs to effectively counteract the disease and its consequences.

Assessment of Droplet Digital PCR for the Detection and Absolute Quantification of Toxoplasma gondii: A Comparative Retrospective Study

Accurate tools for Toxoplasma gondii detection and quantification can be valuable for the early and effective management of toxoplasmosis. Droplet digital PCR (ddPCR) is a next-generation end-point PCR technique with high performance. The objective of the study was to evaluate the performance of ddPCR for the detection and absolute quantification of T. gondii. From January 2019 to October 2020, DNA samples collected at the Laboratory of Parasitology and Mycology of Pitié-Salpêtrière Hospital in Paris were retrospectively analyzed by ddPCR and real-time quantitative PCR (qPCR). To detect T. gondii with the best sensitivity possible, the REP-529 multicopy target was used. For absolute quantification of T. gondii, a specific single-copy target of α-tubulin was designed. T. gondii detection by ddPCR and qPCR was strongly correlated (R2 = 0.93), with a total concordance of 96.7% (n = 145/150). Quantification of T. gondii using ddPCR was successful for 15 of 35 samples showing a parasite load ≥170 copies/mL of DNA eluate using the α-tubulin target. The qPCR REP-529 quantification based on a standard curve was approximate and dependent on the strain genotype, which led to an estimate of parasite copy number 14- to 160-fold superior to the ddPCR result. In total, ddPCR is an effective molecular method for T. gondii detection that shows equivalent performance to qPCR. For robust T. gondii quantification, ddPCR is clearly more accurate than semiquantitative qPCR methods.

Molecular Diagnosis of Toxoplasmosis: Multicenter Evaluation of the Toxoplasma RealCycler Universal PCR Assay on 168 Characterized Human Samples

Real-time PCR plays a crucial role in the diagnosis of toxoplasmosis. In this multicenter study, the Toxoplasma RealCycler Universal assay was assessed for the diagnosis of toxoplasmosis by eight reference laboratories. DNAs from diverse clinical samples were included: 141 characterized samples from patients with different clinical forms of proven toxoplasmosis and 27 from patients without toxoplasmosis were tested in duplicate with the commercial assay. Final diagnosis was affirmed by each center by analysis of clinical settings and biological follow-up. Calibrated Toxoplasma gondii standards and 11 external quality control samples were also included. Discrepant results observed after the first run of commercial PCR were controlled by both reference and commercial PCR assays. Using the commercial assay, the detection threshold varied from 0.01 to 1 tachyzoites/mL, depending on the center. The relationship between crossing point and DNA concentration was linear over 4 log units (r² > 0.99), and PCR efficiencies were satisfactory (89% to 104%). The results of the 11 external quality control samples were concordant after one retesting, but those for 3 clinical samples remained discrepant. Sensitivity and specificity were calculated at 97.8% (95% CI, 97.8%-100%) and 100% (95% CI, 87.2%-100%), respectively. Provided that PCRs are performed at least in duplicate to detect low parasitic loads, Toxoplasma RealCycler Universal PCR showed suitable performances to diagnose the different forms of toxoplasmosis.

Development and validation of a flexible DNA extraction (PAN) method for liquid biopsy of multiple sample types

BACKGROUND

Liquid biopsy is gaining increasing popularity in cancer screening and diagnosis. However, there is no relatively mature DNA isolation method or commercial kit available that is compatible with different LB sample types. This study developed a PAN-sample DNA isolation method (PAN method) for liquid biopsy samples.

METHODS

The PAN method has two key steps, including biosample-specific pretreatments for various LB sample types and high concentration guanidine thiocyanate buffer for lysis and denaturation procedure. Subsequently, the performance of PAN method was validated by a series of molecular analyses.

RESULTS

The PAN method was used to isolate DNA from multiple sample types related to LB, including plasma, serum, saliva, nasopharyngeal swab, and stool. All purified DNA products showed good quality and high quantity. Comparison of KRAS mutation analysis using DNA purified using PAN method versus QIAamp methods showed similar efficiency. Epstein-Barr virus DNA was detected via Q-PCR using DNA purified from serum, plasma, nasopharyngeal swab, and saliva samples collected from nasopharyngeal carcinoma patients. Similarly, methylation sequencing of swab and saliva samples revealed good coverage of target region and high methylation of HLA-DPB1 gene. Finally, 16S rDNA gene sequencing of saliva, swab, and stool samples successfully defines the relative abundance of microbial communities.

CONCLUSIONS

This study developed and validated a PAN-sample DNA isolation method that can be used for different LB samples, which can be applied to molecular epidemiological research and other areas.

Evaluation of Two Commercial Kits on the Automated ELITe InGenius PCR Platform for Molecular Diagnosis of Toxoplasmosis

Molecular diagnosis of toxoplasmosis is essential for establishing the diagnosis of congenital contaminations and for primary infection or reactivation of immunocompromised patients. An integrated extraction and real-time PCR-based system is of particular interest in this context. Commercial kits for automated extraction and amplification steps are now available. Herein, we assessed two commercial PCR assays for this diagnosis, those of Bio-Evolution and Elitech, on the ELITe InGenius platform. The Bio-Evolution assay showed a specificity and a sensitivity of 100% on clinical samples, but a lower analytical detection threshold than the Elitech assay. The latter showed a specificity of 100% and a sensitivity of 96%. The SP1000 cartridges, which allow DNA extraction from 1 mL of template, showed interesting performances on amniotic fluid samples. Overall, the two kits had good performances on the InGenius platform, which offers a turn-key solution suitable for the molecular diagnosis of toxoplasmosis.

Impact of pre-analytic step duration on molecular diagnosis of toxoplasmosis for five types of biological samples

Introduction

Toxoplasma-PCR is essential to diagnose ocular, cerebral, disseminated and congenital toxoplasmosis. This multicenter study evaluated the impact of sample storage duration at +4°C on PCR assay performances in order to propose guidelines for the storage of samples during shipment or/and before PCR.

Materials and methods

Five matrices, amniotic (AF), cerebrospinal (CSF), and bronchoalveolar lavage fluids (BALF), whole blood (WB) and buffy coat (BC), were artificially spiked with different amounts of Toxoplasma gondii (20, 100, 500 tachyzoites per mL of sample) or with previously infected THP1 cells. DNA extractions were performed at day 0 and after 2, 4 and 7 days of storage at +4°C. Each extract was amplified at least twice by real-time PCR.

Results

A total of 252 spiked samples was studied. No increase of crossing point was observed and all samples were positive for AF, BALF, BC and infected THP1-spiked WB after up to 7 days at 4°C. For CSF spiked with 20 parasites/mL, only 50% of PCR reactions were positive at D7 (p<0.05). For WB spiked with type II parasites, all reactions remained positive at D7 but amplifications were significantly delayed from D2; and for WB spiked with RH strain, the proportion of positive reactions decreased at D7.

Conclusion

The storage of clinical samples at +4°C is compatible with the molecular detection of T. gondii parasites. Provided that PCR assays are performed in duplicate, storage of samples is possible up to 7 days. However, from the fifth day onwards, and for samples susceptible to contain low parasitic loads, we recommend to perform the PCR in multiplicate.

Multicenter Comparative Study of Six Cryptosporidium parvum DNA Extraction Protocols Including Mechanical Pretreatment from Stool Samples

BACKGROUND

Nowadays, many commercial kits allow the detection of Cryptosporidium sp. in stool samples after deoxyribonucleic acid (DNA) extraction. Protocols of stool pretreatment have been proposed to optimize oocysts' DNA extraction. Among them, mechanical grinding was reported to improve the performance of Cryptosporidium oocysts' DNA extraction.

METHODS

A multicenter comparative study was conducted within the framework of the French National Reference Center-Expert Laboratory for Cryptosporidiosis. Six extraction systems (i.e., manual or automated) associated with various mechanical pretreatment protocols, were compared for the Cryptosporidium parvum oocyst' DNA extraction, before amplification using the same real-time PCR method targeting.

RESULTS

The sensitivity of real-time PCR assay was unequally impacted by the pretreatment/extraction protocol. We observed significant differences for the lowest concentrations of C. parvum oocysts (i.e., 0-94.4% and 33.3-100% respectively for 10 and 50 oocysts/mL). All in all, the protocol using Quick DNA Fecal/Soil Microbe-Miniprep® manual kit showed the best performances. In addition, optimal performances of mechanical pretreatment were obtained by combining a grinding duration of 60 s with a speed of 4 m/s using Fastprep24® with Lysing Matrix E®.

CONCLUSIONS

Sample pretreatment, as well as the extraction method, needs to be properly adapted to improve the diagnostic performances of the C. parvum DNA amplification methods.

Is Real-Time PCR Targeting Rep 529 Suitable for Diagnosis of Toxoplasmosis in Patients Infected with Non-Type II Strains in North America?

Toxoplasma gondii DNA detection is essential to antenatally diagnose a congenital infection and reactivation of a past infection in an immunocompromised patient. Initially, PCR methods targeted the 35-fold repetitive B1 gene, and more recently, coding sequence Rep 529 has been preferred, as it was reported to be repeated 200- to 300-fold and yielded far better sensitivity than amplification of the B1 sequence. To date, few data are available in regard to the efficacy of Rep 529 for non-type II genotypes. In this study, we compared the results of B1 quantitative PCR (qPCR) with those of two different Rep 529 qPCRs performed on 111 samples in two different laboratories (Rep 529-1 and Rep 529-2). The performances of the 3 qPCRs were also compared according to the genotypes of the isolates for 13 type II and 21 non-type II samples. The performance of the Rep 529 target was superior to that of the B1 target regardless of the genotype (threshold cycle [C_T ] values for the Rep 529-1 and Rep 529-2 qPCRs were lower than those for the B1 qPCR [P < 0.001 and P < 0.01, respectively]). The same results were observed when a comparison was made according to the genotype of the strain (type II and non-type II genotypes). To our knowledge, these results provide the first relative quantitative data revealing that the efficiency of Rep 529 qPCR does not depend on the genotype of T. gondii isolates and that, in fact, it is superior to B1 qPCR.

Risk of congenital toxoplasmosis in women with low or indeterminate anti-Toxoplasma IgG avidity index in the first trimester of pregnancy: an observational retrospective study

OBJECTIVES

Congenital toxoplasmosis (CT) affects one to ten fetuses per 10 000 live newborns in western countries. Without knowing pre-conception serostatus, it is hard to date the infection when anti-Toxoplasma IgG and IgM antibodies are positive at first screening. Although a high IgG avidity index (AI) in the first trimester excludes CT, the same cannot be said of intermediate and low AI. The aim of this study was to estimate the risk of CT when intermediate or low AI is detected in the first trimester of pregnancy.

METHODS

Our observational retrospective study enrolled women with positive anti-Toxoplasma IgG and IgM, and low/intermediate AI in the first trimester of gestation seen at two reference centres in northern Italy between 2006 and 2015. All women received spiramycin. When requested by women, a sample of fluid obtained through amniocentesis was tested with a commercial real-time PCR. CT was defined by positive PCR result confirmed on aborted materials or by newborn follow up.

RESULTS

Overall, 778 first-trimester pregnant women were included; AI was low in 532/778 (68%) and intermediate in 246/778 (32%). Amniocenteses were performed in 528/778 (67.9%), with no fetal loss. In all, 19/778 (2.4%) miscarriages and 15/778 (1.9%) pregnancy terminations were recorded; 9/778 (1.6%) were lost to follow up. In two women, PCR on amniotic fluid was positive, but CT was confirmed in only 1/747 cases (0.13%, 95% CI 0.02%-0.75%).

CONCLUSION

In our study, the risk of CT was much lower than anticipated. These data must be considered when counselling these women.