Comparative evaluation of the QIAsymphony RGQ system with the easyMAG/R-gene combination for the quantitation of cytomegalovirus DNA load in whole blood

Impact of Dextran-Sodium-Sulfate-Induced Enteritis on Murine Cytomegalovirus Reactivation

(1) Background: Ulcerative colitis (UC) is an inflammatory bowel disease that causes inflammation of the intestines, which participates in human cytomegalovirus (HCMV) reactivation from its latent reservoir. CMV-associated colitis plays a pejorative role in the clinical course of UC. We took advantage of a model of chemically induced enteritis to study the viral reactivation of murine CMV (MCMV) in the context of gut inflammation. (2) Methods: Seven-week-old BALB/c mice were infected by 3 × 10³ plaque-forming units (PFU) of MCMV; 2.5% (w/v) DSS was administered in the drinking water from day (D) 30 to D37 post-infection to induce enteritis. (3) Results: MCMV DNA levels in the circulation decreased from D21 after infection until resolution of the acute infection. DSS administration resulted in weight loss, high disease activity index, elevated Nancy index shortening of the colon length and increase in fecal lipocalin. However, chemically induced enteritis had no impact on MCMV reactivation as determined by qPCR and immunohistochemistry of intestinal tissues. (4) Conclusions: Despite the persistence of MCMV in the digestive tissues after the acute phase of infection, the gut inflammation induced by DSS did not induce MCMV reactivation in intestinal tissues, thus failing to recapitulate inflammation-driven HCMV reactivation in human UC.

Deletions of the Plasmodium falciparum histidine-rich protein 2/3 genes are common in field isolates from north-eastern Tanzania

Plasmodium falciparum parasites lacking histidine-rich protein 2 and 3 (pfhrp2/3) genes have been reported in several parts of the world. These deletions are known to compromise the effectiveness of HRP2-based malaria rapid diagnostic tests (HRP2-RDT). The National Malaria Control Programme (NMCP) in Tanzania adopted HRP2-RDTs as a routine tool for malaria diagnosis in 2009 replacing microscopy in many Health facilities. We investigated pfhrp2/3 deletions in 122 samples from two areas with diverse malaria transmission intensities in Northeastern Tanzania. Pfhrp2 deletion was confirmed in 1.6% of samples while pfhrp3 deletion was confirmed in 50% of samples. We did not find parasites with both pfhrp2 and pfhrp3 deletions among our samples. Results from this study highlight the need for systematic surveillance of pfhrp2/3 deletions in Tanzania to understand their prevalence and determine their impact on the performance of mRDT.

Evaluation of four commercial extraction-quantification systems to monitor EBV or CMV viral load in whole blood

BACKGROUND

Measurement of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) viral loads is commonly used to monitor posttransplant patients. Two new systems (eMAG/eSTREAM and Versant/kPCR) have been recently commercialized.

OBJECTIVES

To evaluate the performance of four systems to quantify CMV and EBV in whole blood.

STUDY DESIGN

Three extraction and real-time PCR amplification systems: m2000SP/RT (M2000), eMAG/eSTREAM (EMAG), and Versant/kPCR (KPCR) were compared with our routine system Qiasymphony/RGQ (QS/RGQ). The 4 systems were tested using 3 dilutions in triplicate according to the WHO international standard (WHO-IS) for intra-assay reproducibility; 56 whole blood samples (24 patients, 4 follow-ups) for CMV and 45 samples (27 patients, 3 follow-ups) for EBV.

RESULTS

For CMV, the mean of the WHO-IS (expected value: 4.7 Log IU/ml) was: QS/RGQ=4.84, M2000=4.61, EMAG=4.33, and KPCR=4.79. One patient (10 samples) presented a major underquantification by QS/RGQ. Of the 46 remaining samples, 41 were quantified with QS/RGQ, 43 with M2000, 33 with EMAG and 24 with KPCR. For EBV, the mean of the WHO-IS was: QS/RGQ=4.70, M2000=4.61, EMAG=4.62, and KPCR=4.57. Among the 45 samples, 43 were quantified with QS/RGQ, 39 with M2000, 40 with EMAG and 32 with KPCR.

CONCLUSION

The results obtained with the WHO-IS were very good. The results of patients' samples were well correlated with the announced sensitivity of each system. The elevated threshold of the KPCR CMV assay may be problematic for the follow-up of highly immunocompromised patients who require early introduction of treatment.

Pulmonary cytomegalovirus (CMV) DNA shedding in allogeneic hematopoietic stem cell transplant recipients: Implications for the diagnosis of CMV pneumonia

OBJECTIVES

To date no definitive cut-off value for cytomegalovirus (CMV) DNA load in bronchoalveolar lavage (BAL) fluid specimens has been established to discriminate between CMV pneumonia and pulmonary CMV DNA shedding in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients.

METHODS

The current retrospective study is aimed at assessing the range of CMV DNA loads quantified in BAL fluid specimens from allo-HSCT patients with pneumonia in which different microorganisms were causally involved.

RESULTS

A total of 144 BAL specimens from 123 patients were included. CMV DNA was detected in 56 out of 144 BAL fluid specimens and the median CMV DNA load from patients in whom CMV pneumonia was unlikely or could be tentatively ruled out was 1210 (31-68, 920) IU/ml. The frequency of CMV DNA detection and median CMV DNA loads were comparable, irrespective of the attributable cause of pneumonia. Detection of CMV DNA loads in BAL fluid specimens >500 IU/ml was independently associated with pneumonia-attributable mortality.

CONCLUSIONS

The current study highlights the difficulty in establishing universal CMV DNA load thresholds in BAL fluid specimens for distinguishing between CMV pneumonia and pulmonary CMV DNA shedding, and suggests that the presence of CMV DNA in BAL fluid specimens beyond a certain level may have a deleterious impact on patient outcome.

Community-acquired respiratory virus lower respiratory tract disease in allogeneic stem cell transplantation recipient: Risk factors and mortality from pulmonary virus-bacterial mixed infections

Risk factors (RFs) and mortality data of community‐acquired respiratory virus (CARVs) lower respiratory tract disease (LRTD) with concurrent pulmonary co‐infections in the setting of allogeneic hematopoietic stem cell transplantation (allo‐HSCT) is scarce. From January 2011 to December 2017, we retrospectively compared the outcome of allo‐HSCT recipients diagnosed of CARVs LRTD mono‐infection (n = 52, group 1), to those with viral, bacterial, or fungal pulmonary CARVs LRTD co‐infections (n = 15, group 2; n = 20, group 3, and n = 11, group 4, respectively), and with those having bacterial pneumonia mono‐infection (n = 19, group 5). Overall survival (OS) at day 60 after bronchoalveolar lavage (BAL) was significantly higher in group 1, 2, and 4 compared to group 3 (77%, 67%, and 73% vs 35%, respectively, P = .012). Recipients of group 5 showed a trend to better OS compared to those of group 3 (62% vs 35%, P = .1). Multivariate analyses showed bacterial co‐infection as a RF for mortality (hazard ratio[HR] 2.65, 95% C.I. 1.2‐6.9, P = .017). We identified other 3 RFs for mortality: lymphocyte count <0.5 × 10⁹/L (HR 2.6, 95% 1.1‐6.2, P = .026), the occurrence of and CMV DNAemia requiring antiviral therapy (CMV‐DNAemia‐RAT) at the time of BAL (HR 2.32, 95% C.I. 1.1‐4.9, P = .03), and the need of oxygen support (HR 8.3, 95% C.I. 2.9‐35.3, P = .004). CARV LRTD co‐infections are frequent and may have a negative effect in the outcome, in particular in the context of bacterial co‐infections.

Comparison of two commercial quantitative PCR assays and correlation with the first WHO International Standard for human CMV

Comparability between CMV assays could be facilitated by the first WHO International Standard for human CMV (standard). Standard dilutions were submitted to nucleic acid extraction with Versant kPCR Molecular systems SP or MagNA Pure LC System followed by the kPCR PLX™ CMV DNA (kPCR) or the CMV R-gene™ assay (R-gene), respectively; 139 clinical specimens were tested. Both assays correlated well with the standard (R² > 0.96) and a matrix effect was observed. Quantitative results correlated reasonably between both assays for whole blood (R² = 0.79) and well for other specimen types (R² = 0.93). Quantification differences were within one log₁₀ of the averaged log₁₀ results for 25/27 blood specimens and for 32/33 other specimens. Calibration to the standard did not increase this percentage. In conclusion, results of both assays showed reasonable correlation with each other and good correlation with the standard. Calibration to the standard did not improve comparability of quantitative results.

Automated Nucleic Acid Extraction Systems for Detecting Cytomegalovirus and Epstein-Barr Virus Using Real-Time PCR: A Comparison Study Between the QIAsymphony RGQ and QIAcube Systems

BACKGROUND

Cytomegalovirus (CMV) and Epstein-Barr virus (EBV) are increasingly important in immunocompromised patients. Nucleic acid extraction methods could affect the results of viral nucleic acid amplification tests. We compared two automated nucleic acid extraction systems for detecting CMV and EBV using real-time PCR assays.

METHODS

One hundred and fifty-three whole blood (WB) samples were tested for CMV detection, and 117 WB samples were tested for EBV detection. Viral nucleic acid was extracted in parallel by using QIAsymphony RGQ and QIAcube (Qiagen GmbH, Germany), and real-time PCR assays for CMV and EBV were performed with a Rotor-Gene Q real-time PCR cycler (Qiagen). Detection rates for CMV and EBV were compared, and agreements between the two systems were analyzed.

RESULTS

The detection rate of CMV and EBV differed significantly between the QIAsymphony RGQ and QIAcube systems (CMV, 59.5% [91/153] vs 43.8% [67/153], P=0.0005; EBV, 59.0% [69/117] vs 42.7% [50/117], P=0.0008). The two systems showed moderate agreement for CMV and EBV detection (kappa=0.43 and 0.52, respectively). QIAsymphony RGQ showed a negligible correlation with QIAcube for quantitative EBV detection. QIAcube exhibited EBV PCR inhibition in 23.9% (28/117) of samples.

CONCLUSIONS

Automated nucleic acid extraction systems have different performances and significantly affect the detection of viral pathogens. The QIAsymphony RGQ system appears to be superior to the QIAcube system for detecting CMV and EBV. A suitable sample preparation system should be considered for optimized nucleic acid amplification in clinical laboratories.

Comparison of eMAG™ versus NucliSENS® EasyMAG® performance on clinical specimens

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eMAG™ is a new nucleic acid extraction platform based on magnetic silica technology.

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Performance of eMAG™ and easyMAG^® were compared on various clinical specimens.

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Agreement for virus detection ranged from 84.6% to 95.9%.

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Correlation for virus quantitation displayed R² from 0.802 to 0.995.

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The two platforms showed comparable performance on the clinical specimens tested.

Background

eMAG™ (bioMerieux) is a new nucleic acid extraction platform based on magnetic silica technology, like its predecessor, NucliSENS^® easyMAG^® (bioMerieux). Using the same reagents and disposables, eMAG™ adds further automation, allowing simultaneous extraction of 48 samples directly from primary tubes, and distribution of nucleic acid extracts on PCR strips or in tubes at the end of the extraction process.

Objective

To compare the performance of eMAG™ and easyMAG^® on various clinical specimens.

Study design

Respiratory (n = 199), whole blood (n = 50), plasma (n = 25) and urine (n = 25) specimens were extracted in parallel on both platforms. Both qualitative (respiratory virus, cell control, CMV, EBV, HHV6 and BKV detection) and quantitative (respiratory virus and cell control cycle thresolds, and CMV, EBV, HHV6 and BKV viral loads) results were compared.

Results

Detection of qualitative targets showed good agreement, ranging from 84.6% for whole blood to 95.9% for respiratory specimens. Correlations between quantitative results were good, with R² ranging from 0.802 to 0.995. Quantitative results showed average overall differences below 0.10 log₁₀ copies/mL between eMAG™ and easyMAG^®.

Conclusions

The two platforms showed comparable performance on the types of clinical specimen tested. With higher automation and throughput than easyMAG^®, the eMAG™ platform is likely to be advantageous for laboratories performing a large number of molecular analyses.

Performance of a completely automated system for monitoring CMV DNA in plasma

BACKGROUND

Completely automated systems for monitoring CMV-DNA in plasma samples are now available.

OBJECTIVES

Evaluate analytical and clinical performances of the VERIS™/MDx System CMV Assay(®).

STUDY DESIGN

Analytical performance was assessed using quantified quality controls. Clinical performance was assessed by comparison with the COBAS(®) Ampliprep™/COBAS(®) Taqman CMV test using 169 plasma samples that had tested positive with the in-house technique in whole blood.

RESULTS

The specificity of the VERIS™/MDx System CMV Assay(®) was 99% [CI 95%: 97.7-100]. Intra-assay reproducibilities were 0.03, 0.04, 0.05 and 0.04 log10IU/ml (means 2.78, 3.70, 4.64 and 5.60 log10IU/ml) for expected values of 2.70, 3.70, 4.70 and 5.70 log10IU/ml. The inter-assay reproducibilities were 0.12 and 0.08 (means 6.30 and 2.85 log10IU/ml) for expected values of 6.28 and 2.80 log10IU/ml. The lower limit of detection was 14.6IU/ml, and the assay was linear from 2.34 to 5.58 log10IU/ml. The results for the positive samples were concordant (r=0.71, p<0.0001; slope of Deming regression 0.79 [CI 95%: 0.56-1.57] and y-intercept 0.79 [CI 95%: 0.63-0.95]). The VERIS™/MDx System CMV Assay(®) detected 18 more positive samples than did the COBAS(®) Ampliprep™/COBAS(®) Taqman CMV test and the mean virus load were higher (0.41 log10IU/ml). Patient monitoring on 68 samples collected from 17 immunosuppressed patients showed similar trends between the two assays. As secondary question, virus loads detected by the VERIS™/MDx System CMV Assay(®) were compared to those of the in-house procedure on whole blood. The results were similar between the two assays (-0.09 log10IU/ml) as were the patient monitoring trends.

CONCLUSION

The performances of the VERIS™/MDx System CMV Assay(®) facilitated its routine use in monitoring CMV-DNA loads in plasma samples.

Malaria Diagnosis Across the International Centers of Excellence for Malaria Research: Platforms, Performance, and Standardization

Diagnosis is “the act of identifying a disease, illness, or problem by examining someone or something.” When an individual with acute fever presents for clinical attention, accurate diagnosis leading to specific, prompt treatment often saves lives. As applied to malaria, not only individual patient diagnosis is important but also assessing population-level malaria prevalence using appropriate diagnostic methods is essential for public health purposes. Similarly, identifying (diagnosing) fake antimalarial medications prevents the use of counterfeit drugs that can have disastrous effects. Therefore, accurate diagnosis in broad areas related to malaria is fundamental to improving health-care delivery, informing funding agencies of current malaria situations, and aiding in the prioritization of regional and national control efforts. The International Centers of Excellence for Malaria Research (ICEMR), supported by the U.S. National Institute of Allergy and Infectious Diseases, has collaborated on global efforts to improve malaria diagnostics by working to harmonize and systematize procedures across different regions where endemicity and financial resources vary. In this article, the different diagnostic methods used across each ICEMR are reviewed and challenges are discussed.

Bacterial and fungal DNA extraction from positive blood culture bottles: a manual and an automated protocol

When adapting a gene amplification-based method in a routine sepsis diagnostics using a blood culture sample as a specimen type, a prerequisite for a successful and sensitive downstream analysis is the efficient DNA extraction step. In recent years, a number of in-house and commercial DNA extraction solutions have become available. Careful evaluation in respect to cell wall disruption of various microbes and subsequent recovery of microbial DNA without putative gene amplification inhibitors should be conducted prior selecting the most feasible DNA extraction solution for the downstream analysis used. Since gene amplification technologies have been developed to be highly sensitive for a broad range of microbial species, it is also important to confirm that the used sample preparation reagents and materials are bioburden-free to avoid any risks for false-positive result reporting or interference of the diagnostic process. Here, one manual and one automated DNA extraction system feasible for blood culture samples are described.

Quantification of cytomegalovirus viral load

Cytomegalovirus (CMV), a member of the Herpesviridae family, is worldwide distributed. After the primary infection, CMV induces a latent infection with possible reactivation(s). It is responsible for severe to life-threatening diseases in immunocompromised patients and in foetuses and newborns of infected mothers. For monitoring CMV load, classical techniques based on rapid culture or pp65 antigenemia are progressively replaced by quantitative nuclear acid tests (QNAT), easier to implement and standardize. A large variety of QNAT are available from laboratory-developed assays to fully-automated commercial tests. The indications of CMV quantification include CMV infection during pregnancy and in newborns, and viral surveillance of grafted and non-grafted immunocompromised patients, patients with bowel inflammatory diseases and those hospitalised in intensive care unit. A close cooperation between virologists and clinicians is essential for optimizing the benefit of CMV DNA monitoring.