Characteristics of the ID-NOW™ test for the rapid detection of SARS-CoV-2.

OBJECTIVE: To determine the sensitivity and specificity of the Abbott ID-NOW™ test in the diagnosis of COVID-19. The test is based on the detection of the SARS-CoV-2 gene by isothermal amplification technology. METHODS: From 303 individuals, two nasopharyngeal swabs and one oropharyngeal swab were collected to be tested in parallel by the ID-NOW™ test and PCR test (Allplex™ SARS-CoV-2 Assay). A subgroup of 107 individuals presented to the public collection point for covid-19 at the Motol University Hospital during the dominance of the Delta variant, and the others were tested via the Adult Emergency Admission Department during the dominance of the Omicron variant. RESULTS: Of 297 valid samples, 43 were positive by the PCR assay and 33 were positive by the ID-NOW™ test (sensitivity 76.74%; 95% CI 61.37 to 88.24%). ID-NOW™ detected three samples as positive, but the positivity was not confirmed by PCR (specificity 98.82%; 95% CI 96.59 to 99.76%). A significant increase in sensitivity up to 100% is observed for samples with a higher viral load (with a PCR threshold cycle value below 30 or from patients with symptoms of COVID-19). The Delta or Omicron variant has no significant effect on the sensitivity of the test. CONCLUSION: Due to its ease of use and speed of result, ID-NOW™ is a suitable diagnostic tool for prompt assessment of a patient's infectivity. If, despite the negative ID-NOW™ result, the patient has symptoms of COVID-19, it is advised to perform a classic PCR test for SARS-CoV-2.

The sensitivity of SARS-CoV-2 antigen tests in the view of large-scale testing.

OBJECTIVES: Antigen tests have emerged as an alternative to SARS-CoV-2 diagnostic PCR, thought to be valuable especially for the screening of bigger communities. To check appropriateness of the antigen based testing, we determined sensitivity of two point-of-care antigen tests when applied to a cohort of COVID-19 symptomatic, COVID-19 asymptomatic and healthy persons. METHODS: We examined nasopharyngeal swabs with antigen test 1 (Panbio Covid-19 Ag Rapid Test, Abbott) and antigen test 2 (Standard F Covid-19 Ag FIA, SD Biosensor). An additional nasopharyngeal and oropharyngeal swab of the same individual was checked with PCR (Allplex SARS-nCoV-2, Seegene). Within a 4-day period in October 2020, we collected specimens from 591 subjects. Of them, 290 had COVID-19 associated symptoms. RESULTS: While PCR positivity was detected in 223 cases, antigen test 1 and antigen test 2 were found positive in 148 (sensitivity 0.664, 95%CI 0.599, 0.722) and 141 (sensitivity 0.623, 95%CI 0.558, 0.684) patients, respectively. When only symptomatic patients were analysed, sensitivity increased to 0.738 (95%CI 0.667, 0.799) for the antigen test 1 and to 0.685 (95%CI 0.611, 0.750) for the antigen test 2. The substantial drop in sensitivity to 12.9% (95%CI 0.067, 0.234) was observed for samples with the PCR threshold cycle above > 30. CONCLUSIONS: Low sensitivity of antigen tests leads to the considerable risk of false negativity. It is advisable to implement repeated testing with high enough frequency if the antigen test is used as a frontline screening tool, and to follow with PCR if it is applied to vulnerable populations.

BAL fluid analysis in the identification of infectious agents in patients with hematological malignancies and pulmonary infiltrates.

The present study aims to evaluate the diagnostic yield of bronchoalveolar lavage (BAL) fluid in patients with hematological malignancies and describe the most common pathogens detected in BAL fluid (BALF.) An analysis of 480 BALF samples was performed in patients with hematological malignancies over a period of 7 years. The results of culture methods, PCR, and immunoenzymatic sandwich microplate assays for Aspergillus galactomannan (GM) in BALF were analyzed. Further, the diagnostic thresholds for Aspergillus GM and Pneumocystis jiroveci were also calculated. Microbiological findings were present in 87% of BALF samples. Possible infectious pathogens were detected in 55% of cases; 32% were classified as colonizing. No significant difference in diagnostic yield or pathogen spectrum was found between non-neutropenic and neutropenic patients. There was one significant difference in BALF findings among intensive care units (ICU) versus non-ICU patients for Aspergillus spp. (22% versus 9%, p = 0.03). The most common pathogens were Aspergillus spp. (n = 86, 33% of BAL with causative pathogens) and Streptococcus pneumoniae (n = 46, 18%); polymicrobial etiology was documented in 20% of cases. A quantitative PCR value of > 1860 cp/mL for Pneumocystis jirovecii was set as a diagnostic threshold for pneumocystis pneumonia. The absorbance index of GM in BALF of 0.5 was set as a diagnostic threshold for aspergillosis. The examination of BAL fluid revealed the presence of pathogen in more than 50% of cases and is, therefore, highly useful in this regard when concerning pulmonary infiltrates.

Reduction of Thymoglobuline from 7.5 mg/kg to 6 mg/kg in conditioning regimen extended time to the first cytomegalovirus detection after allogenic haematopoietic stem cell transplantation.

INTRODUCTION: The optimal dosage of anti-thymocyte globulin (ATG) may influence the outcome of patients after allogenic haematopoietic stem cell transplantation (HSCT). The aim of our study was to analyse human cytomegalovirus (CMV) infection data, incidence of graft-versus-host disease and other clinical endpoints comparing two patients cohorts that were administered two different Thymoglobuline Genzyme doses as part of the HSCT conditioning regimen. MATERIALS AND METHODS: Total of 65 adult patients received ATG (7.5 mg/kg or 6 mg/kg) as a part of the fludarabine/busulfan/ATG conditioning regimen. CMV DNAemia was monitored after HSCT using quantitative real-time PCR and preemptive treatment was started for viral loads above 1000 cp/ml. RESULTS: The mild ATG dose reduction extended the time to the first CMV detection after transplantation (28 days for 7.5 mg/kg dose vs. 40 days for 6 mg/kg dose, p = 0.04). But it did not reduce the incidence or influence first anti-CMV treatment onset, the initial viral load, peak viral load in whole blood or the antiviral therapy parameters (all p 0.18). No impact of ATG dose reduction on incidence of graft-versus-host-disease, relapse of underlying disease or mortality within first year after transplantation (all p 0.32) were observed. CONCLUSIONS: The reduced ATG dosages can allow lower toxicity of conditioning regimen while keeping the performance.

[Ganciclovir treatment failure in adult allogeneic hematopoietic stem cell transplant recipients with cytomegalovirus infection--a single centre experience]. / Klinická rezistence lidského cytomegaloviru pri lécbe gancyklovirem u pacientu po alogenní transplantaci hematopoetických bunek--zkusenosti jednoho centra.

OBJECTIVE: To determine the incidence of infection with ganciclovir-resistant cytomegalovirus (CMV) in adult allogeneic hematopoietic stem cell transplant (HSCT) recipients. Clinical resistance or treatment failure was defined as persistent DNAemia or increasing viral load in peripheral blood after 2 weeks of virostatic treatment. The association between the treatment failure and viral resistance was analysed. The presence of ganciclovir-resistant CMV strains was confirmed by genotypic testing able to detect mutations conferring resistance. METHODS: In 2012 and 2014, 40 patients who underwent allogeneic HSCT for hematologic malignancies and were treated for human CMV reactivation/disease were followed up prospectively. In patients with treatment failure, CMV DNA was isolated and analysed by nucleotide sequence analysis of the UL 97 and UL 54 genes conferring resistance to the virostatic agent. RESULTS: The treatment failure occurred in seven patients, but ganciclovir resistance conferring mutations were only detected in two of them (mutations L595F and M460I in the UL 97 gene). Another mutation in the UL 97 gene (N510S) was found in a patient with recurrent CMV replication who needed to be retreated but did not meet the criteria for treatment failure. CONCLUSION: The low incidence of genetically confirmed ganciclovir-resistant CMV isolates in HSCT recipients with relatively common clinical treatment failure suggests that the mechanism underlying slower viral clearance is often other than mutations conferring ganciclovir resistance to the virus.

Analyses of germline, chromosomally integrated human herpesvirus 6A and B genomes indicate emergent infection and new inflammatory mediators.

Human herpesvirus-6A (HHV-6A) is rarer than HHV-6B in many infant populations. However, they are similarly prevalent as germline, chromosomally integrated genomes (ciHHV-6A/B). This integrated form affects 0.1-1 % of the human population, where potentially virus gene expression could be in every cell, although virus relationships and health effects are not clear. In a Czech/German patient cohort ciHHV-6A was more common and diverse than ciHHV-6B. Quantitative PCR, nucleotide sequencing and telomeric integration site amplification characterized ciHHV-6 in 44 German myocarditis/cardiomyopathy and Czech malignancy/inflammatory disease (MI) patients plus donors. Comparisons were made to sequences from global virus reference strains, and blood DNA from childhood-infections from Zambia (HHV-6A mainly) and Japan (HHV-6B). The MI cohort were 86 % (18/21) ciHHV-6A, the cardiac cohort 65 % (13/20) ciHHV-6B, suggesting different disease links. Reactivation was supported by findings of 1) recombination between ciHHV-6A and HHV-6B genes in 20 % (4/21) of the MI cohort; 2) expression in a patient subset, of early/late transcripts from the inflammatory mediator genes chemokine receptor U51 and chemokine U83, both identical to ciHHV-6A DNA sequences; and 3) superinfection shown by deep sequencing identifying minor virus-variants only in ciHHV-6A, which expressed transcripts, indicating virus infection reactivates latent ciHHV-6A. Half the MI cohort had more than two copies per cell, median 5.2, indicative of reactivation. Remarkably, the integrated genomes encoded the secreted-active form of virus chemokines, rare in virus from childhood-infections. This shows integrated virus genomes can contribute new human genes with links to inflammatory pathology and supports ciHHV-6A reactivation as a source for emergent infection.

[Diagnosis of Clostridium difficile infections: comparative study of two immuno enzyme assays with confirmation by PCR and culture followed by PCR ribotyping]. / Diagnostika Clostridium difficile infekcí - porovnávací studie dvou imunoenzymatických metod s konfirmací pomocí PCR a kultivace s následnou ribotypizací kmene*

STUDY OBJECTIVE: Comparison of two commercially avail-able tests for the detection of Clostridium difficile Glutamate Dehydrogenase (GDH) and toxins A and B for their sensitivity and specificity. MATERIAL AND METHODS: Eighty-six stool samples from patients hospitalised in the Motol University Hospital were analysed. GDH and toxins A and B were assayed in parallel by two tests: C. difficile Quik Chek Complete® (Techlab, USA) and Liaison® C. difficile GDH and Toxins AαB (DiaSorin, USA). From the stool samples, nucleic acids were also isolated using the UltraClean® Fecal DNA kit (MoBio Laboratories, USA). The commercially available C. difficile Elite MGB® kit (Nanogen, Italy) was used for the polymerase chain reaction (PCR). Anaerobic culture on C. difficile selective medium (Oxoid) was performed for all positive samples at least in one test. Pure isolates were characterized by PCR ribotyping. RESULTS: Thirty-six (42%) samples were GDH negative and toxin A/B negative by both tests. Twenty (23%) samples were GDH positive and toxin A/B positive by both tests. Nine (10%) samples were GDH positive and toxin negative by both tests, but were positive by PCR. Eleven (13%) samples that were GDH positive and toxin negative by both tests remained negative by PCR. Six (7%) samples only were GDH positive and toxin positive by the Liaison® test alone. Four (5%) samples were GDH-positive by theLiaison® test alone. Culture failure was observed in 11 (13%) samples, of which seven were positive by PCR. PCR was inhibited in five (6%) samples. The following toxigenic ribotypes: AI-3, 001, 002, 012,014, 017, 020, 049, 054, 078, 176, 203, and 413 and non-toxigenic ribotypes: AI-34, AI-61, 010, 485, 495, and 596 were identified. CONCLUSION: The Liaison® test had seven percent higher sensitivity for the detection of toxins A/B. The two-step protocol of the tests is also cost-saving. The savings can be used e.g. for incorporating the PCR techniques into the diagnostic algorithm of the laboratory.

Post-mortem analysis of Candida albicans breakthrough infection during echinocandin treatment in haematopoietic stem cell transplant recipient.

We present case of a girl deceased due to Candida albicans breakthrough invasive infection during the echinocandin treatment after undergoing allogeneic haematopoietic stem cell transplant for relaps of acute myeloid leukaemia. Candida albicans generally susceptible to all antifungal drugs wasn't considered for potential resistance and conventional blood culture positivity was too late to reveal the resistance to echinocandins. Due to severe organ toxicities (liver, kidneys) she received echinocandin as an antifungal prophylaxis, no change was made for the treatment of Candida albicans infection. Later, the molecular analysis proved the mutation S645P known as being responsible for the echinocandin resistance. The post mortem analysis of fungal burden in autopsy samples showed very high levels of Candida DNA in gut, liver, spleen and kidneys.

Alterations of CHEK2 forkhead-associated domain increase the risk of Hodgkin lymphoma.

Checkpoint kinase 2 gene (CHEK2) codes for an important mediator of DNA damage response pathway. Mutations in the CHEK2 gene increase the risk of several cancer types, however, their role in Hodgkin lymphoma (HL) has not been studied so far. The most frequent CHEK2 alterations (including c.470T>C; p.I157T) cluster into the forkhead-associated (FHA) domain-coding region of the CHEK2 gene. We performed mutation analysis of the CHEK2 gene segment coding for FHA domain using denaturing high-performance liquid chromatography in 298 HL patients and analyzed the impact of characterized CHEK2 gene variants on the risk of HL development and progression-free survival (PFS). The overall frequency of CHEK2 alterations was significantly higher in HL patients (17/298; 5.7%) compared to the previously analyzed non-cancer controls (19/683; 2.8%; p= 0.04). Presence of any alteration within the analyzed region of the CHEK2 gene was associated with increased risk of HL development (OR = 2.11; 95% CI = 1.08 - 4.13; p= 0.04). The most frequent I157T mutation was found in 4.0% of HL patients and 2.5% of controls (p = 0.22), however, the frequency of 5 other alterations (excluding I157T) was significantly higher in HL cases and associated with increased risk of HL development (OR = 5.81; 95% CI = 1.12 - 30.12; p= 0.03). PFS in HL patients did not differ between CHEK2 mutation carriers and non-carriers. The predominant I157T mutation together with other alterations in its proximity represent moderate genetic predisposition factor increasing the risk of HL development.

Signature profiles of CMV-specific T-cells in patients with CMV reactivation after hematopoietic SCT.

Depletion of cellular immunity as a consequence of conditioning before allogeneic hematopoietic SCT (HSCT) frequently results in CMV reactivation, which may in turn lead to life-threatening infections and require timely antiviral treatment. We have investigated the functional signatures of CMV-specific CD4+ and CD8+ T-cells in 191 samples from 118 individuals. We compared healthy donors with both patients with high and undetectable viral loads, and those who controlled and did not control their CMV reactivations. Polychromatic flow-cytometric measurements of CD154 (CD40L), intracellular cytokines (IFNγ, IL2) and a degranulation marker (CD107a) allowed us to assess the functional status of various T-cells simultaneously. We found that dual IFNγ/IL2-producing CD8+ T-cells were present in patients controlling their CMV reactivations but absent from non-controllers. CD8+ T-cells that produce only IFNγ were the most abundant subtype, but they most likely represent non-protective memory cells. Distinct functional signatures were examined by hierarchical clustering, and this revealed that, unlike polyfunctional CD8+ T-cells, CD8+ T-cells that produce IFNγ alone were not functioning in concert with other subsets. In conclusion, our study revealed functional signatures that may be useful for immune monitoring, and it could change the interpretation of previous studies that assessed only IFNγ.

[Invasive zygomycosis of the large intestine in a diabetes patient]. / Invazivní zygomykóza tlustého streva u pacienta s diabetem.

Invasive mucormycosis is a rare, serious or even fatal condition. The authors diagnosed and successfully treated the disorder in a 62-year-old diabetes patient. The course of the disease, including justification of the surgical procedure are described in the case review. All treatment options were implemented and, after 121 days of hospitalization, the patient was released for homecare.

Failure of multiple antivirals to affect high HHV-6 DNAaemia resulting from viral chromosomal integration in case of severe aplastic anaemia.

We report a fifty-year-old woman presenting with severe aplastic anaemia (SAA) and prolonged high Human Herpesvirus 6 (HHV6) variant A DNAeamia detected by quantitative PCR. Multiple antiviral treatments failed to affect the HHV6 DNAemia and subsequent immunosuppressive treatment reached only partial improvement as judged by bone marrow examinations. The patient remained dependent on thrombocyte transfusions and G-CSF treatment. After one year of steady high HHV6 DNA load in blood, viral chromosomal integration was proved by demonstrating the viral DNA in hair follicles. This condition appeared to be unconnected with, and to have no effect, on the original SAA.

Low mortality of children undergoing hematopoietic stem cell transplantation from 7 to 8/10 human leukocyte antigen allele-matched unrelated donors with the use of antithymocyte globulin.

Human leukocyte antigen (HLA)-matched sibling donor hematopoietic stem cell transplantation (HSCT) is available for only approximately 30% patients needing HSCT. Use of alternative donors is associated with a high incidence and severity of graft-versus-host disease (GVHD). Here we report our experience with GVHD prophylaxis using pre-transplant rabbit antithymocyte globulin (rATG), in addition to post transplant cyclosporin A and methotrexate. Seventy-five children received unmanipulated grafts from 7 to 10/10 HLA allele-matched unrelated donors. Median follow-up was 25 months (range, 6-65 months). Only 2/75 patients (2.5%) developed acute GVHD grades III-IV, and 17/75 (25%) developed extensive chronic GVHD. Overall survival was 79%. It was similar in patients receiving grafts from 7 or 8/10 to 9 or 10/10 allele-matched donors, and similar in patients receiving peripheral blood stem cells and marrow. Six (11%) patients died owing to relapse, and 10 (13%) due to transplant-related complications. The addition of rATG appears to result in a low incidence of severe GVHD and overall mortality.

[EBV quantification in children after allogeneic hematopoietic stem cell transplantation]. / Kvantifikace EBV u detí po alogenní transplantaci hematopoetických kmenových bunek.

BACKGROUND: Patients undergoing allogeneic hematopoietic stem cell transplantation (AHSCT) are endangered by developing Epstein-Barr virus-related post-transplant lymfoprolipherative disease (EBV-LPD). The aims of the study were to retrospectively characterise the viral loads in four patients who died of this complication, and to test possible risk factors for EBV reactivation in a prospectively observed cohort of children after AHSCT. METHODS AND RESULTS: Serial DNA samples extracted from whole blood from four patients who died of post-transplant EBV-LPD in year 2000 were retrospectively analysed for EBV load using quantitative real-time PCR. First detection of EBV activation preceded death by 24-91 days. All four patients exceeded a viral load of one million EBV copies per 100,000 human genome equivalents. A cohort of 72 children undergoing AHSCT between 2001-2004 was prospectively followed-on using the same quantification method from regularly obtained samples of whole blood, and clinical and laboratory data were recorded on a weekly basis, totalling at 3,896 person-weeks of observation. Approximately one half of the cohort experienced at least one episode of EBV reactivation during the first 100 days after AHSCT, four of the episodes being accompanied with viral loads higher than our provisional threshold of 10,000 copies per 100,000 human genome equivalents. Three of the four patients developed EBV-LPD and were successfully treated by intravenous administration of anti-CD20 antibody. Testing of possible clinical and laboratory predictors of EBV reactivation did not reveal any clinically useful association. CONCLUSIONS: The cornerstone of predicting EBV-LPD in AHSCT is a regular monitoring of EBV viral load using quantitative methods. Using this strategy with a threshold of 10,000 EBV copies per 100,000 human genome equivalents was proved to be effective, as shown by no death of EBV for the study period, compared to four cases in the year before the quantitative monitoring.