The inactivation of Cobalamin by nitrous oxide : application in experimental chemotherapy of leukemia

The subject of this thesis is the investigation of the role of cobalamin in leukemic cell proliferation. This has been studied by the application of the nitrous oxide-induced inactivation of the cobalamin coenzyme function in methionine synthetase. In most of the studies, the well-characterized myeloid leukemia of BN rats (BNML) has been employed as a model for human leukemia. In some studies leukemic bone marrow cells from patients have been used. The results of these studies may lead to a tentative conclusion with regard to the perspectives of cobalamin inactivation in antileukemic chemotherapy. Prior to the presentation of these studies in chapters 3 to 8, some essential experimental methods are described in chapter 2. This involves the BN rat leukemia model, the exposure of rats to nitrous oxide, and the deoxyuridine suppression tes

Rhinovirus viremia in adult patients with high viral load in bronchoalveolar lavages

Molecular basis of virus replication, viral pathogenesis and antiviral strategie

Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield

Introduction Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. Areas covered This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. Expert opinion The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

Anti-leukemic potential of methyl-cobalamin inactivation by nitrous oxide

Myelo‐cytotoxicity of extended nitrous oxide (N2O) inhalation was described almost forty years ago and then incidentally applied already with temporary success for suppressing leukemia. In 1948 the accompanying megaloblastic maturation arrest was explained by inactivation of the methylcobalamin coenzyme and subsequent folate deficiency. We studied the anti‐leukemic effect of N2O on a transplantable acute leukemia in B(rown) N(orway) rats. Progression of this B,N,M(yelocytic)L(eukemia) was measured as spleen and liver weights, and leukemic blood cell counts. The deoxyuridine (dU)‐suppression test provided in vitro indication of the functional folate activity of leukemic cells. Breathing of N2O‐oxygen considerably reduced but did not eradicate, BNML‐proliferation. Addition of anti‐metabolites, interfering with some enzyme in the folate metabolism beyond the methylcobalamin co‐enzyme dependent methionine synthase step, acted at least synergistically. The anti‐leukemic effect of cycloleucine, which reduces S‐adenosyl‐methionine synthesis by inactivation of methionine adenosyltransferase, was moderate but became much stronger with N2O inhalation. Methotrexate, a potent anti‐leukemic agent by inhibiting tetrahydrofolate (THF) generation through inactivation of di‐HF reductase, became highly anti‐BNML, even in low dosage when combined with or preceded by N2O. 5‐Fluorouracil, which inhibits methylene‐THF dependent thymidilate synthase, itself was surprisingly anti‐BNML, but also became much more potent with previous or concomittant N2O exposure. Preliminary dU‐suppression test results with human acute leukemia cells, exposed to N2O and/or folate antagonists in vitro, correlated well with the in vivo BNML‐experiments. Combining the anticobalamin activity of N2O with an anti‐folate therefore seems to be a promising chemotherapeutic approach. Copyrigh

Diagnosis of intrauterine parvovirus B19 infection at birth - value of DNA detection in neonatal blood and dried blood spots

Background: Diagnosis of congenital viral infection at birth is generally attempted by direct detection of the virus by PCR in various neonatal materials. How to reliably diagnose intrauterine infection with parvovirus B19 (B19 V) at birth is unknown.Objectives: To evaluate the performance of B19 V DNA detection in cord blood (CB) or neonatal dried blood spots (DBS) in diagnosing fetal infection. Study design: Two cohorts of children diagnosed prenatally with an intrauterine B19 V infection were included in this study. CB samples of intrauterine B19 V infections that were sent to a reference laboratory for congenital infections in Stuttgart, Germany in the period 1995-2014 were tested in triplicate for B19 V DNA by quantitative PCR. DBS from children with intrauterine B19 V infection that underwent IUT at the LUMC, Leiden, the Netherlands in the period 2009-2014 were tested for B19 V DNA by quantitative B19 V PCR in triplicate.Results: Fourteen of twenty (70 %) CB samples tested positive for B19 V DNA. The positivity rate was 40 % (4/10) in those with a prenatal diagnosis< 20 weeks gestation. When intrauterine B19 V infection was diagnosed thereafter, 100 % (10/10) samples were B19 V DNA positive. Of the thirteen available DBS, twelve (92 %) tested positive. Viral load in CB and DBS corresponded inversely with time from fetal diagnosis to birth.Conclusion: B19 V DNA can be detected in neonatal blood samples of children following intrauterine B19 V infection, although the possibility of false-negatives, even in severe infections, should be considered. B19 V viral load at birth correlates with timing of infection.Research into fetal development and medicin

Infections after auxiliary partial liver transplantation. Experiences in the first ten patients

Summary In ten auxiliary partial liver transplant recipients selective bowel decontamination (SBD) was used to reduce infections due to gram-negative microorganisms and fungi. During SBD no gram-negative infections occurred. Candida peritonitis was observed in one patient. After discontinuation of SBD serious infections of gram-negative origin did occur and three fungal infections were seen. SBD seems to have a favourable effect in reducing infections by gram-negative microorganisms and fungi. Most striking was the number of enterococcal infections that occurred. Five out of ten patients developed enterococcal infections which in two cases contributed to a fatal outcome. These infections occurred after increase of the number of enterococci in faeces and concomitant positive cultures of bile, ascites or wound drains. This increase could be due to the use of SBD. Also, the kind of biliary anastomosis may play an important role in the relatively high incidence of enterococcal infections. In the postoperative period, recurrence of hepatitis B infection in the liver graft was observed in all patients with cirrhosis due to this virus. Problems caused by other viral infections or protozoal infections remained limited in these ten patients. Zusammenfassung Bei Patienten, bei denen eine auxiliäre, partielle Lebertransplantation durchgeführt wurde, wurde die selektive Darmdekontamination (SBD) eingesetzt, um Infektionen durch gramnegative Mikroorganismen und Pilze zu vermindern. Während SBD traten keine Infektionen durch gramnegative Bakterien auf. Bei einem Patienten wurde eine Candida-Peritonitis beobachtet. Nach Beendigung der SBD kam es zu schweren Infektionen durch gramnegative Bakterien, außerdem zu drei Pilzinfektionen. SBD hat offensichtlich einen günstigen Einfluß im Hinblick auf eine Verminderung von Infektionen durch gramnegative Erreger und Pilze. Bemerkenswert hoch war die Zahl der aufgetretenen Enterokokkeninfektionen. Bei fünf der zehn Patienten traten Enterokokkeninfektionen auf, die in zwei Fällen den letalen Ausgang mitbestimmten. Diesen Infektionen gingen ein Anstieg der Enterokokkenzahlen im Stuhl und zugleich positive Kulturen in Galle, Aszites und Wunddrainagen voraus. Es ist möglich, daß die SBD die Zunahme von Enterokokkeninfektionen begünstigte. Auch die Art der Gallengangsanastomose kann hierzu wesentlich beigetragen haben. Bei allen Patienten, bei denen die Zirrhose durch Hepatitis B Virus verursacht war, kam es postoperativ zu einem Rezidiv durch dieses Virus im Lebertransplantat. Probleme durch andere virale oder Protozoeninfektionen hielten sich bei diesen zehn Patienten in Grenzen

Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness

Background: Diagnosis of infections in returning international travellers can be challenging because of the broad spectrum of potential infectious etiologies potentially involved. Viral metagenomic next-generation sequencing (mNGS) has the potential to detect any virus present in a patient sample and is increasingly being used for difficult to diagnose cases. The aim of this study was to analyze the performance of mNGS for viral pathogen detection in the clinical setting of international travellers returning with febrile illness. Methods: Thirty-eight serum samples from international travellers returning with febrile illness and presenting at the outpatient clinic of the Leiden University Medical Center in the Netherlands in the time period 2015-2016 were selected retrospectively. Samples were processed for viral metagenomic sequencing using a probe panel capturing all known vertebrate viruses. Bioinformatic analysis was performed using Genome Detective software for metagenomic virus detection. Metagenomic virus findings were compared with viral pathogen detection using conventional methods. Results: In 8 out of the 38 patients (21%), a pathogenic virus was detected by mNGS. All viral pathogens detected by conventional assays were also detected by mNGS: dengue virus (n=4 patients), Epstein-Barr virus (n=2), hepatitis B virus (n=1). In addition, mNGS resulted in additional pathogenic findings in 2 patients (5%): dengue virus (n=1), and hepatitis C virus (n=1). Non-pathogenic viruses detected were: GB virus C (n=1) and torque teno viruses (n=3). High genome coverage and depth using capture probes enabled typing of the dengue viruses detected. Conclusions: Viral metagenomics has the potential to assist the detection of viral pathogens and co-infections in one step in international travellers with a febrile syndrome. Furthermore, viral enrichment by probes resulted in high genome coverage and depth which enabled dengue virus typing.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

Improved diagnostics in bacterial neonatal meningitis using a next-generation sequencing platform

IntroductionBacterial meningitis in infants is an infrequent but life-threatening condition. Empiric therapy should begin as soon as meningitis is thought likely. Consequently, the causative microorganisms may not always be detected using culturing techniques, as cerebrospinal fluid (CSF) cultures are influenced by antibiotics. Nucleic acid amplification tests, such as polymerase chain reaction (PCR) (multiplex panels), may overcome this limitation but require a priori knowledge of the likely pathogen present within the sample. With this in mind, we investigated to what extent a culture-free, broad-range 16S rRNA gene next-generation sequencing (NGS) platform (MYcrobiota) could add to the microbiological diagnosis of meningitis.MethodsRetrospective cohort study at level III neonatal intensive care unit. Included were all infants with suspected meningitis admitted between 10 November 2017 and 31 December 2020. A comparison was made of the bacterial pathogen detection rate between MYcrobiota and conventional bacterial culture.ResultsIn a 3-year period, 37 CSF samples (diagnostic and follow-up) from 35 infants with proven or possible meningitis were available for MYcrobiota testing. MYcrobiota detected the presence of bacterial pathogens in 11 samples (30%), in contrast with the conventional CSF culture, which detected bacteria in 2 of 36 samples (5.6%).ConclusionAddition of 16S rRNA sequencing to conventional culturing greatly improved the identification of the aetiology of bacterial meningitis compared to culturing of CSF samples alone.Molecular basis of bacterial pathogenesis, virulence factors and antibiotic resistanc

Performance of five metagenomic classifiers for virus pathogen detection using respiratory samples from a clinical cohort

Viral metagenomics is increasingly applied in clinical diagnostic settings for detection of pathogenic viruses. While several benchmarking studies have been published on the use of metagenomic classifiers for abundance and diversity profiling of bacterial populations, studies on the comparative performance of the classifiers for virus pathogen detection are scarce. In this study, metagenomic data sets (n = 88) from a clinical cohort of patients with respiratory complaints were used for comparison of the performance of five taxonomic classifiers: Centrifuge, Clark, Kaiju, Kraken2, and Genome Detective. A total of 1144 positive and negative PCR results for a total of 13 respiratory viruses were used as gold standard. Sensitivity and specificity of these classifiers ranged from 83 to 100% and 90 to 99%, respectively, and was dependent on the classification level and data pre-processing. Exclusion of human reads generally resulted in increased specificity. Normalization of read counts for genome length resulted in a minor effect on overall performance, however it negatively affected the detection of targets with read counts around detection level. Correlation of sequence read counts with PCR Ct-values varied per classifier, data pre-processing (R-2 range 15.1-63.4%), and per virus, with outliers up to 3 log(10) reads magnitude beyond the predicted read count for viruses with high sequence diversity. In this benchmarking study, sensitivity and specificity were within the ranges of use for diagnostic practice when the cut-off for defining a positive result was considered per classifier.Molecular Epidemiolog

The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

Introduction Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. Objectives To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. Study design 88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006-2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. Results By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. Conclusions The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection