Estimation of antimicrobial resistance of Mycoplasma genitalium, Belgium, 2022.

BackgroundAntimicrobial resistance (AMR) of Mycoplasma genitalium (MG) is a growing concern worldwide and surveillance is needed. In Belgium, samples are sent to the National Reference Centre of Sexually Transmitted Infections (NRC-STI) on a voluntary basis and representative or robust national AMR data are lacking.AimWe aimed to estimate the occurrence of resistant MG in Belgium.MethodsBetween July and November 2022, frozen remnants of MG-positive samples from 21 Belgian laboratories were analysed at the NRC-STI. Macrolide and fluoroquinolone resistance-associated mutations (RAMs) were assessed using Sanger sequencing of the 23SrRNA and parC gene. Differences in resistance patterns were correlated with surveillance methodology, socio-demographic and behavioural variables via Fisher's exact test and logistic regression analysis.ResultsOf the 244 MG-positive samples received, 232 could be sequenced for macrolide and fluoroquinolone RAMs. Over half of the sequenced samples (55.2%) were resistant to macrolides. All sequenced samples from men who have sex with men (MSM) (24/24) were macrolide-resistant. Fluoroquinolone RAMs were found in 25.9% of the samples and occurrence did not differ between socio-demographic and sexual behaviour characteristics.ConclusionAlthough limited in sample size, our data suggest no additional benefit of testing MG retrieved from MSM for macrolide resistance in Belgium, when making treatment decisions. The lower occurrence of macrolide resistance in other population groups, combined with emergence of fluoroquinolone RAMs support macrolide-resistance testing in these groups. Continued surveillance of resistance in MG in different population groups will be crucial to confirm our findings and to guide national testing and treatment strategies.

Anti-tumor necrosis factor therapy in Bulgarian pediatric patients with inflammatory bowel disease - an 8-year experience of a referral center.

INTRODUCTION: Anti-tumor necrosis factor (anti-TNF) therapy has become a mainstay in the treatment of patients with inflammatory bowel disease over the past few decades.

Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium.

From early 2020, a high demand for SARS-CoV-2 tests was driven by several testing indications, including asymptomatic cases, resulting in the massive roll-out of PCR assays to combat the pandemic. Considering the dynamic of viral shedding during the course of infection, the demand to report cycle threshold (Ct) values rapidly emerged. As Ct values can be affected by a number of factors, we considered that harmonization of semi-quantitative PCR results across laboratories would avoid potential divergent interpretations, particularly in the absence of clinical or serological information. A proposal to harmonize reporting of test results was drafted by the National Reference Centre (NRC) UZ/KU Leuven, distinguishing four categories of positivity based on RNA copies/mL. Pre-quantified control material was shipped to 124 laboratories with instructions to setup a standard curve to define thresholds per assay. For each assay, the mean Ct value and corresponding standard deviation was calculated per target gene, for the three concentrations (107, 105 and 103 copies/mL) that determine the classification. The results of 17 assays are summarized. This harmonization effort allowed to ensure that all Belgian laboratories would report positive PCR results in the same semi-quantitative manner to clinicians and to the national database which feeds contact tracing interventions.

Influence of diabetes and hypercholesterolemia on laboratory methods for hereditary spherocytosis diagnosis.

INTRODUCTION: Hereditary spherocytosis (HS) is characterized by decreased erythrocyte deformability resulting in hemolytic anemia. This is a heterogeneous disease regarding underlying protein deficiency, disease severity, age at diagnosis and clinical course. Although largely considered as pediatric disease, HS could be initially diagnosed also in elder patients as a result of gallstones or splenomegaly fortuitous finding. Concurrently, common adulthood metabolic disorders like diabetes or dyslipidemia are also known to impair RBC rheology and deformability. Therefore, we aimed to investigate if these diseases affect the screening and diagnostic tools used for HS diagnosis. METHODS: We applied our workflow for HS diagnosis on 95 pathological samples: 29 patients with diabetes, 20 with hypercholesterolemia, 17 with dyslipidemia, 6 with hypertriglyceridemia, 23 with metabolic syndrome (MS). Thus, a total of 73 samples were analyzed by automated reticulocyte analysis, 52 by cryohemolysis test, and 41 by ektacytometry osmoscan analysis as we used two out of the three tests for each individual sample. RESULTS: Applying our screening algorithm based on automated reticulocyte indices, a total of 4 samples (4.2%): one sample (5%) from the diabetes group and three samples (16.7%) from the MS group, positioned into the HS zone. However, no significant difference was found between any of the pathological groups and the controls for the cryohemolysis test or the osmoscan. CONCLUSION: While diabetes and hypercholesterolemia are pathologic conditions known to present with decreased erythrocyte deformability and disturbed rheology, their possible concomitant presence with HS would not interfere with the screening and confirmatory laboratory methods.

Risk Factors for Surgery in Pediatric Patients with Crohn's Disease.

OBJECTIVE: Pediatric Crohn's disease (CD) has a more aggressive phenotype and course than in adults. Many patients develop complications that require surgery. The aim of this study was to identify the factors associated with increased risk for surgical intervention in pediatric patients with CD. SUBJECTS AND METHODS: This study is a retrospective review of medical records. We analyzed the following variables: sex, age at diagnosis, presenting symptoms, duration of symptoms before diagnosis, disease location and severity, the presence of extraintestinal manifestations, and the presence of anti-Saccharomyces cerevisiae antibodies. Univariate analysis using the Mann-Whitney test and Fisher's exact test was performed to detect the factors associated with surgery. Potential risk factors with p < 0.05 were further analyzed using a multivariate binary logistic regression model. RESULTS: Fifty-seven patients (27 girls and 30 boys) were included in the analysis. More than one-fourth of them (28.1%) required surgical management. Female sex (p = 0.043), disease behavior (p = 0.012), and the presence of perianal disease at diagnosis (p < 0.001) were the variables associated with surgical intervention. Stricturing disease (B2) (odds ratio [OR], 24.944; p = 0.016), stricturing and penetrating disease (B2B3) (OR, 28.276; p = 0.011), and the presence of perianal disease at diagnosis (OR, 95.802; p = 0.001) were independent risk factors for surgery. Female sex was associated with surgery without being an independent risk factor. CONCLUSION: Females with B2 or B2B3 or the presence of perianal disease at diagnosis are at a higher risk for surgery and should be considered for more aggressive medical treatments.

The role of SAF-A/hnRNP U in regulating chromatin structure.

Scaffold attachment factor A (SAF-A) or hnRNP U is a nuclear RNA-binding protein with a well-documented role in processing newly transcribed RNA. Recent studies also indicate that SAF-A can oligomerise in an ATP-dependent manner and interact with RNA to form a dynamic nuclear mesh. This mesh is thought to regulate nuclear and chromatin architecture, yet a mechanistic understanding is lacking. Here, we review developments in the field to understand how the SAF-A/RNA mesh affects chromatin organisation in interphase and mitosis. As SAF-A has an intrinsically disordered domain we discuss how the chromatin mesh is related to nuclear phase-separated condensates, which in other situations have been shown to regulate transcription and cell functions. Finally, we infer possible links between diseases emerging from SAF-A mutations and its role in chromatin organisation and regulation.

A Web Based Tool to Support a Personalized Therapeutic Path Through the Use of Psychological Tests.

Psychology tests are tools used to evaluate specific aspects of individual psyche and behavior, in clinical practice and for research purposes. They are validated and standardized both in the administration procedures and interpretation of results. Nowadays, most of these tests are questionnaires administered to patients on paper support. The patient's answers to the questionnaires constitute a basis for self-presentation and self-awareness at the beginning of the therapeutic path. The computer is a valuable aid allowing a quickly consultation of all the answers and highlighting the most salient ones. The main aim of this work was to design, develop and test a computerized support tool for the interpretation of psychological tests that allow good interaction between groups of therapists sharing the same operating modes. The developed system allows: first the storing of the numerical values corresponding to the answers to the questionnaires of the patients; then it creates a complete 'Picture' of the patient and allows the automatic computation of the correlation between the indexes of the various scales. The graphical correlations between scales can be also a valuable aid in finding the outliers, so patients far away from the trend line.

A brief performance evaluation and literature review of Abbott ID Now COVID-19 rapid molecular-based test.

The qualitative ID Now COVID-19 assay combines claimed performance and ease of use that seem to position it as a reliable test for urgent patient management. However, the declared limit of detection (LOD) of 125 genome equivalents/mL is not confirmed by the published studies, which observed a range of LOD varying from 276 to 20.000 copies/mL. We decided to establish the LOD value on more robust basis using serial dilutions of a SARS-CoV-2 culture supernatant sample of defined concentration. Afterwards, we tested the analytical performances of the assay with 23 QCMD external quality control measurements. Hence, taking into consideration the additional dilution in the sample receiver cup, we found a lower 95 % LOD of 64 copies/mL. For its intended use and with the new established LOD, ID Now COVID-19 proved to be a suitable test for the diagnosis of COVID-19 in contagious patients, as proposed by the latest Belgian recommendations.

Integrating an Electronic Health Record System into a Regional Health Information System: An HL7 FHIR Architecture.

This paper presents an architecture which has been developed in order to integrate a routinely used cardiologic EHR system into the health information infrastructure system of the region where the EHR is used. A Service Oriented Approach based on HL7 and FHIR was used, achieving interoperability, security and confidentiality at all levels. The system has been used for about a year and has brought about significant improvements in the provision of care.

Parameter-free molecular super-structures quantification in single-molecule localization microscopy.

Understanding biological function requires the identification and characterization of complex patterns of molecules. Single-molecule localization microscopy (SMLM) can quantitatively measure molecular components and interactions at resolutions far beyond the diffraction limit, but this information is only useful if these patterns can be quantified and interpreted. We provide a new approach for the analysis of SMLM data that develops the concept of structures and super-structures formed by interconnected elements, such as smaller protein clusters. Using a formal framework and a parameter-free algorithm, (super-)structures formed from smaller components are found to be abundant in classes of nuclear proteins, such as heterogeneous nuclear ribonucleoprotein particles (hnRNPs), but are absent from ceramides located in the plasma membrane. We suggest that mesoscopic structures formed by interconnected protein clusters are common within the nucleus and have an important role in the organization and function of the genome. Our algorithm, SuperStructure, can be used to analyze and explore complex SMLM data and extract functionally relevant information.

Reuse of Clinical COVID-19 Patient Data: Pre-Processing for Future Classification.

One of the most important challenges in the scenario of COVID-19 is to design and develop decision support systems that can help medical staff to identify a cohort of patients that is more likely to have worse clinical evolution. To achieve this objective it is necessary to work on collected data, pre-process them in order to obtain a consistent dataset and then extract the most relevant features with advanced statistical methods like principal component analysis. As preliminary results of this research, very influential features that emerged are the presence of cardiac and liver illnesses and the levels of some inflammatory parameters at the moment of diagnosis.

Next-generation osmotic gradient ektacytometry for the diagnosis of hereditary spherocytosis: interlaboratory method validation and experience.

BACKGROUND: Osmotic gradient ektacytometry is part of the laboratory diagnosis process of hereditary spherocytosis (HS) and other red blood cell (RBC) membrane disorders. We here present the experience of two independent institutions with a next-generation ektacytometer, the LoRRca MaxSis analyzer, in HS diagnostic settings. METHODS: Inter- and intra-assay variability and sample stability were analyzed. Samples from patients with HS (n=40), probable HS (n=21), auto-immune hemolytic anemia (n=7), and other pathologies (n=37) were studied. Daily controls were run in parallel with patient samples. Results were expressed as percent of change compared to mean of controls. RESULTS: Analytical performances showed an inter-assay variability between 0.2% and 3%. Samples were stable for 48-72 h depending of temperature storage and anticoagulant used. The following diagnostic cut-offs were established for HS: an increase of more than 21.5% for the osmolality point at the minimal elongation index (O min), a decrease of more than 8.5% for the maximal elongation index (EI max), and a decreased area under the curve (AUC) of more than 18.5% compared to the mean of controls. CONCLUSIONS: As the previous instrument, the next-generation ektacytometer is an efficient tool for laboratory diagnosis of HS. Sample stability and standardized reporting of results allow inter-laboratory exchange and comparison. The most useful parameters for HS diagnosis were AUC, EI max, and O min; unfortunately, this method does not differentiate between HS and auto-immune hemolytic anemia (AIHA), but it distinguishes HS from other hereditary membrane pathologies. It can thus be considered as an intermediate step between screening and diagnostic tests.

Automated reticulocyte parameters for hereditary spherocytosis screening.

The laboratory diagnosis of hereditary spherocytosis (HS) is based on several screening and confirmatory tests; our algorithm includes clinical features, red blood cell morphology analysis and cryohaemolysis test, and, in case of positive screening, sodium dodecyl sulphate polyacrylamide gel electrophoresis as a diagnostic test. Using the UniCel DxH800 (Beckman Coulter) haematology analyser, we investigated automated reticulocyte parameters as HS screening tool, i.e. mean reticulocyte volume (MRV), immature reticulocyte fraction (IRF) and mean sphered cell volume (MSCV). A total of 410 samples were screened. Gel electrophoresis was applied to 159 samples that were positive for the screening tests. A total of 48 patients were diagnosed as HS, and seven were diagnosed as acquired autoimmune haemolytic anaemia (AIHA). Some other 31 anaemic conditions were also studied. From the receiver operating characteristic (ROC) curve analysis, both delta (mean cell volume (MCV)-MSCV) and MRV presented an area under the curve (AUC) of 0.98. At the diagnostic cut-off of 100 % sensitivity, MRV showed the best specificity of 88 % and a positive likelihood ratio of 8.7. The parameters IRF, MRV and MSCV discriminated HS not only from controls and other tested pathologies but also from AIHA contrary to the cryohaemolysis test. In conclusion, automated reticulocyte parameters might be helpful for haemolytic anaemia diagnostic orientation even for general laboratories. In combination with cryohaemolysis, they ensure an effective and time-saving screening for HS for more specialised laboratories.

Two-decade trends in primary Helicobacter pylori resistance to antibiotics in Bulgaria.

Evaluating long-term trends in antibiotic resistance can predict earlier the short-term changes in resistance patterns. The aim of the present study was to compare primary resistance rates in 501 Helicobacter pylori strains in 2007 to 2009 to those in 1990 to 1995 (179 strains) and the antibiotic MICs to detect the 20-year resistance evolution. In 2007 to 2009, strains from children exhibited lower resistance rates to metronidazole (16.4%) and ciprofloxacin (2.7%) than those from adults (27.3% and 10.3%, respectively). In 2008 to 2009, more children (29.3%) harbored clarithromycin-resistant strains compared to the adults (17.4%). Overall clarithromycin resistance rate (19.4%) in 2007 to 2009 was much higher than that in 1990 to 1995 (6.2%). MIC(90) of erythromycin in 1990 to 1995 was 142.2-fold lower than that of clarithromycin in 2007 to 2009. Clarithromycin MIC(90) increased >42-fold since 2001 to 2004. Quinolone resistance rate increased 7.7-fold, being 9.2% in 2007 to 2009 versus 1.2% in 1990 to 1995, with a 5-fold increase in MIC(90). Conversely, the amoxicillin resistance decreased from 3.2% in 1996 to 1999 to 0.4% in 2007 to 2009. The MIC(90)'s of tetracycline remained stable but MIC(50)'s of both metronidazole and tetracycline before 1996 decreased about 4-fold to 2007 to 2009. In conclusion, associations between the resistance evolution and patients' age groups as well as the national outpatient antibiotic use have been found. H. pylori resistance to antibiotics showed many long-term changes, with a more rapid evolution for clarithromycin than for the other antibiotics. Metronidazole and tetracycline did not show a resistance evolution but exhibited a decrease in MIC(50) since 1990. The significant increase in ciprofloxacin resistance was found only by extending the study period to 20 years.

Helicobacter pylori and Helicobacter heilmannii in untreated Bulgarian children over a period of 10 years.

The aims of the study were to evaluate the incidence of Helicobacter pylori and Helicobacter heilmannii in untreated Bulgarian children from 1996 to 2006, to analyse the performance of diagnostic tests, and to look at H. pylori density in specimens by culture. Antral specimens from children with chronic gastritis (n=513), peptic ulcers (n=54) and other diseases (n=91) were evaluated by direct Gram staining (DGS), in-house rapid urease test (RUT) and culture. The living environment and semi-quantitative H. pylori density were assessed in 188 and 328 children, respectively. H. pylori infection was found in children with ulcers (77.8 %), chronic gastritis (64.5 %) and other diseases (36.3 %). Half (51.4 %) of patients aged 1-5 years and 77.4 % of those aged 16-17 years were H. pylori-positive. Of all children, 328 (49.8 %) showed positive DGS, 184 (28 %) had a positive RUT, and 386 (58.7 %) were culture-positive. Unlike gastric mucus specimens, frozen biopsy specimens provided reliable diagnosis. H. heilmannii was observed in two (0.3 %) children. High H. pylori density (growth into all quadrants of plates) was found in 18 % of 328 children evaluated, involving 31 % of ulcer and 16.7 % of non-ulcer patients. H. pylori infection was more common in rural children with chronic gastritis (91.3 %) than in the remainder (66.7 %). In conclusion, H. pylori infection was common in symptomatic Bulgarian children. The infection prevalence was >77 % in patients aged 16-17 years, in children with a duodenal ulcer, and in rural patients. H. heilmannii infection was uncommon. The performance of the bacterial culture was good. The impact of H. pylori density on the clinical expression and eradication of the infection requires further evaluation. The results highlight the need for routine H. pylori diagnosis in rural children with chronic gastritis.

An alternative pathway of NF-kappaB activation results in maturation and T cell priming activity of dendritic cells overexpressing a mutated IkappaBalpha.

Maturation of dendritic cells (DC) is a critical step in the induction of T cell responses and depends on the activation of NF-kappaB transcription factors. Therefore, inhibition of NF-kappaB activation has been proposed as a strategy to maintain DC in an immature stage and to promote immune tolerance. Herein, we generated murine myeloid DC expressing a mutated IkappaBalpha acting as a superrepressor of the classical NF-kappaB pathway (s-rIkappaB DC) to investigate the consequences of NF-kappaB inhibition on the ability of DC to prime T cell responses. Upon in vitro LPS activation, maturation of s-rIkappaB DC was profoundly impaired as indicated by defective up-regulation of MHC class II and costimulatory molecules and reduced secretion of IL-12 p70 and TNF-alpha. In contrast, after injection, s-rIkappaB DC had the same capacity as control DC to migrate to draining lymph node and to induce Th1- and Th2-type cytokine production in a MHC class II-incompatible host mice. Likewise, s-rIkappaB DC pulsed with OVA were as efficient as control DC to induce Ag-specific T cell responses in vivo. Indeed, further in vitro experiments established that s-rIkappaB DC undergo efficient maturation upon prolonged contact with activated T cells via the alternative pathway of NF-kappaB activation triggered at least partly by lymphotoxin beta receptor ligation and involving processing of p100/RelB complexes.

Antibacterial resistance in Helicobacter pylori strains isolated from Bulgarian children and adult patients over 9 years.

The aim of this study was to evaluate the primary, combined and post-treatment antibacterial resistance rates in 1205 Helicobacter pylori strains from non-treated (786 adults, 282 children) and treated (109 adults, 28 children) patients in Bulgaria. Susceptibility was tested by the limited agar dilution method. Overall primary resistance rates to metronidazole, clarithromycin, amoxicillin, tetracycline and both metronidazole and clarithromycin were respectively 15.0, 12.5, 1.5, 3.4 and 4.7% in children and 25.6, 12.6, 0.8, 5.2 and 4.9% in adults. Primary metronidazole resistance in adults was more common than in children, but the differences for other agents tested were not significant. Primary resistance rates were in the range of those reported worldwide. There was no significant increase in primary resistance rates from 1996/1999 to 2003/2004; however, clarithromycin resistance rates exhibited a slight tendency to increase. Post-treatment resistance to amoxicillin was detected in 1.6% of 63 strains. Post-treatment resistance to metronidazole was common (81.6%) and that to clarithromycin was considerable (36%). Alarming emergence of strains with triple resistance to amoxicillin, metronidazole and clarithromycin was found in two non-treated and three treated patients. The results motivate a larger and continuing surveillance of H. pylori resistance in Bulgaria and worldwide.

Activity of Bulgarian propolis against 94 Helicobacter pylori strains in vitro by agar-well diffusion, agar dilution and disc diffusion methods.

Propolis exhibits antimicrobial, anti-inflammatory and other biological effects. The aim of this study was to evaluate the activity of 30 % ethanolic extract of Bulgarian propolis against 94 Helicobacter pylori strains by three methods. By the agar-well diffusion method, only 13.8 % of the strains exhibited no inhibition by 30 microl propolis extract (containing 9 mg propolis) and all isolates were inhibited to some extent by 90 microl of the extract (27 mg propolis) per well. The mean diameters of growth inhibition by 30, 60 or 90 microl propolis extract or 30 microl 96 % ethanol per well were 16.8, 19.2, 27.5 and 8.3 mm, respectively. The propolis extract was more active than the ethanol (P < 0.001). With 90 microl propolis extract per well, 69.4 % of the strains exhibited large diameters of growth inhibition (> or =20 mm) versus 26.6 % with 30 mul per well (P < 0.001). With moist propolis discs, inhibition was detected in more strains (92.1 %) than with dried discs (78.2 %, P < 0.05), with mean inhibitory diameters of 18.7 and 13.8 mm, respectively. By the agar dilution method, 100 and 300 microg propolis ml(-1) inhibited the growth of 57.1 % and 76.2 %, respectively, of the 21 strains tested. In conclusion, Bulgarian propolis had a strong and dose-dependent activity against most of the H. pylori strains tested. Although the effect of propolis on H. pylori in vitro is promising, further microbiological, pharmacological and clinical trials are required.

Risk factors for primary Helicobacter pylori resistance in Bulgarian children.

Risk factors for primary Helicobacter pylori resistance in 186 children with gastroduodenal diseases (44 from villages/small towns and 130 from large towns/cities) in 2000-2003 were tested. Susceptibility was tested by a limited agar dilution method. Overall resistance rates to metronidazole, clarithromycin, tetracycline and both metronidazole and clarithromycin were 14.5, 11.9, 3.3 and 4.3 %, respectively. No amoxycillin resistance was observed. Tetracycline resistance was found in six children aged 7-18 years. Clarithromycin resistance was more common in children from small towns/villages (22.7 %) than in those from large towns/cities (8.5 %, P < 0.05). There were no significant differences (P > 0.05) in resistance rates between children from northern Bulgaria and those from southern regions. Resistance rates in duodenal ulcer patients and other children were, respectively, 10.5 and 15 % (P > 0.20) for metronidazole and 10.5 and 12 % (P > 0.20) for clarithromycin. No combined resistance to metronidazole and clarithromycin was found in 22 children aged 1-7 years and in 34 children living in northern Bulgaria. There were no significant associations of resistance with sex and age group (1-7- versus 8-18-year-old children) for all antibacterial agents tested. In conclusion, primary H. pylori resistance was absent (for metronidazole + clarithromycin) or low (4.5 % for clarithromycin) in children aged 1-7 years. Place of residence was associated with clarithromycin resistance rates.

Helicobacter pylori and Helicobacter heilmannii in children. A Bulgarian study.

The aim of the study was to evaluate the prevalence of Helicobacter pylori and Helicobacter heilmannii among 321 children. Gram staining, urease test and culture were performed. Of all patients, 52.6% were H. pylori positive and 0.3% were H. heilmannii positive. H. pylori infection was associated with chronic gastritis in 57.1%, with duodenal ulcer in 75% and with non-ulcer dyspepsia in 25.6%. This infection was more frequent in children aged 11-18 years than in younger patients. Rapid urease test, culture and direct Gram staining showed 42.3, 96.5 and 78.2% sensitivity and 93.2, 100 and 84.6% specificity, respectively. H. pylori was detected in 60.2% of fresh versus 52.8% of frozen specimens and in 64.8% in gastric biopsy versus 25% in gastric mucus specimens. H. pylori growth was detected after nine to 10 days in 6.2% and after 11 days in 1.2%. Culture exhibited the best accuracy of the three diagnostic methods. Frozen biopsy specimens gave reliable H. pylori detection unlike gastric mucus specimens. Eleven days of incubation for H. pylori is recommended. The study confirms an early acquisition of H. pylori infection in Bulgaria. The incidence of H. heilmannii infection in childhood is uncommon but clinically important.