‘We compared the miDiagnostics COVID-19 PCR Test in an acute regional Hospital setting to the standard of care Covid-19 testing at the time: GeneXpert SARS-CoV-2, Seegene Allplex Sars-CoV-2 and Aries Sars-CoV-2 assays. Nasopharyngeal swabs were collected from 200 symptomatic and asymptomatic patients. A standard of care swab and a study swab were collected in a randomized fashion. In this pooled analysis, 165 swabs were compared to Seegene, 28 to GeneXpert and 5 to Aries. On a total of 198 paired samples, the miDiagnostics test correctly classified 49 samples as positive and 127 samples as negative when compared to the standard of care method. This resulted in a sensitivity of 90.74% and a specificity of 88.19%. The miDiagnostics COVID-19 PCR Test is a viable diagnostic platform for very fast direct PCR diagnosis of Sars-CoV-2. Further studies are still needed to evaluate the performance in other settings and against other test platforms.’

Background Antimicrobial 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. Aim We aimed to estimate the occurrence of resistant MG in Belgium. Methods Between 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. Results Of 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. Conclusion Although 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.

Objectives Antimicrobial resistance of Mycoplasma genitalium (MG) is a growing concern worldwide. Because reliable data on the burden of resistant MG in Belgium are missing, an additional prospective surveillance program was implemented in 2022 to estimate the real burden of resistant MG in Belgium.Methods Belgian laboratories (n=21) provided frozen remnants of MG positive samples to the National Reference Centre of Sexually Transmitted Infections from July to November 2022. The presence of macrolide and fluoroquinolones resistance associated mutations (RAMs) was assessed using Sanger sequencing of the 23SrRNA and parC gene. Differences in resistance patterns were correlated with surveillance methodology, socio-demographic and behavioral variables via Fisher’s exact test and logistic regression analysis.Results Sequencing for both macrolide and fluoroquinolone RAMs was successful for 232/244 MG positive samples. Over half of the samples were resistant to macrolides (55.2%). All MG in samples from men who have sex with men (MSM) (24/24) were resistant to macrolides. The presence of fluoroquinolone RAMs was estimated to be 26% and did not differ with socio-demographic and sexual behaviour characteristics.Conclusions Given the considerable cost of macrolide resistance testing, our data suggest that the use of macrolide resistance testing in MSM does not seem justified in Belgium. However, the lower prevalence of macrolide resistance in other population groups, combined with further emergence of fluoroquinolone resistance provides evidence for macrolide resistance testing in these groups. Continued surveillance of resistance in MG in all groups will be crucial to guide national testing- and treatment strategies.### Competing Interest StatementThe authors have declared no competing interest.### Funding StatementThe prospective study was financed by the Belgian government.### Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The prospective study has been approved by the Institutional review board of the Institute of Tropical Medicine (ITM) (ref: 1594/22) and the Ethics Committee of the University of Antwerp (ref: 3534).I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesThe data supporting the findings of this publication are retained at the Institute of Tropical Medicine, Antwerp and will not be made openly accessible due to ethical and privacy concerns. According to the ITM research data sharing policy, only fully anonymized data can be shared publicly. The data are de-identified (using a unique patient code) but not fully anonymized and it is not possible to fully anonymize them due to the longitudinal nature of the data. Data can however be made available after approval of a motivated and written request to the ITM at ITMresearchdataaccess{at}itg.be. The ITM data access committee will verify if the dataset is suitable for obtaining the study objective and assure that confidentiality and ethical requirements are in place.

PURPOSE:To evaluate and compare the performance of three commercial culture media, two filamentous fungi libraries, and two different protein extraction procedures in MALDI-TOF MS fungal identification.METHODS:A total of 21 quality control samples were cultured on Sabouraud dextrose agar (SDA), ID fungi plate medium (IDFP), and Sabouraud gentamicin chloramphenicol 2 agar (SGC2). For four consecutive days, fungal growths were inoculated on a MALDI target plate both by using a direct transfer technique (DT) and by using a formic acid-ethanol protein extraction procedure (EEP). The MALDI-TOF MS-generated spectra were identified by the MBT Bruker library and the MSI database.RESULTS:Selective culture media (IDFP and SGC2) significantly outperformed the non-selective SDA medium. IDFP was superior to the SGC2 medium for dermatophyte identification. The EEP only demonstrated a benefit over DT in the underperforming SDA medium. The MBT Bruker library outperformed the MSI database in Aspergillus identification while the MSI database outperformed the MBT library in dermatophyte identification. For non-Aspergillus fungi, the libraries performed comparably.CONCLUSION:The results of our study show the necessity of using selective culture media (IDFP and SGC2) for fungal identification with MALDI-TOF MS and demonstrate no significant benefit of the formic acid-ethanol protein extraction technique in these media. Given the relative strengths and weaknesses of the MBT library and the MSI database, it might currently be beneficial to consider these libraries as complementary and employ both databases to achieve optimal fungal identification.

An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country's genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.

The objective of this study was to compare the performance of the Idylla™ Respiratory (IFV-RSV) panel to the GeneXpert Xpert® Flu/RSV assay and establish the performance of a midturbinate swab compared to nasopharyngeal sampling. Considering GeneXpert® assay as imperfect reference standard, a positive percentage agreement between both assays of 98-100% for influenza A and 96-99% for influenza B could be calculated when 354 nasopharyngeal and 325 midturbinate swabs were retrospectively analyzed. Comparing midturbinate samples to nasopharyngeal specimens of 321 subjects, positive percentage agreement varied from 42% to 94% depending on both target virus and assay used. Negative percentage agreements ranged from 98% to 100% for both methods and sample type comparison. The Idylla™ assay showed excellent performance compared to the GeneXpert® assay for the detection of influenza virus. The study also showed a slightly better performance for nasopharyngeal sampling compared to the use of a midturbinate swab.

Treatment of parapneumonic empyema (PE) consists of intravenous antibiotics and, in case of large effusions and persisting fever, pleural chest drain (±intrapleural fibrinolytics) or video-assisted surgical intervention. We standardized the treatment for PE in our tertiary care center choosing a first-step nonsurgical approach. The aim was to evaluate the need for surgery and to collect data on disease course, outcome, and microbiology. For all children treated for PE between 2006 and 2013, data were prospectively collected concerning treatment, length of stay, duration of fever, complications, and causative agent. Of 132 children treated for PE, 20 % needed surgical intervention. Analyzed per year, the need for surgery decreased from almost 40 % in 2007 to 0 % in 2010 again increasing to 40 % although this did not reach statistical significance (p = 0.115). Median duration of “in-hospital fever” was 5 days (IQR, 3–8). The duration of fever correlated with pleural LDH (r = 0.324; p = 0.002) and pleural glucose (r = −0.248; p = 0.021) and was inversely correlated with pleural pH (r = −0.249; p = 0.046). Based on pleural PCR data, 85 % of PE were caused by Streptococcus pneumoniae (40 % serotype 1). Conclusion: After introduction of a standardized primary medical approach (chest drain ± fibrinolysis) for PE in our institution, the need for surgical rescue interventions overall remained at 20 %, which is higher than in some other reports. Difference in microbiology or disease severity could not be proven.

Treatment of PE consist of intravenous antibiotics and in case of large effusions and persisting fever pleural chest drain (± intra-pleural fibrinolytics) or surgical intervention (VATS). We standardized the treatment for PE in our tertiary care center choosing for a first step non-surgical approach. The aim was to have prospective data on outcome and need for surgery on all children treated between 2006 and 2013 for PE. Definition of PE and treating algorithm have been published (Proesmans, M. and K. De Boeck. Eur J Pediatr 2009; 168: 639-45). Data on median length of stay, duration of fever, complications and need for additional surgical therapy. Additionally, data on the causative infectious agents were studied. Results:132 children were treated for PE. Median duration of ‘in hospital fever’ was 5 days (IQR 3-8) and median hospital stay was 13 days (IQR 8-17). The duration of fever was inversely correlated with pleural pH (r= -0.28; p=0.04) and pleural glucose (r=-0.34; p=0.004). The need for surgery dropped progressively from almost 40% in 2007 to 0% in 2010 again increasing to 40% in 2012. Overall, 20% of children needed surgical intervention. Based on pleural PCR data, 85% of PE were caused by S pneumonia (40% serotype 1). Pneumococcal antigen detection had a positive predictive value of 98% with a negative predictive value of 56%. Conclusion: Since 2006 all children with PE are strictly treated according to a standardized approach and outcome is registered prospectively. After an initial drop in the need for surgical intervention, the need for surgical rescue interventions increased again. This may be due to change in serotypes or disease severity.