Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants.

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.

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.

Two fatal autochthonous cases of airport malaria, Belgium, 2020.

We report an outbreak investigation of two fatal cases of autochthonous Plasmodium falciparum malaria that occurred in Belgium in September 2020. Various hypotheses of the potential source of infection were investigated. The most likely route of transmission was through an infectious exotic Anopheles mosquito that was imported via the international airport of Brussels or the military airport Melsbroek and infected the cases who lived at 5 km from the airports. Based on genomic analysis of the parasites collected from the two cases, the most likely origin of the Plasmodium was Gabon or Cameroon. Further, the parasites collected from the two Belgian patients were identical by descent, which supports the assumption that the two infections originated from the bite of the same mosquito, during interrupted feeding. Although airport malaria remains a rare event, it has significant implications, particularly for the patient, as delayed or missed diagnosis of the cause of illness often results in complications and mortality. Therefore, to prevent such severe or fatal outcomes, we suggest a number of public health actions including increased awareness among health practitioners, especially those working in the vicinity of airports, and increased surveillance of exotic mosquito species at airports.

Increasing usage of chlorhexidine in health care settings: blessing or curse? A narrative review of the risk of chlorhexidine resistance and the implications for infection prevention and control.

Chlorhexidine digluconate (CHG) is an antiseptic frequently used in hospitals to prevent healthcare-related infections. It is used in different formulations for skin antisepsis, oral care, patient bathing, and hand hygiene. Also, CHG impregnated vascular catheters and wound dressings contribute to increased exposure of hospital germs to this biocide. In the last decade, concerns are rising about decreasing susceptibility of microorganisms to CHG and its potential cross-resistance with antibiotics. This study reviewed the published data regarding the evidence of reduced CHG susceptibility, the cross-resistance with antibiotics, and the implications for infection control for S. aureus, coagulase-negative staphylococci, E. coli, K. pneumoniae, and P. aeruginosa. Despite incongruity in definitions of "resistance," increased CHG minimal inhibitory values of these pathogens have been described, and different mutations encoding for CHG efflux pumps have been identified. Clinical relevance of species with reduced susceptibility to CHG is debatable and cross-resistance with antibiotics remains controversial. However, some studies link the increased usage of CHG to multidrug resistance, and the potential cross-resistance with colistin for K. pneumoniae is of major concern. More research in this matter is necessary. For infection control, it is advisable to use CHG applications only for indications with a clear patient benefit. It is important to follow manufacturer's instructions, and exposure of microorganisms to sub-lethal CHG concentrations should be avoided.

Molecular detection of Helicobacter pylori and clarithromycin resistance in gastric biopsies: a prospective evaluation of RIDA®GENE Helicobacter pylori assay.

Background: Empirical treatment of Helicobacter pylori (HP) depends on the local prevalence of clarithromycin resistance but data are lacking and culturing of HP is time-consuming. We evaluated RIDA®GENE Helicobacter pylori assay (r-biopharm), a quantitative PCR assay for detecting HP and clarithromycin resistance mutations in gastric biopsies.Material/methods: Gastric biopsies were obtained from each of 436 consecutive patients referred for gastroscopic investigation and results of qPCR were compared to culture and immunohistochemical staining (IHCS).Results: Of 436 samples, 47 were positive for HP by PCR (11%), 42 by culture (9.7%) and 44 by IHCS (10%). Compared to culture, sensitivity and specificity of the qPCR were 100% and 99%, respectively, and 96% and 99% compared to IHCS. The sensitivity and specificity for clarithromycin resistance detection were 92% and 97%, respectively.Conclusions: RIDA®GENE Helicobacter pylori assay reliably and rapidly detects HP and its resistance to clarithromycin in human gastric biopsies.

Performance and potential clinical impact of Alfred60AST (Alifax®) for direct antimicrobial susceptibility testing on positive blood culture bottles.

Rapid pathogen identification (ID) and antimicrobial susceptibility testing (AST) of bacteria-causing bloodstream infections can improve patients' outcome. In this study, we evaluated the performance of Alfred60AST (Alifax) which provides AST directly on positive blood culture (BC) bottles by light scattering. In a selected group of patients with a clinical suspicion of severe sepsis or at risk for infections with multiresistant organisms, we compared Alfred60AST AST results with traditional AST results (Vitek2 (bioMérieux) or disk diffusion). Discrepancy analysis was performed by Etest (bioMérieux) or broth microdilution. In total, 222 samples were evaluated. On 595 susceptibility determinations, 93.4% showed categorical agreement (CA) with the standard method. Eighty-one percent of isolates showed a 100% categorical agreement (CA) which increased to 84.3% after discrepancy analysis. There were 8 very major discrepancies (VMD), 18 major discrepancies (MD), and 13 minor discrepancies (MiD). Most discrepant results were observed for piperacillin-tazobactam (15.6%) and clindamycin (18.9%). Analysis time was 6-6.5 h for a complete Alfred60AST AST result. In addition, we evaluated the behavior of clinicians in adjusting antibiotic therapy according to the routine AST results. In 37% of all patients, antibiotic therapy was altered after reporting of AST result and adjustment was more frequent for Gram-negative than for Gram-positive isolates. With some improvements, Alfred60AST provides accurate and rapid preliminary AST results for organisms causing bloodstream infections and may have at least a potential clinical benefit in about one-third of patients with severe sepsis, by delivering faster results compared with conventional methods.

OPAT: proof of concept in a peripheral Belgian hospital after review of the literature.

Since its introduction in the 1970s in the United States, outpatient parenteral antibiotic/antimicrobial therapy (OPAT) has been adopted internationally for long-term intravenous (IV) treatment of stable infectious diseases. The aim is to provide a safe and successful completion of IV antimicrobial treatment at the ambulatory care center or at home without complications and costs associated with hospitalization. OPAT implementation has been accelerated by progress in vascular access devices, newly available antibiotics, the emphasis on cost-savings, as well as an improved patient comfort and a reduced incidence of health care associated infections with a similar outcome. OPAT utilization is supported by an extensive published experience and guidelines of the British Society of Antimicrobial Chemotherapy and the Infectious Diseases Society of America for adults as well as for children. Despite these recommendations and its widespread adoption, in Belgium OPAT is only fully reimbursed and established for cystic fibrosis patients. Possible explanations for this unpopularity include physician unfamiliarity and a lack of uniform funding arrangements with higher costs for the patient. This article aims to briefly review benefits, risks, indications, financial impact for supporting OPAT in a non-university hospital as standard of care. Our experience with OPAT at the ambulatory care center of our hospital and its subsequent recent introduction in the home setting is discussed.

Highly sensitive assays are mandatory for the differential diagnosis of patients presenting with symptoms of mast cell activation: diagnostic work-up of 38 patients.

Mastocytosis is a heterogeneous disease caused by excessive mast cell (MC) proliferation. Diagnosis of systemic mastocytosis (SM) is based on the presence of major and minor criteria defined by the World Health Organization. Symptoms of MC activation can also occur in patients without SM or without allergic or inflammatory disease. These MC activation syndromes (MCAS) can be divided into primary (monoclonal) MCAS (MMAS) vs. secondary and idiopathic MCAS. In this single center study, the diagnostic work-up of 38 patients with a clinical suspicion of SM and/or with elevated basic tryptase levels is presented. Clinical symptoms, biochemical parameters, results of bone marrow investigation, flow cytometric immunophenotyping, and molecular analysis were retrospectively reviewed. Twenty-three patients were found to have a monoclonal MC disorder of which 19 were diagnosed with SM and 4 with MMAS. In 13/19 SM patients, multifocal MC infiltrates in the bone marrow were found (major criterion), while in 6 the diagnosis was based on the presence of ≥3 minor criteria. Flow cytometric analysis of bone marrow showed CD25 expression of MCs in all patients with SM and MMAS (range: 0.002-0.3% of cells). In bone marrow, the KIT D816V mutation was detected in all SM patients but in only 2 patients with MMAS (range: 0.007-9% mutated cells). Basic tryptase elevation was demonstrated in 16/19 patients with SM but also in 9/19 patients without SM. Our study reveals the heterogeneity of primary MC disorders and the importance of sensitive assays in patients suspected of having SM.