Severity of COVID-19 among Hospitalized Patients: Omicron Remains a Severe Threat for Immunocompromised Hosts.

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the general population in the context of a relatively high immunity gained through the early waves of coronavirus disease 19 (COVID-19), and vaccination campaigns. Despite this context, a significant number of patients were hospitalized, and identifying the risk factors associated with severe disease in the Omicron era is critical for targeting further preventive, and curative interventions. We retrospectively analyzed the individual medical records of 1501 SARS-CoV-2 positive hospitalized patients between 13 December 2021, and 13 February 2022, in Belgium, of which 187 (12.5%) were infected with Delta, and 1036 (69.0%) with Omicron. Unvaccinated adults showed an increased risk of moderate/severe/critical/fatal COVID-19 (crude OR 1.54; 95% CI 1.09-2.16) compared to vaccinated patients, whether infected with Omicron or Delta. In adults infected with Omicron and moderate/severe/critical/fatal COVID-19 (n = 323), immunocompromised patients showed an increased risk of in-hospital mortality related to COVID-19 (adjusted OR 2.42; 95% CI 1.39-4.22), compared to non-immunocompromised patients. The upcoming impact of the pandemic will be defined by evolving viral variants, and the immune system status of the population. The observations support that, in the context of an intrinsically less virulent variant, vaccination and underlying patient immunity remain the main drivers of severe disease.

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.

Viral Evolution and Immunology of SARS-CoV-2 in a Persistent Infection after Treatment with Rituximab.

BACKGROUND: Prolonged shedding of SARS-CoV-2 in immunocompromised patients has been described. Furthermore, an accumulation of mutations of the SARS-CoV-2 genome in these patients has been observed. METHODS: We describe the viral evolution, immunologic response and clinical course of a patient with a lymphoma in complete remission who had received therapy with rituximab and remained SARS-CoV-2 RT-qPCR positive for 161 days. RESULTS: The patient remained hospitalised for 10 days, after which he fully recovered and remained asymptomatic. A progressive increase in Ct-value, coinciding with a progressive rise in lymphocyte count, was seen from day 137 onward. Culture of a nasopharyngeal swab on day 67 showed growth of SARS-CoV-2. Whole genome sequencing (WGS) demonstrated that the virus belonged to the wildtype SARS-CoV-2 clade 20B/GR, but rapidly accumulated a high number of mutations as well as deletions in the N-terminal domain of its spike protein. CONCLUSION: SARS-CoV-2 persistence in immunocompromised individuals has important clinical implications, but halting immunosuppressive therapy might result in a favourable clinical course. The long-term shedding of viable virus necessitates customized infection prevention measures in these individuals. The observed accelerated accumulation of mutations of the SARS-CoV-2 genome in these patients might facilitate the origin of new VOCs that might subsequently spread in the general community.

Evaluation of the SARS-CoV-2 positivity ratio and upper respiratory tract viral load among asymptomatic individuals screened before hospitalization or surgery in Flanders, Belgium.

INTRODUCTION: The incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in the Belgian community is mainly estimated based on test results of patients with coronavirus disease (COVID-19)-like symptoms. The aim of this study was to investigate the evolution of the SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) positivity ratio and distribution of viral loads within a cohort of asymptomatic patients screened prior hospitalization or surgery, stratified by age category. MATERIALS/METHODS: We retrospectively studied data on SARS-CoV-2 real-time RT-PCR detection in respiratory tract samples of asymptomatic patients screened pre-hospitalization or pre-surgery in nine Belgian hospitals located in Flanders over a 12-month period (1 April 2020-31 March 2021). RESULTS: In total, 255925 SARS-CoV-2 RT-PCR test results and 2421 positive results for which a viral load was reported, were included in this study. An unweighted overall SARS-CoV-2 real-time RT-PCR positivity ratio of 1.27% was observed with strong spatiotemporal differences. SARS-CoV-2 circulated predominantly in 80+ year old individuals across all time periods except between the first and second COVID-19 wave and in 20-30 year old individuals before the second COVID-19 wave. In contrast to the first wave, a significantly higher positivity ratio was observed for the 20-40 age group in addition to the 80+ age group compared to the other age groups during the second wave. The median viral load follows a similar temporal evolution as the positivity rate with an increase ahead of the second wave and highest viral loads observed for 80+ year old individuals. CONCLUSION: There was a high SARS-CoV-2 circulation among asymptomatic patients with a predominance and highest viral loads observed in the elderly. Moreover, ahead of the second COVID-19 wave an increase in median viral load was noted with the highest overall positivity ratio observed in 20-30 year old individuals, indicating they could have been the hidden drivers of this wave.

SARS-CoV-2 seroprevalence survey among health care providers in a Belgian public multiple-site hospital.

Although the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is lasting for more than 1 year, the exposition risks of health-care providers are still unclear. Available evidence is conflicting. We investigated the prevalence of antibodies against SARS-CoV-2 in the staff of a large public hospital with multiple sites in the Antwerp region of Belgium. Risk factors for infection were identified by means of a questionnaire and human resource data. We performed hospital-wide serology tests in the weeks following the first epidemic wave (16 March to the end of May 2020) and combined the results with the answers from an individual questionnaire. Overall seroprevalence was 7.6%. We found higher seroprevalences in nurses [10.0%; 95% confidence interval (CI) 8.9-11.2] than in physicians 6.4% (95% CI 4.6-8.7), paramedical 6.0% (95% CI 4.3-8.0) and administrative staff (2.9%; 95% CI 1.8-4.5). Staff who indicated contact with a confirmed coronavirus disease 2019 (COVID-19) colleague had a higher seroprevalence (12.0%; 95% CI 10.7-13.4) than staff who did not (4.2%; 95% CI 3.5-5.0). The same findings were present for contacts in the private setting. Working in general COVID-19 wards, but not in emergency departments or intensive care units, was also a significant risk factor. Since our analysis points in the direction of active SARS-CoV-2 transmission within hospitals, we argue for implementing a stringent hospital-wide testing and contact-tracing policy with special attention to the health care workers employed in general COVID-19 departments. Additional studies are needed to establish the transmission dynamics.

Use of Next-Generation Sequencing for Diagnosis of West Nile Virus Infection in Patient Returning to Belgium from Hungary.

An elderly patient in Belgium who became critically ill after returning from Hungary was tested for pathogens using routine diagnostic tests. All results were negative. However, using next-generation sequencing on a cultured respiratory sample, laboratorians detected a complete West Nile virus genome, similar to strains isolated in southeastern Europe.

A retrospective observational study on the efficacy of colistin by inhalation as compared to parenteral administration for the treatment of nosocomial pneumonia associated with multidrug-resistant Pseudomonas aeruginosa.

BACKGROUND: Colistin is used as last treatment option for pneumonia associated with multidrug-resistant (MDR) Pseudomonas spp.. Literature about the best administration mode (inhalation versus parenteral treatment) is lacking. METHODS: A retrospective study of 20 intensive care patients with a pneumonia associated with MDR P. aeruginosa receiving colistin sulphomethate sodium (Colistineb®) between 2007 and 2009 was performed. A strain was considered multidrug-resistant if it was resistant to at least 6 of the following antibiotics: piperacillin-tazobactam, ceftazidime, cefepime, meropenem, aztreonam, ciprofloxacin, and amikacin. The administration mode, predicted mortality based on the SAPS3 score, SOFA score at onset of the colistin treatment, clinical and microbiological response, and mortality during the episode of the infection were analysed. The non parametric Kruskal-Wallis and Fisher's Exact test were used for statistical analysis of respectively the predicted mortality/SOFA score and mortality rate. RESULTS: Six patients received colistin by inhalation only, 5 were treated only parenterally, and 9 by a combination of both administration modes. All patients received concomitant beta-lactam therapy. The mean predicted mortalities were respectively 72%, 68%, and 69% (p = 0.91). SOFA scores at the onset of the treatment were also comparable (p = 0.87). Clinical response was favorable in all patients receiving colistin by inhalation (6/6) and in 40% (2/5) of the patients receiving colistin parenterally (p = 0.06). In the patients with colistin administered both via inhalation and parenterally, clinical response was favorable in 78% of the patients (7/9) (p = 0.27 as compared to the treatment group receiving colistin only parenterally). When all patients with inhalation therapy were compared to the group without inhalation therapy, a favorable clinical response was present in respectively 87% and 40% (p = 0.06). In none of the patients, the Pseudomonas spp. was eradicated from the follow-up cultures.All patients in the parenterally treated group died. None of the patients receiving colistin by inhalation, and 3 of 9 patients of the combination group eventually died (p = 0.002 and p = 0.03 respectively as compared to the group receiving colistin only parenterally). CONCLUSIONS: Aerosolized colistin could be beneficial as adjunctive treatment for the management of pneumonia due to MDR P. aeruginosa.

Comparison of Vitek identification and antifungal susceptibility testing methods to DNA sequencing and Sensititre YeastOne antifungal testing.

The colorimetric Vitek 2 YST card and the yeast susceptibility test (AST-YS01) were evaluated for their identification efficacy and their use in assessing the in vitro susceptibility of Candida spp. to fluconazole, voriconazole and amphotericin B. Ninety-one percent or 62 of 68 Candida isolates from blood specimens were correctly identified, as compared to determinations of the ITS2 fragment length. The overall essential agreements between Vitek 2 and the Sensititre YeastOne (SYO) colorimetric method were 78.4%, 84.6% and 90.8%, for fluconazole, voriconazole and amphotericin B, respectively. The overall categorical agreements between Vitek 2 and SYO for fluconazole and voriconazole were 76.9% and 96.9%, respectively. The poorest agreement between Vitek 2 and SYO was seen with C. glabrata (n = 27), particularly for fluconazole. The MIC values of 2 C. glabrata strains (3%) could not be determined with the Vitek 2 due to an insufficient growth in the control well. For other Candida species (n = 38) Vitek 2 and SYO showed acceptable agreements.

Central nervous system invasion by community-acquired meticillin-resistant Staphylococcus aureus.

We report a case of community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) bacteraemia with cavernous sinus thrombosis, meningitis and brain abscess in a previously healthy American, who was employed in Belgium. We consecutively reviewed all published cases of CA-MRSA with central nervous system (CNS) involvement. A total of 12 similar cases were found, of which 11 were published in the last 4 years. Predominantly, young previously healthy subjects were affected (median age 28 years). The cases involved brain abscesses (5/12), disseminated disease (4/12), cavernous sinus thrombosis (2/12) and other (1/12). Infection origins were superficial skin infections (5/12), mostly of the face, sinusitis (1/12), otitis media (1/12), other or unknown (5/12). Although, in our review of the literature patients treated with linezolid had a better outcome compared to patients treated with vancomycin, the latter is still the mainstay of therapy for CNS infections associated with MRSA.