Clinical and molecular epidemiological features of critically ill patients with invasive group A Streptococcus infections: a Belgian multicenter case-series.

BACKGROUND: Recent alerts have highlighted an increase in group A streptococcal (GAS) infections since 2022 in Europe and the United States. Streptococcus pyogenes can cause limited skin or mucosal disease, but can also present as severe invasive disease necessitating critical care. We performed a multicenter retrospective study of patients with GAS infections recently admitted to Belgian intensive care units (ICUs) since January 2022. We describe patient characteristics and investigate the molecular epidemiology of the S. pyogenes strains involved. RESULTS: Between January 2022 and May 2023, a total of 86 cases (56 adults, 30 children) with GAS disease were admitted to critical care in the university hospitals of Leuven, Antwerp and Liège. We noted a strikingly high incidence of severe community-acquired pneumonia (sCAP) (45% of adults, 77% of children) complicated with empyema in 45% and 83% of adult and pediatric cases, respectively. Two-thirds of patients with S. pyogenes pneumonia had viral co-infection, with influenza (13 adults, 5 children) predominating. Other disease presentations included necrotizing fasciitis (23% of adults), other severe skin/soft tissue infections (16% of adults, 13% of children) and ear/nose/throat infections (13% of adults, 13% of children). Cardiogenic shock was frequent (36% of adults, 20% of children). Fifty-six patients (65%) had toxic shock syndrome. Organ support requirements were high and included invasive mechanical ventilation (77% of adults, 50% of children), renal replacement therapy (29% of adults, 3% of children) and extracorporeal membrane oxygenation (20% of adults, 7% of children). Mortality was 21% in adults and 3% in children. Genomic analysis of S. pyogenes strains from 55 out of 86 patients showed a predominance of emm1 strains (73%), with a replacement of the M1global lineage by the toxigenic M1UK lineage (83% of emm1 strains were M1UK). CONCLUSIONS: The recent rise of severe GAS infections (2022-23) is associated with introduction of the M1UK lineage in Belgium, but other factors may be at play-including intense circulation of respiratory viruses and potentially an immune debt after the COVID pandemic. Importantly, critical care physicians should include S. pyogenes as causative pathogen in the differential diagnosis of sCAP.

[Does a rapid antibiotic susceptibility test optimize antibiotic therapy of patients with bacteremia ?] / Un antibiogramme rapide optimise-t-il la prise en charge thérapeutique des patients présentant une bactériémie ?

BACKGROUND: We evaluated the contribution of a rapid antibiotic susceptibility test performed directly from a positive blood culture (PBC), the dRAST™, in the management of patients with bacteremia. METHODS: We retrospectively compared the time from sampling to availability of antibiotic susceptibility test (AST) results («time-to-result¼, TTR) between dRAST™ and classic AST (Vitek®2), in 150 patients with bacteremia. The antibiotic treatment of these 150 patients was classified into three categories (optimal, suboptimal, ineffective) according to the time of availability of AST results. RESULTS: Adaptation of antibiotic treatment to optimal therapy following AST results occurred in 46/100 (46 %) of Gram-negative PBC and in 4/50 (2 %) of Gram-positive HP. TTR was significantly lower with dRAST™ compared with classic AST (29:35 (± 08:48) hours versus 50:55 (± 12:45) hours, p < 0.001). CONCLUSION: For patients with bacteremia requiring adjustment of empirical antibiotic therapy based on AST, dRAST™ could allow a faster administration of optimal therapy.

CONTEXTE: Nous avons évalué la contribution d'un antibiogramme rapide réalisé directement à partir d'une hémoculture positive (HP), le dRAST™, dans la prise en charge des patients présentant une bactériémie. Méthodes: Nous avons comparé, rétrospectivement, le délai entre le prélèvement et la disponibilité des résultats d'antibiogramme («temps-pour-résultats¼, TPR) entre le dRAST™ et l'antibiogramme classique (Vitek®2), auprès de 150 patients présentant une bactériémie. Les antibiothérapies de ces 150 patients ont été classés en trois catégories (optimale, suboptimale, inefficace) en fonction du moment d'obtention des résultats de l'antibiogramme. Résultats : L'adaptation du traitement antibiotique en thérapie optimale suite au résultat de l'antibiogramme est survenue chez 46/100 (46 %) des HP à Gram négatif et chez 4/50 (2 %) des HP à Gram positif. Le TPR était significativement plus faible avec le dRAST™ par rapport à l'antibiogramme classique (29:35 (± 08:48) heures versus 50:55 (± 12:45) heures, p < 0,001). CONCLUSION: Pour les patients avec bactériémie nécessitant une adaptation de l'antibiothérapie empirique basée sur l'antibiogramme, le dRAST™ permettrait une administration plus rapide du traitement optimal.

[Renal manifestations of syphilis]. / Manifestations rénales de la syphilis.

Syphilis is an acquired or congenital systemic pathology, currently on the rise in Europe. The clinical manifestations of syphilis are not very specific and variable over time. In this case report, we describe two renal presentations of syphilis in patients followed in a Pre-Exposure Prophylaxis (PrEP) program for the prevention of HIV infection. The specificity of the renal involvement of syphilis, the diagnostic and the therapeutic management will be discussed in this article.

La syphilis est une pathologie systémique acquise ou congénitale, actuellement en recrudescence en Europe. Les manifestations cliniques de la syphilis sont souvent peu spécifiques et variables au cours du temps. Nous décrivons ici deux présentations rénales de la syphilis survenues chez des patients suivis dans un programme de Pre-Exposure Prophylaxis (PrEP) de prévention contre l'infection VIH. La spécificité de l'atteinte rénale de la syphilis, la mise au point diagnostique et la prise en charge thérapeutique seront discutées dans cet article.

Occurrence of Vibrio spp. in Selected Recreational Water Bodies in Belgium during 2021 Bathing Season.

In recent years, a global increase in the number of reports of human vibriosis involving V. cholerae non-O1/O139 (NOVC) and other Vibrio spp. has been observed. In this context, the Belgian National Reference Center for Vibrio conducted an assessment of the presence of Vibrio spp. in recreational waters. Water sampling was performed monthly in different lakes in Wallonia and Flanders, including the North Sea. The collected water was then filtrated and cultured, and Vibrio spp. was quantified according to the Most Probable Number (MPN). Presumptive colonies were confirmed via MALDI-TOF, and PCR for virulence genes was applied if justified. No Vibrio spp. was found in the analyzed water bodies in Wallonia. However, NOVC was isolated from three different lakes in Flanders and from coastal water. In addition, V. alginolyticus and V. parahaemolyticus were also detected in coastal water. No clear impact of the pH and temperature was observed on Vibrio spp. occurrence. Our study demonstrates the presence of Vibrio spp. in different bathing water bodies, mostly in the north of Belgium, and supports the recommendation to include Vibrio spp. as a water quality indicator for bathing water quality assessment to ensure the safety of water recreational users in Belgium.

Multicenter interlaboratory study of routine systems for the susceptibility testing of temocillin using a challenge panel of multidrug-resistant strains.

Accurate susceptibility result of temocillin (TMO) is important for treating infections caused by multidrug-resistant Enterobacterales. This multicenter study aimed to investigate the performance of routine temocillin testing assays against Enterobacterales challenging strains. Forty-seven selected clinical isolates were blindly analyzed by 12 Belgian laboratories using VITEK® 2 (n = 5) and BD Phoenix™ (n = 3) automated systems, ETEST® gradient strip (n = 3), and disk (3 brands) diffusion method (DD; n = 6) for temocillin susceptibility using standardized methodology. Results were interpreted using EUCAST 2023 criteria and compared to the broth microdilution (BMD; Sensititre™ panel) method used as gold standard. Methods' reproducibility was assessed by testing 3 reference strains in triplicate. A total of 702 organism-drug results were obtained against 33 TMO-susceptible and 14 TMO-resistant isolates. Excluding Proteae species (P. mirabilis and M. morganii), the essential agreement rates were excellent (91.5-100%) for all MIC-based methods. The highest category agreement was achieved by ETEST® (97.5%) followed by VITEK® 2 (93.2%), disk diffusion (91.6%), and BD Phoenix™ (88.5%). BD Phoenix™ and paper disk diffusion overcalled resistance (11.5% and 6.8% of major discrepancies, respectively), while ROSCO tablets diffusion and VITEK® 2 generated higher very major discrepancies (7.1% and 4.2% respectively). Inter-assay reproducibility was unsatisfactory using recommended E. coli ATCC 25922 strain but was excellent with E. coli ATCC 35218 and K. pneumoniae ATCC 700603 strains. This interlaboratory study suggests that routine testing methods provide accurate and reproducible TMO categorization results except for Proteae species.

Clinical Outcomes of Third-Generation Cephalosporin Definitive Therapy for Bloodstream Infections Due to Enterobacterales with Potential AmpC Induction: A Single-Center Retrospective Study.

The recommended therapy for severe infections caused by AmpC-inducible Enterobacterales (AmpC-E) typically involves cefepime or carbapenems. In an era of emerging resistance to these antimicrobials, we aim to assess the impact of third-generation cephalosporins (3GCs) vs. alternative antibiotics on clinical outcomes in bloodstream infections (BSIs) due to AmpC-E. We retrospectively included hospitalized adult patients with BSIs caused by 3GC-susceptible AmpC-E between 2012 and 2022, comparing the outcomes of 3GC and non-3GC definitive therapies. The primary outcome was overall treatment failure (OTF), encompassing 90-day all-cause mortality, 90-day reinfection, and 90-day readmission. Secondary outcomes comprised components of the OTF, in-hospital all-cause mortality, and length-of-stay. Within a total cohort of 353 patients, OTF occurred in 46.5% and 41.5% in the 3GC- and non-3GC-therapy groups, respectively (p = 0.36). The 3GC-therapy group exhibited a longer length-of-stay (38 vs. 21 days, p = 0.0003) and higher in-hospital mortality (23.3% vs. 13.4%, p = 0.019). However, the 90-day mortality, 90-day reinfection, and 90-day readmission were comparable between the therapy groups. Subgroup analyses involving high-risk AmpC-E and 3GC vs. standard-of-care yielded similar conclusions. Overall, our findings suggest that 3GC definitive therapy may not result in poorer clinical outcomes for the treatment of BSIs caused by AmpC-E.

Actinomyces israelii and Fusobacterium nucleatum brain abscess in an immunocompetent patient: case report.

Introduction: Brain abscess is the most common focal infectious neurological injury. Until the nineteenth century this condition was fatal, however the development of neuroimaging for early diagnosis, neurosurgery and antibiotic therapy in the twentieth century has led to new therapeutic strategies decreasing mortality from 50 % in the 1970s to less than 10 % nowadays. In this context we report a case of brain abscess with a dental origin. Case report: A immunocompetent man without any addiction presented to the emergency department with dysarthria and frontal headache at home. The clinical examination was normal. Further investigations revealed a polymicrobial brain abscess as a consequence of an ear, nose or throat (ENT) infection with locoregional extension with a dental starting point involving Actinomyces israelii and Fusobacterium nucleatum . In spite of a rapid diagnosis and a neurosurgical management associated with an optimal treatment by a dual therapy made of ceftriaxone and metronidazole the patient unfortunately died. Conclusion: This case report shows that despite a low incidence and a good prognosis following the diagnosis, brain abscesses can lead to patient's death. Thereby, when the patient's condition and urgency allow, a thorough dental examination of patients with neurological signs following the recommendations would improve the diagnosis made by the clinician. The use of microbiological documentation, the respect of pre-analytical conditions, the interaction between the laboratory and the clinicians are indispensable for an optimal management of these pathologies.

Multicenter Performance Evaluation of the Revogene® GBS DS Real-Time PCR Assay for Group B Streptococcus Detection During Labor.

PURPOSE: This study aimed to evaluate the performance and ease of use of the Revogene® GBS DS PCR assay for the intrapartum detection of Group B Streptococcus (GBS) colonization, as compared with intrapartum culture and antenatal culture-based screening. METHODS: Between April and August 2019, 398 women who gave birth in one of the three maternities participating in this study agreed to the collection of a vaginal swab when they arrived in the labor ward. The samples were immediately sent to the adjacent laboratory where they were discharged into the buffer provided with the Revogene® GBS DS assay. Part of the buffer was used to perform the Revogene® GBS DS test, and part of the same buffer was used for GBS culture. RESULTS: The Revogene® GBS DS assay provided a valid result in less than 70 min for 356 (89%) women. The sensitivity of the test was 85.7% (66.4-95.3%). The specificity of the test was 99.1% (97.3-99.8%). The positive predictive value was 88.9% (69.7-97.1%). The negative predictive value was 98.9% (96.9-99.6%). CONCLUSION: The easy-to-use Revogene® GBS DS assay provides a valuable tool for the detection of GBS colonization at the beginning of labor. The sensitivity and turn-around time are adequate. The high number of invalid results needs to be addressed before the Revogene® GBS DS test can be expected to replace the current screening-based approach.

Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data.

Mathematical modelling studies have shown that repetitive screening can be used to mitigate SARS-CoV-2 transmission in primary schools while keeping schools open. However, not much is known about how transmission progresses within schools and whether there is a risk of importation to households. During the academic year 2020-2021, a prospective surveillance study using repetitive screening was conducted in a primary school and associated households in Liège (Belgium). SARS-CoV-2 screening was performed via throat washing either once or twice a week. We used genomic and epidemiological data to reconstruct the observed school outbreaks using two different models. The outbreaker2 model combines information on the generation time and contact patterns with a model of sequence evolution. For comparison we also used SCOTTI, a phylogenetic model based on the structured coalescent. In addition, we performed a simulation study to investigate how the accuracy of estimated positivity rates in a school depends on the proportion of a school that is sampled in a repetitive screening strategy. We found no difference in SARS-CoV-2 positivity between children and adults and children were not more often asymptomatic compared to adults. Both models for outbreak reconstruction revealed that transmission occurred mainly within the school environment. Uncertainty in outbreak reconstruction was lowest when including genomic as well as epidemiological data. We found that observed weekly positivity rates are a good approximation to the true weekly positivity rate, especially in children, even when only 25% of the school population is sampled. These results indicate that, in addition to reducing infections as shown in modelling studies, repetitive screening in school settings can lead to a better understanding of the extent of transmission in schools during a pandemic and importation risk at the community level.

Endovesical instillation of Cidofovir in the treatment of BK polyomavirus hemorrhagic cystitis after allogeneic hematopoietic cell transplantation.

BACKGROUND: Hemorrhagic cystitis (HC) with BK polyomavirus (BKPyV) is a common complication after allogeneic hematopoietic cell transplantation (alloHCT) that may lead to severe discomfort for the patient and significant morbidity (urinary obstruction, increased transfusion requirements and prolonged hospitalization). So far, there is no clear consensus on how to manage this complication. PATIENTS AND METHODS: Here, we report a single-center case series of 9 patients (4 children and 5 adults) treated with cidofovir endovesical (EV) instillation(s) for BKPyV-HC after alloHCT. EV Cidofovir was administered at a dose of 5 mg/kg, for 1 to 3 instillations (with a minimum delay between 2 successive doses of 5 days). RESULTS: Eight out of the 9 treated patients with EV Cidofovir achieved a complete resolution of HC after 1-3 instillation(s), without recurrence of symptomatic infection within the next 3 months. Only 1 adult patient did not improve after treatment and developed severe morbidity (emphysematous cystitis). CONCLUSION: Although this single-center case series of EV cidofovir for BKPyV HC after alloHCT shows encouraging results, only large prospective studies will definitively establish the effectiveness of this therapy.

Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium.

Healthcare workers (HCWs) are known to be at higher risk of developing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections although whether these risks are equal across all occupational roles is uncertain. Identifying these risk factors and understand SARS-CoV-2 transmission pathways in healthcare settings are of high importance to achieve optimal protection measures. We aimed to investigate the implementation of a voluntary screening program for SARS-CoV-2 infections among hospital HCWs and to elucidate potential transmission pathways though phylogenetic analysis before the vaccination era. HCWs of the University Hospital of Liège, Belgium, were invited to participate in voluntary reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed every week from April to December 2020. Phylogenetic analysis of SARS-CoV-2 genomes were performed for a subgroup of 45 HCWs. 5095 samples were collected from 703 HCWs. 212 test results were positive, 15 were indeterminate, and 4868 returned negative. 156 HCWs (22.2%) tested positive at least once during the study period. All SARS-CoV-2 test results returned negative for 547 HCWs (77.8%). Nurses (p < 0.05), paramedics (p < 0.05), and laboratory staff handling respiratory samples (p < 0.01) were at higher risk for being infected compared to the control non-patient facing group. Our phylogenetic analysis revealed that most positive samples corresponded to independent introduction events into the hospital. Our findings add to the growing evidence of differential risks of being infected among HCWs and support the need to implement appropriate protection measures based on each individual's risk profile to guarantee the protection of both HCWs and patients. Furthermore, our phylogenetic investigations highlight that most positive samples correspond to distinct introduction events into the hospital.

Evaluation of the Revogene® GBS DS assay performance for the intrapartum screening of group B streptococcus in comparison with intrapartum culture.

Prevention of perinatal Group B Streptococcus (GBS) transmission is crucial in our effort to prevent Early-onset GBS disease. Here, we established the performance of the Revogene GBS DS assay for the detection of group B streptococcus on intrapartum vaginal samples in a laboratory environment using a prospective noninterventional study design. Intrapartum vaginal swabs were enriched using a selective culture method which served as study reference method. Overall, 119 patients were enrolled with an antenatal and intrapartum Group B Streptococcus colonization prevalence of 12.9% and 11.8%, respectively. Compared to intrapartum culture, the Revogene GBS DS assay had a sensitivity of 92.9% and a specificity of 99.1%, while the antenatal culture displayed a sensitivity 78.6% of and specificity of 96.2%. The Revogene GBS DS assay displayed an acceptable performance according to the European Group B Streptococcus consensus recommendations. Complementary studies in clinical practice are needed to confirm these findings.

Transmission of SARS-CoV-2 After COVID-19 Screening and Mitigation Measures for Primary School Children Attending School in Liège, Belgium.

Importance: Recent data suggest a relatively low incidence of COVID-19 among children. The possible role that children attending primary school may play in the transmission of SARS-CoV-2 remains poorly understood. Objective: To gain a better understanding of the possible role of children in the transmission of SARS-CoV-2. Design, Setting, and Participants: This prospective cohort study was conducted from September 21 to December 31, 2020, in a primary school in Liège, Belgium, among a volunteer sample of 181 children, parents, and school employees. Exposures: Participants were tested for SARS-CoV-2 infection once a week for 15 weeks through throat washing, performed with 5 mL of saline and collected in a sterile tube after approximately 30 seconds of gargling. Quantitative reverse transcription-polymerase chain reaction was performed to detect SARS-CoV-2 infection. Main Outcomes and Measures: In case of test positivity, participants were asked to complete a questionnaire aimed at determining the timing of symptom onset and symptom duration. SARS-CoV-2 genetic sequencing was also performed. Confirmed cases were linked based on available information on known contacts and viral sequences. Results: A total of 181 individuals participated in this study, including 63 children (34 girls [54.0%]; mean [SD] age, 8.6 [1.9] years [range, 5-13 years]) and 118 adults (75 women [63.6%]; mean [SD] age, 42.5 [5.7] years [range, 30-59 years]). Forty-five individuals (24.9%) tested positive: 13 children (20.6%; 95% CI, 10.6%-30.6%) and 32 adults (27.1%; 95% CI, 19.1%-35.7%) (P = .34). Children were more often asymptomatic compared with adults (6 [46.2%; 95% CI, 19.1%-73.3%] vs 4 of 31 [12.9%; 95% CI, 1.3%-24.5%]; P = .04). The median duration of symptoms was shorter in children than in adults (0.00 days [IQR, 0.00-1.00 days] vs 15.00 days [IQR, 7.00-22.00 days]). A reconstruction of the outbreak revealed that most transmission events occurred between teachers and between children within the school. Of the observed household transmission events, most seemed to have originated from a child or teacher who acquired the infection at school. Conclusions and Relevance: Despite the implementation of several mitigation measures, the incidence of COVID-19 among children attending primary school in this study was comparable to that observed among teachers and parents. Transmission tree reconstruction suggests that most transmission events originated from within the school. Additional measures should be considered to reduce the transmission of SARS-CoV-2 at school, including intensified testing.

Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020.

At the end of 2020, several new variants of SARS-CoV-2-designated variants of concern-were detected and quickly suspected to be associated with a higher transmissibility and possible escape of vaccine-induced immunity. In Belgium, this discovery has motivated the initiation of a more ambitious genomic surveillance program, which is drastically increasing the number of SARS-CoV-2 genomes to analyse for monitoring the circulation of viral lineages and variants of concern. In order to efficiently analyse the massive collection of genomic data that are the result of such increased sequencing efforts, streamlined analytical strategies are crucial. In this study, we illustrate how to efficiently map the spatio-temporal dispersal of target mutations at a regional level. As a proof of concept, we focus on the Belgian province of Liège that has been consistently sampled throughout 2020, but was also one of the main epicenters of the second European epidemic wave. Specifically, we employ a recently developed phylogeographic workflow to infer the regional dispersal history of viral lineages associated with three specific mutations on the spike protein (S98F, A222V and S477N) and to quantify their relative importance through time. Our analytical pipeline enables analysing large data sets and has the potential to be quickly applied and updated to track target mutations in space and time throughout the course of an epidemic.

Evaluation of Two Rapid Antigenic Tests for the Detection of SARS-CoV-2 in Nasopharyngeal Swabs.

(1) Background: In the current context of the COVID-19 crisis, there is a need for fast, easy-to-use, and sensitive diagnostic tools in addition to molecular methods. We have therefore decided to evaluate the performance of newly available antigen detection kits in "real-life" laboratory conditions. (2) Methods: The sensitivity and specificity of two rapid diagnostic tests (RDT)-the COVID-19 Ag Respi-Strip from Coris Bioconcept, Belgium (CoRDT), and the coronavirus antigen rapid test cassette from Healgen Scientific, LLC, USA (HeRDT)-were evaluated on 193 nasopharyngeal samples using RT-PCR as the gold standard. (3) Results: The sensitivity obtained for HeRDT was 88% for all collected samples and 91.1% for samples with Ct ≤ 31. For the CoRDT test, the sensitivity obtained was 62% for all collected samples and 68.9% for samples with Ct ≤ 31. (4) Conclusions: Despite the excellent specificity obtained for both kits, the poor sensitivity of the CoRDT did not allow for its use in the rapid diagnosis of COVID-19. HeRDT satisfied the World Health Organization's performance criteria for rapid antigen detection tests. Its high sensitivity, quick response, and ease of use allowed for the implementation of HeRDT at the laboratory of the University Hospital of Liège.

Clinical decision support tool for diagnosis of COVID-19 in hospitals.

BACKGROUND: The coronavirus infectious disease 19 (COVID-19) pandemic has resulted in significant morbidities, severe acute respiratory failures and subsequently emergency departments' (EDs) overcrowding in a context of insufficient laboratory testing capacities. The development of decision support tools for real-time clinical diagnosis of COVID-19 is of prime importance to assist patients' triage and allocate resources for patients at risk. METHODS AND PRINCIPAL FINDINGS: From March 2 to June 15, 2020, clinical patterns of COVID-19 suspected patients at admission to the EDs of Liège University Hospital, consisting in the recording of eleven symptoms (i.e. dyspnoea, chest pain, rhinorrhoea, sore throat, dry cough, wet cough, diarrhoea, headache, myalgia, fever and anosmia) plus age and gender, were investigated during the first COVID-19 pandemic wave. Indeed, 573 SARS-CoV-2 cases confirmed by qRT-PCR before mid-June 2020, and 1579 suspected cases that were subsequently determined to be qRT-PCR negative for the detection of SARS-CoV-2 were enrolled in this study. Using multivariate binary logistic regression, two most relevant symptoms of COVID-19 were identified in addition of the age of the patient, i.e. fever (odds ratio [OR] = 3.66; 95% CI: 2.97-4.50), dry cough (OR = 1.71; 95% CI: 1.39-2.12), and patients older than 56.5 y (OR = 2.07; 95% CI: 1.67-2.58). Two additional symptoms (chest pain and sore throat) appeared significantly less associated to the confirmed COVID-19 cases with the same OR = 0.73 (95% CI: 0.56-0.94). An overall pondered (by OR) score (OPS) was calculated using all significant predictors. A receiver operating characteristic (ROC) curve was generated and the area under the ROC curve was 0.71 (95% CI: 0.68-0.73) rendering the use of the OPS to discriminate COVID-19 confirmed and unconfirmed patients. The main predictors were confirmed using both sensitivity analysis and classification tree analysis. Interestingly, a significant negative correlation was observed between the OPS and the cycle threshold (Ct values) of the qRT-PCR. CONCLUSION AND MAIN SIGNIFICANCE: The proposed approach allows for the use of an interactive and adaptive clinical decision support tool. Using the clinical algorithm developed, a web-based user-interface was created to help nurses and clinicians from EDs with the triage of patients during the second COVID-19 wave.

A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages.

Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of SARS-CoV-2 have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analyzed with gold-standard phylogeographic approaches. To tackle this practical limitation, we here describe and apply a rapid analytical pipeline to analyze the spatiotemporal dispersal history and dynamics of SARS-CoV-2 lineages. As a proof of concept, we focus on the Belgian epidemic, which has had one of the highest spatial densities of available SARS-CoV-2 genomes. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.

Evaluation of the new Id-Fungi plates from Conidia for MALDI-TOF MS identification of filamentous fungi and comparison with conventional methods as identification tool for dermatophytes from nails, hair and skin samples.

OBJECTIVES: We first compare the efficiency of mould/dermatophyte identification by MALDI-TOF MS using a new medium called Id-Fungi plates (IDFP) from Conidia® and two different databases. For the second purpose, we evaluated a new version of the medium supplemented with cycloheximide, Id-Fungi plates Plus (IDFPC) for the direct inoculation of nails, hair and skin samples and compared the efficiency of MALDI-TOF MS identification of dermatophytes to classical methods based on culture and microscopy. METHODS: A total of 71 strains have been cultured IDFP and Sabouraud gentamicin plates (SGC2) and were identified by MALDI-TOF MS. For the evaluation of the combination IDFPC/ MALDI-TOF MS as a method of identification for dermatophytes, 428 samples of hair nails and skin were cultivated in parallel on IDFPC and Sabouraud + cycloheximide medium (SAB-ACTI). RESULTS: For Aspergillus sp and non-Aspergillus moulds, the best performances were obtained on IDFP after maximum 48-h growth, following protein extraction. For dermatophytes, the best condition was using the IDFP at 72 hours, after extended direct deposit. Regarding the direct inoculation of nails, hair skin on IDFPC, 129/428 (30.1%) showed a positive culture against 150/428 (35%) on SAB-ACTI medium. Among the 129 positive strains, the identification by MALDI-TOF MS was correct for 92/129 (71.4%). CONCLUSION: The IDFP allows the generation of better spectra by MALDI-TOF MS compared to SGC2. It facilitates sampling and deposit. Regarding the use of IDFPC, this medium seems less sensitive than SAB-ACTI but among positive strains, the rate of correct identification by MALDI-TOF MS is satisfactory.

A Recurrent Mutation at Position 26340 of SARS-CoV-2 Is Associated with Failure of the E Gene Quantitative Reverse Transcription-PCR Utilized in a Commercial Dual-Target Diagnostic Assay.

Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals while also clearing essential staff to continue to work. At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains, it is prudent to monitor circulating viruses for variants that might compromise these assays. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. As the cobas SARS-CoV-2 assay targets two positions in the genome, the individuals carrying this variant were still called SARS-CoV-2 positive. Whole-genome sequencing of SARS-CoV-2 showed all to carry closely related viruses. Examination of viral genomes deposited on GISAID showed this mutation has arisen independently at least four times. This work highlights the necessity of monitoring SARS-CoV-2 for the emergence of single-nucleotide polymorphisms that might adversely affect RT-PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives.