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OBJECTIVES: This study aimed to evaluate an expanded matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF MS) database for the identification of Haemophilus species other than H. influenzae (Hi). METHODS: A total of 144 Haemophilus species, cultured from respiratory samples from people (living) with cystic fibrosis, were identified with MALDI-TOF MS and 16S rRNA sequencing. Of these, 99 Haemophilus strains showed >99% similarity with the best matching strain in the National Center for Biotechnology Information (NCBI) database and were assigned to a single Haemophilus subspecies using both MALDI-TOF MS and 16S rRNA sequencing. The MS profiles of a subset of strains (n = 58/99) were added to the Bruker MALDI-TOF MS database. Subsequently, 270 different strains that were analyzed previously in a routine setting were re-analyzed. RESULTS: 16S rRNA sequencing reliably identified 99/144 Haemophilus strains (>99% similarity). H. haemolyticus 16S rRNA identification was suboptimal since only 3/21 H. haemolyticus strains attained a similarity of >99% with H. haemolyticus 16S rRNA sequence in the NCBI database. Expansion of the MALDI-TOF MS database improved the number of reliable identifications only moderately for H. haemolyticus, H. influenzae and H. paraphrohaemolyticus (<10%). By contrast, improved identification was more outspoken for H. parahaemolyticus, H. parainfluenzae, H. sputorum and H. pittmaniae (>85%). CONCLUSION: 16S rRNA sequencing is a valuable method for the identification of Haemophilus sp. other than Hi. Expansion of the MALDI-TOF MS database, based on 16S rRNA sequencing results, increased the proportion of reliable identifications and in this study resulted in an increase of 10% of Haemophilus sp. other than Hi strain identifications.
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It is increasingly recognized that interspecies interactions may modulate the pathogenicity of Pseudomonas aeruginosa during chronic lung infections. Nevertheless, while the interaction between P. aeruginosa and pathogenic microorganisms co-infecting the lungs has been widely investigated, little is known about the influence of other members of the lung microbiota on the infection process. In this study, we focused on investigating the impact of Prevotella species isolated from the sputum of people with cystic fibrosis (pwCF) on biofilm formation and virulence factor production by P. aeruginosa. Screening of a representative collection of Prevotella species recovered from clinical samples showed that several members of this genus (8 out 10 isolates) were able to significantly reduce biofilm formation of P. aeruginosa PAO1, without impact on growth. Among the tested isolates, the strongest biofilm-inhibitory activity was observed for Prevotella intermedia and Prevotella nigrescens, which caused a reduction of up to 90% in the total biofilm biomass of several P. aeruginosa isolates from pwCF. In addition, a strain-specific effect of P. nigrescens on the ability of P. aeruginosa to produce proteases and pyocyanin was observed, with significant alterations in the levels of these virulence factors detected in LasR mutant strains. Overall, these results suggest that non-pathogenic bacteria from the lung microbiota may regulate pathogenicity traits of P. aeruginosa, and possibly affect the outcome of chronic lung infections.
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Background: Dysregulation of the gut microbiome has been implicated in Parkinson's disease (PD). This study aimed to evaluate the clinical effects and safety of a single faecal microbiota transplantation (FMT) in patients with early-stage PD. Methods: The GUT-PARFECT trial, a single-centre randomised, double-blind, placebo-controlled trial was conducted at Ghent University Hospital between December 01, 2020 and December 12, 2022. Participants (aged 50-65 years, Hoehn and Yahr stage 2) were randomly assigned to receive nasojejunal FMT with either healthy donor stool or their own stool. Computer-generated randomisation was done in a 1:1 ratio through permutated-block scheduling. Treatment allocation was concealed for participants and investigators. The primary outcome measure at 12 months was the change in the Movement Disorders Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) motor score obtained during off-medication evaluations. Intention-to-treat analysis was performed using a mixed model for repeated measures analysis. This completed trial is registered on ClinicalTrials.gov (NCT03808389). Findings: Between December 2020 and December 2021, FMT procedures were conducted on 46 patients with PD: 22 in the healthy donor group and 24 in the placebo group. Clinical evaluations were performed at baseline, 3, 6, and 12 months post-FMT. Full data analysis was possible for 21 participants in the healthy donor group and 22 in the placebo group. After 12 months, the MDS-UPDRS motor score significantly improved by a mean of 5.8 points (95% CI -11.4 to -0.2) in the healthy donor group and by 2.7 points (-8.3 to 2.9) in the placebo group (p = 0.0235). Adverse events were limited to temporary abdominal discomfort. Interpretation: Our findings suggested a single FMT induced mild, but long-lasting beneficial effects on motor symptoms in patients with early-stage PD. These findings highlight the potential of modulating the gut microbiome as a therapeutic approach and warrant a further exploration of FMT in larger cohorts of patients with PD in various disease stages. Funding: Flemish PD patient organizations (VPL and Parkili), Research Foundation Flanders (FWO), Biocodex Microbiota Foundation.
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Since the onset of the coronavirus disease (COVID-19) pandemic in Belgium, UZ/KU Leuven has played a crucial role as the National Reference Centre (NRC) for respiratory pathogens, to be the first Belgian laboratory to develop and implement laboratory developed diagnostic assays for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and later to assess the quality of commercial kits. To meet the growing demand for decentralised testing, both clinical laboratories and government-supported high-throughput platforms were gradually deployed across Belgium. Consequently, the role of the NRC transitioned from a specialised testing laboratory to strengthening capacity and coordinating quality assurance. Here, we outline the measures taken by the NRC, the national public health institute Sciensano and the executing clinical laboratories to ensure effective quality management of molecular testing throughout the initial two years of the pandemic (March 2020 to March 2022).
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COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/epidemiologia , Bélgica/epidemiologia , Teste para COVID-19 , Pandemias , Técnicas de Laboratório Clínico , Técnicas de Diagnóstico MolecularRESUMO
The aim of this study was to assess the reliability of rapid antigen detection tests (RADT) for Streptococcus pyogenes (GAS) and Streptococcus pneumoniae on pleural fluid samples for diagnosis of parapneumonic effusion/empyema (PPE) and their potential for improving pathogen identification rates. Sixty-three pleural samples were included from 54 patients on which GAS and S. pneumoniae RADT (BinaxNOW), culture, 16S rRNA PCR, and S. pneumoniae-specific PCR were performed. GAS RADT showed a sensitivity of 95.2% and a specificity of 100%. Pneumococcal RADT showed a sensitivity of 100% and specificity of 88.6%. Both RADT increased the pathogen identification rate in PPE compared to culture.
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Empiema Pleural , Empiema , Derrame Pleural , Humanos , Streptococcus pneumoniae/genética , Streptococcus pyogenes/genética , RNA Ribossômico 16S , Reprodutibilidade dos Testes , Empiema/diagnóstico , Derrame Pleural/diagnóstico , Derrame Pleural/microbiologia , Empiema Pleural/diagnóstico , Empiema Pleural/microbiologiaRESUMO
BackgroundThe earliest recognised infections by the SARS-CoV-2 Omicron variant (Pango lineage B.1.1.529) in Belgium and Switzerland suggested a connection to an international water polo tournament, held 12-14 November 2021 in Brno, Czechia.AimTo study the arrival and subsequent spread of the Omicron variant in Belgium and Switzerland, and understand the overall importance of this international sporting event on the number of infections in the two countries.MethodsWe performed intensive forward and backward contact tracing in both countries, supplemented by phylogenetic investigations using virus sequences of the suspected infection chain archived in public databases.ResultsThrough contact tracing, we identified two and one infected athletes of the Belgian and Swiss water polo teams, respectively, and subsequently also three athletes from Germany. In Belgium and Switzerland, four and three secondary infections, and three and one confirmed tertiary infections were identified. Phylogenetic investigation demonstrated that this sporting event played a role as the source of infection, but without a direct link with infections from South Africa and not as a superspreading event; the virus was found to already be circulating at that time in the countries involved.ConclusionThe SARS-CoV-2 Omicron variant started to circulate in Europe several weeks before its identification in South Africa on 24 November 2021. Accordingly, it can be assumed that travel restrictions are usually implemented too late to prevent the spread of newly detected SARS-CoV-2 variants to other regions. Phylogenetic analysis may modify the perception of an apparently clear result of intensive contact tracing.
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COVID-19 , Esportes Aquáticos , Humanos , SARS-CoV-2/genética , Bélgica/epidemiologia , Suíça/epidemiologia , República Tcheca , Filogenia , COVID-19/epidemiologia , AlemanhaRESUMO
IMPORTANCE: People with cystic fibrosis (pwCF) often suffer from chronic lung infections with Pseudomonas aeruginosa. While antibiotics are still commonly used to treat P. aeruginosa infections, there is a high discordance between in vitro and in vivo antibiotic efficacy, which contributes to suboptimal antibiotic therapy. In the present study, we found that isolates from the same sputum sample had highly diverse antibiotic resistance profiles [based on the minimal inhibitory concentration (MIC)], which may explain the reported discrepancy between in vitro and in vivo antibiotic efficacy. Through systematic analysis, we report that pooling nine isolates per sputum sample significantly decreased intrasample diversity in MIC and influenced clinical interpretation of antibiotic susceptibility tests compared to single isolate testing. Hence, pooling of isolates may offer a solution to obtain a consistent MIC test result and could lead to optimizing antibiotic therapy in pwCF and other infectious diseases where diversity in antibiotic resistance is observed.
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Fibrose Cística , Infecções por Pseudomonas , Humanos , Pseudomonas aeruginosa , Fibrose Cística/tratamento farmacológico , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Infecções por Pseudomonas/tratamento farmacológico , Testes de Sensibilidade MicrobianaRESUMO
BACKGROUND: Accumulating evidence shows a role of the hospital wastewater system in the spread of multidrug-resistant organisms, such as carbapenemase producing Enterobacterales (CPE). Several sequential outbreaks of CPE on the geriatric ward of the Ghent University hospital have led to an outbreak investigation. Focusing on OXA-48 producing Citrobacter freundii, the most prevalent species, we aimed to track clonal relatedness using whole genome sequencing (WGS). By exploring transmission routes we wanted to improve understanding and (re)introduce targeted preventive measures. METHODS: Environmental screening (toilet water, sink and shower drains) was performed between 2017 and 2021. A retrospective selection was made of 53 Citrobacter freundii screening isolates (30 patients and 23 environmental samples). DNA from frozen bacterial isolates was extracted and prepped for shotgun WGS. Core genome multilocus sequence typing was performed with an in-house developed scheme using 3,004 loci. RESULTS: The CPE positivity rate of environmental screening samples was 19.0% (73/385). Highest percentages were found in the shower drain samples (38.2%) and the toilet water samples (25.0%). Sink drain samples showed least CPE positivity (3.3%). The WGS data revealed long-term co-existence of three patient sample derived C. freundii clusters. The biggest cluster (ST22) connects 12 patients and 8 environmental isolates taken between 2018 and 2021 spread across the ward. In an overlapping period, another cluster (ST170) links eight patients and four toilet water isolates connected to the same room. The third C. freundii cluster (ST421) connects two patients hospitalised in the same room but over a period of one and a half year. Additional sampling in 2022 revealed clonal isolates linked to the two largest clusters (ST22, ST170) in the wastewater collection pipes connecting the rooms. CONCLUSIONS: Our findings suggest long-term circulation and transmission of carbapenemase producing C. freundii clones in hospital sanitary installations despite surveillance, daily cleaning and intermittent disinfection protocols. We propose a role for the wastewater drainage system in the spread within and between rooms and for the sanitary installations in the indirect transmission via bioaerosol plumes. To tackle this problem, a multidisciplinary approach is necessary including careful design and maintenance of the plumbing system.
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Citrobacter freundii , Águas Residuárias , Humanos , Idoso , Citrobacter freundii/genética , Engenharia Sanitária , Estudos Retrospectivos , Hospitais , Células ClonaisRESUMO
OBJECTIVES: EUCAST breakpoints for short incubation disk diffusion allow rapid antimicrobial susceptibility testing (RAST) directly from positive blood cultures. We evaluate the RAST methodology and assess its potential added value in a setting of low prevalence of multidrug-resistant (MDR) organisms. METHODS: In our two-part study, we performed RAST on 127 clinical blood cultures at 6 and 8 h and determined categorical agreement with direct susceptibility testing. We also measure the impact of susceptibility results on antimicrobial therapy compared to empirical treatment. RESULTS: Categorical agreement was 96.2% at 6 h (575/598 isolate-drug combinations) and 96.6% at 8 h (568/588 combinations). Major errors involved piperacillin/tazobactam in 16 of 31 cases. The second part of our study shows that AST reporting proved essential in correcting ineffective empirical therapy in 6.3% of the patients (8/126). CONCLUSION: EUCAST RAST is an inexpensive and reliable method of susceptibility testing, although care must be taken with reporting piperacillin/tazobactam. In support of RAST implementation, we show that AST remains of great importance in providing effective therapy, even in a setting of low MDR prevalence and elaborate antibiotic guidelines.
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Antibacterianos , Anti-Infecciosos , Humanos , Testes de Sensibilidade Microbiana , Centros de Atenção Terciária , Bélgica , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Bactérias Gram-Negativas , Piperacilina/farmacologia , Piperacilina/uso terapêutico , Tazobactam/farmacologiaRESUMO
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.
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COVID-19 , Pandemias , Humanos , Bélgica/epidemiologia , COVID-19/epidemiologia , Genoma Viral , Genômica , SARS-CoV-2/genética , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
INTRODUCTION: Long term care facilities for elderly (LTCFs) in Europe encountered a high disease burden at the start of the COVID-19 pandemic. Therefore, these facilities were the first to receive COVID-19 vaccines in many European countries. A limited COVID-19 vaccine supply early 2021 resulted in a majority of residents and healthcare workers (HCWs) in LTCFs being vaccinated compared to a minority in the general population. This study exploits this imbalance to assess the efficiency of COVID-19 vaccination in containing outbreaks in LTCFs. METHODS: Exploratory statistics were performed using data from a COVID-19 surveillance system covering all 842 LTCFs in Flanders (the northern region of Belgium). The number and size of COVID-19 outbreaks in LTCFs were compared (1) before and after introducing vaccines and (2) with the status of the pandemic in the general population. Based on individual data from 15 LTCFs, the infection rate and symptoms of vaccinated and unvaccinated residents and HCWs were compared during a COVID-19 outbreak. RESULTS: 95.8% of the residents and 90.9% of the HCWs in Flemish LTCFs were vaccinated before May 30, 2021. Before vaccine introduction, residents in LTCFs were 10 times more likely to test positive for COVID-19 than the general population of Flanders. This ratio reversed after vaccination. Furthermore, after vaccination fewer and shorter outbreaks were observed involving fewer residents. During these outbreaks, vaccinated and unvaccinated residents were equally likely to test positive, but positive vaccinated residents were less likely to develop severe symptoms. In contrast, unvaccinated HCWs were more likely to test positive. CONCLUSION: In the first half of 2021, two-dose vaccination was highly efficient in preventing and containing outbreaks in LTCFs, reducing COVID-19 hospitalizations and deaths. The high likelihood of unvaccinated HCWs to be involved in COVID-19 outbreaks in vaccinated LTCFs emphasizes the importance of vaccinating HCWs.
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COVID-19 , Influenza Humana , Idoso , Bélgica/epidemiologia , COVID-19/epidemiologia , COVID-19/prevenção & controle , Vacinas contra COVID-19 , Surtos de Doenças/prevenção & controle , Humanos , Influenza Humana/prevenção & controle , Assistência de Longa Duração , Pandemias , VacinaçãoRESUMO
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.
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COVID-19 , SARS-CoV-2 , Bélgica/epidemiologia , COVID-19/diagnóstico , COVID-19/epidemiologia , Humanos , Pandemias , Reação em Cadeia da Polimerase em Tempo Real , SARS-CoV-2/genéticaRESUMO
Background: Immunocompromised patients are at increased risk of severe COVID-19 and impaired vaccine response. In this observational prospective study, we evaluated immunogenicity of the BNT162b2 mRNA vaccine in cohorts of primary or secondary immunocompromised patients. Methods: Five clinical groups of immunocompromised patients [primary immunodeficiency (PID) (n=57), people living with HIV (PLWH) (n=27), secondary immunocompromised patients with a broad variety of underlying rheumatologic (n=23) and homogeneous (multiple sclerosis) neurologic (n=53) conditions and chronic kidney disease (CKD) (n=39)] as well as a healthy control group (n=54) were included. Systemic humoral and cellular immune responses were evaluated by determination of anti-SARS-CoV-2 Spike antibodies using a TrimericS IgG assay (Diasorin) and through quantification of interferon gamma release in response to SARS-CoV-2 antigen with QuantiFERON SARS-CoV-2 assay (Qiagen), respectively. Responses were measured at pre-defined time-points after complete vaccination. Results: All healthy controls, PLWH and CKD-patients had detectable antibodies 10 to 14 days (T2) and 3 months (T3) after administration of the second vaccination. In contrast, only 94.5% of the PID, 50.0% of the rheumatologic and 48.0% of neurologic patients developed antibodies at T2 and only 89.1% of the PID, 52.4% of the rheumatologic and 50.0% of neurologic patients developed antibodies at T3. At T3 no significant differences in cellular response between the healthy control group and the PLWH and CKD groups were found, while proportions of reactive subjects were lower in PID and rheumatologic patients and higher in neurologic patients. Humoral and cellular immune responses significantly correlated in the healthy control, PID, PLWH groups for all 3 antigens. Conclusion: Patients with acquired or inherited immune disorders may show variable immune responses to vaccination with the BNT162b2 mRNA vaccine against SARS-CoV-2. Whether humoral, cellular or both immune responses are delayed depends on the patient group, therapy and individual risk factors. These data may guide the counselling of patients with immune disorders regarding vaccination of SARS-CoV-2.
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Artrite Reumatoide , COVID-19 , Insuficiência Renal Crônica , Anticorpos Antivirais , Vacina BNT162 , Vacinas contra COVID-19 , Humanos , Imunidade Humoral , Hospedeiro Imunocomprometido , Estudos Prospectivos , RNA Mensageiro , SARS-CoV-2 , Vacinas Sintéticas , Vacinas de mRNARESUMO
OBJECTIVE: To reduce the inappropriate use of broad-spectrum antibiotics in a 1000+ bed acute tertiary care hospital by the introduction of cascade antimicrobial susceptibility reporting for Enterobacterales. METHODS: Over a 1-year period, we selectively suppressed reporting of susceptibility to the broad-spectrum antibiotics piperacillin-tazobactam (TZP) and meropenem (MEM) for Enterobacterales strains susceptible to amoxicillin-clavulanic acid (AMC) and negative for extended-spectrum ß-lactamase (ESBL). We measured the effects on hospital-wide antibiotic consumption (defined daily doses/1000 admissions) and resistance of Escherichia coli and Klebsiella pneumoniae on two levels. First, we compared resistance and antibiotic use for the antibiotics impacted by the intervention (AMC, TZP and MEM) with control antibiotics that were consistently reported (fluoroquinolones, trimethoprim-sulfamethoxazole and third-generation cephalosporins). Second, we compared the resistance for TZP and MEM with a control pathogen (Pseudomonas aeruginosa) and studied the impact on rate of Clostridioides difficile-associated diarrhoea in our hospital. RESULTS: We observed an overall increased use of AMC relative to overall antibiotic consumption (20.0%, p<0.0001) together with a decreased use of TZP (-11.9%, p=0.049) and unchanged use of MEM (p=0.68) relative to overall antibiotic consumption. As for resistance, the number of ESBL-positive K. pneumoniae strains diminished by 5.9% (p<0.0001). When focusing on intensive care units, the carbapenemase-producing Enterobacterales (CPE) rate also decreased by 4.5% (p=0.0091). For E. coli, no significant difference in ESBL (p=0.33) and CPE (p=0.48) rates were observed. No significant difference in the rate of C. difficile infections was observed (p=0.40). CONCLUSIONS: Restricted susceptibility reporting of TZP and MEM was associated with a significant increased use of AMC and decreased use of TZP relative to overall antibiotic consumption and significant reduction in ESBL- and CPE-positive K. pneumoniae strains.
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Antibacterianos , Clostridioides difficile , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Escherichia coli , Klebsiella pneumoniae , Testes de Sensibilidade MicrobianaRESUMO
INTRODUCTION: The high variability of SARS-CoV-2 serological response after COVID-19 infection hampers its use as indicator of the timing of infection. A potential alternative method is the determination of affinity maturation of SARS-CoV-2 IgG, expressed as the SARS-CoV-2 IgG avidity. METHODS: SARS-CoV-2 IgG concentration and avidity were measured in sera of hospitalized COVID-19 patients sampled at two weeks and ≥12 weeks post symptom onset using an in-house developed protocol based on EUROIMMUN (anti-spike) and EDI™ (anti-nucleocapsid) SARS-CoV-2 IgG ELISA protocols. RESULTS: We included 68 confirmed COVID-19 patients that tested positive for SARS-CoV-2 IgG in both the initial and follow-up specimen sampled at a median of 14 (range 10-18) days and 120 (range 84-189) days, respectively, post symptom onset. The median anti-spike and anti-nucleocapsid SARS-CoV-2 IgG avidity response was 40% (range 9-93%) and 72% (range 27-104%), respectively, for the first sample, and 66% (range 28-90%) and 57% (range 25-94%), respectively, for the second sample. The proportion of SARS-CoV-2 IgG avidity results ≥60% was significantly lower for anti-spike compared to anti-nucleocapsid IgG for initial samples (p< 0.01) and vice versa for follow-up samples (p< 0.01). CONCLUSION: Anti-nucleocapsid SARS-CoV-2 IgG maturation occurs faster and avidity decreases faster than anti-spike IgG, indicating different kinetics of anti-spike and anti-nucleocapsid IgG. Further, affinity maturation after SARS-CoV-2 infection is frequently incomplete.
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COVID-19 , SARS-CoV-2 , Anticorpos Antivirais , Humanos , Imunoglobulina G , Glicoproteína da Espícula de CoronavírusRESUMO
BACKGROUND: Molecular detection of SARS-CoV-2 in respiratory samples is the gold standard for COVID-19 diagnosis but it has a long turnaround time and struggles to detect low viral loads. Serology could help to diagnose suspected cases which lack molecular confirmation. Two case reports are presented as illustration. OBJECTIVES: The aim of this study was to evaluate the performance of several commercial assays for COVID-19 serology. We illustrated the added value of COVID-19 serology testing in suspect COVID-19 cases with negative molecular test. STUDY DESIGN: Twenty-three sera from 7 patients with a confirmed molecular diagnosis of SARS-CoV-2 were tested using 14 commercial assays. Additionally, 10 pre-pandemic sera and 9 potentially cross-reactive sera were selected. We calculated sensitivity and specificity. Furthermore, we discuss the diagnostic relevance of COVID-19 serology in a retrospective cohort of 145 COVID-19 cases in which repetitive molecular and serological SARS-CoV-2 tests were applied. RESULTS: The interpretation of the pooled sensitivity of IgM/A and IgG resulted in the highest values (range 14-71% on day 2-7; 88-94% on day 8-18). Overall, the specificity of the assays was high (range 79-100%). Among 145 retrospective cases, 3 cases (2%) remained negative after sequential molecular testing but positive on final SARS-CoV-2 serology. CONCLUSION: Sensitivity of COVID-19 serological diagnosis was variable but consistently increased at >7 days after symptom onset. Specificity was high. Our data suggest that serology can complement molecular testing for diagnosis of COVID-19, especially for patients presenting the 2nd week after symptom onset or later.
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COVID-19 , SARS-CoV-2 , COVID-19/diagnóstico , Teste para COVID-19 , Humanos , Imunoglobulina M , Estudos Retrospectivos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Sensibilidade e EspecificidadeRESUMO
More than a year after the first identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of the 2019 coronavirus disease (COVID-19) in China, the emergence and spread of genomic variants of this virus through travel raise concerns regarding the introduction of lineages in previously unaffected regions, requiring adequate containment strategies. Concomitantly, such introductions fuel worries about a possible increase in transmissibility and disease severity, as well as a possible decrease in vaccine efficacy. Military personnel are frequently deployed on missions around the world. As part of a COVID-19 risk mitigation strategy, Belgian Armed Forces that engaged in missions and operations abroad were screened (7683 RT-qPCR tests), pre- and post-mission, for the presence of SARS-CoV-2, including the identification of viral lineages. Nine distinct viral genotypes were identified in soldiers returning from operations in Niger, the Democratic Republic of the Congo, Afghanistan, and Mali. The SARS-CoV-2 variants belonged to major clades 19B, 20A, and 20B (Nextstrain nomenclature), and included "variant of interest" B.1.525, "variant under monitoring" A.27, as well as lineages B.1.214, B.1, B.1.1.254, and A (pangolin nomenclature), some of which are internationally monitored due to the specific mutations they harbor. Through contact tracing and phylogenetic analysis, we show that isolation and testing policies implemented by the Belgian military command appear to have been successful in containing the influx and transmission of these distinct SARS-CoV-2 variants into military and civilian populations.
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COVID-19/virologia , Militares , SARS-CoV-2/classificação , SARS-CoV-2/genética , Afeganistão/epidemiologia , Bélgica , COVID-19/epidemiologia , China/epidemiologia , República Democrática do Congo/epidemiologia , Genoma Viral , Genômica , Humanos , Mali/epidemiologia , Epidemiologia Molecular , Mutação , Níger/epidemiologia , Filogenia , Viagem , Sequenciamento Completo do GenomaAssuntos
COVID-19/diagnóstico , Proteínas do Nucleocapsídeo de Coronavírus/metabolismo , Doenças Placentárias/patologia , Complicações Infecciosas na Gravidez/virologia , SARS-CoV-2/genética , Adulto , COVID-19/patologia , COVID-19/virologia , Feminino , Humanos , Imuno-Histoquímica , Morte Materna , Necrose , Fosfoproteínas/metabolismo , Placenta/patologia , Placenta/virologia , Doenças Placentárias/virologia , Gravidez , Complicações Infecciosas na Gravidez/patologia , Terceiro Trimestre da Gravidez , Gravidez de Gêmeos , Risco , Trofoblastos/patologia , Trofoblastos/virologia , Adulto JovemRESUMO
BACKGROUND: Early 2020, a COVID-19 epidemic became a public health emergency of international concern. To address this pandemic broad testing with an easy, comfortable and reliable testing method is of utmost concern. Nasopharyngeal (NP) swab sampling is the reference method though hampered by international supply shortages. A new oropharyngeal/nasal (OP/N) sampling method was investigated using the more readily available throat swab. RESULTS: 35 patients were diagnosed with SARS-CoV-2 by means of either NP or OP/N sampling. The paired swabs were both positive in 31 patients. The one patient who tested negative on both NP and OP/N swab on admission, was ultimately diagnosed on bronchoalveolar lavage fluid. A strong correlation was found between the viral RNA loads of the paired swabs (r = 0.76; P < 0.05). The sensitivity of NP and OP/N analysis in hospitalized patients (n = 28) was 89.3% and 92.7% respectively. CONCLUSIONS: This study demonstrates equivalence of NP and OP/N sampling for detection of SARS-CoV-2 by means of rRT-PCR. Sensitivity of both NP and OP/N sampling is very high in hospitalized patients.
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Teste de Ácido Nucleico para COVID-19 , COVID-19/diagnóstico , Pandemias , SARS-CoV-2/isolamento & purificação , Manejo de Espécimes/métodos , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Orofaringe/virologia , Estudos Prospectivos , Sensibilidade e Especificidade , Adulto JovemRESUMO
To face the continuous emergence of SARS-CoV-2 variants, broadly protective therapeutic antibodies are highly needed. We here focused on the fusion peptide (FP) region of the viral spike antigen since it is highly conserved among alpha- and betacoronaviruses. First, we found that coronavirus cross-reactive antibodies are commonly formed during infection, being omnipresent in sera from COVID-19 patients, in ~50% of pre-pandemic human sera (rich in antibodies against endemic human coronaviruses), and even in feline coronavirus-infected cats. Pepscan analyses demonstrated that a confined N-terminal region of the FP is strongly immunogenic across diverse coronaviruses. Peptide-purified human antibodies targeting this conserved FP epitope exhibited broad binding of alpha- and betacoronaviruses, besides weak and transient SARS-CoV-2 neutralizing activity. Being frequently elicited by coronavirus infection, these FP-binding antibodies might potentially exhibit Fc-mediated effector functions and influence the kinetics or severity of coronavirus infection and disease.