This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical ...Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.
•The majority of hospitalized COVID-19 patients are zinc deficient.•There is a weak correlation between plasma zinc and the length of hospital stay.•cHIS score, described by Webb et al., is ...externally validated in this study.•Current findings do not support plasma zinc as a robust prognostic factor.
Zinc deficiency is associated with impaired antiviral response, cytokine releasing syndrome (CRS), and acute respiratory distress syndrome. Notably, similar complications are being observed during severe SARS-CoV-2 infection.
We conducted a prospective, single-center, observational study in a tertiary university hospital (CUB-Hôpital Erasme, Brussels) to address the zinc status, the association between the plasma zinc concentration, development of CRS, and the clinical outcomes in PCR-confirmed and hospitalized COVID-19 patients.
One hundred and thirty-nine eligible patients were included between May 2020 and November 2020 (median age of 65 years IQR = 54, 77).
Our cohort's median plasma zinc concentration was 57 µg/dL (interquartile range IQR = 45, 67) compared to 74 µg/dL (IQR = 64, 84) in the retrospective non-COVID-19 control group (N = 1513; p < 0.001). Markedly, the absolute majority of COVID-19 patients (96%) were zinc deficient (<80 µg/dL).
The median zinc concentration was lower in patients with CRS compared to those without CRS (-5 µg/dL; 95% CI = -10.5, 0.051; p = 0.048).
Among the tested outcomes, zinc concentration is significantly correlated with only the length of hospital stay (rho = -0.19; p = 0.022), but not with mortality or morbidity. As such, our findings do not support the role of zinc as a robust prognostic marker among hospitalized COVID-19 patients who in our cohort presented a high prevalence of zinc deficiency. It might be more beneficial to explore the role of zinc as a biomarker for assessing the risk of developing a tissue-damaging CRS and predicting outcomes in patients diagnosed with COVID-19 at the early stage of the disease.
Background
The translation of Next-Generation Sequencing (NGS) from research to clinical microbiology is increasing rapidly, but its integration into routine clinical care struggles to catch-up. A ...challenge for clinical laboratories is that the substantial investments made in the required technologies and resources must meet both current and forthcoming needs.
Methods
To get a clinical perspective of these needs, we have sent a survey to infectious diseases clinicians of five hospitals, covering the following topics: NGS knowledge, expected syndromes and patients foreseen to benefit from NGS, and expected impact on antimicrobial prescription.
Results
According to clinicians, benefits of NGS are mostly expected in neurological and respiratory infections diagnostics.
Conclusion
A better dialog between microbiologists and clinicians about hopes and limits of NGS in microbiology may help identifying key investments needed for clinical laboratories, today and tomorrow.
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 (
= 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.
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.
can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a ...second case of Legionnaires' disease in the same ward. While the first case was easily assumed as nosocomial based on the date of symptom onset, the second case required clear typing results to be assigned either as nosocomial and related to the same environmental source as the first case, or community acquired. To untangle this specific question, we applied core-genome multilocus typing (MLST), whole-genome single nucleotide polymorphism and whole-genome MLST methods to a collection of 36 Belgian and 41 international sequence-type 1 (ST1) isolates using both thresholds recommended in the literature and tailored threshold based on local epidemiological data. Based on the thresholds applied to cluster isolates together, the three methods gave different results and no firm conclusion about the nosocomial setting of the second case could been drawn. Our data highlight that despite promising results in the study of outbreaks and for large-scale epidemiological investigations, next-generation sequencing typing methods applied to ST1 outbreak investigation still need standardization regarding both wet-lab protocols and bioinformatics. A deeper evaluation of the
evolutionary clock is also required to increase our understanding of genomic differences between isolates sampled during a clinical infection and in the environment.
Background:
Mycoplasma hominis
and
Ureaplasma
spp. are responsible for opportunistic infections in transplant patients, sometimes causing a life-threatening hyperammonemia syndrome. Both pathogens ...are not identified with standard microbiology techniques, resulting in missed or delayed diagnosis. We present a clinical case that illustrates the added value that next-generation sequencing (NGS) may offer in the diagnosis of respiratory infections in immune-compromised patients.
Results:
A 55 years-old man with idiopathic pulmonary fibrosis underwent double lung transplantation. He received antibiotic prophylaxis with piperacillin-tazobactam and azythromycin. At day 4 post-transplantation (PTx), the patient presented an acute respiratory distress. A broncho-alveolar lavage (BAL) was performed. At day 5 PTx, the patient presented a status epilepticus due to diffuse cerebral oedema. Serum ammonia concentration was 661 μg/dL. BAL bacterial culture was negative. Because of the clinical presentation, special cultures were performed and identified 100.000 CFU/mL of
M. hominis
and
Ureaplasma
spp. and specific PCRs were positive for
M. hominis
and
Ureaplasma parvum
. Antibiotic therapy was shifted to therapeutic dose of azithromycin and doxycycline; within 48 h ammonia serum concentrations returned to normal but the coma persisted several weeks, followed by a persistent frontal lobe syndrome. A follow-up BAL was performed on day 11 Ptx. The
Mycoplasma/Ureaplasma
culture was negative, yet the specific PCRs remained positive. Bacterial culture found 100 CFU/mL of
Staphylococcus aureus
and viral culture was positive for Herpes Simplex Virus-1. These results were confirmed by metagenomic next-generation sequencing (mNGS). In the bacterial fraction, the majority of reads belonged to
Corynebacterium propinquum
(34.7%),
S. aureus
(24.1%) and
Staphylococcus epidermidis
(17.1%). Reads assigned to
M. hominis, Ureaplasma urealyticum
and
parvum
represented 0.71, 0.13, and 0.04% of the bacterial fraction and corresponded to 6.9 × 10
3
, 9.7 × 10
2
, and 3.7 × 10
2
genome equivalents per mL of BAL fluid, respectively. These results are in favor of a cure of the atypical infection.
Conclusions:
mNGS offered added diagnostic and quantitative values compared to PCR tests, which can remain positive after resolved infections. The initiation of appropriate antibiotic therapy would have occurred earlier on, possibly resulting in a better clinical outcome if mNGS had been performed in a routine fashion.
Legionnaires' disease (LD) is a severe bacterial infection causing pneumonia. Surveillance commonly underestimates the true incidence as not all cases are laboratory confirmed and reported to public ...health authorities. The aim of this study was to present indicators for the impact of LD in Belgium between 2013 and 2017 and to estimate its true burden in the Belgian population in 2017, the most recent year for which the necessary data were available.
Belgian hospital discharge data, data from three infectious disease surveillance systems (mandatory notification, sentinel laboratories and the national reference center), information on reimbursed diagnostic tests from the Belgian National Institute for Health and Disability Insurance and mortality data from the Belgian statistical office were used. To arrive at an estimate of the total number of symptomatic cases in Belgium, we defined a surveillance pyramid and estimated a multiplication factor to account for LD cases not captured by surveillance. The multiplication factor was then applied to the pooled number of LD cases reported by the three surveillance systems. This estimate was the basis for our hazard- and incidence-based Disability-Adjusted Life Years (DALYs) calculation. To account for uncertainty in the estimations of the DALYs and the true incidence, we used Monte Carlo simulations with 10,000 iterations.
We found an average of 184 LD cases reported by Belgian hospitals annually (2013-2017), the majority of which were male (72%). The surveillance databases reported 215 LD cases per year on average, 11% of which were fatal within 90 days after diagnosis. The estimation of the true incidence in the community yielded 2674 (95% Uncertainty Interval UI: 2425-2965) cases in 2017. LD caused 3.05 DALYs per case (95%UI: 1.67-4.65) and 8147 (95%UI: 4453-12,426) total DALYs in Belgium in 2017, which corresponds to 71.96 (95%UI: 39.33-109.75) DALYs per 100,000 persons.
This analysis revealed a considerable burden of LD in Belgium that is vastly underestimated by surveillance data. Comparison with other European DALY estimates underlines the impact of the used data sources and methodological approaches on burden estimates, illustrating that national burden of disease studies remain essential.
In the context of rising sea level, many estuaries and bays show an overall trend to sedimentary infilling. Among these coastal environments, the Bay of Somme is a hypertidal tide and wave-dominated ...estuary, filled in by marine sands, with a superficy of 70 km
2
. This study proposes a spatial zonation of the intertidal area of the bay based on the combination of information on sediments, seabed morphology and dynamics. Data come from a surficial sediment sampling campaign and six airborne LiDAR topographic surveys, acquired over the period 2011-2013, providing information on grain size, carbonate content, bedform occurrence and seabed dynamics. The Main Map shows the morpho-sedimentary and -dynamic zonation used as a basis to describe infilling stages in the bay.
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