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.

Effects of cascade reporting of susceptibility profiles for Enterobacterales on broad-spectrum antibiotics use and resistance.

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.

Different long-term avidity maturation for IgG anti-spike and anti-nucleocapsid SARS-CoV-2 in hospitalized COVID-19 patients.

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.

Comparison of the QuantiFERON-TB® Gold Plus on LIAISON® XL and T-SPOT.TB for the diagnosis of latent Mycobacterium tuberculosis infection in a low tuberculosis incidence population.

The current study compared the QuantiFERON-TB® Gold Plus on LIAISON® XL to the T-SPOT.TB for the diagnosis of latent Mycobacterium tuberculosis infection on 125 patient samples. A high agreement of qualitative results (90%) was observed between both methods with 3% major discrepancies, half of which were false negative results with the T-SPOT.TB.

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.

Is monitoring of antiplatelet therapy by light transmission aggregometry dependent on instrument and reagent used?

INTRODUCTION: Light transmission aggregometry (LTA), used to detect clopidogrel resistance in patients under antiplatelet therapy, is prone to multiple variables potentially influencing results and interpretation. Currently, no attention is given to type of aggregometer or reagent used. The aim of this study was to evaluate the interassay variability between two aggregometers (Chronolog700 and TA-8V), using two different ADP reagents (Chrono-Par® and Agro-Bio ADP) in patients under clopidogrel therapy. Additionally, LTA results were correlated to CYP2C19-polymorphism. METHODS: Light transmission aggregometry was performed in 20 healthy individuals and 30 patients using both aggregometers, and applying two different reagents (2.5 and 5 µmol/L). The maximum platelet aggregation (ADPmax ), the platelet aggregation at 6 minutes (ADP6min ), and the percentage of disaggregation at 6 min (ADP%disaggr ) were compared between four applied combinations. Additionally, 23 clopidogrel-resistant patients according to Chronolog700-Chrono-par® ADP reagent analysis were tested for CYP2C19*2 polymorphism. RESULTS: Comparison of the LTA of healthy individuals revealed a significant lower ADPmax , lower ADP6min , and higher ADP%disaggr with the TA-8V aggregometer compared to Chronolog700, regardless of the reagent. In contrast, LTA results in patients are depending on the reagent, with significant higher ADPmax and ADP6min and lower ADP%disaggr using Chrono-Par® compared to Agro-Bio ADP reagent. All intermediate clopidogrel metabolizers (CYP2C19*2 carriers) were correctly classified as clopidogrel resistant using Chrono-Par® , in contrast to the Agro-Bio ADP reagent. CONCLUSION: Light transmission aggregometry in clopidogrel-treated patients is mainly depending on the type of ADP reagent. Comparison of LTA with genotype reveals that the choice of instrument seems less influencing. In contrast, in the healthy individuals, differences could be attributed to the instrument.

Performance of the new ID-fungi plate using two types of reference libraries (Bruker and MSI) to identify fungi with the Bruker MALDI Biotyper.

During the last decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the diagnosis of fungal infections. Recently, a new Conidia ID-fungi plate (IDFP) medium was introduced to facilitate growth and sampling of fungi. This study aimed to evaluate the IDFP for fungal MALDI-TOF MS identification by comparison with a standard fungal growth medium using two reference libraries. A total of 75 filamentous fungal isolates (including 32 dermatophytes) were inoculated on IDFP and Sabouraud-gentamicin-chloramphenicol (SGC) agar and identified by MALDI-TOF MS using formic acid/acetonitrile extraction. Both the commercially available Bruker library (version 2.0) and the public available MSI web application (version 2018) were applied. For 15% of the isolates, a faster growth was noticed on IDFP compared to SGC. IDFP enhanced the performance of fungal identification compared to SGC for both MSI (increase of 16% identifications to genus and 5% to species level) and Bruker library (increase of 22% identifications to genus and 8% to species level). In total, only 73% of the tested isolates were present in the Bruker library compared to 92% for MSI library. No significant difference (P = 0.46) in MALDI score between IDFP and SGC was observed for the MSI library, but scores were significantly (P = 0.03) higher for IDFP when using Bruker library, potentially explained by the prevention of agar contamination by using IDFP since the Bruker database was created from liquid media. IDFP is a promising alternative growth medium for MALDI-TOF MS fungal identification which would strongly benefit from optimizing the Bruker reference library.

Detection of a Large Novel α-Thalassemia Deletion in an Autochthonous Belgian Family.

α-Thalassemia (α-thal) is a common hemoglobinopathy mainly caused by deletion of one or both α-globin genes. We describe an autochthonous Belgian family diagnosed with α-thal trait. Molecular analysis revealed a novel large deletion of at least 170 kb between 226.68 kb (0.2 Mb) and 402.68 kb (0.4 Mb) from the telomere of 16p, leaving the subtelomeric region intact. The deletion includes both α-globin genes (HBA1 and HBA2) but also flanking genes possibly related to non hematological effects: HBQ1, LUC7L, ITFG3, RGS11, ARHGDIG, PDIA2 and AXIN1. These genes are not contained in the region (0.9 and 1.7 Mb from the telomere of 16p) associated with α-thal intellectual disability (ATR-16) syndrome. However, further research is necessary to exclude other potential effects than α-thal in patients with a large deletion at 0.2-0.4 Mb from the telomere of 16p. Genetic counseling is important for carriers of this deletion as homozygosity for the α-globin (- -/) haplotype may lead to Hb Bart's (γ4) hydrops fetalis syndrome.

Smartphone Application Monitoring of Acceleration Forces During Pneumatic Tube System Transport of Emergency Department Patient Samples.

BACKGROUND: The use of pneumatic tube system (PTS) transport has gained considerable popularity in modern hospitals but is also associated with sample hemolysis. The potential contribution of PTS-associated acceleration forces to high hemolysis rates observed in the emergency department (ED) has not been investigated before and can be easily examined nowadays using smartphone applications. The first aim of our study was to investigate whether our PTS induces hemolysis of patient samples obtained from our ED. We also explored a potential correlation between hemolysis index (HI) on the one hand and acceleration forces during PTS transport or other potential causes of hemolysis related to patient characteristics on the other for two different blood sampling techniques. METHODS: Blood samples from 100 ED patients were collected in one Sarstedt S-Monovette® serum tube (PTStransported to laboratory) and two BD Vacutainer® serum tubes (one PTS-transported and one hand-carried). For all serum samples HI was measured. A smartphone was sent along with the samples in order to register accelerations during transport. Patient's erythrocyte sedimentation rate (ESR), mean corpuscular volume (MCV), hematocrit, total cholesterol, low density lipoprotein (LDL), and high-density lipoprotein (HDL) concentration were determined as well. RESULTS: Hemolysis rate was only 1 - 4% and 5% for PTS and hand-carried transport, respectively. Calculated acceleration vector sums for PTS transport from the ED to laboratory reached up to 131.49 m/second2 (13.40 g). No correlation could be demonstrated between HI on the one hand and acceleration forces acting on the samples during PTS transport or ESR, MCV, hematocrit, and HDL concentration on the other. However, an inverse correlation was noted between HI and cholesterol (total and LDL) concentration in serum tubes transported via PTS, though not in those carried by hand. CONCLUSIONS: We demonstrated that our PTS does not induce or contribute to hemolysis of ED patient samples, even at high acceleration vector sums up to 13 g. Technological advancements such as the development of smartphone applications offer the ability to regularly monitor acceleration forces during PTS transport of patient samples. Low total cholesterol and LDL concentrations may affect the erythrocyte membrane fluidity, making erythrocytes more prone to hemolysis.

High anion gap metabolic acidosis induced by cumulation of ketones, L- and D-lactate, 5-oxoproline and acute renal failure.

INTRODUCTION: Frequent causes of high anion gap metabolic acidosis (HAGMA) are lactic acidosis, ketoacidosis and impaired renal function. In this case report, a HAGMA caused by ketones, L- and D-lactate, acute renal failure as well as 5-oxoproline is discussed. CASE PRESENTATION: A 69-year-old woman was admitted to the emergency department with lowered consciousness, hyperventilation, diarrhoea and vomiting. The patient had suffered uncontrolled type 2 diabetes mellitus, underwent gastric bypass surgery in the past and was chronically treated with high doses of paracetamol and fosfomycin. Urosepsis was diagnosed, whilst laboratory analysis of serum bicarbonate concentration and calculation of the anion gap indicated a  HAGMA. L-lactate, D-lactate, ß-hydroxybutyric acid, acetone and 5-oxoproline serum levels were markedly elevated and renal function was impaired. DISCUSSION: We concluded that this case of HAGMA was induced by a variety of underlying conditions: sepsis, hyperglycaemia, prior gastric bypass surgery, decreased renal perfusion and paracetamol intake. Risk factors for 5-oxoproline intoxication present in this case are female gender, sepsis, impaired renal function and uncontrolled type 2 diabetes mellitus. Furthermore, chronic antibiotic treatment with fosfomycin might have played a role in the increased production of 5-oxoproline. CONCLUSION: Paracetamol-induced 5-oxoproline intoxication should be considered as a cause of HAGMA in patients with female gender, sepsis, impaired renal function or uncontrolled type 2 diabetes mellitus, even when other more obvious causes of HAGMA such as lactate, ketones or renal failure can be identified.

Causes, consequences and management of sample hemolysis in the clinical laboratory.

Preanalytical hemolysis of blood samples is a common problem in medical practice, especially in emergency departments. Several potential influences on sample hemolysis have been investigated, including sampling techniques, centrifugation and sample transport. In particular, the use of intravenous catheters and the vacuum sampling technique have often been demonstrated to provoke hemolysis. Other factors playing a role include the use of inappropriate puncture sites, complicated blood sampling, prolonged tourniquet application, underfilling of tubes and excessive shaking of specimens. Training of phlebotomists can play a pivotal role in overcoming these issues. A sample may also undergo hemolysis at the point of centrifugation, more specifically when centrifugation lasts too long or is done repeatedly. Pneumatic tube system (PTS)-transported samples tend to be more strongly affected by hemolysis compared to hand-carried ones, though whether this difference is clinically relevant remains questionable. The velocity at which the sample moves, the distance it covers and the shock forces it sustains all determine to what extent hemolysis occurs during PTS transport. The use of cushion inserts in the carrier to stabilize the samples and the presence of a gel separator in the transported serum tubes may prevent PTS-induced hemolysis. Finally, there is considerable variation between patients in the extent to which samples are prone to hemolysis. Sample hemolysis leads to unreliable laboratory results, delayed diagnosis and patients suffering avoidable discomfort. Specifically, hemolysis may interfere with laboratory results due to release of intracellular components, dilution effects, proteolysis and interference with analytical techniques. There is ongoing debate about how laboratories should deal with results altered by hemolysis. Laboratory specialists should clearly communicate with the ordering clinicians in order to make an informed decision about how to interpret hemolysis-affected analytical results. This review looks into current evidence concerning the causes and consequences of in vitro hemolysis, and aims to explain how to deal with it.