Sniffing out safety: canine detection and identification of SARS-CoV-2 infection from armpit sweat.

Detection dogs were trained to detect SARS-CoV-2 infection based on armpit sweat odor. Sweat samples were collected using cotton pads under the armpits of negative and positive human patients, confirmed by qPCR, for periods of 15-30 min. Multiple hospitals and organizations throughout Belgium participated in this study. The sweat samples were stored at -20°C prior to being used for training purposes. Six dogs were trained under controlled atmosphere conditions for 2-3 months. After training, a 7-day validation period was conducted to assess the dogs' performances. The detection dogs exhibited an overall sensitivity of 81%, specificity of 98%, and an accuracy of 95%. After validation, training continued for 3 months, during which the dogs' performances remained the same. Gas chromatography/mass spectrometry (GC/MS) analysis revealed a unique sweat scent associated with SARS-CoV-2 positive sweat samples. This scent consisted of a wide variety of volatiles, including breakdown compounds of antiviral fatty acids, skin proteins and neurotransmitters/hormones. An acceptability survey conducted in Belgium demonstrated an overall high acceptability and enthusiasm toward the use of detection dogs for SARS-CoV-2 detection. Compared to qPCR and previous canine studies, the detection dogs have good performances in detecting SARS-CoV-2 infection in humans, using frozen sweat samples from the armpits. As a result, they can be used as an accurate pre-screening tool in various field settings alongside the PCR test.

From Delta to Omicron SARS-CoV-2 variant: Switch to saliva sampling for higher detection rate.

Background: Real-time polymerase chain reaction (RT-PCR) testing on a nasopharyngeal swab is the current standard for SARS-CoV-2 virus detection. Since collection of this sample type is experienced uncomfortable by patients, saliva- and oropharyngeal swab collections should be considered as alternative specimens. Objectives: Evaluation of the relative performance of oropharyngeal swab, nasopharyngeal swab and saliva for the RT-PCR based SARS-CoV-2 Delta (B.1.617.2) and Omicron (B.1.1.529) variant detection. Study design: Nasopharyngeal swab, oropharyngeal swab and saliva were collected from 246 adult patients who presented for SARS-CoV-2 testing at the screening centre in Ypres (Belgium). RT-PCR SARS-CoV-2 detection was performed on all three sample types separately. Variant type was determined for each positive patient using whole genome sequencing or Allplex SARS-CoV-2 variants I and II Assay. Results and conclusions: Saliva is superior compared to nasopharyngeal swab for the detection of the Omicron variant. For the detection of the Delta variant, nasopharyngeal swab and saliva can be considered equivalent specimens. Oropharyngeal swab is the least sensitive sample type and shows little added value when collected in addition to a single nasopharyngeal swab.

Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium.

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.

Prevalence and clinical relevance of colonization with methicillin-resistant Staphylococcus aureus in the obstetric population.

BACKGROUND AND AIMS: Routine screening for Methicillin-Resistant Staphylococcus aureus (MRSA) in pregnant women is common practice in many hospitals. However, little is known on its prevalence and clinical relevance in this population. In this prospective longitudinal study, we aimed to investigate the MRSA prevalence in our obstetric population, the rate of vertical transmission of MRSA and the potential clinical relevance of MRSA colonization for both mother and child. A possible correlation between GBS and MRSA colonization was also investigated. MATERIALS AND METHODS: MRSA screening samples were collected at 35-37 weeks of gestation (from mother), at delivery and at discharge (from mother and newborn). All samples were analyzed by conventional microbiological methods and MRSA strains were subjected to spa-typing to investigate genetic similarity. The medical records of all positive mother-child pairs were analyzed to detect the occurrence of clinical infection in the postpartum period. RESULTS: 679 mother-child pairs were included between June 2014 and July 2016. Maternal MRSA positivity rate was 1.3% at 35-37 weeks (vaginal/anorectal), 3.1% at delivery (nose/throat) and 3.6% at discharge (nose/throat). MRSA positivity in neonates was 0.3% at delivery and increased to 3% at discharge (nose/umbilicus). Almost all MRSA positive children were born to MRSA positive mothers (OR 120.40, 95% CI: 38.42-377.32). Genetic similarity of the MRSA strains found in mother and child was illustrated for all but one case. 57.7% of the cases of MRSA colonization in our cohort were associated with livestock exposure. 31% of the MRSA positive mothers developed an infectious complication in the postpartum period. No neonatal infectious complications were observed. GBS positivity was not a predictive factor for MRSA colonization in our cohort. CONCLUSION: The rate of MRSA colonization (overall 4.3%) in our obstetric population is similar to that described in the literature and that of the general population admitted to our hospital in the same period. Maternal MRSA colonization appeared to be an important risk factor for neonatal colonization. Whereas mothers were at higher risk of developing infectious morbidity in the postpartum period, no neonatal infectious complications were observed. We observed no correlation between GBS and MRSA colonization.

Antibody response against SARS-CoV-2 spike protein and nucleoprotein evaluated by four automated immunoassays and three ELISAs.

OBJECTIVES: The aim was to determine the antibody response against SARS-CoV-2 spike protein and nucleoprotein using four automated immunoassays and three ELISAs for the detection of total Ig antibodies (Roche) or IgG (Abbott, Diasorin, Snibe, Euroimmun, Mikrogen) in COVID-19 patients. METHODS: Sensitivity and dynamic trend to seropositivity were evaluated in 233 samples from 114 patients with moderate, severe or critical COVID-19 confirmed with PCR on nasopharyngeal swab. Specificity was evaluated in 113 samples collected before January 2020, including 24 samples from patients with non-SARS coronavirus infection. RESULTS: Sensitivity for all assays was 100% (95% confidence interval 83.7-100) 3 weeks after onset of symptoms. Specificity varied between 94.7% (88.7-97.8) and 100% (96.1-100). Calculated at the cut-offs that corresponded to a specificity of 95% and 97.5%, Roche had the highest sensitivity (85.0% (79.8-89.0) and 81.1% (76.6-85.7), p < 0.05 except vs. Abbott). Seroconversion occurred on average 2 days earlier for Roche total Ig anti-N and the three IgG anti-N assays (Abbott, Mikrogen, Euroimmun) than for the two IgG anti-S assays (Diasorin, Euroimmun) (≥50% seroconversion day 9-10 vs. day 11-12 and p < 0.05 for percent seropositive patients day 9-10 to 17-18). There was no significant difference in the IgG antibody time to seroconversion between critical and non-critical patients. DISCUSSION: Seroconversion occurred within 3 weeks after onset of symptoms with all assays and on average 2 days earlier for assays detecting IgG or total Ig anti-N than for IgG anti-S. The specificity of assays detecting anti-N was comparable to anti-S and excellent in a challenging control population.

Target-Controlled Infusion of Cefepime in Critically Ill Patients.

Attainment of appropriate pharmacokinetic-pharmacodynamic (PK-PD) targets for antimicrobial treatment is challenging in critically ill patients, particularly for cefepime, which exhibits a relative narrow therapeutic-toxic window compared to other beta-lactam antibiotics. Target-controlled infusion (TCI) systems, which deliver drugs to achieve specific target drug concentrations, have successfully been implemented for improved dosing of sedatives and analgesics in anesthesia. We conducted a clinical trial in an intensive care unit (ICU) to investigate the performance of TCI for adequate target attainment of cefepime. Twenty-one patients treated with cefepime according to the standard of care were included. Cefepime was administered through continuous infusion using TCI for a median duration of 4.5 days. TCI was based on a previously developed population PK model incorporating the estimated creatinine clearance based on the Cockcroft-Gault formula as the input variable to calculate cefepime clearance. A cefepime blood concentration of 16 mg/liter was targeted. To evaluate the measured versus predicted plasma concentrations, blood samples were taken (median of 10 samples per patient), and total cefepime concentrations were measured using ultraperformance liquid chromatography-tandem mass spectrometry. The performance of the TCI system was evaluated using Varvel criteria. Half (50.3%) of the measured cefepime concentrations were within ±30% around the target value of 16 mg liter-1 The wobble was 11.4%, the median performance error (MdPE) was 21.1%, the median absolute performance error (MdAPE) was 32.0%, and the divergence was -3.72% h-1 Based on these results, we conclude that TCI is useful for dose optimization of cefepime in ICU patients. (This study has been registered at ClinicalTrials.gov under identifier NCT02688582.).

Fluorescent in situ hybridization can be used as a complementary assay for the diagnosis of Tropheryma whipplei infection.

BACKGROUND: Immunohistochemistry and Periodic acid-Schiff (PAS) staining have been routinely used for the diagnosis of Whipple's disease (WD). However, these methods present limitations. As a result, the last years, Fluorescence in situ hybridization (FISH) has been increasingly used as a complementary tool for the diagnosis of WD from various tissue samples. CASE REPORT: In this study, we visualized, by FISH, Tropheryma whipplei within macrophages of a lymph node from a patient with WD. Moreover, we report in this study a patient with a pulmonary biopsy compatible with WD by PAS, immunostaining and FISH, although the specific molecular assays for T. whipplei were negative. Sequencing analysis of the 16S rDNA revealed a T. whipplei-related species with unknown classification. CONCLUSION: FISH can be a valuable method for the detection of Tropheryma species in formalin-fixed paraffin-embedded tissues. FISH cannot replace the other already approved diagnostic techniques for WD, it can be used as a complementary tool and can provide supplementary information in a relatively short time.

Target-Controlled Continuous Infusion for Antibiotic Dosing: Proof-of-Principle in an In-silico Vancomycin Trial in Intensive Care Unit Patients.

OBJECTIVES: In this in-silico study, we investigate the clinical utility of target-controlled infusion for antibiotic dosing in an intensive care unit setting using vancomycin as a model compound. We compared target-controlled infusion and adaptive target-controlled infusion, which combines target-controlled infusion with data from therapeutic drug monitoring, with conventional (therapeutic drug monitoring-based) vancomycin dosing strategies. METHODS: A clinical trial simulation was conducted. This simulation was based on a comprehensive database of clinical records of intensive care unit patients and a systematic review of currently available population-pharmacokinetic models for vancomycin in intensive care unit patients. Dosing strategies were compared in terms of the probability of achieving efficacious concentrations as well as the potential for inducing toxicity. RESULTS: Adaptive target-controlled infusion outperforms rule-based dosing guidelines for vancomycin. In the first 48 h of treatment, the probability of target attainment is significantly higher for adaptive target-controlled infusion than for the second-best method (Cristallini). Probability of target attainments of 54 and 72% and 47 and 59% for both methods after 24 and 48 h, respectively. Compared to the Cristallini method, which is characterized by a probability of attaining concentrations above 30 mg.L-1 > 65% in the first few hours of treatment, adaptive target-controlled infusion shows negligible time at risk and a probability of attaining concentrations above 30 mg.L-1 not exceeding 25%. Finally, in contrast to the other methods, the performance of target-controlled infusion is consistent across subgroups within the population. CONCLUSIONS: Our study shows that adaptive target-controlled infusion has the potential to become a practical tool for patient-tailored antibiotic dosing in the intensive care unit.

Multicenter evaluation of the revised RIDA® QUICK test (N1402) for rapid detection of norovirus in a diagnostic laboratory setting.

The updated RIDA® QUICK (N1402) immunochromatographic assay (R-Biopharm) for detection of norovirus was evaluated during a prospective, multicenter study using 771 stool samples from patients with gastroenteritis. Compared to real-time reverse transcriptase polymerase chain reaction (RT-rtPCR) as gold standard, the RIDA® QUICK had an overall sensitivity of 72.8% (91/125) and a specificity of 99.5% (640/643). Genotype analysis of the polymerase (ORF1) and capsid (ORF2) region of the genome indicated that the RIDA® QUICK assay could detect a broad range of genotypes including new variants (15 of 125 positive samples) which were detected by an in-house SYBR®Green RT-rtPCR, but not by the RIDA® GENE PCR PG1415 (R-Biopharm) and mostly not by the RIDA® GENE PCR PG1405 and the Xpert® Norovirus assay (Cepheid). The RIDA® QUICK can be used to reliably confirm norovirus in stool samples, but a negative result does not definitively exclude the presence of norovirus.

Nontuberculous mycobacteria among pulmonary tuberculosis patients: a retrospective Belgian multicenter study.

OBJECTIVES: Currently, there are no European data about the frequency and clinical significance of nontuberculous mycobacteria (NTM) grown from respiratory samples during the treatment of tuberculosis (TB). We determined the frequency and clinical significance of NTM isolated before or during pulmonary tuberculosis treatment in Belgian laboratories. METHODS: We conducted a nationwide retrospective multicenter cohort study on the co-isolation of TB and NTM in Belgium. Starting from laboratory data between 2006 and 2013, possible TB-NTM co-isolations were searched for. RESULTS: A total of 2569 unique culture-positive pulmonary tuberculosis cases were included in the study. Only 35 (1.4%) of these TB cases had an NTM co-isolated, and two of these 35 fulfilled the ATS criteria for NTM lung disease. CONCLUSION: A very low prevalence of 1.4% NTM co-isolations was found in Belgian patients with culture-proven pulmonary TB.

A model-based analysis of the predictive performance of different renal function markers for cefepime clearance in the ICU.

OBJECTIVES: Several population pharmacokinetic models for cefepime in critically ill patients have been described, which all indicate that variability in renal clearance is the main determinant of the observed variability in exposure. The main objective of this study was to determine which renal marker best predicts cefepime clearance. METHODS: A pharmacokinetic model was developed using NONMEM based on 208 plasma and 51 urine samples from 20 ICU patients during a median follow-up of 3 days. Four serum-based kidney markers (creatinine, cystatin C, urea and uromodulin) and two urinary markers [measured creatinine clearance (CLCR) and kidney injury molecule-1] were evaluated as covariates in the model. RESULTS: A two-compartment model incorporating a renal and non-renal clearance component along with an additional term describing haemodialysis clearance provided an adequate description of the data. The Cockcroft-Gault formula was the best predictor for renal cefepime clearance. Compared with the base model without covariates, the objective function value decreased from 1971.7 to 1948.1, the median absolute prediction error from 42.4% to 29.9% and the between-subject variability in renal cefepime clearance from 135% to 50%. Other creatinine- and cystatin C-based formulae and measured CLCR performed similarly. Monte Carlo simulations using the Sanford guide dose recommendations indicated an insufficient dose reduction in patients with a decreased kidney function, leading to potentially toxic levels. CONCLUSIONS: The Cockcroft-Gault formula was the best predictor for cefepime clearance in critically ill patients, although other creatinine- and cystatin C-based formulae and measured CLCR performed similarly.

What about confidence intervals? A word of caution when interpreting PTA simulations.

OBJECTIVES: In the field of antimicrobial chemotherapy, readers are increasingly confronted with population pharmacokinetic models and the ensuing simulation results with the purpose to improve the efficiency of currently used therapeutic regimens. One such type of analysis is Monte Carlo (MC) simulations in support of dose selection. At the moment, results of these MC simulations consist of predictions for the typical individual/population only. The uncertainty associated with the parameters, from which the simulations are derived, is completely ignored. Here, we highlight the importance of and the need to include parameter uncertainty in PTA simulations. METHODS: Using MC simulation with parameter uncertainty, we estimated CIs around PTA curves. The added benefit of this approach was illustrated using, on the one hand, a population pharmacokinetic model developed in-house for a ß-lactam antibiotic and, on the other hand, results from a previously published PTA analysis. RESULTS: Our examples illustrate that proper clinical decision-making requires more than the typical PTA curve. Therefore, authors should be encouraged to provide an estimate of the uncertainty along with their simulations and to take this into account when interpreting the results. We feel that CIs around PTA curves provide this information in a comprehensive manner without requiring advanced knowledge on the underlying modelling approaches from the reader. CONCLUSIONS: We believe that this approach should be advocated by all stakeholders in antibiotic stewardship programmes to safeguard the quality of clinical decision-making in the future.

Evaluation of Three Hemoglobin A1c Point-of-Care Instruments.

BACKGROUND: Hemoglobin A1c is currently used both for monitoring and diagnosing patients with diabetes mellitus. Point-of-care (POC) instruments have been proposed to improve glycemic control of patients with diabetes by providing a rapid result if the analytical performance is acceptable. However, the performance of most current POC devices is unsatisfactory. In this study, we evaluated 3 POC devices: cobas b101 (Roche), Afinion (Alere) and B-Analyst (Menarini). METHODS: The CLSI protocols EP-5 and EP-9 were applied to investigate precision, accuracy, and bias. Bias was compared with an ion-exchange chromatography method (Adams Arkray HA-8160, Menarini) of which the accuracy was assessed by three secondary reference methods (SRMs) and a capillary zone electrophoresis-based laboratory method (Capillarys Flex Piercing 2, Sebia). RESULTS: Using the IFCC units (mmol/mol), total CV's for cobas b101, Afinion and B-Analyst ranged from 2.0 to 3.9%, from 2.3 to 3.7% and from 2.3 to 2.9%, respectively, compared to a total CV ranging from 0.9 to 1.2% for the Adams Arkray HA-8160. A high correlation was found between the HA-8160 and the three POC devices (r = 0.992, r = 0.968, r = 0.998 for cobas b101, Afinion and B-Analyst, respectively). However, all three showed a significant bias of -2.2 mmol/mol, -2.2 mmol/mol and 0.5 mmol/mol, respectively. CONCLUSIONS: Only the B-Analyst met the current HbA1c quality specifications for precision, whereas cobas b101 and Afinion failed on the low level. Significant bias was observed for all three POC instruments. As low precision and bias are required for both monitoring and diagnosis of diabetes, we believe that POC devices should be carefully selected.

How is the Xpert MRSA Gen 3 assay (Cepheid) performing on pooled eSwab medium?

The performance of the Xpert MRSA Gen 3 was compared to the Xpert MRSA on pooled eSwab media from nose, throat, and perineum using broth enriched cultured as gold standard. A lower specificity was found for the Xpert MRSA Gen 3 compared to the Xpert MRSA (91.8% versus 97.9%; P<0.05).

Multicenter evaluation of BD Veritor System and RSV K-SeT for rapid detection of respiratory syncytial virus in a diagnostic laboratory setting.

The recently introduced BD Veritor System RSV laboratory kit (Becton Dickinson, Sparks, MD, USA) with automatic reading was evaluated and compared with the RSV K-SeT (Coris BioConcept, Gembloux, Belgium) for the detection of respiratory syncytial virus (RSV) using 248 nasopharyngeal aspirates of children younger than 6 years old with respiratory tract infection. Compared to reverse transcriptase polymerase chain reaction as gold standard, both tests had an identical sensitivity of 78.1% and a specificity of 96.8% and 95.8% for the BD Veritor System and RSV K-SeT, respectively. Both antigen tests can be used to reliably confirm RSV in young children. However, a negative result does not definitively exclude the presence of RSV.

Prosthetic valve endocarditis caused by Bordetella holmesii, an Acinetobacter lookalike.

We report a case of fulminant endocarditis on a prosthetic homograft aortic valve caused by Bordetella holmesii, which was successfully managed by surgical valve replacement and antibiotic treatment. B. holmesii, a strictly aerobic, small, Gram-negative coccobacillus, has been implicated as an infrequent cause of a pertussis-like syndrome and other respiratory illnesses. However, B. holmesii is also a rare cause of septicaemia and infective endocarditis, mostly in immunocompromised patients. To our knowledge, this is the first report of B. holmesii endocarditis on a prosthetic aortic valve. Routine laboratory testing initially misidentified the strain as Acinetobacter sp. Correct identification was achieved by 16S rRNA gene and outer-membrane protein A (ompA) gene sequencing. Interestingly, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry also produced an accurate species-level identification. Subsequent susceptibility testing and review of the literature revealed ceftazidime, cefepime, carbapenems, aminoglycosides, fluoroquinolones, piperacillin/tazobactam, tigecycline and colistin as possible candidates to treat infections caused by B. holmesii.

Erythrocyte indices in the assessment of iron status in dialysis-dependent patients with end-stage renal disease on continuous erythropoietin receptor activator versus epoetin beta therapy.

BACKGROUND: European guidelines stress that iron status should be regularly assessed for the optimal management of renal anemia. These guidelines include the hemoglobin content of reticulocytes and the percentage of hypochromic RBC as markers for functional iron deficiency. Recently, equivalents of these indices have become available on the automated hematology analyzer Sysmex XE-2100, these being reticulocyte hemoglobin equivalent (Ret-He) and DF-HYPO XE, respectively. METHODS: In a prospective study, we closely monitored these parameters in dialysis-dependent patients with end-stage renal disease during the switch from a first-generation epoetin (EPO) once weekly to a third-generation EPO [continuous erythropoietin receptor activator (CERA)] once monthly. As a control, patients staying on EPO beta were monitored. RESULTS: During follow-up, no changes in erythrocyte indices were noticed in the EPO beta group. By contrast, in the CERA group, a decrease in Ret-He and an increase in DF-HYPO XE were transiently found 7-10 days after administration. The transient state of functional iron deficiency could not be prevented by extra intravenous iron. CONCLUSION: Fluctuations in Ret-He and DF-HYPO XE have to be taken into account when these parameters are used for the assessment of iron-deficient states. We suggest that a fixed time point in the CERA schedule should be chosen for iron monitoring.

Use of medicinal plants and pharmaceuticals by indigenous communities in the Bolivian Andes and Amazon.

OBJECTIVE: To investigate, by means of household surveys, the use of medicinal plants and pharmaceuticals in Apillapampa, a large Andean community of Quechua peasants, and in six small communities of Yuracaré-Trinitario "slash-and-burn" cultivators of the National Park Isiboro-Secure (the NPIS) in the Bolivian Amazon. METHODS: A total of 12% of households in Apillapampa and nearly all households in the NPIS were interviewed about their use of medicinal plants and pharmaceuticals for treating illnesses. Informants were also asked to name any medicinal plants they knew. FINDINGS: In spite of the presence of a primary health care service (PHC) with medical doctor in Apillapampa, an equal number of informants used medicinal plants and pharmaceuticals. In the NPIS, the prevalent use of medicinal plants or pharmaceuticals in any community depended on the distance of the community from the nearest village and from a PHC with medical doctor (r = 0.85 and r = -0.96; both P = 0.05. The NPIS communities' knowledge of plants expressed as the average number of medicinal plants mentioned correlated positively and negatively with distance from the nearest village and use of pharmaceuticals, respectively (r= 0.95, P < 0.005 and r = -0.90, P < 0.05, respectively). CONCLUSION: The cultural importance of traditional medicine and the physical isolation of communities, both in general and from PHCs, are factors that influence the use of and knowledge about medicinal plants.