Physician-directed microbiological testing versus syndromic multiplex PCR in gastroenteritis.

INTRODUCTION: Syndromic multiplex PCR testing is an alternative to conventional stool testing based on physician-directed request forms. The objective of this study was to compare the etiologic yield of conventional microbiological testing based on physician-directed request forms with that of rapid syndromic testing. In addition, the adequacy of the clinician ordering, which is an important piece of the diagnostic stewardship, was evaluated. MATERIALS AND METHODS: Physician-directed conventional microbiological testing and extensive molecular syndromic testing with the Fast Track Diagnostics Gastroenteritis Kit were performed in parallel on 1238 samples to evaluate the contribution of a multiplex panel to the diagnostic process of gastroenteritis. RESULTS: A potential causative pathogen was identified in 18.4% of stool samples by standard microbiological testing and in 41.3% of stool samples tested using the syndromic panel. Only 15.1% of the request forms could be considered successful of which 88.2% were labeled inadequate. Conventional physician-directed based testing missed the etiologic diagnosis in 32.3% of the specimens (excluding sapovirus and astrovirus). Bacterial infections were theoretically not missed as bacterial stool culture was requested on all stool samples, but in 28.6% of the cases, no isolate could be recovered. In 36.9% of the samples testing positive for a viral pathogen, no viral testing was requested. In addition, 72.5% of all samples positive for a parasite were clinically suspected by the physician. CONCLUSION: This study suggests that syndromic multiplex PCR assays are a better strategy for pathogen detection in patients with gastroenteritis than physician-directed laboratory testing based on the clinical presentation.

Semi-quantitative assessment of gastrointestinal viruses in stool samples with Seegene Allplex gastrointestinal panel assays: a solution to the interpretation problem of multiple pathogen detection?

PURPOSE: The aim of the study was to determine and evaluate the clinical usefulness of pathogen specific semi-quantitative cut-offs in stool samples with multiple pathogen detections. METHODS: The PCR (Seegene Allplex Gastrointestinal Virus Assay) data from 4527 positive samples received over 16 months were retrospectively analyzed to investigate the distribution of the Ct values of each individual viral pathogen. By using interquartile ranges for each viral pathogen, pathogen specific semi-quantitative cut-offs were determined. RESULTS: After a thorough analysis of the Ct values, a well-founded decision to exclude all results with a Ct value higher than 35 was made. This approach made it possible to generate a more nuanced report and to facilitate clinical interpretation in case of mixed infections by linking a lower Ct value of a pathogen to a greater likelihood of being a relevant causative pathogen. Moreover, not reporting viral pathogens with a Ct value higher than 35 led to a significant reduction (p < 0.0001) of reported mixed infections compared to oversimplified qualitative or qualitative reporting. CONCLUSION: By omitting very high Ct values and reporting semi-quantitatively, value was added to the syndromic reports, leading to an easier to read lab report, especially in mixed infections.

Binding of temocillin to plasma proteins in vitro and in vivo: the importance of plasma protein levels in different populations and of co-medications.

BACKGROUND: Temocillin plasma protein binding (PPB) in healthy individuals is reported to be ∼85% but had not been studied in patients. OBJECTIVES: To obtain normative data on temocillin PPB in patients in relation to infection and impact of co-medications widely used in ICU. METHODS: Plasma was obtained from healthy individuals (Group #1), non-ICU patients with UTI (Group #2), ICU patients with suspected/confirmed ventriculitis (Group #3) or with sepsis/septic shock (Group #4). Total and unbound temocillin concentrations were measured in spiked samples from temocillin-naive donors (in vitro) or in plasma from temocillin-treated subjects (in vivo). The impact of diluting plasma, using pharmaceutical albumin, or adding drugs potentially competing for PPB was tested in spiked samples. Data were analysed using a modified Hill-Langmuir equation taking ligand depletion into account. RESULTS: Temocillin PPB was saturable in all groups, both in vitro and in vivo. Maximal binding capacity (Bmax) was 1.2-2-fold lower in patients. At 20 and 200 mg/L (total concentrations), the unbound fraction reached 12%-29%, 23%-42% and 32%-52% in Groups #2, #3, #4. The unbound fraction was inversely correlated with albumin and C-reactive protein concentrations. Binding to albumin was 2-3-fold lower than in plasma and non-saturable. Drugs with high PPB but active at lower molar concentrations than temocillin caused minimal displacement, while fluconazole (low PPB but similar plasma concentrations to temocillin) increased up to 2-fold its unbound fraction. CONCLUSIONS: Temocillin PPB is saturable, 2-4-fold lowered in infected patients in relation to disease severity (ICU admission, hypoalbuminaemia, inflammation) and only partially reproducible with albumin. Competition with other drugs must be considered for therapeutic concentrations to be meaningful.

Pitfalls of SARS-CoV-2 antigen testing at emergency department.

BACKGROUND: Current method for diagnosis of SARS-CoV-2 infection is an RT-PCR test on the nasopharyngeal or oropharyngeal swab. Rapid diagnosis is essential for containing viral spread and triage of symptomatic patients presenting to hospital ER departments. As a faster alternative to RT-PCR, we evaluated a SARS-Cov-2 Rapid Antigen test in symptomatic patients presenting to hospital ER departments. METHODS: We evaluated the diagnostic performance of the Roche SARS-CoV-2 Rapid Antigen test (SD Biosensor) for detection of SARS-CoV-2 compared to RT-PCR. RESULTS: Our study showed inferior performance of the SARS-CoV-2 Rapid Antigen test for detection of SARS-CoV-2. Firstly, because of the lack of specificity, which is potentially life-threatening due to the association of nosocomial-acquired SARS-CoV-2 infection. Secondly, with a sensitivity of 45.5%, it is impossible to rule out SARS-CoV-2 infection, resulting in reflex PCR-testing. Comparison of viral load in RT-PCR positive samples with corresponding antigen results showed a significant difference between antigen positive and negative samples. COVID-19 infection will not be detected in patients admitted to the hospital in an early or late phase, typically associated with low viral loads. Sensitivity increases when testing within 5-7 symptomatic days, but the implementation of this cut-off is impractical in ER settings. However, diagnostic performance is better to detect high viral load (> = 5 log10 copies/mL) linked with contagiousness. CONCLUSION: Our study showed inferior performance of the Roche SARS-CoV-2 Rapid Antigen test (SD Biosensor) for detection of SARS-CoV-2 which limits its use as a diagnostic gatekeeper in ER departments, but is able to differentiate contagious individuals.

First report of a prosthetic joint infection with Fannyhessea (Atopobium) vaginae.

This case describes a 77-year-old woman with dysregulated type II diabetes, presenting with a prosthetic joint infection and bacteremia. Computed tomography (CT) of the pelvis and sacrum revealed manifest periprosthetic collections, suggestive of a septic arthritis with loosening of the hip prosthesis. Synovial fluid grew Fannyhessea vaginae, identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). To our knowledge, this is the first report of a prosthetic joint infection due to this organism.

Antimicrobial resistance of Helicobacter pylori in West Flanders - Belgium: an observational cross-sectional study.

OBJECTIVES: Data on Helicobacter pylori (HP) resistance in Belgium are largely based on the patient population of Brussels and Wallonia. Notably Brussels harbours a large proportion of patients with a migration background which might not be representative for other parts of the country. METHODS: An observational cross-sectional study was performed in the province of West Flanders, Belgium for collecting gastric biopsies to examine the resistance of HP. The study population consisted of patients who underwent a gastroduodenoscopy for any medically indicated purpose. Rapid urease testing (RUT) was performed on all biopsies and cultures were only started if the RUT showed positive. RESULTS: 512 patients participated of whom 495 were eligible for analysis: 438 in first line testing and 57 in second line. The growth of HP was successful in 88.9% (n = 88/99) of which 52.3% (n = 46/88) resulted in an antibiogram. The resistance rate in first line was based on 37 succeeded antibiograms and showed 13.5% resistance for clarithromycin (95% confidence interval; 2.5% to 24.5%); 29.7% for metronidazole; 29.7% for levofloxacin; 11.4% for rifampicin; 2.7% for amoxicillin and 0% for tetracycline. CONCLUSION: The primary clarithromycin resistance rate of HP could still be slightly under 15% in West Flanders, Belgium. This might implicate a clarithromycin-based triple therapy is an option for first line empiric eradication in this region according to the Maastricht V/Florence consensus although conclusions must be interpreted with caution due to the rather small sample size. Further testing in Flanders is recommended to confirm these results.

Comparison of Two Commercial Colorimetric Broth Microdilution Tests for Candida Susceptibility Testing: Sensititre YeastOne versus MICRONAUT-AM.

Two colorimetric broth microdilution antifungal susceptibility tests were compared, Sensititre YeastOne and MICRONAUT-AM for nine antifungal agents. One hundred clinical Candida isolates were tested, representing a realistic population for susceptibility testing in daily practice. The reproducibility characteristics were comparable. Only for fluconazole, caspofungin, 5-flucytosine and amphotericin B, an essential agreement of ≥90% could be demonstrated. Sensititre minimal inhibitory concentrations (MICs) were systematically higher than MICRONAUT MICs for all antifungals, except for itraconazole. CLSI clinical breakpoints (CBPs) and epidemiological cut-off values (ECVs) were used for Sensititre MICs while for MICRONAUT the EUCAST CBPs and ECVs were used. Only fluconazole, micafungin, and amphotericin B had a categorical agreement of ≥90%. For fluconazole, micafungin, and amphotericin B the susceptibility proportions were comparable. Susceptibility proportion of posaconazole and voriconazole was higher using the MICRONAUT system. For itraconazole and anidulafungin, the susceptibility proportion was higher using Sensititre. It was not possible to determine the true MIC values or the correctness of a S/I/R result since both commercial systems were validated against a different reference method. These findings show that there is a significant variability in susceptibility pattern and consequently on use of antifungals in daily practice, depending on the choice of commercial system.

A Lemierre-like syndrome caused by Staphylococcus aureus: an emerging disease.

Despite its clear definition, Lemierre's syndrome is frequently used to describe any septic thrombophlebitis of the jugular vein. We report a Lemierre-like syndrome caused by Staphylococcus aureus without an oropharyngeal infection and present a systematic synthesis of reported cases to date of Lemierre-like syndrome caused by S. aureus. In addition to our case, 24 cases were found. In contrast to the classical picture, S. aureus is associated with an oropharyngeal infection in less than half of the cases. Another striking feature is the significant proportion of patients being very young and the fact that all 25 cases were published in the last 17 years. S. aureus is a rare, but emerging cause of Lemierre-like syndrome. Adequate patient care rests on a high index of suspicion, prompt initiation of antibiotic therapy and early detection and management of metastatic abscesses.BULLET POINT SUMMARYThe term Lemierre's syndrome should be reserved for the classic triad of bacteraemia caused by anaerobic pathogens (primarily Fusobacterium necrophorum), evidence of internal jugular venous thrombosis, and a history of recent oropharyngeal infection.Similar syndromes not caused by anaerobic organisms or without history of an oropharyngeal infection should be named Lemierre-like syndrome and may be a more challenging diagnosis.Staphylococcus aureus is a cause of Lemierre-like syndrome, especially in very young children (<2 years old).The Staphylococcus aureus Lemierre-like syndrome is an emerging clinical syndrome.Adequate patient care is based on a high index of suspicion, prompt initiation of broad-spectrum antibiotics and active detection and management of metastatic abscesses.

Atopobium deltae sp. nov., isolated from the blood of a patient with Fournier's gangrene.

A Gram-stain-positive, obligately anaerobic, short rod, designated strain HHRM1715(T), was isolated from the blood of a patient with Fournier's gangrene, complicated by sepsis. On the basis of 16S rRNA gene sequence analysis, strain HHRM1715(T) was shown to belong to the genus Atopobium and was most closely related to Atopobium minutum (95 % similarity). The results of 16S rRNA-gene-based phylogenetic analysis, cellular fatty acid analysis and differential biochemical tests, showed that strain HHRM1715(T) represented a novel species of the genus Atopobium. We therefore describe Atopobium deltae sp. nov. with HHRM1715(T) ( = LMG 27987(T) = CCUG 65171(T)) as the type strain and propose an emended description of the genus Atopobium with regard to the DNA G+C content.

Sepsis with an Atopobium-like species in a patient with Fournier's gangrene.

Atopobium species are Gram-positive, anaerobic, catalase-negative, fastidious bacteria belonging to the family Coriobacteriaceae. We report the isolation of an Atopobium-like species in a patient with Fournier's gangrene and highlight the role of 16S rRNA gene sequencing in the identification of fastidious organisms in the clinical laboratory.

A case of Candida lambica fungemia misidentified as Candida krusei in an intravenous drug abuser.

Only a handful of cases of human Candida lambica infections have been published up to now. We report a Candida lambica fungemia in a young intravenous drug abuser. Using a popular chromogenic agar and a commercial phenotyping gallery, the fungus was initially misidentified as Candida krusei. Key tests to distinguish these closely related species are maximum growth temperature and assimilation of certain substrates present in more elaborate phenotyping assays. Definite confirmation is possible using molecular techniques. Susceptibility testing of the isolate demonstrated amphotericin B (MIC 0.125 microg/ml) susceptible, flucytosine (MIC 2 microg/ml) susceptible, itraconazole (MIC 0.064 microg/ml) susceptible, voriconazole (MIC 1 microg/ml) susceptible, and fluconazole (MIC >64 microg/ml, resistant).

Determination of anti-neutrophil cytoplasmic antibodies in small vessel vasculitis: Comparative analysis of different strategies.

BACKGROUND: Anti-neutrophil cytoplasmic antibodies (ANCA) are associated with primary small vessel vasculitis (SVV). Proteinase-3 (PR3)-ANCA are primarily associated with Wegener granulomatosis, whereas myeloperoxidase (MPO)-ANCA are primarily associated with microscopic polyangiitis (MPA) and vasculitic Churg-Strauss syndrome. We evaluated whether a strategy that is based on screening with ELISA or fluoroenzymeimmunoassay (FEIA) is an accurate alternative to screening with indirect immunofluorescence (IIF). METHODS: C-ANCA and P-ANCA were determined by IIF and PR3-ANCA and MPO-ANCA were determined by ELISA (Inova) or FEIA (Phadia) on 326 patients (38 with newly diagnosed SVV and 288 diseased controls). RESULTS: Specificity and positive likelihood ratios were higher for ELISA and FEIA than for IIF. Post-test probability for SVV of a positive test result was higher for ELISA and FEIA than for IIF. Decision tree analysis in which several testing strategies were compared revealed that a testing strategy that is based on screening with ELISA or FEIA had an expected clinical utility that was comparable to screening with IIF and confirming with ELISA or FEIA. The highest expected clinical utility was found when both IIF and ELISA or FEIA were performed on all samples. CONCLUSIONS: A strategy based on screening for ANCA with ELISA or FEIA (without prior IIF) is a valuable alternative to screening with IIF and confirming with ELISA or FEIA.