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.

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.

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.

Using online periodontal case-based discussions to synchronize theoretical and clinical undergraduate dental education

BACKGROUND

Clinical experience is important in undergraduate dental education, but (suitable) patients to learn from are often lacking. Online case-based discussions were introduced to overcome patient dependency and to synchronize theoretical with clinical education.

MATERIALS AND METHODS

Undergraduate dental students in groups of 5-7 discussed online clinical case reports presenting either minor (2nd year) or complex periodontal pathology (3rd year). Each case consisted of a brief patient history, extra- and intra-oral clinical pictures, periodontal chart, peri-apical and/or orthopantomographic radiographs. Students had to discuss diagnosis and treatment planning. Questionnaires assessed students' and supervisors' general appreciation (score on 20), time investment and opinions about organisation, relation case/course content, future planning, learning effect and online environment (5-point Likert scale). A crossover design with three tests (pre-test, test in between and post-test) was used to investigate whether the frequency of case introduction (one case per week vs. one case element per week) had an effect on learning. Data was analysed with descriptive statistics (questionnaires) and repeated measures ANOVA (crossover design).

RESULTS

Students (n=119) and supervisors (n=9) highly appreciated the exercise. Students reported spending on average 74 min per week to read a case, prepare and post messages. Supervisors' total time investment was 342 min per semester to create a case, provide online feedback and to prepare a live-discussion. No significant differences in test-scores were found between the two modalities of case introduction.

CONCLUSION

Online case-based discussions, in conjunction with a theoretical course, are valuable additions to the dental curriculum, especially to reinforce the transition from theory to clinical practice.

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).