VIDAS3® TB-IGRA assay: evaluation of performance characteristics in a predominantly low risk, low incidence population

OBJECTIVES

To evaluate the analytical performance of the TB-IGRA® assay on the VIDAS3 platform (bioMérieux) when testing a predominantly low risk population in a low incidence area.

RESULTS

Eighty-eight percent of the results were concordant between QuantiFERON®-TB Gold-Plus (QFT®-Plus, QIAGEN) and TB-IGRA®. All 12 of 99 (12.1%) discordant results were determined positive only with the TB-IGRA® assay. In 11 of 12 of these discordant cases, no explanation could be found in the medical record. Five of these discrepant results were probably caused by the use of contaminated stimulation reagents. The remaining 6 discrepant samples were also part of the reproducibility experiment and only 2 results were reproducible positive. Overall, in the reproducibility experiment 5 of 25 (20.0 %) results were not repeatable.

CONCLUSIONS

the TB-IGRA® assay seems prone to contamination. Besides, we documented a reproducibility of only 80.0% with the TB-IGRA® assay.

Ruminococcus gnavus bacteremia, an uncommon presentation of a common member of the human gut microbiota: case report and literature review

Case report: We present a case of a 66-year-old female diagnosed with R. gnavus bacteremia associated with fecal peritonits secondary to small-bowel herniation and perforation. Identification  as R. gnavus was delayed because of absence of this species in the MALDI-TOF MS database (Vitek MS, bioMérieux). Identification was provided by 16S rRNA gene sequencing. Review: R. gnavus, a Gram-positive, strictly anaerobic bacterium, is a member of the human gut microbiota. Dysbiosis in the gut microbiota, with increased amounts of R. gnavus, has been described in inflammatory bowel disease. R. gnavus has only been reported occasionally as the cause of infections. Hence the potential pathogenicity is not yet fully recognized, and data regarding the antimicrobial susceptibility profile are rare. Identification of anaerobic bacteria such as R. gnavus is greatly accelerated  as a result of the introduction of MALDI-TOF MS. However, as illustrated in this case report, an extensive and up-to-date MALDI-TOF MS database is necessary for providing an accurate identification.

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.

Staphylococcus petrasii subsp. pragensis subsp. nov., occurring in human clinical material

Seven coagulase-negative, oxidase-negative and novobiocin-susceptible staphylococci assigned tentatively as Staphylococcus petrasii were investigated in this study in order to elucidate their taxonomic position. All strains were initially shown to form a genetically homogeneous group separated from remaining species of the genus Staphylococcus by using a repetitive sequence-based PCR fingerprinting with the (GTG)5 primer. Phylogenetic analysis based on 16S rRNA gene, hsp60, rpoB, dnaJ, gap and tuf sequences showed that the group is closely related to Staphylococcus petrasii but separated from the three hitherto known subspecies, S. petrasii subsp. petrasii, S. petrasii subsp. croceilyticus and S. petrasii subsp. jettensis. Further investigation using automated ribotyping, MALDI-TOF mass spectrometry, fatty acid methyl ester analysis, DNA-DNA hybridization and extensive biotyping confirmed that the analysed group represents a novel subspecies within S. petrasii, for which the name Staphylococcus petrasii subsp. pragensis subsp. nov. is proposed. The type strain is NRL/St 12/356(T) ( = CCM 8529(T) = LMG 28327(T)).

Persistence of frequently transmitted drug-resistant HIV-1 variants can be explained by high viral replication capacity

Background

In approximately 10% of newly diagnosed individuals in Europe, HIV-1 variants harboring transmitted drug resistance mutations (TDRM) are detected. For some TDRM it has been shown that they revert to wild type while other mutations persist in the absence of therapy. To understand the mechanisms explaining persistence we investigated the in vivo evolution of frequently transmitted HIV-1 variants and their impact on in vitro replicative capacity.

Results

We selected 31 individuals infected with HIV-1 harboring frequently observed TDRM such as M41L or K103N in reverse transcriptase (RT) or M46L in protease. In all these samples, polymorphisms at non-TDRM positions were present at baseline (median protease: 5, RT: 6). Extensive analysis of viral evolution of protease and RT demonstrated that the majority of TDRM (51/55) persisted for at least a year and even up to eight years in the plasma. During follow-up only limited selection of additional polymorphisms was observed (median: 1).

To investigate the impact of frequently observed TDRM on the replication capacity, mutant viruses were constructed with the most frequently encountered TDRM as site-directed mutants in the genetic background of the lab strain HXB2. In addition, viruses containing patient-derived protease or RT harboring similar TDRM were made. The replicative capacity of all viral variants was determined by infecting peripheral blood mononuclear cells and subsequently monitoring virus replication. The majority of site-directed mutations (M46I/M46L in protease and M41L, M41L + T215Y and K103N in RT) decreased viral replicative capacity; only protease mutation L90M did not hamper viral replication. Interestingly, most patient-derived viruses had a higher in vitro replicative capacity than the corresponding site-directed mutant viruses.

Conclusions

We demonstrate limited in vivo evolution of protease and RT harbouring frequently observed TDRM in the plasma. This is in line with the high in vitro replication capacity of patient-derived viruses harbouring TDRM compared to site-directed mutant viruses harbouring TDRM. As site-directed mutant viruses have a lower replication capacity than the patient-derived viruses with similar mutational patterns, we propose that (baseline) polymorphisms function as compensatory mutations improving viral replication capacity.

Reclassification of Staphylococcus jettensis De Bel et al. 2013 as Staphylococcus petrasii subsp. jettensis subsp. nov. and emended description of Staphylococcus petrasii Pantucek et al. 2013

The type and clinical strains of two recently described coagulase-negative species of the genus Staphylococcus, Staphylococcus petrasii and Staphylococcus jettensis, were compared using dnaJ, tuf, gap, hsp60 and rpoB gene sequences, DNA-DNA hybridization, ribotyping, repetitive sequence-based PCR fingerprinting and extensive biochemical characterization. Based on the results, the species description of S. petrasii has been emended and S. jettensis should be reclassified as a novel subspecies within S. petrasii for which the name Staphylococcus petrasii subsp. jettensis subsp. nov. is proposed. The type strain is SEQ110(T) ( = LMG 26879(T) = CCUG 62657(T) = DSM 26618(T) = CCM 8494(T)).

Staphylococcus jettensis sp. nov., a coagulase-negative staphylococcal species isolated from human clinical specimens

Eight coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human clinical specimens at two different Belgian medical facilities. All strains were non-motile, Gram-stain-positive, catalase-positive cocci. DNA G+C content, peptidoglycan type, menaquinone pattern, the presence of teichoic acid and cellular fatty acid composition were in agreement with the characteristics of species of the genus Staphylococcus . Sequencing of the 16S rRNA gene and four housekeeping genes (dnaJ, tuf, gap and rpoB) demonstrated that these strains constitute a separate taxon within the genus Staphylococcus . Less than 41 % DNA–DNA hybridization with the most closely related species of the genus Staphylococcus ( Staphylococcus haemolyticus , Staphylococcus hominis and Staphlococcus lugdunensis ) was observed. Key biochemical characteristics that allowed these bacteria to be distinguished from their nearest phylogenetic neighbours are arginine dihydrolase positivity, ornithine decarboxylase negativity and inability to produce acid aerobically from d-mannose, α-lactose and turanose. Acid is produced aerobically from trehalose. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus jettensis sp. nov. The type strain is SEQ110T ( = LMG 26879T = CCUG 62657T = DSM 26618T).

RegaDB: community-driven data management and analysis for infectious diseases

Summary: RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.

Availability and implementation: Source code, binaries and documentation are available on http://rega.kuleuven.be/cev/regadb. RegaDB is written in the Java programming language, using a web-service-oriented architecture.

Contact:pieter.libin@rega.kuleuven.be

HIV-1 low-level viraemia assessed with 3 commercial real-time PCR assays show high variability

Background

Current real-time PCR-based HIV-1 viral load (VL) assays allow the detection of residual viraemia in antiretroviral-treated patients. The clinical outcome of HIV1 patients experiencing low-level replication (<50 cop/mL) in comparison with fully suppressed patients is currently debated. We analysed variability of 3 VL assays <50 cop/mL, and evaluated the reproducibility of viral blips <100 cop/mL.

Methods

Three commercial VL assays were tested: Versant HIV-1 RNA 1.0 kPCR (Siemens), Abbott Realtime HIV-1, and Cobas Ampliprep/Cobas Taqman HIV-1 v2.0 (Roche). Ten replicates of a reference sample at 4 low target dilutions were tested to evaluate assay variability. Prospective collection of 181 clinical samples with detectable VL <50 cop/mL was used to evaluate intra-and inter-assay variability by triplicate testing. Samples from 26 patients experiencing a viral blip were retested.

Results

All assays showed substantial variability at low VL level: the coefficient of variation at 100, 50, 25 and 12 cop/mL ranged respectively from 32 to 44%, 35 to 68%, 41 to 83% and 33 to 77%. In the intra-assay evaluation of repeatability, 52.5 to 57.5% of detectable VL <50 cop/mL tested in triplicate showed at least one fully undetected result. Variability was similar in the inter-assay arm. The VL blips could only be reproduced in 19% of cases.

Conclusions

The most recent versions of widespread commercial VL assays showed substantial variability at low levels and residual viraemia could not be consistently reproduced. Patient outcome studies comparing residual VL to full suppression are therefore biased when using commercial assays.

Case report: Infrapatellar bursitis caused by Prototheca wickerhamii

A 54-year-old immunocompetent man presented with an infrapatellar bursitis caused by Prototheca wickerhamii. Because of clinical and microbiological relapse two weeks after bursectomy, six weekly injections of 5 mg of conventional amphotericin B were chosen for intrabursal treatment. Four months after completion of the treatment, the patient remains cured.

Antimicrobial susceptibility of Streptococcus pneumoniae isolates from vaccinated and non-vaccinated patients with a clinically confirmed diagnosis of community-acquired pneumonia in Belgium

We assessed the in vitro susceptibility of Streptococcus pneumoniae isolates from patients with confirmed community-acquired pneumonia (CAP) to β-lactams, macrolides and fluoroquinolones and the association of non-susceptibility and resistance with serotypes/serogroups (STs/SGs), patient's risk factors and vaccination status. Samples (blood or lower respiratory tract) were obtained in 2007-2009 from 249 patients (from seven hospitals in Belgium) with a clinical and radiological diagnosis of CAP [median age 61 years (11.6% aged <5 years); 85% without previous antibiotic therapy; 86% adults with level II Niederman's severity score]. MIC determination (EUCAST breakpoints) showed for: (i) amoxicillin, 6% non-susceptible; cefuroxime (oral), 6.8% resistant; (ii) macrolides: 24.9% erythromycin-resistant [93.5% erm(B)-positive] but 98.4% telithromycin-susceptible; and (iii) levofloxacin and moxifloxacin, all susceptible. Amongst SGs: ST14, all resistant to macrolides and most intermediate to β-lactams; SG19 (>94% ST19A), 73.5% resistant to macrolides and 18-21% intermediate to β-lactams; and SG6, 33% resistant to clarithromycin. Apparent vaccine failures: 3/17 for 7-valent vaccine (children; ST6B, 23F); 16/29 for 23-valent vaccine (adults ST3, 7F, 12F, 14, 19A, 22F, 23F, 33F). Isolates from nursing home residents, hospitalised patients and patients with non-respiratory co-morbidities showed increased MICs for amoxicillin, all β-lactams, and β-lactams and macrolides, respectively. Regarding antibiotic susceptibilities: (i) amoxicillin is still useful for empirical therapy but with a high daily dose; (ii) cefuroxime axetil and macrolides (but not telithromycin) are inappropriate for empirical therapy; and (iii) moxifloxacin and levofloxacin are the next 'best empirical choice' (no resistant isolates) but levofloxacin will require 500 mg twice-daily dosing for effective coverage.