Inaccuracy of routine susceptibility tests for detection of erythromycin resistance of Campylobacter jejuni and Campylobacter coli

In The Netherlands, both an increase in and regional differences in erythromycin resistance of Campylobacter jejuni and Campylobacter coli have been reported. To determine the accuracy of routine tests for erythromycin resistance, 48 erythromycin-resistant isolates from various laboratories that participate in the Dutch surveillance of Campylobacter infections were reinvestigated. Initial susceptibility testing for erythromycin had been performed by disk diffusion in six and MIC-based methods in two laboratories. Reinvestigation was carried out using broth microdilution as a reference standard, as well as E-test and genetic resistance testing. Of 36 C. jejuni isolates reported by the initial laboratories as erythromycin-resistant, four (11%) and five (14%) were confirmed as erythromycin-resistant using broth microdilution according to CLSI and EUCAST resistance criteria, respectively. Erythromycin resistance was found in eight of 12 (67%) C. coli isolates according to both criteria. Results of E-tests were in accordance with these results in all isolates. Resistance-associated mutations in the 23S rRNA gene (A2059G and A2058T) were found in all isolates showing high-level resistance, whereas none were found in susceptible isolates. Routine determination of the erythromycin resistance of C. jejuni and C. coli shows unacceptable interlaboratory variation. In the absence of standardized protocols and interpretive criteria for disk diffusion, and while we await the development of easily applicable and reliable methods for molecular resistance testing, the use of broth microdilution remains the best method

Prevention and treatment of bronchopneumonia in mice caused by mouse-adapted variant of avian H5N2 influenza A virus using monoclonal antibody against conserved epitope in the HA stem region.

The effects of monoclonal antibody (MAb) C179 recognizing a conformational epitope in the middle of the hemagglutinine (HA) stem region were examined in a mouse model in the experiments of prevention and treatment of lethal bronchopneumonia caused by influenza A virus of H5 subtype. To model the lethal infection, avian nonpathogenic strain A/mallard duck/Pennsylvania/ 10218/84 (H5N2) was adapted to mice. This resulted in highly pathogenic pneumovirulent mouse-adapted (MA) variant, which was characterized.

Comparison of the GeneFinder (TM) COVID-19 Plus RealAmp Kit on the sample-to-result Platform ELITe InGenius to the national reference method: an added value of N gene target detection?

Background: Due to the emergence of the coronavirus disease 2019 (COVID-19) pandemic there is an urgent need for rapid and accurate testing on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).Objectives: The aim of this study was to assess the diagnostic performance of the GeneFinderTMCOVID-19 Plus RealAmp Kit on the ELITe InGenius sample-to-result platform, which is a commercial nucleic acid amplification test (NAT) targeting genes of SARS-CoV-2.Study design: Patients were eligible between March 18 and May 27, 2020, when they had respiratory symptoms that were suspected for COVID-19. The InGenius platform was compared to routine in-house NAT that was validated according to the national reference.Results: Of 128 randomly selected patients, 58 (45 %) tested positive and 55 (43 %) tested negative in both platforms. Sensitivity of the InGenius platform was 100 % (95 % confidence interval 94-100). In the remaining 15 (12 %) cases E and RdRp genes were not detected in both platforms but the nucleoprotein (N) gene was tested positive by the InGenius platform. All solitary N gene positive cases were confirmed by a N-gene specific in-house validated NAT, and most of these patients could also be considered positive based on other recently available COVID-19 positive respiratory samples or highly suspected radiological findings.Conclusion: The InGenius platform for SARS-CoV-2 detection has excellent sensitivity, is easy to use and provides fast results. The inclusion of the N gene as a third gene target may further increase sensitivity for the diagnosis of COVID-19 in comparison to the national reference method.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

G protein variation in respiratory syncytial virus group A does not correlate with clinical severity

Respiratory syncytial virus group A strain variations of 28 isolates from The Netherlands collected during three consecutive seasons were studied by ana

Clinical performance of two new, fully integrated molecular platforms used for HIV-1, HBV and HCV viral load analysis, the NeuMoDx 288 and the Alinity m

Background: Viral load (VL) determination in patients with human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV) and hepatitis C virus (HCV) is essential for proper patient management and follow-up. New molecular platforms have been developed to fully automate these diagnostic assays.Objective: Evaluation of the clinical performance of HIV-1, HBV and HCV VL assays on the Alinity m (Abbott) and NeuMoDx (Qiagen) molecular platforms.Method: Test panels of the three viruses have been compiled of 100 plasma and/or serum samples per target containing non-detectable, non-quantifiable and quantifiable VLs. All samples were retrospectively tested on the Alinity m and NeuMoDx platforms according to manufacturers' instructions. Results: A total of 74, 86 and 66 samples with valid results for both platforms were included in the HIV-1, HBV and HCV analysis respectively. Overall qualitative agreement of the assays on both platforms was 78% for HIV-1, 93% for HBV and 100% for HCV. Quantitative agreement (less than 0.5 log difference) was shown to be 68% for HIV-1, 68% for HBV and 94% for HCV.Conclusion: The Alinity m and NeuMoDx HCV assay have a comparable performance. Quantification differences in the HIV-1 assay were mostly apparent in the lower VLs and under-quantification of the NeuMoDx HBV assay was observed.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield

Introduction Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. Areas covered This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. Expert opinion The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

Increasing diagnostic possibilities using the geneLEAD VIII platform for detection of SARS-CoV-2

At the time SARS-CoV-2 was identified as the cause of coronavirus disease 2019 (COVID-19) no in vitro diagnostic (IVD) tests were available since it was a new virus. Very shortly after the release of the genomic sequence of SARS-CoV-2, laboratory-developed tests (LDTs) were developed, made available and implemented in several laboratories in the Netherlands and globally. In this study, the performance of an E-gene Sarbeco specific realtime reverse-transcriptase PCR (RT-PCR) was verified on the open modus of the geneLEAD VIII sample-to-answer platform. The results obtained from 134 clinical samples, of which 63 had been tested positive, showed almost complete concordance compared to the same PCR on the routine diagnostic systems and that was validated according to the national reference standard. The only discordant sample tested positive using the routine diagnostic workflow with a cycle threshold (CT) value of 37.7, while the sample tested negative using the geneLEAD VIII workflow. In addition, good performance was achieved in analyzing a blinded SARS-CoV-2 external quality assurance (EQA) panel. Implementation of the geneLEAD VIII platform as routine diagnostic tool resulted in testing 871 clinical samples with 115 positive results. In conclusion, the geneLEAD VIII SARSCoV-2 workflow presented in this study showed excellent diagnostic performance and with a rapid turnaround time of approximately two hours it proved a valuable option for STAT SARS-CoV-2 testing in the absence of (rapid, CE-IVD) point-of-care testing platforms.Molecular basis of virus replication, viral pathogenesis and antiviral strategie

A revision of the spider genera Drassodes and Tivodrassus (Araneae, Gnaphosidae) in North America. American Museum novitates ; no. 2593

29 p. : ill., maps ; 26 cm.Includes bibliographical references (p. 28-29)."Seven North American species of Drassodes and four of Tivodrassus are diagnosed and described. The usefulness of various genitalic characters for species discrimination in Drassodes is discussed. Five new species are described: D. mirus from the Rocky Mountains, D. angulus from California, and T. pecki, T. reddelli, and T. farias from Mexico. Drassodes saccatus (Emerton) is removed from the synonymy of D. neglectus (Keyserling) and considered a valid species. Five specific names are newly synonymized: D. phanus (Chamberlin) and D. yavapainus (Chamberlin), both with D. gosiutus Chamberlin; and D. centralis F.O.P.-Cambridge, D. celes Chamberlin, and D. robinsoni Chamberlin, all with D. saccatus (Emerton). The males of D. louisianus Roddy and T. ethophor Chamberlin and Ivie are described for the first time. Drassodes perditus Banks is transferred to Herpyllus"--P. [1]

A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters

The recently observed increase in invasive Streptococcus pyogenes infections causes concern in Europe. However, conventional molecular typing methods lack discriminatory power to aid investigations of outbreaks caused by S. pyogenes. Therefore, there is an urgent need for high-resolution molecular typing methods to assess genetic relatedness between S. pyogenes isolates. In the current study, we aimed to develop a novel high-resolution core-genome multilocus sequence typing (cgMLST) scheme for S. pyogenes and compared its discriminatory power to conventional molecular typing methods. The cgMLST scheme was designed with the commercial Ridom SeqSphere+ software package. To define a cluster threshold, the scheme was evaluated using publicly available data from nine defined S. pyogenes outbreaks in the United Kingdom. The cgMLST scheme was then applied to 23 isolates from a suspected S. pyogenes outbreak and 117 S. pyogenes surveillance isolates both from the Netherlands. MLST and emm-typing results were used for comparison to cgMLST results. The allelic differences between isolates from defined outbreaks ranged between 6 and 31 for isolates with the same emm-type, resulting in a proposed cluster threshold of </p

A two minute liquid based sample preparation for rapid SARS-CoV2 real-time PCR screening: a multicentre evaluation

Background: Apart from major health concerns associated to the SARS-coronavirus-2 (SARS-CoV-2) pandemic, also the diagnostic workflow encountered serious problems. Limited availability of kit components, buffers and even plastics has resulted in suboptimal testing procedures worldwide. Alternative workflows have been implemented to overcome these difficulties. Recently a liquid based sample prep has been launched as solution to overcome limitations in relation to nucleic acid extraction.Objective: Multicenter evaluation of the QlAprep& Viral RNA UM kit (QIA P&A) for rapid sample preparation and real-time PCR detection of SARS-CoV-2 in comparison to standardized laboratory testing methods.Study design: Selected samples of the routine diagnostic workflow at Clinical Microbiology Laboratories of four Dutch hospitals have been subjected to the rapid QIA P&A protocol and the results have been compared to routine diagnostic data.Results: Combining results of manual and automated procedures, a total of 377 clinical samples of which 202 had been tested positive with a wide range of C-T values, showed almost complete concordance in the QIA P&A assay for samples up to C-T values of 33 with one exception of C-T 31. Prospectively 60 samples were tested and also showed 100 % concordance with 5 positives. The method has been automated by two centres.Conclusions: Despite an input of only 8 mu L of clinical sample, the QIA P&A kit showed good performance for sample preparation and amplification of SARS-CoV-2 and can contribute as a rapid molecular testing strategy in managing the CoV-2 pandemic.Molecular basis of virus replication, viral pathogenesis and antiviral strategie