Multicenter clinical evaluation of the Luminex Aries Flu A/B & RSV assay for pediatric and adult respiratory tract specimens

ABSTRACT Influenza A and B viruses and respiratory syncytial virus (RSV) are three common viruses implicated in seasonal respiratory tract infections and are a major cause of morbidity and mortality in adults and children worldwide. In recent years, an increasing number of commercial molecular tests have become available to diagnose respiratory viral infections. The Luminex Aries Flu A/B &amp; RSV assay is a fully automated sample-to-answer molecular diagnostic assay for the detection of influenza A, influenza B, and RSV. The clinical performance of the Aries Flu A/B &amp; RSV assay was prospectively evaluated in comparison to that of the Luminex xTAG respiratory viral panel (RVP) at four North American clinical institutions over a 2-year period. Of the 2,479 eligible nasopharyngeal swab specimens included in the prospective study, 2,371 gave concordant results between the assays. One hundred eight specimens generated results that were discordant with those from the xTAG RVP and were further analyzed by bidirectional sequencing. Final clinical sensitivity values of the Aries Flu A/B &amp; RSV assay were 98.1% for influenza A virus, 98.0% for influenza B virus, and 97.7% for RSV. Final clinical specificities for all three pathogens ranged from 98.6% to 99.8%. Due to the low prevalence of influenza B, an additional 40 banked influenza B-positive specimens were tested at the participating clinical laboratories and were all accurately detected by the Aries Flu A/B &amp; RSV assay. This study demonstrates that the Aries Flu A/B &amp; RSV assay is a suitable method for rapid and accurate identification of these causative pathogens in respiratory infections.</jats:p

Diversity of Rhodopirellula and related planctomycetes in a North Sea coastal sediment employing carB as molecular marker.

Rhodopirellula is an abundant marine member of the bacterial phylum Planctomycetes. Cultivation studies revealed the presence of several closely related Rhodopirellula species in European coastal sediments. Because the 16S rRNA gene does not provide the desired taxonomic resolution to differentiate Rhodopirellula species, we performed a comparison of the genomes of nine Rhodopirellula strains and six related planctomycetes and identified carB, coding for the large subunit of carbamoylphosphate synthetase, as a suitable molecular marker. In this study, we investigated the diversity of Rhodopirellula in coastal intertidal surface sediments of Sylt island, North Sea, using the 16S rRNA and carB genes as molecular markers. The carB clone and pyrosequencing libraries revealed the presence of 12 species of Rhodopirellula and of 66 species in closely related undescribed genera, a diversity that was not detected with a 16S rRNA gene library. This study demonstrates that the carB gene is a powerful molecular marker for detecting Rhodopirellula species in the environment and may be used for the taxonomic evaluation of new strains

Competition between Nitrospira spp. and Nitrobacter spp. in nitrite-oxidizing bioreactors

In this work the question was addressed if in nitrite-oxidizing activated sludge systems the environmental competition between Nitrobacterspp. and Nitrospira spp., which only recently has been discovered to play a role in these systems, is affected by the nitrite concentrations. Two parallel chemostats were inoculated with nitrifying-activated sludge containing Nitrospira and operated under identical conditions. After addition of Nitrobacter to both chemostats, the nitrite concentration in the influent of one of the chemostats was increased such that nitrite peaks in the bulk liquid of this reactor were detected. The other chemostat served as control reactor, which always had a constant nitrite influent concentration. The relative cellular area (RCA) of Nitrospira and Nitrobacter was determined by quantitative fluorescence in situ hybridization (FISH). The nitrite perturbation stimulated the growth of Nitrobacter while in the undisturbed control chemostat Nitrospira dominated. Overall, the results of this experimental study support the hypothesis that Nitrobacter is a superior competitor when resources are abundant, while Nitrospira thrive under conditions of resource scarcity. Interestingly, the dominance of Nitrobacter over Nitrospira, caused by the elevated nitrite concentrations, could not be reverted by lowering the available nitrite concentration to the original level. One possible explanation for this result is that when Nitrobacter is present at a certain cell density it is able to inhibit the growth of Nitrospira. An alternative explanation would be that the length of the experimental period was not long enough to observe an increase of the Nitrospira population. (c) 2006 Wiley Periodicals, Inc

Nitrifying and heterotrophic population dynamics in biofilm reactors: effects of hydraulic retention time and the presence of organic carbon

Two biofilmreactors operated with hydraulic retention times of 0.8 and 5.0 h were used to study the links between population dynamics and reactor operation performance during a shift in process operation from pure nitrification to combined nitrification and organic carbon removal. The ammonium and the organic carbon loads were identical for both reactors. The composition and dynamics of the microbial consortia were quantified by fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes combined with confocal laser scanning microscopy, and digital image analysis. In contrast to past research, after addition of acetate as organic carbon nitrification performance decreased more drastically in the reactor with longer hydraulic retention time. FISH analysis showed that this effect was caused by the unexpected formation of a heterotrophic microorganism layer on top of the nitrifying biofilm that limited nitrifiers oxygen supply. Our results demonstrate that extension of the hydraulic retention time might be insufficient to improve combined nitrification and organic carbon removal in biofilm reactors.Ministério da Ciência, Tecnologia e Ensino Superior. Fundação para a Ciência e a Tecnologia (FCT) - PRAXIS XXI BD/15943/98). Deutscher Akademischer Austauschdienst (A/99/06961). European Comission - T.M.R. BioToBio project. Deutsche Forschungsgemeinschaft

Chitin mixed in potting soil alters lettuce growth, the survival of zoonotic bacteria on the leaves and associated rhizosphere microbiology

Chitin is a promising soil amendment for improving soil quality, plant growth, and plant resilience. The objectives of this study were twofold. First, to study the effect of chitin mixed in potting soil on lettuce growth and on the survival of two zoonotic bacterial pathogens, Escherichia colt O157:H7 and Salmonella enterica on the lettuce leaves. Second, to assess the related changes in the microbial lettuce rhizosphere, using phospholipid fatty acid (PLFA) analysis and amplicon sequencing of a bacterial 16S rRNA gene fragment and the fungal ITS2. As a result of chitin addition, lettuce fresh yield weight was significantly increased. S. enterica survival in the lettuce phyllosphere was significantly reduced. The E. coli O157:H7 survival was also lowered, but not significantly. Moreover, significant changes were observed in the bacterial and fungal community of the lettuce rhizosphere. PLFA analysis showed a significant increase in fungal and bacterial biomass. Amplicon sequencing showed no increase in fungal and bacterial biodiversity, but relative abundances of the bacterial phyla Acidobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Proteobacteria and the fungal phyla Ascomycota, Basidiomycota, and Zygomycota were significantly changed. More specifically, a more than 10-fold increase was observed for operational taxonomic units belonging to the bacterial genera Cellvibrio, Pedobacter, Dyadobacter, and Streptomyces and to the fungal genera Lecanicillium and Mortierella. These genera include several species previously reported to be involved in biocontrol, plant growth promotion, the nitrogen cycle and chitin degradation. These results enhance the understanding of the response of the rhizosphere microbiome to chitin amendment. Moreover, this is the first study to investigate the use of soil amendments to control the survival of S. enterica on plant leaves

Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria

Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study

Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification

The substrate fluorescein-tyramide was combined with oligonucleotide probes directly labeled with horseradish peroxidase to improve the sensitivity of in situ hybridization of whole fixed bacterial cells. Flow cytometry and quantitative microscopy of cells hybridized by this technique showed 10- to 20-fold signal amplifications relative to fluorescein-manolabeled probes. The application of the new technique to the detection of natural bacterial communities resulted in very bright signals; however, the number of detected cells was significantly lower than that detected with fluorescently monolabeled, rRNA-targeted oligonucleotide probes

Comparison of the Panther Fusion and BD MAX GBS Assays for Detection of Group B Streptococcus in Prenatal Screening Specimens.

Streptococcus agalactiae, or Group B Streptococcus (GBS) is the cause of early and late-onset GBS disease in neonates and can present as septicemia, meningitis, and pneumonia. Our objective was to compare the performance of two FDA-approved nucleic acid amplification tests (NAATs), the Panther Fusion and BD MAX™ systems, for detection of group B Streptococcus (GBS) in vaginal-rectal screening specimens. A total of 510 vaginal-rectal prepartum specimens were tested simultaneously in both NAATs following broth enrichment. Assay agreement was calculated using the kappa statistics. Overall agreement between assays was 99.0% (505/510; 95% CI: 0.951 to 0.997; kappa = 0.974). Discordant results were re-tested with both assays and by standard culture. The assays were also compared for workflow characteristics, including time to first results (TFR), total turnaround time (TAT), number of return visits to load additional specimens, and hands-on time (HoT).Using a standard run size of 60 specimens/day, the Panther Fusion assay had a longer time to TFR (2.4 vs. 2.0 hours), but showed a shorter overall TAT for all 60 samples (3.98 vs. 7.18 hours) due to an increased initial sample loading capacity, required less labor (35.0 vs. 71.3 sec/sample) and fewer return visits for loading additional specimens (0 vs. 2). The Panther Fusion system also had a larger sample loading capacity (120 vs. 24 samples) and greater 8-hour throughput (335 vs. 96 samples). In summary, the Panther Fusion GBS assay has comparable clinical performance to the BD MAX GBS assay, but provides a faster TAT, less HoT, and higher throughput

Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment-water interface of two lakes and the Baltic Sea

The functional gene amoA was used to compare the diversity of ammonia-oxidizing bacteria (AOB) in the water column and sediment-water interface of the two freshwater lakes Plusssee and Schöhsee and the Baltic Sea. Nested amplifications were used to increase the sensitivity of amoA detection, and to amplify a 789-bp fragment from which clone libraries were prepared. The larger part of the sequences was only distantly related to any of the cultured AOB and is considered to represent new clusters of AOB within the Nitrosomonas/Nitrosospira group. Almost all sequences from the water column of the Baltic Sea and from 1-m depth of Schöhsee were related to different Nitrosospira clusters 0 and 2, respectively. The majority of sequences from Plusssee and Schöhsee were associated with sequences from Chesapeake Bay, from a previous study of Plusssee and from rice roots in Nitrosospira-like cluster A, which lacks sequences from Baltic Sea. Two groups of sequences from Baltic Sea sediment were related to clonal sequences from other brackish/marine habitats in the purely environmental Nitrosospira-like cluster B and the Nitrosomonas-like cluster. This confirms previous results from 16S rRNA gene libraries that indicated the existence of hitherto uncultivated AOB in lake and Baltic Sea samples, and showed a differential distribution of AOB along the water column and sediment of these environment

Are the fathers alright? A systematic and critical review of studies on gay and bisexual fatherhood

The purpose of the present systematic and critical review was to assess the findings and to identify the gaps in the literature concerning gay and bisexual fathers. A comprehensive search of relevant literature using electronic databases and reference lists for articles published until December 2016 was conducted. A total of 63 studies, spanning from 1979 to 2016, were collected. More than half of the studies were published after 2011 and the overwhelming majority were conducted in the United States. Nine themes were identified in the studies reviewed: (1) Pathways to fatherhood; (2) Motivations for fatherhood; (3) Parenting experiences and childrearing; (4) Family life and relationship quality; (5) Gender and father identities and gender-role orientation; (6) Disclosure of sexual identity; (7) Social climate; (8) Father’s psychosocial adjustment; and (9) Children’s psychosocial adjustment. It was found that research on gay fatherhood appears to be more heterogeneous than on lesbian motherhood, perhaps because of the variety of pathways to parenthood (via co-parenting, adoption, fostering, or surrogacy). Two-father families are becoming more visible in research on sexual minority parenting and gradually transforming the conceptualization of parenting in family research