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  • Are More Specimens Always Better? Microbiologic Diagnosis of Periprosthetic Joint Infections
    01/15/2018
  • “Seq”ing the bacterial genes necessary for growth-arrest
    01/12/2018
  • Assessing risk factors for infection with carbapenem-resistant Enterobacteriaceae
    01/12/2018
  • Market Your Clinical Lab Skills when Applying to Graduate School
    01/10/2018
  • New ASM Press author encourages all to enjoy the puzzle-like nature of bioinformatics
    01/09/2018
  • January 2018 ASMClinMicro News Round-Up
    01/08/2018
  • Ensuring Medical Device and Pharmaceutical Safety: An Interview With an Industrial Microbiologist
    01/03/2018
  • The mycobiome, fungal dysbiosis, and health in the gut.
    12/22/2017
  • In Case You Missed It - top 2017 mBiosphere posts
    12/21/2017
  • Best of Bugs & Drugs 2017
    12/14/2017

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  • Tuesday, 16 January 2018

    Background: Bacterial vaginosis (BV) is a prevalent multifactorial disease of women in their reproductive years characterized by a shift from the healthy Lactobacillus sp. dominated microbial community towards a highly diverse anaerobic community. BV can initially be cured by antibiotic therapy in most women, but the high recurrence frequency represents a serious challenge. Moreover, for unknown reasons, a small number of women does not respond to therapy. In a clinical study, out of 37 women diagnosed with BV, 31 were successfully treated with a single peroral dose of metronidazole, while 6 still had BV after treatment. Here, we performed a...

  • Tuesday, 16 January 2018

    Nanoparticles accumulate a plethora of host factors on their surface (protein corona) in biological fluids, which influence the nanoparticle activity. Here we provide evidence for the existence of a rich viral protein corona and show its implications for viral infectivity, immune cell activation and catalysis of amyloid aggregation. We demonstrate that respiratory syncytial virus (RSV), a major cause of respiratory tract infections, accumulates a distinctive protein corona in different biofluids including: human plasma, human bronchoalveolar lavage fluid, non-human primate plasma and fetal bovine serum. Additionally, corona pre-coating differentially affects viral infectivity and its ability to activate human monocyte-derived dendritic cells...

  • Tuesday, 16 January 2018

    Drugs that target protein synthesis are well-validated for use as antimicrobials, yet specific high throughput (HTP) methods to screen for those targeting malaria are lacking. Here, we have developed a cell free in vitro translation (IVT) assay for the human malaria parasite, Plasmodium falciparum, which reconstitutes the native parasite protein translation machinery. Combining clarified IVT lysate with a click beetle luciferase reporter gene fused to untranslated regions of Pf histidine-rich proteins (hrp)-2 and 3, the HTP IVT assay accurately reports protein translation in a 384-well plate format using a standard spectrofluorometer. We validate the assay as effective in detecting compounds...

  • Monday, 15 January 2018

    Citrobacter rodentium is a mouse-restricted pathogen that has long been used as an in vivo model for two important human intestinal pathogen enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC). And yet, in contrast to E. coli, little is known about the bacteriophages (phages), bacterial viruses, that infect C. rodentium, reflecting in part a need to isolate and comparatively analyze phages associated with this bacterial species. Here, we isolated two novel virulent phages CrRp3 and CrRp10 that infect C. rodentium and conduct in vitro and comparative genomic studies with other, related phages. Whole-genome analyses revealed that CrRp3 and CrRp10...

  • Monday, 15 January 2018

    Detection of viruses in the environment is heavily dependent on PCR-based approaches that require reference sequences for primer design. While this strategy can accurately detect known viruses, it will not find novel genotypes, nor emerging and invasive viral species. In this study, we investigated the use of viromics, i.e. high-throughput sequencing of the biosphere viral fraction, to detect human/animal pathogenic RNA viruses in the Conwy river catchment area in Wales, UK. Using a combination of filtering and nuclease treatment, we extracted the viral fraction from wastewater, estuarine river water and sediment, followed by RNASeq analysis on the Illumina HiSeq platform...

  • Monday, 15 January 2018

    Crop disease outbreaks are commonly associated with the clonal expansion of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site 16S rDNA survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct pathogenic sublineages. The coexistence of diverse sublineages suggests that in contrast to crop systems, no single strain has been able to overtake these A....

  • Monday, 15 January 2018

    Geothermal springs are model ecosystems to systematically investigate microbial biogeography as they i) represent discrete, homogenous habitats; ii) are abundantly distributed across multiple geographical scales; iii) span broad geochemical gradients; and iv) have simple community structures with reduced metazoan interactions. Taking advantage of these traits, we undertook the largest known consolidated study of geothermal ecosystems (http://1000springs.org.nz) to determine factors that influence biogeographical patterns. Rigorously standardised methodologies were used to measure microbial communities, 46 physicochemical parameters, and metadata from 1,019 hotspring samples across New Zealand. pH was found to be the primary influence on diversity in springs < 70 {degrees}C with...

  • Friday, 12 January 2018

    Since persister cells survive antibiotic treatments through dormancy and resuscitate to reconstitute infections, it is imperative to determine the rate at which these cells revive. Using two sets of Escherichia coli persister cells, those arising naturally at low levels and those generated at high levels by ceasing transcription via rifampicin pretreatment (shown to be bona fide persisters through seven sets of experiments), we used microscopy of single cells to determine that persisters have low levels of antibiotic-corrupting proteins and that their resuscitation is heterogeneous and includes cells that grow immediately. In all, five phenotypes were found for persister cell resuscitation:...

  • Friday, 12 January 2018

    The library preparation step is a major source of bias in NGS-based studies. Several PCR-related factors might negatively influence the application of NGS tools in environmental studies and diagnostics. Among the most understudied factors are DNA polymerases. In our study, we evaluated the effect of DNA polymerase type on the characterisation of bacterial communities, more precisely Legionella, using a genus-specific NGS approach. The assay with proof-reading high fidelity KAPA HiFi showed better amplification yield than the one with widely used non-proofreading HotStarTaq. Legionella community richness metrics were significantly overestimated with HotStarTaq. However, the choice of DNA polymerase did not significantly...

  • Friday, 12 January 2018

    Ambient temperature filter dried vaccine formulations have been proposed to simultaneously achieve thermostability and offer a ready-to-use immunisation device that combines reconstitution and injection. Vaccine concentration should be uniform at the point of injection, but the uniformity following direct reconstitution of filter-dried vaccines has not been reported. We present here a study of vaccine mixing and release following dissolution of filter-dried model protein and toxoid antigens within a single syringe, filter and needle unit. Release was better for filters made from glass than cellulose. Without additional mixing, uniformity was poor and only 41% of input protein was released from protein...

  • Friday, 12 January 2018

    Enveloped viruses gain entry into host cells by fusing with cellular membranes, a step required for virus replication. Coronaviruses, including the severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and infectious bronchitis virus (IBV), fuse at the plasma membrane or use receptor-mediated endocytosis and fuse with endosomes depending on the cell or tissue type. The virus Spike (S) protein mediates fusion with the host cell membrane. We have shown previously that an Abl kinase inhibitor, imatinib, significantly reduces SARS-CoV and MERS-CoV viral titers and prevents endosomal entry by HIV SARS S and MERS S pseudotyped virions....

  • Thursday, 11 January 2018

    New assays for quantitative imaging and sequencing have yielded great progress towards understanding the organizational principles of chromosomes. Yet, even for the well-studied model bacterium Escherichia coli, many basic questions remain unresolved regarding chromosomal (sub-)structure, its mechanics and dynamics, and the link between structure and function. Here we resolve the spatial organization of the circular chromosome of bacteria by directly imaging the chromosome in live E. coli cells with a broadened cell shape. The chromosome was observed to exhibit a torus topology with a 4.2-micron toroidal length and 0.4-micron bundle thickness. On average, the DNA density along the chromosome shows...

  • Thursday, 11 January 2018

    Streptomycetes make up the largest genus of actinobacteria, living predominantly in soil and decaying vegetation. The bacteria are widely known for their filamentous morphologies and their capacity to synthesize antibiotics and other biologically active molecules. More than a decade ago, we and others identified 22 genomic islands that Streptomyces coelicolor M145 possesses and other Streptomyces strains lack. One of these genomic islands, Genomic Island (GI) 6, encodes an extracytoplasmic function (ECF) sigma factor that we were characterizing in separate work. Here we report that artificial induction of the ECF sigma factor, which is encoded by SCO3450, causes the transcription of...

  • Wednesday, 10 January 2018

    Background: Antibiotics have been spread widely in environments, asserting profound effects on environmental microbes as well as antibiotic resistance genes (ARGs) within these microbes. Therefore, investigating the associations between ARGs and bacterial communities become an important issue for environment protection. Ocean microbiomes are potentially large ARG reservoirs, but the marine ARG distribution and its associations with bacterial communities remain unclear. Methods: we have utilized the big-data mining techniques on ocean microbiome data to analysis the marine ARGs and bacterial distribution on a global scale, and applied comprehensive statistical analysis to unveil the associations between ARG contents, ocean microbial community structures,...

  • Wednesday, 10 January 2018

    The recent Zika virus (ZIKV) and chikungunya virus (CHIKV) epidemics highlight the explosive nature of arthropod-borne (arbo) viruses transmitted by Aedes aegypti mosquitoes. Vector competence and the extrinsic incubation period (EIP) are two key entomological parameters used to assess the public health risk posed by arboviruses. These are typically measured empirically by offering mosquitoes an infectious bloodmeal and temporally sampling mosquitoes to determine infection and transmission status. This approach has been used for the better part of a century; however, it does not accurately capture the biology and behavior of many mosquito vectors which refeed frequently (every 2-3 days). Here...

  • Tuesday, 09 January 2018

    Measurements of the carbon stable isotope ratio ({delta}13C) are widely used in biology to address major questions regarding food sources and metabolic pathways used by organisms. Measurement of these so called stable carbon isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals have led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide limited taxonomic resolution, such as with the use of lipid biomarkers, or are limited in throughput, such as NanoSIMS imaging of single cells. Here we present "direct Protein-SIF" and...

  • Tuesday, 09 January 2018

    While the structure and regulatory networks that govern the activity of the type-six secretion system (T6SS) of Vibrio cholerae are becoming increasingly clear, we know less about the role of the T6SS in disease. Under laboratory conditions, V. cholerae uses the T6SS to outcompete many Gram-negative species, including other V. cholerae strains and human commensal bacteria. However, the role of these interactions has not been resolved in an in-vivo setting. We used the Drosophila melanogaster model of cholera to define the contribution of the T6SS to V. cholerae pathogenesis. Here, we demonstrate that interactions between the T6SS and host commensals...

  • Tuesday, 09 January 2018

    Surface proteins of Staphylococcus aureus are secreted across septal membranes for assembly into the bacterial cross-wall. This localized secretion requires the YSIRK/GXXS motif signal peptide, however the mechanisms supporting precursor trafficking are not known. We show here that the signal peptide of staphylococcal protein A (SpA) is cleaved at the YSIRK/GXXS motif. A signal peptide mutant defective for cleavage can be crosslinked to SecA, SecDF and LtaS. SecA depletion blocks precursor targeting to septal membranes, whereas deletion of secDF diminishes SpA secretion into the cross-wall. Depletion of LtaS blocks lipoteichoic acid synthesis and promotes precursor trafficking to peripheral membranes. We...

  • Monday, 08 January 2018

    Background: Agricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear. Methods: We performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities. Results:...

  • Monday, 08 January 2018

    Background: Universal access to drug susceptibility testing is key to ending TB. UKMYC5 is a 96-well microtitre plate designed by the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) which has potential to determine, at low cost, the MICs for 14 different anti-TB drugs, including several new and repurposed compounds. It is a dry-format plate and therefore easy to transport and store. Objectives: Determine how long to incubate the plates before reading, and the optimal reading method. Establish the reproducibility of the UKMYC5 plate and compare it to established methods. Methods: UKMYC5 plates were tested by seven laboratories on...

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