Inference of Antibiotic Resistance and Virulence among Diverse Group A Streptococcus Strains Using emm Sequencing and Multilocus Genotyping Methods

Background

Group A Streptococcus pyogenes (GAS) exhibits a high degree of clinically relevant phenotypic diversity. Strains vary widely in terms of antibiotic resistance (AbR), clinical severity, and transmission rate. Currently, strain identification is achieved by emm typing (direct sequencing of the genomic segment coding for the antigenic portion of the M protein) or by multilocus genotyping methods. Phenotype analysis, including critical AbR typing, is generally achieved by much slower and more laborious direct culture-based methods.

Methodology/Principal Findings

We compare genotype identification (by emm typing and PCR/ESI-MS) with directly measured phenotypes (AbR and outbreak associations) for 802 clinical isolates of GAS collected from symptomatic patients over a period of 6 years at 10 military facilities in the United States. All independent strain characterization methods are highly correlated. This shows that recombination, horizontal transfer, and other forms of reassortment are rare in GAS insofar as housekeeping genes, primary virulence and antibiotic resistance determinants, and the emm gene are concerned. Therefore, genotyping methods offer an efficient way to predict emm type and the associated AbR and virulence phenotypes.

Conclusions/Significance

The data presented here, combined with much historical data, suggest that emm typing assays and faster molecular methods that infer emm type from genomic signatures could be used to efficiently infer critical phenotypic characteristics based on robust genotype: phenotype correlations. This, in turn, would enable faster and better-targeted responses during identified outbreaks of constitutively resistant or particularly virulent emm types.     

Role of Tropomyosin in Formin-mediated Contractile Ring Assembly in Fission Yeast

Like animal cells, fission yeast divides by assembling actin filaments into a contractile ring. In addition to formin Cdc12p and profilin, the single tropomyosin isoform SpTm is required for contractile ring assembly. Cdc12p nucleates actin filaments and remains processively associated with the elongating barbed end while driving the addition of profilin-actin. SpTm is thought to stabilize mature filaments, but it is not known how SpTm localizes to the contractile ring and whether SpTm plays a direct role in Cdc12p-mediated actin polymerization. Using “bulk” and single actin filament assays, we discovered that Cdc12p can recruit SpTm to actin filaments and that SpTm has diverse effects on Cdc12p-mediated actin assembly. On its own, SpTm inhibits actin filament elongation and depolymerization. However, Cdc12p completely overcomes the combined inhibition of actin nucleation and barbed end elongation by profilin and SpTm. Furthermore, SpTm increases the length of Cdc12p-nucleated actin filaments by enhancing the elongation rate twofold and by allowing them to anneal end to end. In contrast, SpTm ultimately turns off Cdc12p-mediated elongation by “trapping” Cdc12p within annealed filaments or by dissociating Cdc12p from the barbed end. Therefore, SpTm makes multiple contributions to contractile ring assembly during and after actin polymerization.     

Antioxidant Activity of Sulfur and Selenium: A Review of Reactive Oxygen Species Scavenging,Glutathione Peroxidase,and Metal-Binding Antioxidant Mechanisms

It is well known that oxidation caused by reactive oxygen species (ROS) is a major cause of cellular damage and death and has been implicated in cancer, neurodegenerative, and cardiovascular diseases. Small-molecule antioxidants containing sulfur and selenium can ameliorate oxidative damage, and cells employ multiple antioxidant mechanisms to prevent this cellular damage. However, current research has focused mainly on clinical, epidemiological, and in vivo studies with little emphasis on the antioxidant mechanisms responsible for observed sulfur and selenium antioxidant activities. In addition, the antioxidant properties of sulfur compounds are commonly compared to selenium antioxidant properties; however, sulfur and selenium antioxidant activities can be quite distinct, with each utilizing different antioxidant mechanisms to prevent oxidative cellular damage. In the present review, we discuss the antioxidant activities of sulfur and selenium compounds, focusing on several antioxidant mechanisms, including ROS scavenging, glutathione peroxidase, and metal-binding antioxidant mechanisms. Findings of several recent clinical, epidemiological, and in vivo studies highlight the need for future studies that specifically focus on the chemical mechanisms of sulfur and selenium antioxidant behavior.     

Silver Ions Increase Auxin Efflux Independently of Effects on Ethylene Response

Silver nitrate and aminoethoxyvinylglycine (AVG) are often used to inhibit perception and biosynthesis, respectively, of the phytohormone ethylene. In the course of exploring the genetic basis of the extensive interactions between ethylene and auxin, we compared the effects of silver nitrate (AgNO₃) and AVG on auxin responsiveness. We found that although AgNO₃ dramatically decreased root indole-3-acetic acid (IAA) responsiveness in inhibition of root elongation, promotion of DR5-β-glucuronidase activity, and reduction of Aux/IAA protein levels, AVG had more mild effects. Moreover, we found that that silver ions, but not AVG, enhanced IAA efflux similarly in root tips of both the wild type and mutants with blocked ethylene responses, indicating that this enhancement was independent of ethylene signaling. Our results suggest that the promotion of IAA efflux by silver ions is independent of the effects of silver ions on ethylene perception. Although the molecular details of this enhancement remain unknown, our finding that silver ions can promote IAA efflux in addition to blocking ethylene signaling suggest that caution is warranted in interpreting studies using AgNO₃ to block ethylene signaling in roots.     

Hurricane disturbance in a temperate deciduous forest: patch dynamics, tree mortality, and coarse woody detritus

Patch dynamics, tree injury and mortality, and coarse woody detritus were quantified to examine the ecological impacts of Hurricane Fran on an oak-hickory-pine forest near Chapel Hill, NC. Data from long-term vegetation plots (1990–1997) and aerial photographs (1998) indicated that this 1996 storm caused patchy disturbance of intermediate severity (10–50% tree mortality; Woods, J Ecol 92:464–476, 2004). The area in large disturbance patches (>0.1 ha) increased from <1% to approximately 4% of the forested landscape. Of the forty-two 0.1-ha plots that were studied, 23 were damaged by the storm and lost 1–66% of their original live basal area. Although the remaining 19 plots gained basal area (1–15% increase), across all 42 stands basal area decreased by 17% because of storm impacts. Overall mortality of trees >10 cm dbh was 18%. The basal area of standing dead trees after the storm was 0.9 m²/ha, which was not substantially different from the original value of 0.7 m²/ha. In contrast, the volume and mass of fallen dead trees after the storm (129 m³/ha; 55 Mg/ha) were 6.1 and 7.9 times greater than the original levels (21 m³/ha; 7 Mg/ha), respectively. Uprooting was the most frequent type of damage, and it increased with tree size. However, two other forms of injury, severe canopy breakage and toppling by other trees, decreased with increasing tree size. Two dominant oak species of intermediate shade-tolerance suffered the largest losses in basal area (30–41% lost). Before the storm they comprised almost half of the total basal area in a forest of 13% shade-tolerant, 69% intermediate, and 18% shade-intolerant trees. Recovery is expected to differ with respect to vegetation (e.g., species composition and diversity) and ecosystem properties (e.g., biomass, detritus mass, and carbon balance). Vegetation may not revert to its former composition; however, reversion of biomass, detritus mass, and carbon balance to pre-storm conditions is projected to occur within a few decades. For example, the net change in ecosystem carbon balance may initially be negative from losses to decomposition, but it is expected to be positive within a decade after the storm. Repeated intermediate-disturbance events of this nature would likely have cumulative effects, particularly on vegetation properties.     

Elevated CO2 will not select for enhanced growth in white spruce despite genotypic variation in response

The effect of elevated atmospheric CO₂ on plant growth has been well-documented in the literature. However, few studies have quantified intra-specific genetic variation in growth response, and the potential for natural and artificial selection to act upon this variation. This study examined intra-specific variation in growth response to elevated CO₂ in 29 genotypes of white spruce (Picea glauca), a widely distributed and economically important species of the boreal forest region in North America. Trees were exposed to either ambient (370 μL L^?1) or twice-ambient CO₂ (740 μL L^?1). The opportunity for selection (i.e. the relative variation in fitness) was determined at low and high CO₂ levels with size as a measure of fitness and heritability of this variation determined. There was considerable variation among the genotypes in size and response to elevated CO₂. The increase in mass at elevated CO₂ ranged from 23% to 108% depending upon genotype. In spite of this variation, the genetic correlation between the two environments approached unity, as genotype variance was much greater than the genotype×CO₂ variance. Elevated CO₂ had no effect on heritability of the size-related traits we examined, and either had no effect on opportunity for selection, or decreased it. We conclude that selection at elevated atmospheric CO₂ is unlikely to increase mean plant size in white spruce beyond that observed for present day populations grown at elevated CO₂, despite the substantial genetic variation in CO₂ response displayed by this species.     

A Cell Cycle Timer for Asymmetric Spindle Positioning

The displacement of the mitotic spindle to one side of a cell is important for many cells to divide unequally. While recent progress has begun to unveil some of the molecular mechanisms of mitotic spindle displacement, far less is known about how spindle displacement is precisely timed. A conserved mitotic progression mechanism is known to time events in dividing cells, although this has never been linked to spindle displacement. This mechanism involves the anaphase-promoting complex (APC), its activator Cdc20/Fizzy, its degradation target cyclin, and cyclin-dependent kinase (CDK). Here we show that these components comprise a previously unrecognized timer for spindle displacement. In the Caenorhabditis elegans zygote, mitotic spindle displacement begins at a precise time, soon after chromosomes congress to the metaphase plate. We found that reducing the function of the proteasome, the APC, or Cdc20/Fizzy delayed spindle displacement. Conversely, inactivating CDK in prometaphase caused the spindle to displace early. The consequence of experimentally unlinking spindle displacement from this timing mechanism was the premature displacement of incompletely assembled components of the mitotic spindle. We conclude that in this system, asymmetric positioning of the mitotic spindle is normally delayed for a short time until the APC inactivates CDK, and that this delay ensures that the spindle does not begin to move until it is fully assembled. To our knowledge, this is the first demonstration that mitotic progression times spindle displacement in the asymmetric division of an animal cell. We speculate that this link between the cell cycle and asymmetric cell division might be evolutionarily conserved, because the mitotic spindle is displaced at a similar stage of mitosis during asymmetric cell divisions in diverse systems.     

Evolutionary Dynamics of Human Rotaviruses: Balancing Reassortment with Preferred Genome Constellations

Group A human rotaviruses (RVs) are a major cause of severe gastroenteritis in infants and young children. Yet, aside from the genes encoding serotype antigens (VP7; G-type and VP4; P-type), little is known about the genetic make-up of emerging and endemic human RV strains. To gain insight into the diversity and evolution of RVs circulating at a single location over a period of time, we sequenced the eleven-segmented, double-stranded RNA genomes of fifty-one G3P[8] strains collected from 1974 to 1991 at Children''s Hospital National Medical Center, Washington, D. C. During this period, G1P[8] strains typically dominated, comprising on average 56% of RV infections each year in hospitalized children. A notable exception was in the 1976 and 1991 winter seasons when the incidence of G1P[8] infections decreased dramatically, a trend that correlated with a significant increase in G3P[8] infections. Our sequence analysis indicates that the 1976 season was characterized by the presence of several genetically distinct, co-circulating clades of G3P[8] viruses, which contained minor but significant differences in their encoded proteins. These 1976 lineages did not readily exchange gene segments with each other, but instead remained stable over the course of the season. In contrast, the 1991 season contained a single major clade, whose genome constellation was similar to one of the 1976 clades. The 1991 clade may have gained a fitness advantage after reassorting with as of yet unidentified RV strain(s). This study reveals for the first time that genetically distinct RV clades of the same G/P-type can co-circulate and cause disease. The findings from this study also suggest that, although gene segment exchange occurs, most reassortant strains are replaced over time by lineages with preferred genome constellations. Elucidation of the selective pressures that favor maintenance of RVs with certain sets of genes may be necessary to anticipate future vaccine needs.     

Structure of the Ctr1 copper trans'PORE'ter reveals novel architecture

Copper is essential for biological processes such as free radical detoxification, mitochondrial respiration and iron metabolism. A central player in copper homeostasis is the high-affinity integral plasma membrane copper transporter Ctr1. However, the precise mechanisms by which Ctr1 functions are not known. Here, we highlight an important breakthrough in our understanding of how Ctr1 facilitates Cu(I) movement across membranes: the publication of structural details for human Ctr1 obtained from 2D crystallography and electron microscopy.