Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there is growing awareness of the emergence of multidrug-resistant lineages in community settings around the world. One such lineage is ST772-MRSA-V, which has disseminated globally and is increasingly prevalent in India. Here, we present the complete genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage from India, and investigate its genomic characteristics in regards to antibiotic resistance and virulence factors.

Results

Sequencing using single-molecule real-time technology resulted in the assembly of a single continuous chromosomal sequence, which was error-corrected, annotated and compared to nine draft genome assemblies of ST772-MRSA-V from Australia, Malaysia and India. We discovered numerous and redundant resistance genes associated with mobile genetic elements (MGEs) and known core genome mutations that explain the highly antibiotic resistant phenotype of DAR4145. Staphylococcal toxins and superantigens, including the leukotoxin Panton-Valentinin Leukocidin, were predominantly associated with genomic islands and the phage φ-IND772PVL. Some of these mobile resistance and virulence factors were variably present in other strains of the ST772-MRSA-V lineage.

Conclusions

The genomic characteristics presented here emphasize the contribution of MGEs to the emergence of multidrug-resistant and highly virulent strains of community-associated MRSA. Antibiotic resistance was further augmented by chromosomal mutations and redundancy of resistance genes. The complete genome of DAR4145 provides a valuable resource for future investigations into the global dissemination and phylogeography of ST772-MRSA-V.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1599-9) contains supplementary material, which is available to authorized users.     

The Proportion of Three Foundation Plant Species and Their Genotypes Influence an Arthropod Community: Restoration Implications for the Endangered Southwestern Willow Flycatcher

As part of a restoration project, multiple genotypes of two tree species, Fremont cottonwood (Populus fremontii) and Goodding's willow (Salix gooddingii), and one shrub species, Coyote willow (S. exigua), were experimentally planted in different proportions at the Palo Verde Ecological Reserve near Blythe, California, U.S.A. These common woody plant species are important to the endangered southwestern willow flycatcher, providing perch, nesting, and foraging habitat. We conducted this study to evaluate plant species proportion and plant genotype effects on the arthropod community, the prey base for the endangered southwestern willow flycatcher. Three patterns emerged. First, plant species proportions were important; the arthropod community had the greatest richness and diversity (H′) when Goodding's willow proportion was high and Fremont cottonwood proportion was lower; that is, fewer Fremont cottonwoods are required to positively affect overall arthropod diversity. Second, we found significant genotypic effects, for all three plant species, on arthropod species accumulation. Third, while both planting proportion and genotype effects were significant, we found that the effect of planting proportion on arthropod richness was about twice as large as the effect of plant genotype. This shows that both plant species proportions and genotype should be utilized in restoration projects to maximize habitat heterogeneity and arthropod richness. Similar studies can determine which planting proportion and specific genotypes may result in a more favorable arthropod prey base for the southwestern willow flycatcher and other species of concern. Greater attention to planting design and genotype can result in significant gains in diversity at little or no additional project cost.     

Drought-induced mortality of a foundation species (<Emphasis Type="Italic">Juniperus monosperma</Emphasis>) promotes positive afterlife effects in understory vegetation

Climate change-induced droughts have contributed to large-scale die-offs of dominant tree species throughout much of the southwestern United States. These mortality events provide ecologists with the opportunity to determine whether afterlife effects associated with the die-off occur and the potential implications for future ecosystem changes. We studied both the afterlife and interaction effects of condition (dead trees, living trees, and open areas) on understory vegetation in a Juniperus monosperma woodland of northern Arizona 7 years after a major mortality event. Five major findings resulted: (1) there was a positive afterlife effect on understory plants, in which vegetation under dead junipers contained almost double the amount of cover; (2) the competitive effect on understory plants was exemplified by a 1.3 times greater cover and 1.6 additional species in open areas compared to under living junipers; (3) plant community composition significantly differed by aspect and condition; (4) the highly invasive cheatgrass (Bromus tectorum) was 1.5 times greater under dead junipers compared to live junipers; and (5) litter depth and light availability were negatively and positively correlated with plant cover, respectively, but weakly correlated with afterlife effects. Our results indicate that mortality events can promote changes in understory vegetation through afterlife effects. In ecosystems where foundation species suffer high rates of mortality, changes in plant population dynamics and ecosystem function may promote an altered trajectory in community composition with the potential to increase the presence of invasive species. Continued species die-offs associated with climate change-induced drought may contribute to an increased occurrence and legacy of afterlife effects.     

Herbivore host-associated genetic differentiation depends on the scale of plant genetic variation examined

Herbivore adaptation to plant genetic variation can lead to reproductive isolation and the formation of host-associated lineages (host-associated differentiation, or HAD). Plant genetic variation exists along a scale, ranging from variation among individual plant genotypes to variation among plant species. Along this scale, herbivores may adapt and diverge at any level, yet few studies have examined whether herbivore differentiation exhibits scaling with respect to host variation (e.g., from genotypes to species). Determining at which level(s) herbivore differentiation occurs can provide insight into the importance of plant genetic variation on herbivore evolution. Previous studies have found strong genetic differentiation in the eriophyid mite, Aceria parapopuli, between hybrid Populus hosts and parental Populus species, but minimal neutral-locus differentiation among individual trees of the same species. We tested whether genetic differentiation in A. parapopuli scales with genetic variation in its Populus hosts. Using mite ITS1 sequence data collected among host species and among host populations, two key patterns emerged. (1) We found strong differentiation of A. parapopuli among Populus species, supporting the hypothesis that plant species differences drive reproductive isolation and HAD. (2) We did not find evidence of host-driven genetic differentiation in mites at the level of plant populations, suggesting that this level of plant variation is insufficiently strong to drive differentiation at a neutral locus. In combination with previous studies, we found that HAD occurs at the higher levels of plant genetic variation, but not at lower levels, and conclude that HAD depends on the scale of plant genetic variation examined.     

Global remodelling of cellular microenvironment due to loss of collagen VII

The mammalian cellular microenvironment is shaped by soluble factors and structural components, the extracellular matrix, providing physical support, regulating adhesion and signalling. A global, quantitative mass spectrometry strategy, combined with bioinformatics data processing, was developed to assess proteome differences in the microenvironment of primary human fibroblasts. We studied secreted proteins of fibroblasts from normal and pathologically altered skin and their post‐translational modifications. The influence of collagen VII, an important structural component, which is lost in genetic skin fragility, was used as model. Loss of collagen VII had a global impact on the cellular microenvironment and was associated with proteome alterations highly relevant for disease pathogenesis including decrease in basement membrane components, increase in dermal matrix proteins, TGF‐β and metalloproteases, but not higher protease activity. The definition of the proteome of fibroblast microenvironment and its plasticity in health and disease identified novel disease mechanisms and potential targets of intervention.     

Autoantibodies and Sjogren’s Syndrome in Multiple Sclerosis,a Reappraisal

Background

Rheumatologic diseases may cause neurologic disorders that mimic multiple sclerosis (MS). A panel of serum autoantibodies is often obtained as part of the evaluation of patients suspected of having MS.

Objectives

To determine, in light of recently revised diagnostic criteria for MS, neuromyelitis optica, and Sjogren’s Syndrome, if testing for autoantibodies in patients with a confirmed diagnosis of MS would reveal a frequency or demonstrate a clinical utility divergent from previous reports or lead to identification of undiagnosed cases of Sjogren’s Syndrome.

Methods

Convenience sample cross-sectional study of MS patients recruited from the OHSU Multiple Sclerosis Center.

Results

Autoantibodies were detected in 38% (35/91) of patients with MS and were not significantly associated with disease characteristics or severity. While four patients had SSA antibodies, none met diagnostic criteria for Sjogren’s Syndrome.

Conclusions

Rheumatologic autoantibodies are frequently found in MS patients and are not associated with disease severity or systemic rheumatologic disease. Our demonstration of the low specificity of these autoantibodies suggests that the diagnostic utility and cost-effectiveness of testing is not supported when there is strong clinical suspicion of MS and low clinical suspicion of rheumatologic disease.     

Arabidopsis monothiol glutaredoxin, AtGRXS17, is critical for temperature-dependent postembryonic growth and development via modulating auxin response

Global environmental temperature changes threaten innumerable plant species. Although various signaling networks regulate plant responses to temperature fluctuations, the mechanisms unifying these diverse processes are largely unknown. Here, we demonstrate that an Arabidopsis monothiol glutaredoxin, AtGRXS17 (At4g04950), plays a critical role in redox homeostasis and hormone perception to mediate temperature-dependent postembryonic growth. AtGRXS17 expression was induced by elevated temperatures. Lines altered in AtGRXS17 expression were hypersensitive to elevated temperatures and phenocopied mutants altered in the perception of the phytohormone auxin. We show that auxin sensitivity and polar auxin transport were perturbed in these mutants, whereas auxin biosynthesis was not altered. In addition, atgrxs17 plants displayed phenotypes consistent with defects in proliferation and/or cell cycle control while accumulating higher levels of reactive oxygen species and cellular membrane damage under high temperature. Together, our findings provide a nexus between reactive oxygen species homeostasis, auxin signaling, and temperature responses.     

Plant genetic effects on soils under climate change

Background

Many biological questions about N availability and the N cycle require knowledge of the abundance and identity of molecules comprising the pool of organic N. Moreover, basic knowledge of the molecular composition of the soil solution can give rise to new hypotheses via data-driven or inductive reasoning.

Scope

This paper examines the composition of organic N molecules in the soil solution. Our perception of organic N in the soil solution is shaped by analytical approaches, and thus I briefly review approaches for sampling and analysis of the soil solution. I give examples of hypotheses generated by knowledge of the molecular composition of organic N and conclude by suggesting priorities for future research.

Conclusions

Studies of the molecular composition of organic N are very much in their infancy. Amino acids, their oligomers and polymers are consistently large components of the pool of organic N. The soil solution also contains organic N compounds from at least another 12 compound classes, but almost nothing is known about their functional significance. Uncovering the role of these other compounds in the N cycle would enrich our understanding of organic N and the N cycle, and place studies of amino acids and their polymers in a broader context.