The High Diversity of MRSA Clones Detected in a University Hospital in Istanbul

Background: To characterize the methicillin-resistant Staphylococcus aureus (MRSA) clones present in Istanbul, 102 MRSA isolates collected during a 5-year period at the Istanbul Medical Faculty Hospital were characterized using microarray analysis and phenotypic resistance profiles.Methods: Resistance to methicillin was detected with a cefoxitin disk diffusion assay and confirmed with a MRSA-agar and MRSA detection kit. Antimicrobial susceptibility testing was performed by a disk diffusion assay and interpreted according to the 2012 guidelines of the Antibiogram Committee of the French Society for Microbiology. Decreased susceptibility to glycopeptides was confirmed using the population analysis profile-area under the curve (PAP-AUC) method. The presence of the mecA gene was detected by polymerase chain reaction. Bacterial DNA was extracted according to the manufacturer''s recommended protocol using commercial extraction kits. Strains were extensively characterized using the DNA microarray.Results: Isolates were grouped into six clonal complexes. The most frequently detected clone was the Vienna/Hungarian/Brazilian clone (ST239-MRSA-III), which accounted for 53.9% of the isolates. These isolates were resistant to multiple antibiotics, particularly penicillin, tetracycline, rifampicin, kanamycin, tobramycin, gentamicin, levofloxacin, erythromycin, lincomycin and fosfomycin. Furthermore, three isolates were detected by population analysis profile as heterogeneous vancomycin-intermediate S. aureus (hVISA). The UK-EMRSA-15 clone (ST22-MRSA-IV PVL negative) was detected in 9.8% of the isolates and was mainly susceptible to all anti-staphylococcal antibiotics. Seven isolates (6.9%) were positive for PVL genes and were assigned to the CC80-MRSA-IV clone (European CA-MRSA clone, three isolates), ST8-MRSA-IV clone (USA300 clone, two isolates, one ACME-positive) or ST22-MRSA-IV clone (“Regensburg EMRSA” clone, two isolates). All other clones were detected in one to six isolates and corresponded to well-known clones (e.g., Pediatric clone, Dublin EMRSA clone, WA MRSA-54/63, WA MRSA-1/57).Conclusions: This work highlighted both the high prevalence of ST239-MRSA-III clone and the large diversity of the other MRSA clones detected in a university hospital in Istanbul.     

Antigenic diversity and size diversity of Plasmodium falciparum antigens in isolates from Gambian patients. I. S-antigens

Ring-stage asexual parasites of P. falciparum were collected from six Gambian children and the S-antigens radiolabelled by 3H-glycine uptake during in vitro culture up to rupture of infected cells and merozoite release. Ouchterlony double diffusion of boiled culture supernatants against a panel of adult Gambian sera identified one S-antigen precipitin arc for five isolates and two precipitin arcs for one isolate. Five of the six isolates were serologically distinct. Analysis of S-antigens by comparison of SDS-polyacrylamide gel electrophoresis patterns of heat-treated soluble proteins revealed a more complex pattern of 3H-labelled S-antigens that was different for each isolate. There were between two and six different 3H-labelled bands for each isolate in the size range of molecular weight 137 000 to 285 000. This result confirms the large size range of S-antigens identified with culture adapted P. falciparum. Several bands were relatively weakly labelled with 3H-glycine, suggesting that natural isolates contain one or two predominant S-antigen phenotypes and several other S-antigen phenotypes expressed by minor parasite subpopulations. Immunoprecipitation was performed using a panel of sera from Gambian adults, or, acute and 3 week convalescent sera from the same patients used for S-antigen radiolabelling. Adult sera generally immunoprecipitated some of the S-antigens in each isolate, including antigens that must represent extremely minor parasite subpopulations since they could not be seen in the patterns of non-immunoprecipitated heat-stable proteins. Sera from convalescent children were generally negative on immunoprecipitation, even with the homologous isolate. In one case we observed the acquisition of specific immunoprecipitating antibody to one of the homologous S-antigens during the convalescent period. The antigenic and structural complexity of S-antigens in natural isolates that have not been submitted to the selection pressure of adaptation for in vitro culture is clearly greater than for culture adapted P. falciparum.     

First overview of the Culicoides Latreille (Diptera: Ceratopogonidae) livestock associated species of Reunion Island,Indian Ocean

This study establishes the first faunistic inventory of livestock associated Culicoides (Diptera: Ceratopogonidae) species of Reunion Island (Indian Ocean), where bluetongue and epizootic hemorrhagic disease are regularly recorded. Single night-catches were performed at 41 sites using light suction traps at altitudes ranging from 0 to 1525 m, from March to April 2005. Five species were recorded: Culicoides imicola, Culicoides bolitinos, Culicoides enderleini, Culicoides grahamii, and Culicoides kibatiensis, among which at least the first three species are known to be involved in virus transmission to ruminants and equids. This is the first record of C. bolitinos, C. kibatiensis, and C. enderleini on the island. C. imicola was the most abundant species along the sea coast. C. bolitinos was more abundant inland and on two sites on the east coast. C. kibatiensis and C. grahamii were less abundant than the other three species and limited to two foci.     

CCHF virus variants in Pakistan and Afghanistan: Emerging diversity and epidemiology

BackgroundCrimean Congo hemorrhagic fever (CCHF) has been reported from more than 30 countries in Africa, Asia, Eastern Europe and Middle East. The disease is considered endemic in Pakistan and neighboring countries like Iran and Afghanistan.ObjectivesThis study aimed to explore the genetic diversity of CCHF virus (CCHFV) detected in Pakistan and Afghanistan based on analysis of partial S-segment sequences.Study designDuring 2011, one hundred samples satisfying the CCHF case definition were tested by (ELISA) and RT-PCR for detection of IgM antibodies and viral RNA, respectively. Phylogenetic analysis was carried out on partial S-segment nucleotide sequences using MEGA 5.0.ResultsOut of one hundred collected during 2011, 49 (49%) were positive for CCHF either by ELISA/RT-PCR or both. The mean age of the CCHFV positive cases was 30.32 years (range 18–56 years) and overall mortality rate was 20.4%. All CCHF virus isolates from this study clustered with strains previously reported from Pakistan, Iran and Afghanistan within the Asia-1 genogroup. Four distinct sub-clades were found circulating within Asia-1 genogroup. Six CCHFV strains found in Pakistan and Afghanistan grouped into a new sub-clade-D.ConclusionsData from this study shows that endemic foci of CCHFV span the international border between Pakistan and Afghanistan with genetically diverse variants circulating in this region. Our findings emphasize to establish a laboratory based surveillance program and devise health policy measures to control CCHF infection especially in Baluchistan.     

A Unique Evolution of the S2 Gene of Equine Infectious Anemia Virus in Hosts Correlated with Particular Infection Statuses

Equine infectious anemia virus (EIAV) is a member of the Lentivirus genus in the Retroviridae family that exhibits a genomic structure similar to that of HIV-1. The S2 accessory proteins play important roles in viral replication in vivo and in viral pathogenicity; however, studies on S2 evolution in vivo are limited. This study analyzed the evolutionary characteristics of the S2 gene of a pathogenic EIAV strain, EIAV_LN40, in four experimentally infected horses. The results demonstrated that 14.7% (10 of 68 residues) of the stable amino acid mutations occurred longitudinally in S2 during a 150-day infection period. Further analysis revealed that six of the ten mutated residues were positively selected during the infection. Alignment and phylogenetic analyses showed that the S2 gene sequences of viruses isolated from the infected horses at the early stage of EIAV_LN40 infection were highly homologous and similar to the vaccine-specific sequence. The S2 gene variants isolated from the febrile episodes and late phase of infection became homologous to the S2 gene sequence of the inoculating EIAV_LN40 strain. Our results indicate that the S2 gene evolves in diversity and divergence in vivo in different stages of EIAV infection and that this evolution correlates with the pathogenicity of the virus.     

Vectorial capacity and genetic diversity of Anopheles annularis (Diptera: Culicidae) mosquitoes in Odisha,India from 2009 to 2011

Anopheles annularis is one of the major vectors of malaria in Odisha, India. The present study was undertaken to determine the vectorial capacity and assess the genetic diversity of An. annularis collected from different endemic regions of Odisha. Mosquitoes were collected from thirteen endemic districts using standard entomological collection methods from 2009 to 2011. Sibling species of An. annularis were identified by PCR-RFLP and sequencing of D3 region of 28S ribosomal DNA (rDNA) region. Plasmodium falciparum (Pf) sporozoite rate and human blood fed percentage (HBF) were estimated by multiplex PCR using Pf and human specific primers. Genetic diversity of An. annularis was estimated by ISSR markers. Out of 1647 An. annularis collected, 1353 (82.15%) were collected by mechanical aspirators and 294 (17.85%) by light trap. 49 (2.97%) were positive for human blood and 18 (1.09%) were positive for Pf sporozoite. PCR-RFLP and sequencing analyses detected only An annularis A in the study areas. Overall genetic differentiation among An. annularis populations was moderate (F_ST = 0.048) and showed significant correlation between genetic distance and geographic distance (r = 0.882; P < 0.05). Angul population proved to be genetically unique and was highly divergent F_ST > 0.110) from other populations, suggesting low gene flow between them. The study indicated that only An. annularis A was found in Odisha with potential vectorial capacity that can play a major role in malaria transmission. ISSR markers proved to be useful molecular tools to evaluate genetic variability in An. annularis populations.     

Nonrandom,diversifying processes are disproportionately strong in the smallest size classes of a tropical forest

A variety of ecological processes influence diversity and species composition in natural communities. Most of these processes, whether abiotic or biotic, differentially filter individuals from birth to death, thereby altering species’ relative abundances. Nonrandom outcomes could accrue throughout ontogeny, or the processes that generate them could be particularly influential at certain stages. One long-standing paradigm in tropical forest ecology holds that patterns of relative abundance among mature trees are largely set by processes operating at the earliest life cycle stages. Several studies confirm filtering processes at some stages, but the longevity of large trees makes a rigorous comparison across size classes impossible without long-term demographic data. Here, we use one of the world’s longest-running, plot-based forest dynamics projects to compare nonrandom outcomes across stage classes. We considered a cohort of 7,977 individuals in 186 species that were alive in 1971 and monitored in 13 mortality censuses over 42 y to 2013. Nonrandom mortality with respect to species identity occurred more often in the smaller rather than the larger size classes. Furthermore, observed nonrandom mortality in the smaller size classes had a diversifying influence; species richness of the survivors was up to 30% greater than expected in the two smallest size classes, but not greater than expected in the larger size classes. These results highlight the importance of early life cycle stages in tropical forest community dynamics. More generally, they add to an accumulating body of evidence for the importance of early-stage nonrandom outcomes to community structure in marine and terrestrial environments.Processes that operate nonrandomly with respect to species identity contribute to the structure of natural communities (1–3). Evidence from diverse rain forests includes demographic transitions from seeds to seedlings (4, 5), at the seedling (6, 7) and sapling stages (8) and among large trees (9–12). Although the relative contributions of nonrandom processes at each life cycle stage to determining patterns of abundance and diversity in the mature canopy are unknown, one long-standing paradigm is that community assembly is mediated primarily by events occurring from seed dispersal through seedling germination and small-sapling establishment (13–17). However, despite suggestive patterns (6, 7, 18, 19), evidence is lacking for the comparative strength of early-stage dynamics in determining canopy abundance and diversity.Numerous studies demonstrate significant interspecific variation in the susceptibility of tropical tree seedlings to postgermination hazards, including natural enemies (20, 21), adverse climatic or edaphic conditions (22), physical damage (23), and the crowding or shared-enemies effects of con- and heterospecific neighbors (24, 25). In other words, the per capita probability of seedling mortality is nonrandom because the probability of death is not the same for all individuals in a local community – it is dependent to some degree on species identity. In plant communities in which generation times are relatively short, experiments have demonstrated that nonrandom mortality through these early transitions can be sufficiently strong to affect the species composition of mature plants (26–29). Such demonstrations are impossible in studies of a few decades or less in duration when generation times are long and even juveniles live for several decades or centuries, such as in many tropical forests. Even so, some hypotheses explicitly identify stressors that affect plants at the earliest life cycle stages (such as pests and pathogens, 13, 14, 30) as disproportionately influential. In addition, some empirical studies find a lack of support for nonrandom processes operating among larger stems (31, 32). Together these hypotheses and observations provide the rationale underpinning the considerable body of research on seed and seedling dynamics in tropical forests worldwide. However, no empirical or experimental assessment has been made of the relative contributions across life cycle stages from nonrandom mortality.Here, we evaluate the comparative contribution of early-stage dynamics using a multidecadal study of a tropical forest dynamics plot initiated by one of us (J.H.C.) in 1963 at a site in north Queensland, Australia. We considered a cohort of 7,977 individuals in 186 species that were alive on the plot in 1971, from tiny seedlings to large canopy trees, whose fates were monitored in 13 mortality censuses over 42 y to 2013. Individuals were assigned to one of six size classes (

From the Cover: Amazonian functional diversity from forest canopy chemical assembly

Patterns of tropical forest functional diversity express processes of ecological assembly at multiple geographic scales and aid in predicting ecological responses to environmental change. Tree canopy chemistry underpins forest functional diversity, but the interactive role of phylogeny and environment in determining the chemical traits of tropical trees is poorly known. Collecting and analyzing foliage in 2,420 canopy tree species across 19 forests in the western Amazon, we discovered (i) systematic, community-scale shifts in average canopy chemical traits along gradients of elevation and soil fertility; (ii) strong phylogenetic partitioning of structural and defense chemicals within communities independent of variation in environmental conditions; and (iii) strong environmental control on foliar phosphorus and calcium, the two rock-derived elements limiting CO₂ uptake in tropical forests. These findings indicate that the chemical diversity of western Amazonian forests occurs in a regionally nested mosaic driven by long-term chemical trait adjustment of communities to large-scale environmental filters, particularly soils and climate, and is supported by phylogenetic divergence of traits essential to foliar survival under varying environmental conditions. Geographically nested patterns of forest canopy chemical traits will play a role in determining the response and functional rearrangement of western Amazonian ecosystems to changing land use and climate.Foliage is a locus of chemical investment undertaken by plants to capture and use sunlight for carbon gain under changing environmental conditions and compete with coexisting individuals and species. Plants acquire essential chemical elements from soils, and they synthesize a wide variety of compounds in their leaves to support multiple interdependent physiological processes. Uptake of nitrogen and phosphorus plus the internal production of photosynthetic pigments, including chlorophyll and carotenoids, are required for light capture and carbon fixation in foliage (1). Soluble carbon, primarily comprised of sugars, starch, pectins, and lipids, is then synthesized to meet the energy requirements of the entire plant (2). Other macro- and micronutrients (e.g., calcium) underpin critical leaf functions, such as stomatal conductance and cell wall development. To support the carbon capture process, foliar structural compounds, such as lignin and cellulose, are synthesized to provide strength and longevity (3), and polyphenols are generated for chemical defense (4). Variation in this leaf chemical portfolio expresses multiple strategies evolved in plants to maximize fitness through growth and longevity in any given environment.Despite our understanding of plant chemical and physiological processes, the way that environment and evolution interact to determine geographic variation in plant canopy chemistry remains a mystery. In turn, this shortfall sets a fundamental limit on our knowledge of the core determinants of functional diversity in and across ecosystems, with cascading limits on our understanding of biogeographic and biogeochemical processes. Although much research has either focused on plant functional trait differentiation among coexisting species in communities (5) or emphasized trait convergence in response to environmental filters, such as climate and soils (6), few studies have examined the interconnections between phylogeny and environment in determining functional diversity by way of canopy chemistry (7). This gap is particularly true in the tropics, where our understanding of the interplay between evolution and environmental factors is perhaps weakest because of high plant diversity and a poor understanding of plant community assembly (8). Today, we know very little about canopy chemical traits at community to biome scales in the tropics (9).Western Amazonian forests are a case in point. The forested corridor stretching from Colombia to Bolivia and from the Andean tree line to the Amazon lowlands harbors thousands of plant species arranged in communities distributed across widely varying elevation, geologic, soil, and hydrologic conditions (10, 11). Although the general biological diversity of the region is coming into focus (12, 13), the functional diversity of the forest remains unknown. To understand the regional assembly of forest functional traits and their underlying controls in Amazonia, we must determine the degree to which canopy chemistry is environmentally filtered and phylogenetically partitioned as well as how chemical traits are organized within and among communities. If chemical traits are plastic among coexisting taxa, then biological diversity may be decoupled from functional diversity. Alternatively, if there exists strong phylogenetic organization of canopy chemical traits, then biological diversity may express functional trait diversity and vice versa. Determining the connection between functional and biological diversity may help to explain how so many species coexist within communities and how communities differ throughout the region (14).Here, we are interested in chemical diversity among coexisting tropical canopy tree species and their evolved responses to regional environmental filters thought to limit functional trait divergence. Thus, we developed chemical trait portfolios for tree canopies spread along a 3,500-m elevation gradient stretching from lowland Amazonia to the Andean tree line in Peru (SI Methods and Tables S1 and S2). We assessed the role of taxonomy as well as within- (intraspecific) and between-species (interspecific) variations in determining community and regional chemical assembly. Our study incorporated 2,420 canopy tree species in 19 forests along the elevation gradient, and our sampling included the majority of canopy tree species known to occur in the western Amazon (11, 12). Because submontane to montane Andean forests exist primarily on younger geologic surfaces, whereas lowland forests occur on a mosaic of young to old substrates, we also considered the role of soils in mediating canopy chemical trait distributions. We asked two questions. (i) How does the canopy chemistry of western Amazonian forests vary with elevation? (ii) How much of the variation is explained by taxonomy compared with plasticity within taxa? We focused on light capture and growth traits (including N, P, and photosynthetic pigments) as well as structure and defense traits (total C, lignin, cellulose, and phenols). We also considered Ca as a key element regulating foliar metabolism and nutrient cycling in humid tropical ecosystems (15, 16), and we measured δ¹³C and soluble carbon as indicators of performance (17). Finally, we assessed sources of variation in leaf mass per area (LMA), a foliar structural property expressing plant investment strategies based on multiple chemical and physiological traits (18).     

Increasing homogeneity in global food supplies and the implications for food security

The narrowing of diversity in crop species contributing to the world’s food supplies has been considered a potential threat to food security. However, changes in this diversity have not been quantified globally. We assess trends over the past 50 y in the richness, abundance, and composition of crop species in national food supplies worldwide. Over this period, national per capita food supplies expanded in total quantities of food calories, protein, fat, and weight, with increased proportions of those quantities sourcing from energy-dense foods. At the same time the number of measured crop commodities contributing to national food supplies increased, the relative contribution of these commodities within these supplies became more even, and the dominance of the most significant commodities decreased. As a consequence, national food supplies worldwide became more similar in composition, correlated particularly with an increased supply of a number of globally important cereal and oil crops, and a decline of other cereal, oil, and starchy root species. The increase in homogeneity worldwide portends the establishment of a global standard food supply, which is relatively species-rich in regard to measured crops at the national level, but species-poor globally. These changes in food supplies heighten interdependence among countries in regard to availability and access to these food sources and the genetic resources supporting their production, and give further urgency to nutrition development priorities aimed at bolstering food security.A shared axiom of ecology and nutrition is that, within certain ranges, diversity enhances the health and function of complex biological systems. Species diversity has been shown to stimulate productivity, stability, ecosystem services, and resilience in natural (1–5) and in agricultural ecosystems (6–13). Likewise, variation in food species contributing to diet has been associated with nutritional adequacy (14–17) and food security (18).The development of sedentary agricultural societies and further rise of modern agriculture is generally considered to have led to a decline in the total number of plant species upon which humans depend for food (19, 20), particularly the wild, semidomesticated, and cultivated vegetables and fruits, spices, and other food plants that supplemented staple crops with the provision of micronutrients and that bolstered food security historically during crop failures (21). Harlan (20) warned that

most of the food for mankind comes from a small number of crops and the total number is decreasing steadily. In the United States in the past 40 years, many vegetables and fruits have disappeared from the diet, and the trend is going on all over the world. More and more people will be fed by fewer and fewer crops.

More recent analyses of dietary transition in developing countries in association with globalization have noted increases in the diversity of plants contributing to diets locally, along with a Westernization transition in preference of energy-dense foods (i.e., animal products, plant oils, and sugars) over cereals, pulses, and vegetables, and of particular major crop plants within these food categories over traditional crops (22, 23). The impact of such changes on overall crop diversity worldwide has not been comprehensively documented, although recent changes in varietal and allelic level diversity of some crops have been investigated (24–26). Given the potential food security implications of narrowing of the diversity of crop species both in production systems and in food supplies, an assessment of the global state of crop plant species diversity is warranted.Here we examine changes in the diversity of the portfolio of crop species upon which humans primarily depend for food security in regard to calories, protein, fat, and food weight. Using national per capita food supply data published by the Food and Agriculture Organization (FAO) of the United Nations, we analyzed trends in the richness, abundance, and composition of measured crop commodities in the food supplies of 152 countries comprising 98% of the world’s population from 1961 to 2009.