Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages.

USA500 isolates are clonal complex 8 (CC8) Staphylococcus aureus strains closely related to the prominent community- and hospital-associated USA300 group. Despite being relatively understudied, USA500 strains cause a significant burden of disease and are the third most common methicillin-resistant S. aureus (MRSA) strains identified in the U.S. Emerging Infections Program (EIP) invasive S. aureus surveillance. To better understand the genetic relationships of the strains, we sequenced the genomes of 539 USA500 MRSA isolates from sterile site infections collected through the EIP between 2005 and 2013 in the United States. USA500 isolates fell into three major clades principally separated by their distribution across different U.S. regions. Clade C1 strains, found principally in the Northeast, were associated with multiple IS256 insertion elements in their genomes and higher levels of antibiotic resistance. C2 was associated with Southern states, and E1 was associated with Western states. C1 and C2 strains all shared a frameshift in the gene encoding AdsA surface-attached surface protein. We propose that the term "USA500" should be used for CC8 strains sharing a recent common ancestor with the C1, C2, and E1 strains but not in the USA300 group.IMPORTANCE In this work, we have removed some of the confusion surrounding the use of the name "USA500," placed USA500 strains in the context of the CC8 group, and developed a strategy for assignment to subclades based on genome sequence. Our new phylogeny of USA300/USA500 will be a reference point for understanding the genetic adaptations that have allowed multiple highly virulent clonal strains to emerge from within CC8 over the past 50 years.

Lenalidomide with or without erythropoietin in transfusion-dependent erythropoiesis-stimulating agent-refractory lower-risk MDS without 5q deletion.

After failure of erythropoiesis-stimulating agents (ESAs), lenalidomide (LEN) yields red blood cell (RBC) transfusion independence (TI) in 20-30% of lower-risk non-del5q myelodysplastic syndrome (MDS). Several observations suggest an additive effect of ESA and LEN in this situation. We performed a randomized phase III study in 131 RBC transfusion-dependent (TD, median transfusion requirement six RBC units per 8 weeks) lower-risk ESA-refractory non-del5q MDS. Patients received LEN alone, 10 mg per day, 21 days per 4 weeks (L arm) or LEN (same schedule) + erythropoietin (EPO) beta, 60,000 U per week (LE arm). In an intent-to-treat (ITT) analysis, erythroid response (HI-E, IWG 2006 criteria) after four treatment cycles (primary end point) was 23.1% (95% CI 13.5-35.2) in the L arm and 39.4% (95% CI 27.6-52.2) in the LE arm (P=0.044), while RBC-TI was reached in 13.8 and 24.2% of the patients in the L and LE arms, respectively (P=0.13). Median response duration was 18.1 and 15.1 months in the L and LE arms, respectively (P=0.47). Side effects were moderate and similar in the two arms. Low baseline serum EPO level and a G polymorphism of CRBN gene predicted HI-E. Combining LEN and EPO significantly improves erythroid response over LEN alone in lower-risk non-del5q MDS patients with anemia resistant to ESA.

Indoor noise exposure at home: a field study in the family of urban schoolchildren.

This article aims at evaluating indoor noise levels at home and investigating the factors that may influence their variability. An 8-day noise measurement campaign was conducted in the homes of 44 schoolchildren attending the public primary schools of Besançon (France). The presence of the inhabitants in the dwelling and the noisy events occurring indoors and outdoors was daily collected using a time-location-activity diary (TLAD); 902 time periods were analyzed. The indoor noise level increased significantly with the outdoor noise level, along with the duration of the presence or level of activity of the inhabitants at home. However, this effect may vary according to the period of day and the day of the week. Moreover, a significant part of the day and evening indoor noise level variability was explained when considering the TLAD variables: 46% and 45% in the bedroom, 54% and 39% in the main room, respectively. Our results highlight the complexity of the indoor environment in the dwellings of children living in an urban area. Combining the inhabitant presence and indoor noise source descriptors with outdoor noise levels and other dwelling or inhabitant characteristics could improve large-scale epidemiological studies. However, additional efforts are still needed, particularly during the night period.

[Exacerbations of asthma in Guadeloupe (French West Indies) and volcanic eruption in Montserrat (70 km from Guadeloupe)]. / Exacerbations d'asthme en Guadeloupe et éruption volcanique à Montserrat (70 km de la Guadeloupe).

INTRODUCTION: This study evaluates the impact of the ash cloud emitted in February 2010 during the eruption of the Soufrière Hill volcano of the island of Montserrat (70 km from Guadeloupe), on asthma exacerbations registered by the emergency hospital services in the archipelago of Guadeloupe in February 2010. METHODS: We first recorded the clinical features and outcome of each adult patient admitted as an emergency with an acute asthma exacerbation during this period, then compared the admission rates for asthma exacerbation, concentrations of particulates and chemical pollutants, and climatic parameters before, during, and after exposure to the ash cloud. Then, using a generalized linear model defined by a Poisson regression, we calculated the risks related to these factors. RESULTS: There was an increase in acute asthma admissions during and after exposure to the ash cloud (2.44/day versus 5.6/day, P<0.003). PM10 (particles<10 microns) were the major particulate pollution episodes (mean: 223 µg/m(3)). Asthmatics admitted acutely during the period of pollution were young adults (35 [18-49] years old), and the majority had asthma classified as intermittent (57%, n=27). In multivariate analysis, PM10 were a risk factor for acute asthma presentations during this period (aRR 2.89, 95% [from 1.69 to 4.93]). CONCLUSIONS: This study describes the clinical data and outcome of adult patients admitted to emergency asthma exacerbation during the eruption of the Soufrière Hills Volcano in Montserrat and indicates that there was a significant impact of the ash plume on respiratory health, mainly in patients with intermittent asthma.

Outlier loci highlight the direction of introgression in oaks.

Loci considered to be under selection are generally avoided in attempts to infer past demographic processes as they do not fit neutral model assumptions. However, opportunities to better reconstruct some aspects of past demography might thus be missed. Here we examined genetic differentiation between two sympatric European oak species with contrasting ecological dynamics (Quercus robur and Quercus petraea) with both outlier (i.e. loci possibly affected by divergent selection between species or by hitchhiking effects with genomic regions under selection) and nonoutlier loci. We sampled 855 individuals in six mixed forests in France and genotyped them with a set of 262 SNPs enriched with markers showing high interspecific differentiation, resulting in accurate species delimitation. We identified between 13 and 74 interspecific outlier loci, depending on the coalescent simulation models and parameters used. Greater genetic diversity was predicted in Q. petraea (a late-successional species) than in Q. robur (an early successional species) as introgression should theoretically occur predominantly from the resident species to the invading species. Remarkably, this prediction was verified with outlier loci but not with nonoutlier loci. We suggest that the lower effective interspecific gene flow at loci showing high interspecific divergence has better preserved the signal of past asymmetric introgression towards Q. petraea caused by the species' contrasting dynamics. Using markers under selection to reconstruct past demographic processes could therefore have broader potential than generally recognized.

Detecting the footprints of divergent selection in oaks with linked markers.

Genome scans are increasingly used to study ecological speciation, providing a useful genome-wide perspective on divergent selection in the presence of gene flow. Here, we compare current approaches to detect footprints of divergent selection in closely related species. We analyzed 192 individuals from two interfertile European temperate oak species using 30 nuclear microsatellites from eight linkage groups. These markers present little intraspecific differentiation and can be used in combination to assign individual genotypes to species. We first show that different outlier detection tests give somewhat different results, possibly due to model constraints. Second, using linkage information for these markers, we further characterize the signature of divergent selection in the presence of gene flow. In particular, we show that recombination estimates for regions with outlier markers are lower than those for a control region, in line with a prediction from ecological speciation theory. Most importantly, we show that analyses at the haplotype level can distinguish between truly divergent (bi-directional) selection and positive selection in one of the two species, offering a new and improved method for characterizing the speciation process.

Multiplexed microsatellite markers for genetic studies of beech.

European beech (Fagus sylvatica L.) is one of the economically most important broadleaved tree species in Europe and has become a model for studying climate change effects on forests. Multiplex PCR of microsatellites is a fast and cost-effective technique allowing high-throughput genotyping. Here we present the procedure used to develop two multiplex kits (8-plexes) for European beech. We paid particular attention to quality control throughout all steps of the multiplex kits development (null allele detection, error rate measurements, linkage disequilibrium). Preliminary assays suggest that the 16 amplified loci are largely devoid of null alleles and allow rapid and cost-effective genotyping of beech with low error rates. The two kits, which differ in their levels of polymorphism, most likely due to marker origin, were also informative in seven other beech species tested.

Current trends in microsatellite genotyping.

Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.

Two highly validated multiplexes (12-plex and 8-plex) for species delimitation and parentage analysis in oaks (Quercus spp.).

Multiplex PCR is a fast and cost-effective technique allowing increased genotyping throughput of microsatellites. We developed two multiplexes for Quercus petraea and Q. robur, a 12-plex of EST-SSRs (eSSRs) and an 8-plex of genomic SSRs (gSSRs). We studied the origin of allele calling errors at the human reader and software levels. We showed that the robustness of allele identification can be improved by binning on raw peak sizes prior to genetic data analysis. We checked through simulation the power of these markers for species delimitation and hybrid detection. The resolution achieved with all 20 markers was greatly improved compared to that of previous studies based on a subset of the markers. Preliminary PCR tests suggest that these multiplexes might be useful to study other oak species as well. The strategy used for multiplex microsatellite development (from PCR conditions to the definition of allele calling rules) should be broadly applicable.

Species relative abundance and direction of introgression in oaks.

Successful hybridisation and subsequent introgression lead to the transfer of genetic material across species boundaries. In this process, species relative abundance can play a significant role. If one species is less abundant than the other, its females will receive many heterospecific gametes, increasing mate-recognition errors and thus hybridisation rate. Moreover, first-generation hybrids will also more likely mate with the more abundant species, leading to asymmetric introgression. These predictions have important fundamental consequences, especially during biological invasions or when a rare species threatened by extinction is surrounded by individuals from a related species. However, experimental tests in nature of the importance of the relative abundance of each species on hybridisation dynamics remain scarce. We assess here the impact of species relative abundance on hybridisation dynamics among four species from the European white oak species complex. A total of 2107 oak trees were genotyped at 10 microsatellite markers and Bayesian clustering methods were used to identify reference trees of each species. We then used these reference trees to simulate purebred and hybrid genotypes to determine optimal threshold for genetic assignment. With this approach, we found widespread evidence of hybridisation between all studied oak species, with high occurrence of hybrids, varying from 11% to 31% according to stand and sampling strategies. This finding suggests that hybridisation is a common phenomenon that plays a significant role in evolution of this oak species complex. In addition, we demonstrate a strong impact of species abundance on both hybridisation rate and introgression directionality.

Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex).

Powerful and accurate detection of first-generation (F1) hybrids and backcrosses in nature is needed to achieve a better understanding of the function and dynamics of introgression. To document the frequency of ongoing interspecific gene exchange between two Mediterranean evergreen oaks, the cork oak (Quercus suber) and the holm oak (Q. ilex), we analyzed 1487 individuals originating from across the range of the two species using eight microsatellite loci and two Bayesian clustering approaches (implemented in the programs STRUCTURE and NEWHYBRIDS). Simulated data were used to assess the differences between the two clustering methods and to back up the choice of the threshold value for the posterior probability to discriminate admixed from pure individuals. We found that the use of STRUCTURE resulted in the highest power to detect hybrids, whereas NEWHYBRIDS provided the highest accuracy. Irrespective of the approach, the two species were clearly distinguished as independent genetic entities without any prior information. In contrast with previous reports, we found no evidence for unidirectional introgression. The overall hybridization rate was very low (<2% of introgressed individuals). Only two individuals were identified as F1 hybrids and five as early backcrosses. This work shows that the combined application of the two complementary Bayesian approaches and their systematic validation with simulations, fit for the case at hand, helps gain resolution in the identification of admixed individuals.

Lipoprotein (a) and risk of ischemic stroke in young adults.

UNLABELLED: Lipoprotein (a) [Lp(a)] is a LDL-particle linked to apoprotein (a) [apo(a)]. High Lp(a) plasma level is a risk factor for coronary heart disease and, in older men, for ischemic stroke. The role of Lp(a) as a risk factor for ischemic stroke in young adults is uncertain. METHODS: Lp(a) concentration was prospectively measured in 100 consecutive patients with acute ischemic stroke (58 men and 42 women) aged 18-55 years, and in 100 controls matched for age and gender. RESULTS: The distribution of Lp(a) concentration was skewed toward the highest and median tertiles in male patients. In multivariate logistic regression analyses adjusting on classical risk factors for ischemic stroke and lipid variables, Lp(a) concentration in the highest and medium tertiles compared with the lowest tertile was significantly associated with ischemic stroke in men (OR 3.55, 95% CI 1.33-9.48, p = 0.012), but was not in women (OR 0.42, 95% CI 0.14-1.26, p = 0.12). Although large vessel atherosclerosis was more common in men than in women, there were no differences in Lp(a) concentration according to the cause of ischemic stroke. CONCLUSION: Among subjects aged 18-55 years, a slightly elevated Lp(a) concentration was strongly and independently associated with ischemic stroke in men, but not in women. Further studies are required to elucidate the mechanisms underlying this gender-specific association.

Anestesia en un caso de urticaria a frígore / No disponible

No disponible

Contrasting effects of long distance seed dispersal on genetic diversity during range expansion.

Currently many attempts are made to reconstruct the colonization history of plant species after the last ice age. A surprising finding is that during the colonization phase genetic diversity did not decrease as much as expected. In this paper we examine whether long distance seed dispersal events could play a role in the unexpected maintenance of genetic diversity during range expansion. This study is based on simulations carried out with a maternally inherited haploid locus using a cellular automaton. The simulations reveal a close relationship between the frequency of long distance seed dispersal events and the amount of genetic diversity preserved during colonization. In particular, when the colonized region is narrow, a complete loss of genetic diversity results from the occurrence of very rare long distance dispersal (LDD) events. We call this phenomenon the 'embolism effect'. However, slightly higher rates of LDD events reverse this effect, up to the point that diversity is better preserved than in a pure diffusion model. This phenomenon is linked to the reorganization of the genetic structure during colonization and is called the 'reshuffling effect'.

[Partial replacement of obsolete prosthetic implants]. / Problèmes posés par le remplacement partiel des implants tombés en désuétude.

Thanks to better technique for cemented prostheses or to better osteointegration of porous coated implants, a long term survival can be expected for joint prostheses. Wear of the bearing surfaces resulting in osteolysis, metallosis and even rupture has become the main threat after several years. In such cases, revising all the parts of a stable and well fixed implant may cause fractures, loss of bone and thus need an extensive reconstruction. Revising only the worn out parts might be preferable, provided that they still are available. Data collected by the SFHG (French Hip and Knee Society) and AVIO group show that 45% of hip revisions and 16% of knee revisions are partial ones. The need for a total exchange instead of a partial one appeared in 6.4% of knee revisions and 2.8% of hip revisions, because parts were no longer available. These problems linked to a longer life expertancy of the patients and the increasing number of hip and knee arthroplasties will be met more and more often by orthopedic surgeons. When parts identical to the worn out ones are still on the market, there is no problem. When their production has been given up, but the company has kept their references and accepts to make a single element it may be possible to obtain the missing unit. The increased cost of such a fabrication, however is not nowadays supported by an appropriate price. But in a few remaining cases without enough industrial references, a custom-made part had to be done to allow partial replacement, with the benefit of an adapted price. Care must be taken to observe the regulations. The surgeon endorses full responsibility not only for the surgical procedure but also for the choice of the implanted device. For custom-made products he is responsible for the technical data given to the company. The patient must be thoroughly informed, and his opinion taken into account in the operative decision. As a revision arthroplasty aims at restoring a good function, the procedure should suit best the patient's health condition and try and avoid any hazard. Rejecting the option of partial replacement just because of parts unavailability is not acceptable when it seems the safest way to get the best result. Help can come from orthopedic surgeons themselves, if they give to their patient precise reports on the primary arthroplasty. The technical references of all the devices devoted to joint arthroplasty should not only be collected by public health services (AFSSAPS) but they should also be available to orthopedic surgeons. The real production cost of prosthetic elements should be taken into account in order to encourage the companies to deliver parts that are not on the market anymore.

Chloroplast DNA variation of Quercus rubra L. in North America and comparison with other Fagaceae.

Quercus rubra is one of the most important timber and ornamental tree species from eastern North America. It is a widespread species growing under variable ecological conditions. Chloroplast DNA variation was studied by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) in 290 individuals from 66 populations sampled throughout the natural range. A total of 12 haplotypes were detected, with one found in 75% of the trees. Population differentiation is relatively low (G(ST) = 0.46), even when similarities between haplotypes are taken into account (N(ST) = 0.50), pointing to a weak phylogeographical structure. Furthermore, no spatial structure of genetic diversity could be detected. The genetic differentiation increased northwards, reflecting the postglacial history of Q. rubra. The unusual aspect of this study was the low level of chloroplast DNA genetic differentiation in Q. rubra compared to that typically observed in other oak species. Palynological evidence indicates that during the last glacial maximum, Q. rubra had one major distribution range with populations located relatively far to the north, resulting in only modest movement northwards when climate improved, whereas European white oaks were largely restricted to the southern European peninsulas and experienced extensive movements during the postglacial period. The contrasted geographical features and levels of tree species richness of both continents might further explain why congeneric species sharing similar life history traits have genetic structures that are so different.

Rangewide phylogeography of a bird-dispersed Eurasian shrub: contrasting Mediterranean and temperate glacial refugia.

We studied the phylogeography of alder buckthorn (Frangula alnus), a bird-dispersed shrub or small tree distributed over most of Europe and West Asia and present in three of the four main refugia of West Palaearctic temperate woody plants: the Iberian Peninsula, the Balkans and Anatolia. A total of 78 populations from 21 countries were analysed for chloroplast DNA variation using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and 21 different haplotypes were distinguished. We found a very strong overall population differentiation (GST = 0.81) and phylogeographical structure, and a sharp contrast between the haplotype-rich refugia and the almost completely uniform area of postglacial colonization. The haplotype network comprises three lineages made up of haplotypes from the Iberian Peninsula, Anatolia with the Caucasus, and temperate Europe. The Iberian and the Anatolian branches represent parts of a major lineage that spans over the whole northern Mediterranean Basin and some neighbouring areas and probably dates back to the Tertiary. Many haplotypes of this lineage are distributed locally and most populations are fixed for a single haplotype; these populations have apparently been very stable since their establishment, experiencing negligible gene flow and few mutations. The temperate European lineage consists of one very widespread and abundant plus six locally distributed haplotypes. Four of them are located in Southeast Europe, the putative refugium of all extant temperate European populations. Contrary to populations from Iberia and Anatolia, F. alnus populations from the southeastern European refugium have most genetic variation within populations. Bird-mediated seed dispersal has apparently allowed not only a very rapid postglacial expansion of F. alnus but also subsequent regular seed exchanges between populations of the largely continuous species range in temperate Europe. In contrast, the disjunct F. alnus populations persisting in Mediterranean mountain ranges seem to have experienced little gene flow and have therefore accumulated a high degree of differentiation, even at short distances. Populations from the southern parts of the glacial refugia have contributed little to the postglacial recolonization of Europe, but their long-term historical continuity has allowed them to maintain a unique store of genetic variation.