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International audience; Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.

International audience; Since the start of COVID-19 pandemic the Republic of Djibouti, in the horn of Africa, has experienced two epidemic waves of the virus between April and August 2020 and between February and May 2021. By May 2021, COVID-19 had affected 1.18% of the Djiboutian population and caused 152 deaths. Djibouti hosts several foreign military bases which makes it a potential hot-spot for the introduction of different SARS-CoV-2 strains. We genotyped fifty three viruses that have spread during the two epidemic waves. Next, using spike sequencing of twenty-eight strains and whole genome sequencing of thirteen strains, we found that Nexstrain clades 20A and 20B with a typically European D614G substitution in the spike and a frequent P2633L substitution in nsp16 were the dominant viruses during the first epidemic wave, while the clade 20H South African variants spread during the second wave characterized by an increase in the number of severe forms of COVID-19.

Located from 35° to 45° latitude in both hemispheres, the transition zone is an important region with respect to the planktonic biogeography of the sea. However, to the best of our knowledge, there have been no reports on the existence of a tintinnid community in the transition zone. In this research, tintinnids along two transects across the North Pacific Transition Zone (NPTZ) were investigated in summer 2016 and 2019. Eighty-three oceanic tintinnid species were identified, 41 of which were defined as common oceanic species. The common oceanic species were further divided into five groups: boreal, warm water type I, warm water type II, transition zone, and cosmopolitan species. Undella californiensis and Undella clevei were transition zone species. Other species, such as Amphorides minor, Dadayiella ganymedes, Dictyocysta mitra, Eutintinnus pacificus, Eutintinnus tubulosus, Protorhabdonella simplex, and Steenstrupiella steenstrupii, were the most abundant in the NPTZ but spread over a much larger distribution region. Species richness showed no obvious increase in the NPTZ. Boreal, transition zone, and warm water communities were divided along the two transects. Tintinnid transition zone community mainly distributed in regions with water temperatures between 15 and 20°C. The tintinnid lorica oral diameter size classes were dominated by the 24–28 μm size class in three communities, but the dominance decreased from 66.26% in the boreal community to 48.85% in the transition zone community and then to 22.72% in the warm water community. Our research confirmed the existence of tintinnid transition zone species and community. The abrupt disappearance of warm water type I species below 15°C suggested that this group could be used as an indicator of the northern boundary of the NPTZ.

Off the coast of Vietnam, two recent events seem to have contributed to the death of coral reefs: the rapid invasion of a small marine snail called Drupella, and the emergence of a disease that spreads over corals. We decided to investigate whether there is a link between the corals, the snails, and the disease. We analyzed the mucus covering the surface of corals, both in healthy corals and those infested by Drupella snails. Mucus produced by corals is usually full of helpful microbes, protecting the corals from harmful microbes that can make them ill or kill them. Our analyses showed that, when Drupella eats corals, the snail also removes one of the corals’ primary defenses by eliminating most of the tiny protectors in their mucus. This allows harmful microbes to cause additional damage to the corals.

International audience; The current Coronavirus Disease 2019 (COVID-19) pandemic, with more than 111 million reported cases and 2,500,000 deaths worldwide (mortality rate currently estimated at 2.2%), is a stark reminder that coronaviruses (CoV)-induced diseases remain a major threat to humanity. COVID-19 is only the latest case of betacoronavirus (β-CoV) epidemics/pandemics. In the last 20 years, two deadly CoV epidemics, Severe Acute Respiratory Syndrome (SARS; fatality rate 9.6%) and Middle East Respiratory Syndrome (MERS; fatality rate 34.7%), plus the emergence of HCoV-HKU1 which causes the winter common cold (fatality rate 0.5%), were already a source of public health concern. Betacoronaviruses can also be a threat for livestock, as evidenced by the Swine Acute Diarrhea Syndrome (SADS) epizootic in pigs. These repeated outbreaks of β-CoV-induced diseases raise the question of the dynamic of propagation of this group of viruses in wildlife and human ecosystems. SARS-CoV, SARS-CoV-2, and HCoV-HKU1 emerged in Asia, strongly suggesting the existence of a regional hot spot for emergence. However, there might be other regional hot spots, as seen with MERS-CoV, which emerged in the Arabian Peninsula. β-CoVs responsible for human respiratory infections are closely related to bat-borne viruses. Bats are present worldwide and their level of infection with CoVs is very high on all continents. However, there is as yet no evidence of direct bat-to-human coronavirus infection. Transmission of β-CoV to humans is considered to occur accidentally through contact with susceptible intermediate animal species. This zoonotic emergence is a complex process involving not only bats, wildlife and natural ecosystems, but also many anthropogenic and societal aspects. Here, we try to understand why only few hot spots of β-CoV emergence have been identified despite worldwide bats and bat-borne β-CoV distribution. In this work, we analyze and compare the natural and anthropogenic environments associated with the emergence of β-CoV and outline conserved features likely to create favorable conditions for a new epidemic. We suggest monitoring South and East Africa as well as South America as these regions bring together many of the conditions that could make them future hot spots.

International audience; An organism responds to the invading pathogens such as bacteria, viruses, protozoans, and fungi by engaging innate and adaptive immune system, which functions by activating various signal transduction pathways. As invertebrate organisms (such as sponges, worms, cnidarians, molluscs, crustaceans, insects, and echinoderms) are devoid of an adaptive immune system, and their defense mechanisms solely rely on innate immune system components. Investigating the immune response in such organisms helps to elucidate the immune mechanisms that vertebrates have inherited or evolved from invertebrates. Planarians are non-parasitic invertebrates from the phylum Platyhelminthes and are being investigated for several decades for understanding the whole-body regeneration process. However, recent findings have emerged planarians as a useful model for studying innate immunity as they are resistant to a broad spectrum of bacteria. This review intends to highlight the research findings on various antimicrobial resistance genes, signaling pathways involved in innate immune recognition, immune-related memory and immune cells in planarian flatworms.

One dominant ecological trait in the dimly-lit deep-sea is the ability of organisms to emit bioluminescence. Despite its many ecological roles in deep-sea ecosystems, the presence of inherent bioluminescence in marine sponges has been debated for more than a century. This work reports repeated observations of luminescence from six individuals of an undescribed carnivorous sponge species (Cladorhizidae) sampled near 4,000 m depth off Monterey Bay (CA, United States). These are the first fully documented records of bioluminescence in the phylum Porifera. Videos and photographs of the sponges’ bioluminescence were recorded on board after collection and in vitro bioluminescence assays indicate that the bioluminescence system is a coelenterazine-based luciferase. Coelenterazine luciferin is already described in various organisms such as cnidarians, chaetognaths, copepods, cephalopods, ctenophores, ostracods, and some mysid or decapod shrimps. Based on these observations we discuss new ecological hypotheses of functional traits such as bioluminescence and carnivory in deep sea organisms.

International audience; Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50 degrees C to 60 degrees C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

Microbial food web (MFW) in the seawater encompasses the smallest organisms: viruses, autotrophic prokaryotes and heterotrophic prokaryotes (HP), nanoflagellates, eukaryotic phytoplankton and ciliates. For many years, scientists investigated the MFW structure differences in distinct water masses. However, the MFW structure seasonal variation in coastal areas remains poorly documented. In this study, we report on the seasonal and spatial variations of the MFW structure in the temperate Sanggou Bay in four successive seasons, from spring to winter. With a temperature increase from 1.90 to 24.20°C, HP biomass increased from 3.77 to 135.77 μg C dm–3, almost covering the whole variation range for the global ocean. The autotrophic (AUTO) components, including Synechococcus, phototrophic picoeukaryotes (PEUK) and pigmented nanoflagellates (PNF), exhibited biomass variation ranges as large as previously reported. The MFW structure seasonal variation was driven by MFW relative biomasses (biomass ratios of MFW components to HP). With the increase of HP biomass, PNF and PEUK relative biomasses increased more rapidly than those of other groups while that of ciliates slightly decreased. The HETE:AUTO (biomass ratio of heterotroph to autotroph organisms) decreased with temperature, it was 1 in other seasons. Cluster analyses distinguished Inside Bay and Outside Bay on the basis of hydrological characteristics. Consistently, the two subdivisions of Sanggou Bay exhibited different MFW structures as well as distinct tintinnid communities. The main MFW structure difference between Inside and Outside Bay was the biomass ratios of AUTO components to HP. Our results showed that the variations of autotrophic component biomass ratios relative to HP were the main factor responsible for the MFW structure seasonal variation. The spatial difference in MFW structure as well as in tintinnid taxonomic composition between Inside and Outside Bay was linked to the semienclosed nature of the Bay that does not favor efficient mixing with outside Yellow Sea waters.

The Mediterranean region has been shown to be particularly exposed to climate change, with observed trends that are more pronounced than the global tendency. In forecast studies based on a RCP 8.5 scenario, there seems to be a consensus that, along with an increase in temperature and salinity over the next century, a reduction in the intensity of deep-water formation and a shallowing of the mixed layer (especially in the North-Western Mediterranean Sea (MS)) are expected. By contrast, only a few studies have investigated the effects of climate change on the biogeochemistry of the MS using a 3D physical/biogeochemical model. In this study, our aim was to explore the impact of the variations in hydrodynamic forcing induced by climate change on the biogeochemistry of the MS over the next century. For this purpose, high-resolution simulations under the RCP 8.5 emission scenario have been run using the regional climate system model CNRM-RCSM4 including the NEMO-MED8 marine component, coupled (off-line) with the biogeochemical model Eco3M-Med. The results of this scenario first highlight that most of the changes in the biogeochemistry of the MS will occur (under the RCP 8.5 scenario) after 2050. They suggest that the MS will become increasingly oligotrophic, and therefore less and less productive (14 % decrease in integrated primary production in the Western Basin and in the Eastern Basin). Significant changes would also occur in the planktonic food web, with a reduction (22 % in the Western Basin and 38 % in the Eastern Basin) of large phytoplankton species abundance in favour of small organisms. Organisms will also be more and more N-limited in the future since NO3 concentrations are expected to decline more than those of PO4 in the surface layer. All these changes would mainly concern the Western Basin, while the Eastern Basin would be less impacted.

Coastal and open ocean regions of the Western Tropical South Pacific ocean have been identified as a hotspot of N2 fixation. However, the environmental factors driving the temporal variability of abundance, composition, and activity of diazotrophs are still poorly understood, especially during the winter season. To address this, we quantified N2 fixation rates and the abundance of seven diazotroph phylotypes (UCYN-A1 symbiosis, UCYN-B, UCYN-C, Trichodesmium, Het-1, Het-2, and Het-3) on a monthly basis during two full years (2012 to 2014) at four stations along a coast to open ocean transect in the New Caledonian lagoon. The total nifH gene concentration (sum of all nifH gene copies) clearly decreased from the barrier reef to the shore. Apart from UCYN-B, which peaked at very high abundances (10 6–10 8 nifH gene copies L -1) at two occasions at the coastal station, the UCYN-A1 symbiosis was the most abundant group at all stations, accounting for 79% of the total nifH gene copy counts along the transect (average abundance 4.2 +/- 10.3 x 10 4 nifH gene copies L-1). The next most abundant groups were in order Trichodesmium (accounting for 14% of the total nifH gene copies), Het-groups (6% of the total) and UCYN-C (1% of the total). Statistical analyses reveal that the UCYN-A1 symbiosis and Het groups were associated with cold (25°C) waters, low NOx and PO4 3- concentrations, strong and (mostly) easterly winds. Average N2 fixation rates over the survey were 6.5 +/- 6.7 nmol N L-1 d-1 and did not differ significantly among seasons. The year to year variability was more pronounced with average integrated rates significantly higher in the second year of the survey (162 +/- 122 mmol N m-2 d-1) than the first year (66 +/-91 mmol N m-2 d-1). This dataset suggests that seasonality is less pronounced than previously thought, and that relatively high N2 fixation rates are maintained in the New Caledonian lagoon all year long, despite seasonal changes in the diazotroph community composition.

International audience; The biological fixation of dinitrogen (N 2) by marine microbes called "diazotrophs" sustains ∼50% new production in the ocean, boosting CO 2 absorption by photoautotrophs and thus contributing to the mitigation of climate change. New environmental conditions sustaining N 2 fixation have been revealed in recent years, enabling more accurate forecasting of future nitrogen inputs and localized hot spots. However, at present the paucity and biased geographical coverage of N 2 fixation and diazotroph diversity measurements impede attempts to reconcile global nitrogen budgets with observed rates. Most studies have been conducted at disparate spatiotemporal scales, including: (i) discrete and short duration measurements in small seawater volumes isolated from the environment, and (ii) spatial extrapolations and global models of diazotrophy projected over decades to centuries. We argue that this knowledge gap lies at the fine scales: dynamic seawater structures < 200 km wide and < 2 months lifetime. However, the spatiotemporal resolution of conventional oceanographic cruises, with stations separated by tens to hundreds of kilometers, is too poor to resolve fine scale processes. Bridging this gap requires leveraging high spatiotemporal resolution measurements. Here we present and discuss the advantages and disadvantages of contemporary methods and equipment able to provide high-resolution measurements at sea. We also provide insights into high-resolution sampling approaches to be developed in the near future. Increasing the spatiotemporal resolution of diazotroph activity and diversity will provide more realistic quantifications of nitrogen fluxes in the dynamic ocean.

International audience; The oceanic biological carbon pump (BCP) regulates the Earth carbon cycle by transporting part of the photosynthetically fixed CO 2 into the deep ocean. Suppressing this mechanism would result in an important increase of atmospheric CO 2 level. The BCP occurs mainly in the form of (1) organic carbon (OC) particles sinking out the surface ocean, of (2) neutrally buoyant OC (dissolved or particulate) entrained by downward water masses movements and/or mixing, and of (3) active transport of OC by migrating animals such as zooplankton and fishes. These various pools of OC differ in size since their sinking, production and decomposition rates vary spatially and temporally. Moreover, the OC transported to depths via these various export pathways as well as their decomposition pathways all have different ecological origins and therefore may response differently to climate changes. Currently, most ocean biogeochemical models do not resolve these various of OC pathways explicitly; rather, they imply that OC is therein created and destroyed equally. In addition, the organic composition of these various pools is largely unknown, especially at depths below 500 m. Here, known processes of OC export from the surface ocean to the mesopelagic zone (100-1000 m) are briefly reviewed. Three OC export pathways and some of their sub-categories are considered. I refer to published studies of OC fluxes associated with the specific downward export pathways and identify gaps that need to be addressed to better understand the OC fluxes associated with the BCP.

International audience; Invasive fungal infections, such as aspergillosis, candidiasis, and cryptococcosis, have significantly increased among immunocompromised people. To tackle these infections the first and most decisive step is the accurate identification of the causal pathogen. Routine identification of invasive fungal infections has progressed away from culture-dependent methods toward molecular techniques, including DNA barcoding, a highly efficient and widely used diagnostic technique. Fungal DNA barcoding previously relied on a single barcoding region, the internal transcribed spacer (ITS) region. However, this allowed only for 75% of all fungi to be correctly identified. As such, the translational elongation factor 1α (TEF1α) was recently introduced as the secondary barcode region to close the gap. Both loci together form the dual fungal DNA barcoding scheme. As a result, the ISHAM Barcoding Database has been expanded to include sequences for both barcoding regions to enable practical implementation of the dual barcoding scheme into clinical practice. The present study investigates the impact of the secondary barcode on the identification of clinically important fungal taxa, that have been demonstrated to cause severe invasive disease. Analysis of the barcoding regions was performed using barcoding gap analysis based on the genetic distances generated with the Kimura 2-parameter model. The secondary barcode demonstrated an improvement in identification for all taxa that were unidentifiable with the primary barcode, and when combined with the primary barcode ensured accurate identification for all taxa analyzed, making DNA barcoding an important, efficient and reliable addition to the diagnostic toolset of invasive fungal infections.

International audience; The presence of Acinetobacter baumannii was demonstrated in body lice, however, little is known about the mechanism of natural lice infection. In 2013 and 2014, cross-sectional one-day studies were therefore performed within two Marseille homeless shelters to assess the presence of A. baumannii DNA on human skin, blood and in body lice collected from the same homeless individuals. All 332 participants completed questionnaires, were examined for dermatologic signs, and provided four skin samples (hair, neck, armpits, and pelvic belt), blood samples and body lice (if any). We developed a new real-time PCR tool targeting the ompA/motB gene for the detection of A. baumannii for all collected samples. Blood culture was also performed. Body lice were found in 24/325 (7.4%) of subjects. We showed a prevalence of A. baumannii DNA skin-carriage in 33/305 (10.8%) of subjects. No difference was found in A. baumannii DNA prevalence according to body sites. A strong association between body lice infestation (OR = 3.07, p = 0.029) and A. baumannii DNA skin-carriage was noted. In lice, A. baumannii DNA was detected in 59/219 arthropods (26.9%). All blood cultures and real-time PCR on blood samples were negative for A. baumannii. Lice probably get infected with A. baumannii while biting through the colonized skin and likely transmit the bacteria in their feces. We found no evidence that lice facilitate the invasion of A. baumannii into the blood stream. Further investigations are needed to compare phenotypic and genotypic features of A. baumannii isolates from human skin and lice from the same individuals.

Vielzeuf, Daniel ... et al.-- 18 pages, 9 figures, 3 tables, supplementary material https://www.frontiersin.org/articles/10.3389/feart.2018.00167/full#supplementary-material, The concentration and spatial distribution of major (Ca, Mg) and trace elements (Na, Sr, S, Li, Ba, Pb, and U) in different Corallium skeletons (C. rubrum, C. japonicum, C. elatius, C. konojoi) have been studied by electron microprobe (EMP) and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). EMP data show positive Na-Mg and negative Na-S and Mg-S correlations in all skeletons. LA-ICPMS data display additional Sr-Mg, Li-Mg, and U-Mg positive correlations. Medullar zones in the skeletons, corresponding to fast growing zones, are systematically richer in Mg, Na, Sr, Li, and U and poorer in S than the surrounding slow growing zones. These spatial distributions are mostly interpreted in terms of growth kinetics combined with steric effects influencing the incorporation of impurities in biogenic calcites. This interpretation is in agreement with available experimental data on kinetic effects on the incorporation of elements in calcite. At a different scale, annual growth rings in annular slow growing zones show oscillations in Mg, Na, Sr, and S. These chemical oscillations probably result from growth rate variations: fast growth would produce rings enriched in Mg, Sr, and Na, while slow growth would produce rings enriched in Ca, S and organic matter. From previous studies in C. rubrum, the Mg-rich rings would develop during the spring to fall period while the S-rich rings would form immediately after (late fall and winter). Analytical traverses performed in annular zones of different Corallium skeletons indicate that Mg, Na, Sr, Li, and U decrease from core to rim. This observation indicates that radial growth rate decreases as the colony gets older. Contrary to Mg, Na, Sr, Li, S, and U, barium and lead concentrations are identical in medullar and annular zones and appear independent of growth kinetics. Thus, concentrations in Corallium skeletons could provide indications on Ba and Pb contents in the oceans. Barium and lead concentrations are higher in Mediterranean than in Pacific precious corals, these two elements can be used to discriminate C. rubrum from C. japonicum, and contribute enforcing regulations on the trade of precious corals, This work has been supported by the Centre National de la Recherche Scientifique (CNRS), by the Institut National des Sciences de l’Univers (INSU) through grant INTERRVIE 2017 to DV, by the Agence Nationale pour la Recherche (ANR) through ANR CoRo 2011-2015, by the Centre Interdisciplinaire de Nanoscience de Marseille (CINaM) through internal grants, and by the European Union COST action TD0903

International audience; A rapid analytical method including one-single solid-phase extraction (SPE) procedure followed by gas and liquid chromatography coupled with high resolution mass spectrometry detection (GC–MS and LC–HRMS respectively) was developed for the quantification of 40 organic compounds (1.6 < log K ow < 9.5) in seawater including both legacy and emerging contaminants, with a focus on the most common plastic organic additives. This new method allowed for the analyses of nine organophosphate esters (OPEs), seven phthalates (PAEs), six bisphenols (BPs), five perfluorinated compounds (PFCs), and thirteen legacy organochlorinated compounds (OCs, including polychlorobiphenyles and pesticides) with recoveries in the ranges of 57–124% for OPEs, 52–163% for PAEs, 64–118% for BPs, 63–124% for PFCs, and 40–95% for OCs. As a result of (i) strict cleanup protocols, (ii) material, and solvent selection, and (iii) the use of an ISO 6 cleanroom for sample treatment, the procedural blank levels were always lower than 5 ng L −1 , even for the most abundant and ubiquitous compounds like tris-(2-chloro, 1-methylethyl) phosphate (TCPP) and diethylhexyl phthalate (DEHP). The quantification limits were in the ranges of 0.03–0.75 ng L −1 for OPEs, 0.03–0.25 ng L −1 for PAEs, 0.1–5 ng L −1 for BPs, 0.1–8 ng L −1 for PFCs, and 0.02–1.1 ng L −1 for OCs, matching seawater analysis requirements. Dissolved water phase samples collected in Marseille Bay (NW Mediterranean Sea) were analyzed using the developed method reveling the concentration of PAEs up to 140 ng L −1 (DEHP) and that of OCs up to 70 ng L −1 (α-endosulfan). For the first time, we also provided the concentrations of OPEs (TCPP up to 450 ng L −1), BPs (bisphenol S up to 123 ng L −1), and PFCs (PFOS up to 5 ng L −1) in this area. A sampling station close to the municipal waste water treatment plant outfall exhibited the highest concentration levels for all compounds.

An accurate understanding of the biogeochemistry of dissolved phosphate pool in the upper waters of P-depleted oceanic regions is constrained by the low sensitivity of routine phosphate measurements. In this study, by using the sensitive Liquid Waveguide Capillary Cell method, we report the first extensive cross-basin survey of nanomolar dissolved inorganic phosphate (DIP) and dissolved organic phosphate (DOP) concentration in P-depleted surface waters of the Mediterranean Sea during the stratification period. In the north western Mediterranean Sea (NWMS), DIP above the mixed layer depth (MLD) ranged between 4.9 and 26.5 nM. Along an E-W transect crossing Ionian and Tyrrhenian Seas (E-W transect), DIP above the MLD was lower, ranging between 0.9 and 11.4 nM. Contrarily to the traditional view of a depleted and invariant surface dissolved phosphate pool, a significant vertical variability of DIP and DOP was revealed in upper waters. A positive gradient of DIP was observed above the phosphacline, between the MLD and the deep chlorophyll maximum (DCM) depth, suggesting a potential diffusion of new phosphate to near-surface waters, even under stratified conditions. Interestingly, despite this apparent DIP availability, a significant negative gradient of DOP concentration was observed in the same layer. Finally, the positive gradient in DIP coincided with a significant increase in N:P ratio, suggesting a higher rate of increase of N than of P. The results obtained in this study indicate that acquiring nanomolar DIP data is a sine qua non condition for the comprehension and prediction of the biogeochemical functioning of P-depleted oceanic regions, such as the Mediterranean Sea.

International audience; The presence of the giant virus of amoeba Marseillevirus has been identified at many different sites on the human body, including in the bloodstream of asymptomatic subjects, in the lymph nodes of a child with adenitis, in one adult with Hodgkin's disease, and in the pharynx of an adult. A high seroprevalence of the Marseillevirus has been recorded in the general population. Whether Marseillevirus can disseminate and persist within a mammal after entry remains unproven. We aimed to assess the ability of the virus to disseminate and persist into healthy organisms, especially in the lymphoid organs. Parenteral inoculations were performed by intraperitoneal injection (in rats and mice) or intravenous injection (in rats). Airway inoculation was performed by aerosolization (in mice). Dissemination and persistence were assessed by using PCR and amebal co-culture. Serologies were performed by immunofluorescent assay. Pathological examination was conducted after standard and immunohistochemistry staining. After intraperitoneal inoculation in mice and rats, Marseillevirus was detected in the bloodstream during the first 24 h. Persistence was noted until the end of the experiment, i.e., at 14 days in rats. After intravenous inoculation in rats, the virus was first detected in the blood until 48 h and then in deep organs with infectious virus detected until 14 and 21 days in the liver and the spleen, respectively. Its DNA was detected for up to 30 days in the liver and the spleen. After aerosolization in mice, infectious Marseillevirus was present in the lungs and nasal associated lymphoid tissue until 30 days post inoculation but less frequently and at a lower viral load in the lung than in the nasal associated lymphoid tissue. No other site of dissemination was found after aerosol exposure. Despite no evidence of disease being observed, the 30-day long persistence of Marseillevirus in rats and mice, regardless of the route of inoculation, supports the hypothesis of an infective potential of the virus in certain conditions. Its constant and long-term detection in nasal associated lymphoid tissue in mice after an aerosol exposure suggests the involvement of naso-pharyngeal associated lymphoid tissues in protecting the host against environmental Marseillevirus.

Molecular-based allergy diagnosis yields multiple biomarker datasets. The classical diagnostic score for allergic bronchopulmonary aspergillosis, a severe disease usually occurring in asthmatic patients and people with cystic fibrosis, comprises succinct immunological criteria formulated in 1977: total IgE, anti-Aspergillus fumigatus IgE, anti-Aspergillus fumigatus “precipitins”, and anti-Aspergillus fumigatus IgG. Progress achieved over the last four decades led to multiple IgE and IgG(4) Aspergillus fumigatus biomarkers available with quantitative, standardized, molecular-level reports. These newly available biomarkers have not been included in the current diagnostic criteria, either individually or in algorithms, despite persistent underdiagnosis of allergic bronchopulmonary aspergillosis. Large numbers of individual biomarkers may hinder their use in clinical practice. Conversely, multivariate analysis using new tools may bring about a better chance of less diagnostic mistakes. We report here a proof-of-concept work consisting of a three-step multivariate analysis of Aspergillus fumigatus IgE, IgG and IgG4 biomarkers through a combination of principal component analysis, hierarchical ascendant classification and classification and regression tree multivariate analysis. The resulting diagnostic algorithms might show the way for novel criteria and improved diagnostic efficiency in Aspergillus fumigatus-sensitized patients at risk for allergic bronchopulmonary aspergillosis.

International audience; Coral reefs are highly productive ecosystems thriving in nutrient-poor waters. Their productivity depends largely on the availability of nitrogen, the proximate limiting nutrient for primary production. In reefs, the major nitrogen pathways include regeneration, nitrification, ammonification and dinitrogen (N 2) fixation. N 2 fixation is performed by prokaryotes called " diazotrophs " that abound in coral rubbles, sandy bottoms, microbial mats, or seagrass meadows. Corals, which are the main reef builders, have developed a partnership with dinoflagellates which transform dissolved inorganic nitrogen into amino acids and protein, and with diazotrophs to gain diazotrophically-derived nitrogen (DDN). Pioneering studies found active diazotrophic cyanobacteria in the corals' mucus and/or tissue, and later high throughput sequencing efforts have described diverse communities of non-cyanobacterial diazotrophs associated with scleractinian corals. Yet, the metabolic processes behind these associations and how they benefit corals are currently not well understood. While genomic studies describe the diversity of diazotrophs and isotopic tracer experiments quantify N 2 fixation rates, combined advanced methods are needed to elucidate the mechanisms behind the transfer of DDN to the coral holobiont and whether these mechanisms change according to the identity of the diazotrophs or coral species. Here we review our current knowledge on N 2 fixation in corals: the diversity and localization of diazotrophs in the coral holobiont, the environmental factors controlling N 2 fixation, the fate of DDN within the coral symbiosis as well as its potential role in coral resilience. We finally summarize the unknowns: are the diversity, abundance and localization of diazotrophs within the holobiont species-and/or site-specific? Do they have an impact on DDN production? What are the metabolic mechanisms implicated? Do they change spatially, temporally or according to environmental factors? We encourage scientists to undertake research efforts to tackle these questions in order to shed light on nitrogen cycling in reef ecosystems and to understand if coral-associated N 2 fixation can improve coral's resilience in the face of climate change.

In the Western Tropical South Pacific (WTSP) Ocean, a hotspot of dinitrogen fixation has been identified. The survival of diazotrophs depends, among others, on the availability of dissolved iron (DFe) largely originating, as recently revealed, from shallow hydrothermal sources located along the Tonga-Kermadec arc that fertilize the Lau Basin with this element. On the opposite, these fluids, released directly close to the photic layer, can introduce numerous trace metals at concentrations that can be toxic to surface communities. Here, we performed an innovative 9-day experiment in 300 L reactors onboard the TONGA expedition, to examine the effects of hydrothermal fluids on natural plankton communities in the WTSP Ocean. Different volumes of fluids were mixed with non-hydrothermally influenced surface waters (mixing ratio from 0 to 14.5%) and the response of the communities was studied by monitoring numerous stocks and fluxes (phytoplankton biomass, community composition, net community production, N2 fixation, thiol production, organic carbon and metal concentrations in exported material). Despite an initial toxic effect of hydrothermal fluids on phytoplankton communities, these inputs led to higher net community production and N2 fixation rates, as well as elevated export of organic matter relative to control. This fertilizing effect was achieved through detoxification of the environment, rich in potentially toxic elements (e.g., Cu, Cd, Hg), likely by resistant Synechococcus ecotypes able to produce strong binding ligands, especially thiols (thioacetamide-like and glutathione-like compounds). The striking increase of thiols quickly after fluid addition likely detoxified the environment, rendering it more favorable for phytoplankton growth. Indeed, phytoplankton groups stressed by the addition of fluids were then able to recover important growth rates, probably favored by the supply of numerous fertilizing trace metals (notably Fe) from hydrothermal fluids and new nitrogen provided by N2 fixation. These experimental results are in good agreement with in-situ observations, proving the causal link between the supply of hydrothermal fluids emitted at shallow depth into the surface layer and the intense biological productivity largely supported by diazotrophs in the WTSP Ocean. This study highlights the importance of considering shallow hydrothermal systems for a better understanding of the biological carbon pump.

IntroductionKidney transplant recipients (KTRs) are at high risk of severe COVID-19, even when they are fully vaccinated. Additional booster vaccinations or passive immunization with prophylactic monoclonal antibodies are recommended to increase their protection against severe COVID-19.MethodsHere, we describe the neutralization of SARS-CoV-2 Delta, Omicron BA.1, BA.2, BA.4, and BA.5 variants, firstly by 39 serum samples from vaccinated KTRs exhibiting anti-spike antibody concentrations ≥264 binding antibody units (BAU)/mL and, secondly, by tixagevimab/cilgavimab.ResultsNo neutralization was observed for 18% of the KTRs, while serum from only 46% of patients could neutralize the five variants. Cross-neutralization of the Delta and Omicron variants occurred for 65–87% of sera samples. The anti-spike antibody concentration correlated with neutralization activity for all the variants. The neutralization titers against the Delta variant were higher in vaccinated KTRs who had previously presented with COVID-19, compared to those KTRs who had only been vaccinated. Breakthrough infections occurred in 39% of the KTRs after the study. Tixagevimab/cilgavimab poorly neutralizes Omicron variants, particularly BA.5, and does not neutralize BQ.1, which is currently the most prevalent strain.DiscussionAs a result, sera from seropositive vaccinated KTRs had poor neutralization of the successive Omicron variants. Several Omicron variants are able to escape tixagevimab/cilgavimab.

Marine plankton have different biogeographical distribution patterns. However, it is not clear how the entire plankton assemblage is composed of these species with distinct biogeographical patterns. Tintinnina (tintinnids) is single-celled planktonic protozoa commonly used as model organisms in planktonic studies. In this research, we investigated the organization of Tintinnina assemblages along the Atlantic Meridional Transect (AMT) spanning over 90 degrees of latitude during the 29th AMT cruise (2019). Tintinnina with high frequency of occurrence was classified into four biogeographic distribution patterns (equatorial, gyre, frontal, and deep Chl a maximum) according to their vertical and horizontal distribution. All species falling within each distribution pattern formed a sub-assemblage. Equatorial sub-assemblage dominated in upper waters of the equatorial zone and gyre centres. Equatorial and frontal sub-assemblages co-dominated in upper waters of the frontal zones. Deep Chlorophyll a maximum Layer (DCM) sub-assemblage dominated in the DCM waters. Some Tintinnina species with high abundance could be used as indicator species of sub-assemblages. The Tintinnina assemblages in the northern and southern hemispheres exhibited asymmetry in terms of species composition. The latitudinal gradient of Tintinnina species richness was bimodal, which was shaped by the superposition of the species number of the four sub-assemblages with latitude. The result of this study contributes to the understanding of Tintinnina assemblage in the equatorial zone and subtropical gyres of the Pacific and Indian Ocean. It is also valuable for predicting the influence of global warming on changes in Tintinnina distribution and species richness.

A powerful eruption within the Hunga Tonga-Hunga Ha’apai (HTHH) volcano (20.64°S, 175.19°W) in the Kingdom of Tonga, occurred on 15 January 2022. The volcanic blast was enormous, leading many scientists to investigate the full impact and magnitude of this event via satellite observations. In this study, we describe a new ocean color signature from a discolored water patch created by the HTHH eruption using NASA and CMEMS products of satellite-derived biological and optical properties. Elevated surface chlorophyll-a concentration (Chl-a) between 0.15 to 2.7 mg.m-3 was not associated with phytoplankton growth, but to basalt-andesitic ash material expelled by the volcano and into the ocean, which resulted in erroneous Chl-a estimates. Distribution of the patch over time was aligned with CMEMS ocean currents for 19 days. The gradual decrease of light attenuation or diffuse attenuation coefficient for downward irradiance at 490 nm, Kd(490), was interpreted as due to the sinking of ash particles with time. It is suggested that due to high porosity of 30-40%, a density close to that of seawater, ash particles stay suspended in the water column for more than 10 days with sustained high values of satellite-derived Chl-a, Kd(490), and particulate backscattering coefficient at 443 nm. The high attenuation of light due to ash, reducing the penetration depth to less than 10 meters during the first period after the eruption may have had implications on ecological processes and biogeochemical cycles in Tongan waters.

International audience; In hydrothermal environments, diffuse fluids emanations provide optimal conditions for the development of iron-rich microbial mats. Here, we present a unique spatial and temporal study of phylogenetic and chemical data from this type of mats and their associated hydrothermal fluids from two sites of the Lucky Strike Hydrothermal Field (EMSO-Azores deep-sea observatory), collected annually from 2016 to 2020. Our metabarcoding analyses reveal a completely different microbial community at each site, linked to the distinctive chemical composition of the diffuse fluids nourishing the mats. Capelinhos site is dominated by microorganisms with metabolisms related to iron, methane, and reduced sulphur compounds, coming from hydrothermal fluids, while North Tour Eiffel site presents higher abundances of microorganisms with metabolisms related to nitrogen, organic and oxidized sulphur compounds, coming from seawater. We present for the first time the yearly evolution of these mats over a five-year period. This analysis reveals similar variations of the microbial communities over time at both sites, indicating a regional Lucky Strike influence on the temporal scale. We also highlight more diversified microbial communities at both sites in 2016, pointing out the occurrence of a geological event that could have affected them during this specific year. Except for this year, our study shows that the communities of iron-rich microbial mats remain stable over time at both sites.

BackgroundCarbapenemase-producing Enterobacteriaceae (CPE) represent an increasing threat to public health, especially in hospitals.ObjectivesTo investigate an outbreak of CPE in a thoracic-oncology unit by using whole genome sequencing (WGS) and to describe the control measures taken to limit the epidemic, including fecal microbiota transplantation (FMT).MethodsA retrospective study between December 2016 and October 2017 was performed to investigate an outbreak of CPE in a thoracic-oncology unit at the North Hospital in Marseille, France. The isolates were identified, and antimicrobial susceptibility tests were performed. All CPE were sequenced using MiSeq and/or MinIon technologies. Nucleotide variations between plasmids and similarity within the same species were investigated. The origin of this outbreak, its spread, and the decolonization of patients in the ward were also studied.ResultsFour Citrobacter freundii, one Enterobacter cloacae and four E. hormaechei OXA-48 carbapenemase producers were isolated in eight patients hospitalized the same year in a thoracic-oncology ward. The blaOXA-48 gene was present in a Tn1999.2 transposon located in IncL/M plasmids, with single nucleotide variants (SNV) ranging from 0 to 5. All C. freundii strains belonged to the same ST22 and had more than 99.6% similarity between them. Two strains of E. hormaechei ST1007 were almost identical at 99.98%, while the others belonged to a different ST (ST98, ST114, ST133). No single source was identified. FMT resulted in decolonization in 4/6 patients.ConclusionsWGS demonstrated the dissemination of the blaOXA-48 gene by both clonal (C. freundii ST22 and E. hormaechei ST1007) and plasmid spread (pOXA-48 IncL/M). The origin of this outbreak appeared to be both external and internal to the ward. This evidence of cross-infection supports the urgent need for the implementation of infection control measures to prevent CPE dissemination.

Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.

International audience; Multiple days assessments are frequent for the evaluation of candidates to living kidney donation, combined with an early GFR estimation (eGFR). Living kidney donation is questionable when eGFR is 55 years) in a population of 1825 French living kidney donors with a median follow-up of 5.9 years. In donors younger than 45, postdonation eGFR, absolute- and relative-eGFR variation were not different between the three groups. For older donors, postdonation eGFR was higher in S90 than in S80 or Sage but other comparators were identical. Postdonation eGFR slope was comparable between all groups. Our results are in favour of in-depth screening for all candidates to donation with a normal eGFR for age.

Tissue-specific mouse models are essential tools to decipher the role of each cell compartment and/or their expressed genes in the pathophysiology of diseases. Here, we describe a new knock-in mouse model allowing expression of both the fluorescent protein tdTomato and the CRE recombinase selectively in the basophil compartment under the control of the Mcpt8 gene. These “CT-M8” mice did not show any abnormalities in their peripheral distribution of major immune cell populations nor their basophil function. CT-M8 mice allowed the identification of basophils by immunofluorescence and flow cytometry and basophil-specific Cre-mediated floxed gene deletion. Breeding of our CT-M8 mice with the ROSA26flox-stop-DTA mice led to the generation of basophil-deficient mice with no detectable abnormalities in other cell compartments. These mice were then used to document basophil involvement in systemic lupus erythematosus (SLE) pathophysiology since we previously reported by transient depletion of these cells during the course of an ongoing disease that they support and amplify autoantibody production in two distinct lupus-like mouse models (Lyn−/− and pristane-induced). Here, constitutive basophil deficiency prevented pristane-induced lupus-like disease development by limiting autoantibody titers and renal damages. Therefore, basophils have a nonredundant role in pristane-induced lupus-like disease and are involved in both its induction and amplification. This CT-M8 new mouse model will allow us to finely decipher the role of basophils and their expressed genes in health and disease.

International audience; Whipple’s disease (WD) is a chronic multisystemic infection caused by Tropheryma whipplei . If this bacterium presents an intracellular localization, associated with rare diseases and without pathognomonic signs, it is often subject to a misunderstanding of its physiopathology, often a misdiagnosis or simply an oversight. Here, we report the case of a patient treated for presumed rheumatoid arthritis. Recently, this patient presented to the hospital with infectious endocarditis. After surgery and histological analysis, we discovered the presence of T. whipplei . Electron microscopy allowed us to discover an atypical bacterial organization with a very large number of bacteria present in the extracellular medium in vegetation and valvular tissue. This atypical presentation we report here might be explained by the anti-inflammatory treatment administrated for our patient’s initial diagnosis of rheumatoid arthritis.

Vγ9Vδ2 T cells have been reported to participate to the immune response against infectious diseases such as the Q fever caused by Coxiella burnetii infection. Indeed, the number and proportion of Vγ9Vδ2 T cells are increased during the acute phase of Q fever. Human Vγ9Vδ2 T cell responses are triggered by phosphoantigens (pAgs) produced by pathogens and malignant cells, that are sensed via the membrane receptors butyrophilin-3A1 (BTN3A1) and -2A1 (BTN2A1). Here, by using CRISPR-Cas9 inactivation in THP-1 cells, we show that BTN3A and BTN2A are required to Vγ9Vδ2 T cell response to C. burnetii infection, though not directly involved in the infection process. Furthermore, C. burnetii-infected monocytes display increased BTN3A and BTN2A expression and induce Vγ9Vδ2 T cell activation that can be inhibited by specific antagonist mAb. More importantly, we show that the antimicrobial functions of Vγ9Vδ2 T cells towards C. burnetii are enhanced in the presence of an BTN3A activating antibody. This supports the role of Vγ9Vδ2 T cells in the control of C. burnetii infection and argues in favor of targeting these cells as an alternative treatment strategy for infectious diseases caused by intracellular bacteria.

International audience; Cannabidiol (CBD), a safe, non-intoxicating cannabis component, is growing in popularity in Europe and worldwide. However, CBD EU regulation is blurry, and consequent labelling and product quality issues may have implications for public health. There is therefore a need to assess the prevalence and perceived harmfulness of CBD use in EU countries, as well as to characterise CBD users. We aimed to do so in the French population. Methods In December 2021, an online survey was conducted in a sample respecting the French adult population structure for key demographic variables. Sociodemographic, behavioural and CBD perception data were collected. Three separate regressions were performed to identify correlates of i) having heard of CBD, ii) using CBD, iii) perceived harmfulness of CBD. A hierarchical classification was also performed to identify profiles of CBD users. Results The study sample comprised 1969 adults, of whom 69.2% had heard of CBD and 10.1% used it. Less than half (46.8%) of the former considered it harmful. Having heard of CBD was associated with younger age, being born in France, tobacco use, and cannabis use. CBD use was associated with younger age, tobacco use, cannabis use, poor self-reported general health status, and positive perception of alternative medicines. Cluster analysis revealed four different CBD user profiles based on socio-demographics and behavioural characteristics. Conclusion Ten percent of the adults in this French study used CBD, and several user profiles emerged. Our results indirectly advocate clearer European CBD regulations to ensure safe and high-quality products.

International audience; Planktonic Foraminifera are ubiquitous marine protozoa inhabiting the upper ocean. During life, they secrete calcareous shells, which accumulate in marine sediments, providing a geological record of past spatial and temporal changes in their community structure. As a result, they provide the opportunity to analyze both current and historical patterns of species distribution and community turnover in this plankton group on a global scale. The FORCIS project aims to unlock this potential by synthesizing a comprehensive global database of abundance and diversity observations of living planktonic Foraminifera in the upper ocean over more than 100 years starting from 1910. The database will allow for unravelling the impact of multiple global-change stressors acting on planktonic Foraminifera in historical times, using an approach that combines statistical analysis of temporal diversity changes in response to environmental changes with numerical modeling of species response based on their ecological traits.

International audience; Tick-borne encephalitis virus’ (TBEV) geographic range and the human incidence are increasing throughout Europe, putting a number of non-endemic regions and countries at risk of outbreaks. In spring 2020, there was an outbreak of tick-born encephalitis (TBE) in Ain, Eastern France, where the virus had never been detected before. All patients but one had consumed traditional unpasteurised raw goat cheese from a local producer. We conducted an investigation in the suspected farm using an integrative One Health approach. Our methodology included (i) the detection of virus in cheese and milk products, (ii) serological testing of all animals in the suspected farm and surrounding farms, (iii) an analysis of the landscape and localisation of wooded area, (iv) the capture of questing ticks and small mammals for virus detection and estimating enzootic hazard, and (v) virus isolation and genome sequencing. This approach allowed us to confirm the alimentary origin of the TBE outbreak and witness in real-time the seroconversion of recently exposed individuals and excretion of virus in goat milk. In addition, we identified a wooded focus area where and around which there is a risk of TBEV exposure. We provide the first TBEV isolate responsible for the first alimentary-transmitted TBE in France, obtained its full-length genome sequence, and found that it belongs to the European subtype of TBEV. TBEV is now a notifiable human disease in France, which should facilitate surveillance of its incidence and distribution throughout France.

Convalescent plasma therapy has been described as an attractive approach to treat critically ill patients with COVID-19 (Coronavirus disease 2019). The selection of convalescent plasma donors (CPD) is commonly based on neutralizing antibody titer. A better understanding of the quality of immune responses following COVID-19 will enable the optimization of convalescent donors' selection in convalescent plasma programs. The involvement of SARS-CoV-2 specific T cells in the induction and persistence of high affinity anti-SARS-CoV-2 neutralizing antibody is still poorly investigated. In this study, 115 CPD who presented SARS-CoV-2 and who were eligible for plasma donation were included. Comprehensive analysis of T cells together with humoral responses were performed in regards of sex, age and blood group type. High frequency of T cell responses against SARS-CoV-2 related protein such as spike glycoprotein (80.0%), nucleocapsid (NCAP) (70.4%) and membrane protein (VME1) (74.8%) were detected in CPD by ex vivo IFN-γ and TNF-α ELISpot assays. Among CPD responders, most exhibited poly-specific T cell responses (75%) defined by the ability to mount responses against at least two SARS-CoV-2 antigens. We found a positive correlation between the magnitude and the poly-specificity of anti-SARS-CoV-2 T cell responses in CPD. Notably, both the magnitude and poly-specificity of SARS-CoV-2 T cell responses were highly correlated with neutralizing antibody titer in CPD. The present study highlights that the poly-specificity and strength of SARS-CoV-2 specific T cell responses predicts neutralizing antibody titer following COVID-19. These observations show the interest to combine T cell assays and antibody titer for the selection of CPD and to a latter extend to assess COVID-19 vaccine efficacy in at-risk patients.

In this study, the abundance and properties (size, shape, and polymer type) of microplastics (MPs) in sea surface water samples, collected during two sampling campaigns over 2018–2019, in four coastal areas of the Mediterranean Sea (Saronikos Gulf, LIgurian Sea, Gulf of Lion, and Gabes Gulf) were investigated. Coupled hydrodynamic/particle drift model simulations with basin-scale Mediterranean and high resolution nested models were used to provide a better understanding on the variability of the abundance/size of MPs, originating from wastewater and river runoff, in the four areas. Different size classes of MPs were considered in the model, taking into account biofouling induced sinking, as a possible mechanism of MPs removal from the surface. The Gabes Gulf showed the highest mean MPs abundance (0.073–0.310 items/m2), followed by Ligurian Sea (0.061–0.134 items/m2), Saronikos Gulf (0.047–0.080 items/m2), and Gulf of Lion (0.029–0.032 items/m2). Overall, the observed MPs abundance and size distribution was reasonably well reproduced by the model in the four different areas, except an overestimation of small size contribution in Saronikos Gulf. The basin-scale simulation revealed a strong decrease of smaller size MPs in offshore areas, due to biofouling induced sinking, with larger (floating) MPs being able to travel longer distances in the open sea. A significant impact of waves drift and advection of MPs from non-local sources was identified from model simulations, particularly in the Gulfs of Lion and Gabes, having a stronger effect on larger microplastics. In Gabes Gulf, most MPs originated from offshore areas, being mainly (floating) larger size classes, as suggested by the observed quite small contribution of

Pharmaceutical products (PPs) are considered as emerging micropollutans in wastewaters, river and seawaters, and sediments. The biodegradation of PPs, such as ciprofloxacin, amoxicillin, sulfamethoxazole, and tetracycline by enzymes in aqueous solution was investigated. Laccase from Trametes versicolor was immobilized on silica monoliths with hierarchical meso-/macropores. Different methods of enzyme immobilization were experienced. The most efficient process was the enzyme covalent bonding through glutaraldehyde coupling on amino-grafted silica monoliths. Silica monoliths with different macropore and mesopore diameters were studied. The best support was the monolith featuring the largest macropore diameter (20 µm) leading to the highest permeability and the lowest pressure drop and the largest mesopore diameter (20 nm) ensuring high enzyme accessibility. The optimized enzymatic reactor (150 mg) was used for the degradation of a PP mixture (20 ppm each in 30 ml) in a continuous recycling configuration at a flow rate of 1 ml/min. The PP elimination efficiency after 24 h was as high as 100% for amoxicillin, 60% for sulfamethoxazole, 55% for tetracycline, and 30% for ciprofloxacin.

International audience; There is increasing interest today in how the arts contribute to individual and community wellbeing. This scoping review identified and examined ways in which the arts have been used to address wellbeing in communities in the United States. The review examined 44 publications, with combined study populations representing a total of 5,080 research participants, including marginalized populations. It identified the types of artistic practices and interventions being conducted, research methods, and outcomes measured. It highlights positive associations found across a broad spectrum of psychological, physical, and social outcomes, including improvements in self-esteem and identity formation, cognition, physical balance, and physical conditioning. It also reports negative outcomes of arts interventions that may be underreported. The study identifies the need for core outcomes sets and reporting guidelines for advancing evidence synthesis in this area.

At river mouths, fluvial jets and longshore currents (LSCs) generated by waves interact hydrodynamically. This idealized numerical modeling study simulates a large number of hydro-morphodynamic conditions (650) to explore the emergent hydrodynamics determined by different mouth bar volumes and geometries, river discharge, wave heights, and directions and their potential stress on river-mouth development. We find that in the absence of a river-mouth bar (RMB), interactions are driven by momentum balances, expressed either as the balance of wave momentum flux (Mw) and jet momentum flux (Mj), or the balance of river jet discharge (QJet) and longshore current discharge (QLSC). When a RMB is present, the topography modifies the structure of the jet by spreading it, and we quantify this mechanism through the lateral jet transfer rate (LJT). Secondly, topography generates complex longshore wave-driven circulation as a result of the protruding shoreface which serves as a platform on which counter LSCs develop. The balance in QJet/QLSC may be used as an indication of the type of circulation. High and oblique waves favor longshore circulation and RMB bypass, whereas low waves and normal-to-coast angles generate diverging LSCs on the mouth bar crest which interrupts the longshore circulation. A quantification of the dynamic diversion is proposed in the form of the non-dimensional Dynamic diversion index (DyD), which scales with the product of Mj and Mw, and can account for the absolute strength of hydrodynamic interactions occurring at river mouths. RMB morphology can affect DyD in multiple ways by strengthening or by weakening the interactions. The DyD effect seems to increase with increasing RMB size, indicating that the RMB scale regulates the interplay of the wave-driven circulation and the river jet which further controls the adjacent topography changes.

International audience; Dispersal is a central process that affects population growth, gene flow, and ultimately species persistence. Here we investigate the extent to which gene flow occurs between fragmented populations of the deep-water brown algae Ericaria zosteroides (Turner) Greville (Sargassaceae, Fucales). These investigations were performed at different spatial scales from the bay of Marseille (western Provence) to Corsica. As dispersal of zygotes is shown to be limited over distances beyond a few meters, we used a multidisciplinary approach, based on Lagrangian modeling and population genomics to test the hypothesis that drifting of fertile parts of thallus (eggs on fertile branches), mediated by ocean currents, enable occasional gene flow between populations. Therefore we assessed the respective contribution of oceanographic connectivity, geographical isolation, and seawater temperatures to the genetic structure of this species. The genetic structure was assessed using 10,755 neutral SNPs and 12 outlier SNPs genotyped by dd-RAD sequencing in 261 individuals of E. zosteroides. We find that oceanographic connectivity is the best predictor of genetic structure, while differentiation in outlier SNPs can be explained by the depth of populations, as emphasized by the minimum seawater temperature predictor. However, further investigations will be necessary for clarifying how depth drives adaptive genetic differentiation in E. zosteroides. Our analyses revealed that local hydrodynamic conditions are correlated with the very high divergence of one population in the Bay of Marseille. Overall, the levels of gene flow mediated by drifting were certainly not sufficient to counteract differentiation by local genetic drift, but enough to allow colonization several kilometers away. This study stresses the need to consider secondary dispersal mechanisms of presumed low dispersal marine species to improve inference of population connectivity.

The determination of copper (Cu) speciation and its bioavailability in natural waters is an important issue due to its specific role as an essential micronutrient but also a toxic element at elevated concentrations. Here, we report an improved anodic stripping voltammetry (ASV) method for organic Cu speciation, intended to eliminate the important problem of surface-active substances (SAS) interference on the voltammetric signal, hindering measurements in samples with high organic matter concentration. The method relies on the addition of nonionic surfactant Triton-X-100 (T-X-100) at a concentration of 1 mg L−1. T-X-100 competitively inhibits the adsorption of SAS on the Hg electrode, consequently 1) diminishing SAS influence during the deposition step and 2) strongly improving the shape of the stripping Cu peak by eliminating the high background current due to the adsorbed SAS, making the extraction of Cu peak intensities much more convenient. Performed tests revealed that the addition of T-X-100, in the concentration used here, does not have any influence on the determination of Cu complexation parameters and thus is considered "interference-free." The method was tested using fulvic acid as a model of natural organic matter and applied for the determination of Cu speciation in samples collected in the Arno River estuary (Italy) (in spring and summer), characterized by a high dissolved organic carbon (DOC) concentration (up to 5.2 mgC L−1) and anthropogenic Cu input during the tourist season (up to 48 nM of total dissolved Cu). In all the samples, two classes of ligands (denoted as L1 and L2) were determined in concentrations ranging from 3.5 ± 2.9 to 63 ± 4 nM eq Cu for L1 and 17 ± 4 to 104 ± 7 nM eq Cu for L2, with stability constants logKCu,1 = 9.6 ± 0.2–10.8 ± 0.6 and logKCu,2 = 8.2 ± 0.3–9.0 ± 0.3. Different linear relationships between DOC and total ligand concentrations between the two seasons suggest a higher abundance of organic ligands in the DOM pool in spring, which is linked to a higher input of terrestrial humic substances into the estuary. This implies that terrestrial humic substances represent a significant pool of Cu-binding ligands in the Arno River estuary.

Background: Idarucizumab has been included in guidelines for the management of bleeding or surgical procedure in dabigatran-treated patients without need for biological monitoring. The aim of the study was to assess the prognostic value of dabigatran plasma level before reversal to test the hemostatic efficacy of idarucizumab. The secondary objectives were (i) to analyze plasma dabigatran level according to the risk of rebound and (ii) to evaluate the incidence of post-reversal non-favorable clinical outcomes (including thromboembolism, bleeding, antithrombotic, and death) and antithrombotic resumption.Methods and Results: This was an observational multicentric cohort study, which included all French patients who required idarucizumab for dabigatran reversal. Between May 2016 and April 2019, 87 patients from 21 French centers were enrolled. Patients received idarucizumab for overt bleeding (n = 61), urgent procedures (n = 24), or overdose without bleeding (n = 2). Among patients with major bleeding (n = 57), treatment with idarucizumab was considered effective in 44 (77.2%) of them. Patients who did not achieve effective hemostasis after reversal had a significantly higher mean level of plasma dabigatran at baseline (524.5 ± 386 vs. 252.8 ng/mL ± 235, p = 0.033). Furthermore, patients who did not achieve effective hemostasis after reversal had less favorable outcomes during follow-up (46.2 vs. 81.8%, p = 0.027). ROC curve identified a cutoff of 264 ng/mL for dabigatran level at admission to be predictive of ineffective hemostasis. No plasma dabigatran rebound was observed after reversal in patients with dabigatran plasma level < 264 ng/mL at baseline.Conclusion: This retrospective study shows that dabigatran level before reversal could predict hemostatic effectiveness and dabigatran plasma rebound after idarucizumab injection.

The “One Health” concept recognizes that human health is connected to animal health and to the ecosystems. Coxiella burnetii–induced human Q fever is one of the most widespread neglected zoonosis. The main animal reservoirs responsible for C. burnetii transmission to humans are domesticated ruminants, primarily goats, sheep, and cattle. Although studies are still too sparse to draw definitive conclusions, the most recent C. burnetii serosurvey studies conducted in herds and farms in Africa, North Africa, Arabian Peninsula, and Asia highlighted that seroprevalence was strikingly higher in dromedary camels (Camelus dromedarius) than in other ruminants. The C. burnetii seroprevalence in camel herds can reach more than 60% in Egypt, Saudi Arabia, and Sudan, and 70 to 80% in Algeria and Chad, respectively. The highest seroprevalence was in female camels with a previous history of abortion. Moreover, C. burnetii infection was reported in ticks of the Hyalomma dromedarii and Hyalomma impeltatum species collected on camels. Even if dromedary camels represent 5 million tons/year of both raw and pasteurized milk according to the Food and Agriculture Organization) sustained by a rapid increase of population (growth rate: 2.26–3.76 per year in North Africa), dromedary camel breeding tends to increase from the Maghreb to the Arabic countries. Because of possible long-term persistence of C. burnetii in camel hump adipocytes, this pathogen could represent a threat for herds and breeding farms and ultimately for public health. Because this review highlights a hyperendemia of C. burnetii in dromedary camels, a proper screening of herds and breeding farms for C. burnetii is urgently needed in countries where camel breeding is on the rise. Moreover, the risk of C. burnetii transmission from camel to human should be further evaluated.

International audience; Electron microscopy is a powerful tool in the field of microbiology. It has played a key role in the rapid diagnosis of viruses in patient samples and has contributed significantly to the clarification of virus structure and function, helping to guide the public health response to emerging viral infections. In the present study, we used scanning electron microscopy (SEM) to study the infectious cycle of SARS-CoV-2 in Vero E6 cells and we controlled some key findings by classical transmission electronic microscopy (TEM). The replication cycle of the virus was followed from 1 to 36 h post-infection. Our results revealed that SARS-CoV-2 infected the cells through membrane fusion. Particles are formed in the peri-nuclear region from a budding of the endoplasmic reticulum-Golgi apparatus complex into morphogenesis matrix vesicae. New SARS-CoV-2 particles were expelled from the cells, through cell lysis or by fusion of virus containing vacuoles with the cell plasma membrane. Overall, this cycle is highly comparable to that of SARS-CoV. By providing a detailed and complete SARS-CoV-2 infectious cycle, SEM proves to be a very rapid and efficient tool compared to classical TEM.

International audience; Platelets are the cornerstone of hemostasis. However, their exaggerated aggregation induces deleterious consequences. In several diseases, such as infectious endocarditis and sepsis, the interaction between platelets and bacteria leads to platelet aggregation. Despite platelet involvement, no antiplatelet therapy is currently recommended in these infectious diseases. We aimed here, to evaluate,in vitro, the effect of antiplatelet drugs on platelet aggregation induced by two of the bacterial pathogens most involved in infectious endocarditis,Staphylococcus aureusandStreptococcus sanguinis. Blood samples were collected from healthy donors (n = 43). Treated platelet rich plasmas were incubated with three bacterial strains of each species tested. Platelet aggregation was evaluated by Light Transmission Aggregometry. CD62P surface exposure was evaluated by flow cytometry. Aggregate organizations were analyzed by scanning electron microscopy. All the strains tested induced a strong platelet aggregation. Antiplatelet drugs showed distinct effects depending on the bacterial species involved with different magnitude between strains of the same species. Ticagrelor exhibited the highest inhibitory effect on platelet activation (p

The human opportunistic pathogen Pseudomonas aeruginosa orchestrates the expression of many genes in a cell density-dependent manner by using quorum sensing (QS). Two acyl-homoserine lactones (AHLs) are involved in QS circuits and contribute to the regulation of virulence factors production, biofilm formation, and antimicrobial sensitivity. Disrupting QS, a strategy referred to as quorum quenching (QQ) can be achieved using exogenous AHL-degrading lactonases. However, the importance of enzyme specificity on quenching efficacy has been poorly investigated. Here, we used two lactonases both targeting the signal molecules N-(3-oxododecanoyl)-L-homoserine lactone (3-oxo-C-12 HSL) and butyryl-homoserine lactone (C-4 HSL) albeit with different efficacies on C-4 HSL. Interestingly, both lactonases similarly decreased AHL concentrations and comparably impacted the expression of AHL-based QS genes. However, strong variations were observed in Pseudomonas Quinolone Signal (PQS) regulation depending on the lactonase used. Both lactonases were also found to decrease virulence factors production and biofilm formation in vitro, albeit with different efficiencies. Unexpectedly, only the lactonase with lower efficacy on C-4 HSL was able to inhibit P. aeruginosa pathogenicity in vivo in an amoeba infection model. Similarly, proteomic analysis revealed large variations in protein levels involved in antibiotic resistance, biofilm formation, virulence and diverse cellular mechanisms depending on the chosen lactonase. This global analysis provides evidences that QQ enzyme specificity has a significant impact on the modulation of QS-associated behavior in P. aeruginosa PA14.

Marseilleviruses comprise a family of large double-stranded DNA viruses belonging to the proposed order ``Megavirales.'' These viruses have a circular genome of similar to 370 kbp, coding hundreds of genes. Over a half of their genes are associated with AT-rich putative promoter motifs, which have been demonstrated to be important for gene regulation. However, the transcriptional profile of Marseilleviruses is currently unknown. Here we used RNA sequencing technology to get a general transcriptional profile of Marseilleviruses. Eight million 75-bp-long nucleotide sequences were robustly mapped to all 457 genes initially predicted for Marseillevirus isolate T19, the prototype strain of the family, and we were able to assemble 359 viral contigs using a genome-guided approach with stringent parameters. These reads were differentially mapped to the genes according to the replicative cycle time point from which they were obtained. Cluster analysis indicated the existence of three main temporal categories of gene expression, early, intermediate and late, which were validated by quantitative reverse transcription polymerase chain reaction assays targeting several genes. Genes belonging to different functional groups exhibited distinct expression levels throughout the infection cycle. We observed that the previously predicted promoter motif, AAATATTT, as well as new predicted motifs, were not specifically related to any of the temporal or functional classes of genes, suggesting that other components are involved in temporally regulating virus transcription. Moreover, the host transcription machinery is heavily altered, and many genes are down regulated, including those related to translation process. This study provides an overview of the transcriptional landscape of Marseilleviruses.

International audience; Colistin is considered as a last resort antibiotic. The re-use of this antibiotic highlighted the emergence of colistin resistance mediated by chromosomal and plasmidic resistance mechanisms. Five colistin-resistant Klebsiella pneumoniae strains from Laos and Thailand were analyzed by Next Generation Sequencing (NGS) approaches to determine their colistin resistance mechanisms. Antimicrobial susceptibility testing, conjugation and transformation were performed on these strains. Moreover, whole genome sequencing (WGS) combining Illumina (MiSeq) and Oxford Nanopore technologies (MinION) was realized to obtain closed genomes and plasmids. Resistome analyses as well as location of mcr genes and its genetic environments were done in silico. All five strains had colistin MIC of 32 mg/L and were positive for mcr-3 variants including additionally positive for a mcr-8 variant gene. The novel variants were named mcr-3.21, mcr-3.26, mcr-3.28, and mcr-8.3 genes. The mcr-3 variants genes were located on plasmids IncP1, IncFII, and IncI1 type, while mcr-8.3 gene was found on an IncFII type plasmid. The genetic environment of mcr-3.21 and mcr-3.26 genes were composed of a composite transposon ISKpn40-mcr-3-dgkA-ISKpn40. Concerning mcr-8.3 gene, a similar genetic environment of mcr-8.1 gene surrounded by ISIX2 and IS903B was observed. To the best of our knowledge, this is the first description of the novel variants mcr-3.21, mcr-3.26, mcr-3.28 and mcr-8.3 genes as well as the first study on co-occurrence of mcr-3 and mcr-8 genes. Spread and evolution of mcr genes should be monitored.

International audience; Staphylococcus lugdunensis is a commensal bacterium of human skin that has emerged as a virulent Coagulase-Negative Staphylococcus in both community-acquired and healthcare associated infections. Genotyping methods have shown a clonal population structure of this pathogen but failed to identify hypervirulent lineages. Here, complete genomes of three pathogenic and three carriage S. lugdunensis strains were obtained by Single-Molecule sequencing (PacBio) and compared to 15 complete genomes available in GenBank database. The aim was to identify (i) genetic determinants specific to pathogenic or carriage strains or specific to clonal complexes (CCs) defined by MultiLocus Sequence Typing, and (ii) antibiotic resistance genes and new putative virulence factors encoded or not by mobile genetic elements (MGE). Comparative genomic analysis did not show a strict correlation between gene content and the ability of the six strains to cause infections in humans and in a Galleria mellonella infection model. However, this study identified new MGEs (five prophages, two genomic islands and one plasmid) and genetic variations of some putative virulence-associated loci, especially in CC3 strains. For a clonal population, high variability and eight CC-dependent genetic organizations were observed for the ess locus, which encodes a putative type VII secretion system (T7SS) homologous to that of S. aureus. Further phenotypic and functional studies are needed to characterize this particular CC3 and to evaluate the role of T7SS in the virulence of S. lugdunensis.