In recent years, novel β-lactam-inhibitor combinations (imipenem-relebactam (I/R), meropenem-vaborbactam (M/V), aztreonam-avibactam (A/A)) have been commercialized and some are not yet on the market (cefepime-zidebactam (C/Z)). The objective of this study was to evaluate the efficacy of these β-lactam-β-lactamase inhibitors (BL/BLIs) combinations against a wide collection of French clinical multiresistant Enterobacterales isolates and to assess the performance of the E-test MIC method for I/R and M/V. BL/BLIs MICs were determined by broth microdilution on a collection of 200 ESBL-producing and 414 carbapenem-resistant clinical Enterobacterales (K. pneumoniae (271), E. coli (245), E. cloacae complex (48), other species (50)) including 292 carbapenemase-producing isolates. E-test method was evaluated for the determination of I/R and M/V MICs using 131 isolates from this collection. All the combinations were active against most ESBL-producing isolates (99-100 %), but C/Z and A/A MIC90 were lower than that of I/R and M/V (2mg/L and 2mg/L versus 8mg/L and 8mg/L). The M/V and I/R E-tests performances were close to those required by the FDA recommendations: Categorical agreement (CA) and Essential agreement (EA) ≥ 90 %, Major discrepancy (MD) and Very major discrepancy (VMD) < 3 %): 96.9 % (CA), 92.4 % (EA), 1.2 % (MD), 6.1 % (VMD) for I/R and 94.7 % (CA), 96.9 % (EA), 4.1 % (MD), 8.8 % (VMD) for M/V. This work confirmed the interest of C/Z and A/A combinations against carbapenem-resistant Enterobacterales isolates compared with M/V and I/R. Additionally, the findings indicate that the E-test method can be used for the determination of M/V and I/R MIC for E. coli and K. pneumoniae strains.

Streptococcus pneumoniae infection is considered an uncommon cause of arthritis in adults. To determine the clinical and microbiological characteristics of pneumococcal septic arthritis, we retrospectively studied a large series of cases among adult patients during the 2010-2018 conjugate vaccine era in France. We identified 110 patients (56 women, 54 men; mean age 65 years), and cases included 82 native joint infections and 28 prosthetic joint infections. Most commonly affected were the knee (50/110) and hip (25/110). Concomitant pneumococcal infections were found in 37.2% (38/102) and bacteremia in 57.3% (55/96) of patients, and underlying conditions were noted for 81.4% (83/102). Mortality rate was 9.4% (8/85). The proportion of strains not susceptible to penicillin was 29.1% (32/110). Of the 55 serotyped strains, 31 (56.4%) were covered by standard pneumococcal vaccines; however, several nonvaccine serotypes (mainly 23B, 24F, and 15A) had emerged, for which susceptibility to β-lactams was low.

Extended-spectrum β-lactamases producing Enterobacteriaceae (ESBL-E) are emerging worldwide in hospitals and in the community. The aim of the present study was designed to characterize the extended-spectrum β-lactamase (ESBL) types in clinical isolates of Enterobacteriaceae and their clonal dissemination in the intensive care unit (ICU) of Laghouat hospital, Algeria. During the study period (from March 2011 to September 2014), 247Enterobacteriaceae were isolated from various clinical specimens. Fifty six (22.67%) Enterobacteriaceae isolates were found to ESBL-producers: (48.21%) K. pneumonia, (28.57%), E. coli and (23.21%) E. cloacae. All ESBL-producing isolates were multidrug resistant. The genetic analysis showed that all ESBL-producing Enterobacteriaceae isolates were produced CTX-M-15, whereas TEM-4 was detected in only one isolate with 01.78% (1/56). ERIC-PCR analysis showed that the isolates are genetically unrelated. Our results underline the need for continuous surveillance of the high prevalence and evolution of this CTX-M-15 type β-lactamase in the intensive care unit of Laghouat hospital, Algeria.

Two lateral flow immunochromatographic assays are currently available for the rapid detection of CTX-M enzymes in Enterobacterales, RESIST CTX-M (Coris BioConcept, Gembloux, Belgium) and NG-Test CTX-M MULTI (NG Biotech, Guipry, France). The NG-Test CTX-M MULTI is designed to detect all CTX-M enzymes. The RESIST CTX-M detects CTX-M from the M-15 and the M-14 group for V1.0, CTX-M from the M-15 and the M-14/M-8 groups for V1.1. The performances of the two versions of the RESIST CTX-M test (V1.0 and V1.1) and the NG-Test CTX-M MULTI were assessed against a collection of 140 non-redundant Enterobacterales isolates characterized for their content in β-lactamases. β-lactamases content was established from genotypic analysis to collect a broad diversity of resistance mechanisms and bacterial strains, including 74 ESBL-producing strains (CTX-M (n = 56), other ESBLs (n = 18) either alone or associated with other β-lactamases), 22 strains overproducing chromosomal AmpC, 13 strains producing plasmid-encoded AmpC, 7 carbapenemase-producing strains, 3 strains combining the production of several β-lactamases other than ESBL and 21 strains that produced other β-lactamases. The sensitivity and specificity of NG-Test CTX-M MULTI for detecting CTX-M were 98.2

OBJECTIVES:To assess a new MS approach in detection of antimicrobial resistance (AMR) mechanisms in Enterobacterales and its usefulness in the routine practice of a national reference centre for carbapenemase-producing enterobacteria (CPE). METHODS:A tool utilizing LC coupled with tandem MS (LC-MS/MS) in multiple reaction monitoring mode was tested in the direct and concurrent detection of 13 AMR enzymes. These comprised carbapenemases, extended-spectrum β-lactamases (ESBLs), AmpC-like cephalosporinases, aminoglycoside-modifying enzymes (AMEs) and 16S rRNA methylases. The study included 357 Enterobacterales isolates largely from Polish hospitals (2000-23), including 292 CPE, collected by the National Reference Centre for Susceptibility Testing. The isolates were short-read sequenced to determine their resistomes, and subjected to MIC evaluation. RESULTS:The number of target AMR genes in the isolates was 1128 without defective and duplicated copies. When possible to deduce, the MIC patterns indicated activity of most of the genes/enzymes. The LC-MS/MS assay showed >95% sensitivity in the identification of KPC-, NDM-, VIM-, IMP- and OXA-48-type carbapenemases, CTX-M-like ESBLs, CMY-2- and DHA-type AmpCs, Aac(3)-II- and Aac(6')-Ib-like AMEs and the ArmA 16S rRNA methylase, but only 66.7% and 44.4% of GES-type ESBLs/carbapenemases and RmtB/C-like methylases, respectively. Detection specificity was almost 100% for all of the enzymes. CONCLUSIONS:The study demonstrated good performance of the assay against multiple clinically-relevant AMR mechanisms, including main carbapenemase types, and its usefulness in a CPE reference centre was confirmed. However, further studies, e.g. with other bacterial populations, AMR mechanisms and clinical samples, are necessary to characterize its full diagnostic potential.

Salinization is predicted to intensify due to climate change, impacting biodiversity and ecosystem functioning. Amphibians, particularly embryos and larvae, are highly susceptible to environmental salinity. Yet, local adaptation may cause differing vulnerabilities between coastal and inland populations. In this study, we investigated the physiological, behavioural, and life-history responses to environmental salinity (0, 2 and 4 g.l-1) of embryos and larvae of a widespread amphibian species (spined toad, Bufo spinosus) from salt-exposed (coastal) and salt-free (inland) populations. Moderate salinity (4 g.l-1) altered embryonic and larval development in both populations, causing increased malformations, decreased body size and survival, and altered behavior, but did not affect telomere length or oxidative status. Individuals exposed to low salinity (2 g.l-1) performed better across most traits. However, moderate salinity had stronger negative effects on coastal individuals, indicating a lack of local adaptation and overall lower performance compared to their inland counterparts. These findings suggest that increasing salinity will have varied impacts on organisms depending on their population origins and developmental stages.

Association between ileal colonization by Adherent-Invasive Escherichia coli (AIEC) and Crohn's disease (CD) has been widely described in high-incidence Western countries but remains unexplored in Asian countries with a fast increase in CD incidence. In the PACIFIC study, we compared the characteristics of AIEC pathobionts retrieved from ileal biopsies of CD patients enrolled in France (FR) and Hong Kong (HK). The prevalence of AIEC was similar in France (24.5%, 25/102) and Hong Kong (30.0%, 18/60) (p = 0.44). No difference was observed between the two populations of AIEC regarding adhesion and invasion levels. When tested for antibiotic resistance, the proportion of AIEC strains resistant to ampicillin, piperacillin, tobramycin, and gentamicin was significantly higher in HK AIEC strains compared to French strains. AIEC strains from FR or HK population were both able to persist in the mice intestine (DSS-treated CEABAC10 mice model). Moreover, genomic analysis of 25 FR and 17 hK AIEC strains using next-generation sequencing revealed the co-existence of several virulence factors associated with enteric E. coli pathotypes, although no single virulence factor was significantly associated with either country of origin or AIEC status. In vitro, all AIEC strains (FR and HK) were sensitive to the EcoActive (TM) phage cocktail, suggesting that it could be a promising option to target AIEC in CD across the world.

Migratory shorebird populations are declining worldwide, showing an apparent inability to respond to the interplaying challenges emerging along their flyways. Within the East Atlantic Flyway, non-breeding populations show moderate to strong declines in Sub-Saharan Africa, contrasting with stable or increasing trends in Europe. Local factors are insufficient to explain the opposite tendencies and, therefore, investigating migratory strategies and connectivity of these populations may help identifying the drivers of their demography. We followed the migratory journeys of 20 grey plovers (Pluvialis squatarola) from their wintering grounds in Guinea-Bissau (West Africa), Portugal and France (Europe) using tracking devices. Grey plovers wintering in Africa and Europe were found to share breeding grounds at European Russia and Western Siberia, revealing low migratory connectivity in the Eastern Atlantic population. All individuals followed a “skipping” migratory strategy, flying mostly mid-distance bouts, and using an unexpected large network of stopover sites to re-fuel usually for short periods. We identified 66 different stopover sites along the West African, European and Russian/Siberian coasts. All birds stopped at the Wadden Sea in both migratory periods, highlighting the importance of this region and the risk for a potential bottleneck. Low migratory connectivity and similar migratory strategies shared by grey plovers wintering in Europe and West Africa do not support their contrasting population trends.

Although coastal ecosystems are naturally submitted to temporal variations of salinity, salinization has been increasing over time threatening coastal biodiversity. Species that exploit such habitats can thus be exposed to brackish water at different life stages. However, the impacts of variations of salinity on wildlife remain poorly understood. This is particularly true for coastal amphibians, due to the strong dependency of early life stages (embryos and larvae) on aquatic environments. In order to investigate the effect of salinity during egg laying and embryonic and larval development of coastal amphibians, we used a full-factorial design to expose reproductive adults, eggs, and larvae of coastal spined toads ( Bufo spinosus ) to fresh (0 g.l −1 ) or brackish water (4 g.l −1 ). At egg laying, we evaluated parental investment in reproduction. During embryonic and larval development, we assessed effects on survival, development, and growth. We highlighted strong effects of environmental salinity on reproduction (reduced egg laying time, marginally reduced egg size, and reduced investment in reproduction). Responses to salinity were highly dependent on the developmental stages of exposure (stronger effects when individuals were exposed during embryonic development). These effects carried over when exposure occurred at egg laying or during embryonic development, highlighting the importance of the environmental conditions during early life on ontogenetic trajectories. We also highlighted partial compensation when individuals were transferred back to freshwater. Whether the magnitude of these responses can allow coastal biodiversity to overcome the observed detrimental effects of salinization remain to be assessed.

Farmland birds are among the most threatened species in Europe, largely as a result of the intensification of agriculture leading to widespread biodiversity losses. Ground-breeding shorebirds in grassland and arable habitats are particularly exposed to human threats and predation in highly modified landscapes; however, parts of their populations still breed in natural habitats and could provide a reservoir for threatened populations. This study aimed to improve our knowledge of the spatio-temporal use of breeding habitats by Eurasian curlew Numenius arquata arquata in a core area of the population in remote north-eastern Europe. A total of 83 adult birds across Europe were tagged with GPS devices between 2014 and 2022 to analyse their home-range sizes, habitat use and hatching success. Birds were distributed at breeding sites from 52°N to 66°N between Finland and the Ural Mountains. Forty-one percent of individuals nested in bogs, 33% in grassland, and 20% in abandoned farmland. Birds nested predominantly in bogs at northern latitudes and in grassland at southern latitudes, while abandoned farmland was mainly used at intermediate latitudes. The mean home range was largest for birds breeding predominantly in grassland while birds in bogs had the highest hatching success rate. Russia and Finland host the core population of the subspecies N. a. arquata during breeding period, which is essential for preserving the species on a European scale. Their survival may depend on well-preserved bogs and the maintenance of grassland areas, given that large areas of abandoned farmland are destined to become either forest or to be reclaimed for cereal crops or fodder grass in the short and medium terms. Given the large breeding populations in both countries, Russia and Finland have major responsibilities to maintain these essential populations on a biogeographical scale.

The MAST® D72C test is a phenotypical test which can detect ESBL and AmpC production in Enterobacterales. It can also identify the suspected presence of carbapenemase. The aim of the present study was to assess the sensitivity and specificity of this test and to discuss its usefulness in laboratories, especially those that use only an automated AST system. The performance of the MAST® D72C test was assessed against a collection of 119 non-redundant Enterobacterales isolates characterized for their content in β-lactamases, and compared with that of the reference double disk synergy test. β-lactamase content was established from phenotypic and genotypic analyses to collect a broad diversity of resistance mechanisms and bacterial strains, including 30 ESBL-producing strains, 32 strains overproducing chromosomal AmpC, 10 strains producing plasmid-encoded AmpC, 12 carbapenemase-producing strains, 13 strains combining the production of several β-lactamases, and 22 strains that produced other β-lactamases. The sensitivity and specificity for ESBL-detection were comparable with those of the synergy test, 75 versus 72.5

Coastal wetlands are naturally subjected to salinity, which is expected to increase through global climate changes. Most species will be affected by these changes, leading to major consequences for community structure and ecosystem functioning. We investigated variation of salinity of temporary wetlands across spatial (1,000 m from the ocean) and temporal (across three breeding season) scales relevant to coastal biodiversity and used amphibians (six species, sampled across one breeding season) as a model to investigate the consequences of the spatio-temporal variation of salinity in 24 ponds situated on the Atlantic coast of France. We show that salinity is a highly dynamic environmental variable that varies widely both across spatial and temporal scales. The spatio-temporal dynamics of salinity are a critical factor structuring amphibian communities that affect the main amphibian phylogenetic groups (caudates vs. anurans) differently. Temporal variation in salinity disrupts the match between salinity selected by reproductive adults and those experienced later by their developing offspring, which negatively affect reproductive success. Future changes in coastal salinity are likely to affect the structure and functioning of these ecosystems, excluding salt-intolerant species and eventually leading to less diverse communities of salt-tolerant species.

Coastal, and to a lesser extend inland wetlands, are critical habitats for wintering shorebirds. Given the significant population declines of most shorebird species worldwide, the current degradation of coastal habitats through climate change and human activities raises severe conservation concerns. In order to ensure sufficient and adequate habitats and maintain the populations, a thorough understanding of space use by wintering shorebirds is urgently required. However, overwintering strategies have rarely been investigated throughout the entire range of a shorebird species. This study thus aimed to investigate the spatio-temporal use of wintering habitats by Eurasian curlew Numenius arquata on a European scale, using a large international dataset. A total of 204 adult curlews were tagged with GPS devices at different wintering and breeding sites across Europe between 2014 and 2021, and the data were used to analyse home range size, habitat use, and phenology. The birds were faithful to their wintering sites throughout the winter. Their home ranges were small compared with other shorebirds but highly variable between individuals (533 ± 449 ha). Winter home range areas did not differ in relation to sex or body mass, but were weakly related to the wintering latitude, particularly linked to the many birds wintering in the Wadden Sea. Curlews used a high diversity of coastal and inland habitats, with higher occurrences on mudflats and saltmarshes. Despite the inter-individual variability in space use, the high wintering-site fidelity shown by this near-threatened species raises concerns about its capacity to respond to environmental modifications in coastal regions.

According to the Island rule, insular populations exhibit gigantism in small species and dwarfism in large species. These contexts offer opportunities to test for complementary aspects pertaining to the evolution of body size, and particularly sexual size dimorphism (SSD). ‘Rensch's rule' states that SSD should vary with increasing body size, depending on the larger sex. As a consequence, it is expected that dwarfism or gigantism occurring in insular populations should influence the magnitude of SSD. Using anuran amphibians as a study system (because most anuran species express a female‐biased SSD and a marked lability in size), we investigated our hypothesis both in a specific comparison of continental and insular populations of a widespread coastal amphibian, and using a large‐scale analysis across anurans (10 species across 62 sites). Both datasets yielded similar results, with increasing body size in insular populations reducing the magnitude of SSD through an increase of male body size, as expected by Rensch's rule. Detailed data on insular populations considering both sexes are scarce, and future studies are required to complement the existing literature in order to test for the validity of our hypothesis at a wider scale and to infer the mechanistic causes of size variations, which remain unknown. In addition, further investigations are required to explore the consequences of insularity on the magnitude of SSD including various taxa (e.g. mammals, birds, lizards and snakes) in which the Island rule has found support, and considering taxa in which males are the larger sex. Keywords: amphibians, body size, insularity, Island rule, Rensch's rule, sexual dimorphism

1. Body size is a critical component of organismal biology. Body size is known to be influenced by a plethora of environmental conditions, among which exposure to large scale variations of salinity has been comparatively overlooked. Yet, exposure to salinity is known to affect energetic allocation toward growth and reproduction.2. In this study, we investigated the morphological differences between inland and coastal individuals of spined toads (Bufo spinosus) in Western France.3. We measured adult morphology both outside and during the reproductive season on 190 individuals, and assessed reproduction in pairs originating from inland (N = 20) and coastal (N = 30) environments.4. Overall, we found that adult coastal toads were smaller and lighter than inland individuals. Reproductive correlates of these differences included lower fecundity and smaller egg size (but higher egg density) in coastal females. Interestingly, these differences were not allometric correlates of body size, as coastal females invested proportionally less in all components of reproduction (fecundity, egg size and egg protection).5. These results suggest altered resource allocation to growth and reproduction in coastal amphibians, which may be related to the marked spatial gradient of salinity (measured in reproductive ponds) and the associated costs of osmoregulation (higher osmolality in coastal individuals), for which local adaptation and higher tolerance to salinity remains to be tested.

Coastal freshwater ecosystems play major roles as reservoirs of biodiversity and provide many ecosystem services and protection from extreme weather events. While they are of particular importance worldwide, they are affected by a large variety of anthropogenic threats, among which salinization has been less studied, particularly regarding large temporal and spatial data sets based on real case scenarios, while salinity can impact biodiversity and ecosystem functioning. In this study, we investigated the variations of salinity across long-term (1996-2020) and seasonal (monthly records) temporal scales and spatial (varying distance to the coastline) scales in water bodies of two typical temperate coastal wetlands situated on the Atlantic coast of France. We complemented our analyses with models of sea water levels computed at both sites across 2000-2020. Our detailed data set allowed for highlighting that salinity in ponds varied seasonally (higher during summer, due to decreased precipitation and higher temperature), but also spatially (higher closer to the seashore, which pattern increased through time). Over the long term, decreased precipitation but not increased temperature induced increasing salinity. We also highlighted contrasted long-term patterns of salinity changes on these two coastal wetlands, with one site were salinity decreased over time linked to the responses to marine flood, allowing to document the temporal dy-namics of salinity following a massive intrusion of sea water. Complementarily, at both sites, water levels at high tides increased through time, a pattern which can induce additional salinization. To our knowledge, our study is the first to investigate long-term changes in salinity in coastal wetlands through natural processes (e.g. seaspray, seasonal variations) and ongoing climate perturbations (e.g. marine surges linked to extreme weather events, increased temperature and decreased precipitations).

Enterobacterales bloodstream infections are life-threatening and require rapid, targeted antibiotherapy based on antibiotic susceptibility testing (AST). A new method using Muller-Hinton Rapid-SIR (MHR-SIR) agar (i2a, Montpellier, France) allows complete direct AST (dAST) to be read from positive blood culture bottles (BCBs) for all Enterobacterales species after 6–8 h of incubation. We evaluated (i) the performance of dAST from positive BCBs on MHR-SIR agar using two different inoculum protocols; (ii) the categorical agreement between dAST results obtained with MHR-SIR agar vs. those obtained with Muller-Hinton (MH) agar; and (iii) the ability of the MHR-SIR medium to detect β-lactam resistant Enterobacterales. Finally, we estimated the saved turnaround time (TAT) with MHR-SIR compared with MH agar in our 24/7 laboratory. Our results showed that the most suitable inoculation protocol for dAST on MHR-SIR agar was 1 drop of BCB/5 mL H2O. For monomicrobial Enterobacterales BCBs, dAST performed on MHR-SIR medium showed 99.3% categorical agreement with AST on MH agar. Furthermore, MHR-SIR agar allows early detection of β-lactam resistance mechanisms, including AmpC hyperproduction, extended-spectrum β-lactamase, and carbapenemase. Finally, TAT reduction in our 24/7 laboratory was 16 h, enabling a significantly faster provision of antibiotic advice.

The environment is heterogeneous across spatial and temporal scales, and the behavioural responses required to adjust individuals' needs to resource availability across such variable environments should be under selective pressure. Coastal wetlands are characterized by a diversity of habitats ranging from fresh-to salt water; and individuals occurring in such complex habitats need to adjust their habitat use based on their osmotic status. In this study, we experimentally tested whether an amphibian species (Pelophylax sp.) occurring in coastal wetlands was able to discriminate and select between different salinity concentrations (0, 4, 8 and 12 g.l(-1)) and whether hydric status (hydrated versus dehydrated) influenced salinity-dependent water selection. We found that frogs selected water based on salinity differentially between hydrated and dehydrated individuals, with the later favoring lower salinities likely to improve their osmotic status. Interestingly, we highlighted the ability of frogs to select lower salinity before having access to water, suggesting that frogs can assess water salinity without actual contact. In coastal wetlands where salinity of water bodies can dynamically vary through space and time, such behavioural osmoregulation process is potentially a key factor affecting individual movements, habitat choice and thus species distribution. Our study further highlights the importance of salinity-dependent habitat heterogeneity and especially the presence of freshwater environments as structuring factors for the amphibian community.

Coastal ecosystems are among the most diverse and productive systems on earth, but they are threatened by various anthropogenic pressures. To understand the magnitude of these constraints on biodiversity, it is essential to assess habitat use of coastal species, which can be challenging in the complex matrix of habitats in coastal environments. The stable isotope method is a powerful tool to assess foraging habitat, as marine influences on the trophic web should decrease with increasing distance from the ocean. In this study, we evaluated whether isotopic values (delta N-15, delta C-13 and delta S-34) can be useful to assess habitat use in a coastal amphibian, the western spadefoot toad (Pelobates cultripes). In two coastal wetlands of the French Atlantic coast, we captured individuals from 20 to 1300 m from the seashore in order to assess whether isotopic values were related to the distance to the coastline, and we combined this dataset with data on osmolality that correlate to distance to the ocean in this species. We found divergent site-specific responses, presumably linked to the site-specific extent of a recent marine submersion, highlighting the long-lasting effects of such extreme weather event on trophic webs. In both sites however, we found a larger isotopic niche closer to the seashore suggesting wider diet or prey depending on wider resources near the sea. Overall, our results suggest that isotopic values can provide insights on habitat use depending on site-specific characteristics. Combining isotopic values with other metrics (e.g., osmolality) allows to better understand isoscapes in a site-specific context.