[Ecology: The blind spot in pathology research]. / Écologie : l'angle mort de la recherche en ACP.

INTRODUCTION: The 2015 Paris Agreement has been the first restrictive agreement in the fight against climate change. The newer generations of pathologists, who feel more anxiety due to environmental problems than their predecessors, are asked to publish research works while they are harder and harder to and in a context of demographical tensions. We wanted to measure the rise of ecology research in pathology since the Paris Agreement. MATERIAL & METHODS: Over a ten years study period (2013-2022), we have identified via PubMed the number of articles in which forty-three terms taken from the sustainable development vocabulary appeared in ten renowned international pathology journals, selected for their SJR index from ScimagoJr and their impact factor, plus the Annales de pathologie, and compared their means of incidence between the 2013-2015 (m1) and 2016-2022 (m2) periods. The same process has been applied for "artificial intelligence", "deep learning" and "digital pathology". RESULTS: A total of 1336 articles have been identified. Only "digital pathology" (fromm1=8,33 to m2=23,29; p=0,010) and "deep learning" (fromm1=0 to m2=10,14; p=0,034) saw their incidence rise significantly. A significant decrease has been observed with "biological" (fromm1=70,00 to m2=56,86; p=0,020). DISCUSSION-CONCLUSIONS: Pathology reacts to trends but research in ecology has remained in the blind spot since 2015. However there seems to be an awakening as editorials, articles and communications in congress have blossomed the last two years.

Whole genome sequencing of mesorhizobia isolated from northern Canada.

Rhizobia are soil-dwelling bacteria that can form N2-fixing symbioses with legume plant species (Fabaceae). These bacteria are globally distributed; however, few studies have examined the genomics of rhizobia that live in cold environments. Here, we isolated and characterized three rhizobial strains from legume nodules collected at a pair of distant low Arctic tundra and boreal forest sites in northern Canada. Phylogenetic and average nucleotide identity measurements suggested that the three strains are members of the genus Mesorhizobium, and that each strain represents a novel genospecies. Intriguingly, whereas most mesorhizobia contain the classical determinants of nodulation and nitrogen fixation on their chromosome, whole genome sequencing revealed that all three strains carry these genes on large symbiotic megaplasmids of ∼750 to ∼1000 kb. Phylogenetic and sequence analyses of the common nodulation genes revealed highly conserved alleles amongst these northern mesorhizobia, leading us to propose that they belong to a novel symbiovar that we termed symbiovar oxytropis. Interestingly, these nod gene alleles are uncommon in mesorhizobia isolated from similar plant hosts in other climatic regions, suggesting potential functional adaptive differences.

Environmental DNA bioassays corroborate field data for detection of overwintering species at risk Blanding's turtles (Emydoidea blandingii).

Environmental DNA (eDNA) is gaining traction in conservation ecology as a powerful tool for detecting species at risk. We developed a quantitative polymerase chain reaction assay to detect a DNA amplicon fragment of the mitochondrial nicotinamide adenine dinucleotide locus of the Blanding's turtle (Emydoidea blandingii) for detecting overwintering individuals. Seventy-eight water samples were collected from 17 wetland sites in Ontario, Canada. We used traditional field data to identify a priori positive and negative control sites. Fifty percent of positive control sites amplified. Detection was related to the number of individuals estimated from field observations in at least one region surveyed. Positive control sites had lower total dissolved solids and electrical conductivity in relation to negative control sites. Shedding rates were within the same order of magnitude for brumating and active turtles. We recommend collecting additional samples at a larger number of locations to maximize detection. Recommended sampling design changes may overshadow the additional effects of water chemistry and low eDNA shedding rates. eDNA offers tremendous potential to practitioners conducting species at risk assessments in environmental consulting by providing a faster, more efficient method of detection compared with traditional surveys.

Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River.

Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilms, and suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the phylum level, different niche communities were highly similar to each other and across locations. However, there were significant differences in the abundance of specific genera among the different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though suspended load communities collected by any means remained stably diverse across locations. Although there was an influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as a means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.

[Microbial ecology, the understanding of the invisible living]. / L'écologie microbienne, pour une appréhension du vivant invisible.

Microorganisms are invisible to the naked eye. Hospital hygiene practices are therefore based on the representation that caregivers have of them. This difficulty can generate irrational behavior and fear of blame. Conversely, a better knowledge of the specificities of this invisible living world favors a rationalization of care practices. To do this, caregivers will be able to appropriate the major concepts of microbiology, particularly microbial ecology.

[For more eco-friendly care]. / Pour des soins plus écoresponsables.

The word given to the teams, caregivers and patients who, in the field, carry out reflections and initiatives in favor of sustainable development reflects their commitment. It is an educational and institutional challenge and a strong individual and collective awareness that is expressed.

[Sustainable development and daily care of the patient]. / Développement durable et prise en charge journalière du patient.

How can we actively participate in sustainable development when we are nurses, orderlies or health care agents? Are nurses simply executors, users of equipment and consumers of products or, on the contrary, major contributors to the evolution towards more eco-responsible care practices? A shared reflection and a commitment from all hospital staff could encourage active participation in health establishments.

Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities.

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%-98% less H2 oxidation and 54%-99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

Gas seepage pockmark microbiomes suggest the presence of sedimentary coal seams in the Öxarfjörður graben of northeastern Iceland.

Natural gas seepage pockmarks are found off- and onshore in the Öxarfjörður graben, Iceland. The bacterial communities of two onshore seepage sites were analysed by 16S rRNA gene amplicon sequencing; the geochemical characteristics, hydrocarbon content, and the carbon isotope composition of the sites were also determined. While one site was found to be characterised by biogenic origin of methane gas, with a carbon isotope ratio (δ13C (‰)) of -63.2, high contents of organic matter and complex hydrocarbons, the other site showed a mixed origin of the methane gas (δ13C (‰) = -26.6) with geothermal characteristics and lower organic matter content. While both sites harboured Proteobacteria as the most abundant bacterial phyla, the Deltaproteobacteria were more abundant at the geothermal site and the Alphaproteobacteria at the biogenic site. The Dehalococcoidia class of phylum Chloroflexi was abundant at the geothermal site while the Anaerolineae class was more abundant at the biogenic site. Bacterial strains from the seepage pockmarks were isolated on a variety of selective media targeting bacteria with bioremediation potential. A total of 106 strains were isolated and characterised, including representatives from the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. This article describes the first microbial study on gas seepage pockmarks in Iceland.

Characterization and comparison of poorly known moth communities through DNA barcoding in two Afrotropical environments in Gabon 1.

Biodiversity research in tropical ecosystems-popularized as the most biodiverse habitats on Earth-often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.

Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline.

Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.

Physiological traits and relative abundance of species as explanatory variables of co-occurrence pattern of cultivable bacteria associated with chia seeds.

Deciphering the rules defining microbial community assemblage is envisioned as a promising strategy to improve predictions of pathogens colonization and proliferation in food. Despite the increasing number of studies reporting microbial co-occurrence patterns, only a few attempts have been made to challenge them in experimental or theoretical frameworks. Here, we tested the hypothesis that observed variations in co-occurrence patterns can be explained by taxonomy, relative abundance, and physiological traits of microbial species. We used PCR amplicon sequencing of taxonomic markers to assess distribution and co-occurrence patterns of bacterial and fungal species found in 25 chia (Salvia hispanica L.) samples originating from eight different sources. The use of nutrient-rich and oligotrophic media enabled isolation of 71 strains encompassing 16 bacterial species, of which five corresponded to phylotypes represented in the molecular survey. Tolerance to different growth inhibitors and antibiotics was tested to assess the physiological traits of these isolates. Divergence of physiological traits and relative abundance of each pair of species explained 69% of the co-occurrence profile displayed by cultivable bacterial phylotypes in chia. Validation of this ecological network conceptualization approach to more food products is required to integrate microbial species co-occurrence patterns in predictive microbiology.

Need for integrative thinking to fight against emerging infectious diseases. Proceedings of the 5th seminar on emerging infectious diseases, March 22, 2016 - current trends and proposals.

We present here the proceedings of the 5th seminar on emerging infectious diseases, held in Paris on March 22nd, 2016, with seven priority proposals that can be outlined as follows: encourage research on the prediction, screening and early detection of new risks of infection; develop research and surveillance concerning transmission of pathogens between animals and humans, with their reinforcement in particular in intertropical areas ("hot-spots") via public support; pursue aid development and support in these areas of prevention and training for local health personnel, and foster risk awareness in the population; ensure adapted patient care in order to promote adherence to treatment and to epidemic propagation reduction measures; develop greater awareness and better education among politicians and healthcare providers, in order to ensure more adapted response to new types of crises; modify the logic of governance, drawing from all available modes of communication and incorporating new information-sharing tools; develop economic research on the fight against emerging infectious diseases, taking into account specific driving factors in order to create a balance between preventive and curative approaches.

Bacterial keratitis treated by strengthened antibiotic eye drops: An 18 months review of clinical cases and antibiotic susceptibilities.

PURPOSE: To describe, in patients treated for infectious keratitis, the microorganisms identified and their antibiotic susceptibility over a period of 18 months. METHOD: Retrospective, descriptive, non-comparative study. Medical and biological data were extracted from the patients' file treated with strengthened antibiotic eye drops at Angers University Hospital between January 2015 and June 2016. The main elements noted were the bacteria involved and their susceptibility to antibiotics. Patients' visual acuity at the start and end of treatment was compared. RESULTS: Forty-eight patients were included. Almost one bacterium was identified in 31 patients, totalling 43 pathogens of 24 different species. The most frequently found microorganisms were Gram-positive cocci (55.8%), including Staphylococcus Aureus (14.0%) and Epidermidis (14.0%). All Gram-negative bacilli amounted to 30.2% of the identified bacteria, including 9.3% of Pseudomonas aeruginosa. None of the Gram-positive cocci were resistant to vancomycin and all Gram-negative bacilli were susceptible to ceftazidime and amikacin. Following treatment with at least one of the three antibiotic eye drops produced by our pharmacy (amikacin at 50mg/mL, ceftazidime at 50mg/mL and vancomycin at 25mg/mL), patients' visual acuity was significantly improved (P=0.043). CONCLUSION: The study helped identify the bacterial ecology of patients admitted for infectious keratitis. Among the bacteria identified, none were found to be resistant to any of the three strengthened antibiotic eye drops produced by the hospital pharmacy. These eye drops allowed for a rapid and effective treatment of patients and the improvement of their visual acuity before even identifying the bacteria.

Ten years of barcoding at the African Centre for DNA Barcoding.

The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of a global initiative to accurately and rapidly survey biodiversity using short DNA sequences. The mitochondrial cytochrome c oxidase 1 gene (CO1) was rapidly adopted as the de facto barcode for animals. Following the evaluation of several candidate loci for plants, the Plant Working Group of the Consortium for the Barcoding of Life in 2009 recommended that two plastid genes, rbcLa and matK, be adopted as core DNA barcodes for terrestrial plants. To date, numerous studies continue to test the discriminatory power of these markers across various plant lineages. Over the past decade, we at the ACDB have used these core DNA barcodes to generate a barcode library for southern Africa. To date, the ACDB has contributed more than 21 000 plant barcodes and over 3000 CO1 barcodes for animals to the Barcode of Life Database (BOLD). Building upon this effort, we at the ACDB have addressed questions related to community assembly, biogeography, phylogenetic diversification, and invasion biology. Collectively, our work demonstrates the diverse applications of DNA barcoding in ecology, systematics, evolutionary biology, and conservation.

International Barcode of Life: Focus on big biodiversity in South Africa.

Participants in the 7th International Barcode of Life Conference (Kruger National Park, South Africa, 20-24 November 2017) share the latest findings in DNA barcoding research and its increasingly diversified applications. Here, we review prevailing trends synthesized from among 429 invited and contributed abstracts, which are collated in this open-access special issue of Genome. Hosted for the first time on the African continent, the 7th Conference places special emphasis on the evolutionary origins, biogeography, and conservation of African flora and fauna. Within Africa and elsewhere, DNA barcoding and related techniques are being increasingly used for wildlife forensics and for the validation of commercial products, such as medicinal plants and seafood species. A striking trend of the conference is the dramatic rise of studies on environmental DNA (eDNA) and on diverse uses of high-throughput sequencing techniques. Emerging techniques in these areas are opening new avenues for environmental biomonitoring, managing species-at-risk and invasive species, and revealing species interaction networks in unprecedented detail. Contributors call for the development of validated community standards for high-throughput sequence data generation and analysis, to enable the full potential of these methods to be realized for understanding and managing biodiversity on a global scale.

Chiropody/Podiatry: Interprovincial Differences in Profession Formation.

The regulation of foot health care professionals varies across provinces in Canada. In Ontario, the regulated health profession is chiropody. Chiropodists are foot specialists with a limited scope of practice. In contrast, British Columbia and five other provinces regulate podiatrists, who are highly trained foot physicians with an extensive scope of practice. This article explores the history of chiropody/podiatry in Ontario and British Columbia from the early 1900s through the 1980s in order to understand how professional development in this field took such divergent paths within Canada. In so doing, it not only sheds light on a health practice that has received little scholarly attention, but it also highlights the centrality of inter-professional conflict and state actors' agendas to professional regulatory outcomes.

Species Distribution Modelling of Aedes aegypti in two dengue-endemic regions of Pakistan.

OBJECTIVES: Statistical tools are effectively used to determine the distribution of mosquitoes and to make ecological inferences about the vector-borne disease dynamics. In this study, we utilised species distribution models to understand spatial patterns of Aedes aegypti in two dengue-prevalent regions of Pakistan, Lahore and Swat. Species distribution models can potentially indicate the probability of suitability of Ae. aegypti once introduced to new regions like Swat, where invasion of this species is a recent phenomenon. METHODS: The distribution of Ae. aegypti was determined by applying the MaxEnt algorithm on a set of potential environmental factors and species sample records. The ecological dependency of species on each environmental variable was analysed using response curves. We quantified the statistical performance of the models based on accuracy assessment and spatial predictions. RESULTS: Our results suggest that Ae. aegypti is widely distributed in Lahore. Human population density and urban infrastructure are primarily responsible for greater probability of mosquito occurrence in this region. In Swat, Ae. aegypti has clumped distribution, where urban patches provide refuge to the species in an otherwise hostile heterogeneous environment and road networks are assumed to have facilitated in passive-mediated dispersal of species. CONCLUSIONS: In Pakistan, Ae. aegypti is expanding its range northwards; this could be associated with rapid urbanisation, trade and travel. The main implication of this expansion is that more people are at risk of dengue fever in the northern highlands of Pakistan.

Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.

Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies.

Diagnosis of vibriosis in the era of genomics: lessons from invertebrates.

Global changes linked to increases in temperature and ocean acidification, but also to more direct anthropogenic influences such as aquaculture, have caused a worldwide increase in the reports of Vibrio-associated illnesses affecting humans and also animals such as shrimp and molluscs. Investigation of the emergence of Vibrio pathogenesis events requires the analysis of microbial evolution at the gene, genome and population levels, in order to identify genomic modifications linked to increased virulence, resistance and/or prevalence, or to recent host shift. From a more applied point of view, the elucidation of virulence mechanisms is a prerequisite to devising prophylactic methods to fight infectious agents. In comparison with human pathogens, fairly little is known about the requirements for virulence in vibrios pathogenic to animals. However, the advent of genome sequencing, especially next-generation technologies, the possibility of genetically manipulating most of the Vibrio strains, and the recent availability of standardised animals for experimental infections have now compensated for the considerable delay in advancement of the knowledge of non-model pathogens such as Vibrio and have led to new scientific questions.

Nous assistons actuellement à un accroissement mondial du nombre de maladies imputables à Vibrio rapportées aussi bien chez l'homme que chez des espèces animales comme les crevettes et les mollusques, dû aux changements planétaires liés à l'augmentation des températures et à l'acidification des océans, parmi d'autres influences plus directement associées à l'activité humaine, notamment l'aquaculture. Les études sur la pathogenèse de l'émergence de Vibrio recourent à des analyses de l'évolution microbienne tant au niveau génétique et génomique qu'à l'échelle des populations, de manière à identifier les modifications génomiques associées à l'accroissement de la virulence, de la résistance et/ou de la prévalence, ainsi que l'extension récente des spécificités d'hôte. D'un point de vue plus pratique, l'élucidation des mécanismes de virulence est une condition préalable à la conception de méthodes prophylactiques permettant de lutter contre les agents infectieux. Les critères de virulence des Vibrio pathogènes pour les animaux sont beaucoup moins connus que ceux des agents pathogènes affectant l'être humain. Néanmoins, l'avènement des techniques de séquençage du génome, en particulier celles de nouvelle génération, la possibilité de soumettre la plupart des souches de Vibrio à des manipulations génétiques et la standardisation récente de modèles animaux pour des essais d'infection expérimentale ont permis de rattraper une grande partie du retard des connaissances sur les agents pathogènes non utilisés comme modèles tels que Vibrio, en suscitant de nouvelles questions scientifiques.

Los cambios planetarios ligados no solo al incremento de las temperaturas y la acidificación de los océanos, sino también a factores antrópicos que ejercen una influencia más directa, como la acuicultura, se han traducido en un aumento mundial del número de casos notificados de patologías asociadas a Vibrio, ya sea en el ser humano o en animales como camarones o moluscos. Para investigar la aparición de episodios patógenos causados por Vibrio es preciso analizar la evolución microbiana a nivel génico, genómico y poblacional con el fin de determinar las modificaciones genómicas relacionadas con un aumento de la virulencia, la resistencia y/o la prevalencia o con un cambio reciente de organismo anfitrión. Desde un punto de vista más aplicado, para concebir métodos profilácticos destinados a combatir a los agentes infecciosos es indispensable dilucidar previamente los mecanismos de la virulencia. En comparación con los patógenos humanos, poco se sabe acerca de los factores que determinan la virulencia en los vibrios patógenos para los animales. Sin embargo, gracias al advenimiento de la secuenciación genómica, en especial de las técnicas de secuenciación de próxima generación, a la posibilidad de manipular genéticamente la mayoría de las cepas de Vibrio y a la existencia desde hace poco tiempo de animales estandarizados con los que proceder a infecciones experimentales, ya se ha podido compensar el considerable retraso que existía en el conocimiento de patógenos que no constituyen «organismos modelo¼ para la ciencia, como es el caso de Vibrio, lo que a su vez ha abierto nuevos interrogantes científicos.