Recherches sur l’écosystème de la forêt subéquatoriale de basse Côte-d’Ivoire VII. Conclusions générales

La forêt tropicale pluvieuse, qui couvre encore de vastes surfaces, constitue le type le végétation terrestre le plus complexe et le moins bien connu. Les études dont les principaux résultats sont exposés ici ont été conduites dans deux massifs bien repré sentatifs de la forêt équatoriale sempervirente de Côte-d’Ivoire : le parc national du Banco sur sol sableux, la réserve de Yapo sur sol argilo-sableux et gravillonnaire. L’orientation des recherches a été fondée sur la notion d 'écosystème, entité fonctionnelle caractérisée par sa structure et ses relations d’échanges d’énergie et de matière entre les constituants de la biocoenose et leur milieu non vivant. La complexité de l’écosystème de la forêt tropicale pluvieuse a conduit les auteurs à limiter les études au niveau trophique des producteurs et à ses relations avec l’environnement climatique et édaphique. Le régime climatique comporte une double alternance annuelle d’importance inégale de saisons à forte pluviosité et à faible pluviosité et une seule oscillation du flux de rayonnement solaire et de la température moyenne. Ce rythme climatique complexe introduit une évolution saisonnière de l’activité biologique. Une autre caractéristique fondamentale des forêts étudiées est leur état d’équilibre avec leur environnement en l’absence d’exploitation. Cet équilibre comporte en fait une évolution cycli que en chaque point du peuplement, dont la mort sur pied ou par chute des grands arbres constitue le traumatisme initial. L’organisation structurale et la richesse spécifique tendent à assurer une exploitation maximale du milieu dans l’espace et dans le temps. La biomasse végétale très importante et le dévelop pement de la surface foliaire relative en sont les conséquences. La productivité primaire nette reste cependant faible : sa contribution à l’accroissement de la biomasse ligneuse et à la production de litière a fait l’objet de mesures. Quant à la pro ductivité nette de l’ensemble de l’écosystème, qui est en équilibre climacique avec le milieu, celle-ci est nulle, le bois et la litière produits étant consommés par les chaînes d’hétérotrophes. Les cycles de la matière organique, de l’eau et des bioéléments majeurs ont été analysés. L’importance des flux entre compar timents par rapport aux stocks accumulés dans ceux-ci est un caractère capital du fonctionnement de ce type d’écosystème. La disparition rapide de la litière en donne une image particulière ment apparente, quoique les chaînes de détritivores et de décomposeurs soient très complexes dans cette phase. Ces différentes caractéristiques d’état et de flux dans l’écosystème étudié comportent des variations saisonnières cycli ques sous la dépendance des facteurs climatiques : il en est ainsi des termes du bilan hydrique, notamment les réserves d’eau du sol et l’évapotranspiration, de l’accroissement en épaisseur des troncs, de la chute de litière et de sa vitesse de décomposition, des transferts dans les cycles des éléments minéraux. L’étude parallèle de trois stations a mis en évidence des différences quantitatives dans la production primaire, les compo santes du bilan hydrique, le stock et la vitesse de décomposition de la matière organique, les caractéristiques des cycles biogéo chimiques. La comparaison avec les résultats obtenus dans d’autres forêts tropicales sempervirentes de basse altitude en équilibre et non exploitées, en Afrique, dans l’Asie du Sud-Est et en Amérique, montre une grande similitude de la forêt ivoirienne avec celles-ci.Results are presented on production studies carried out in subequatorial forest ecosystems in the Ivory Coast. The work was carried out between 1966 and 1974, within the framework of the International Riological Programme. Separate papers deal with : the geographic setting of the work ; inventory and structure of woody vegetation ; water balance ; plant biomass, primary production and cycling of organic material ; biogeochemical cycle. A final chapter presents an overview of the main conclusions of the studies undertaken, and their relation to other work on tropical forests in different parts of the world. Studies were centred on two areas of evergreen tropical forest near to Abidjan in the Ivory Coast, in the Ranco Natio nal Park (3000 ha total area, two study sites, sandy soils) and in the Yapo reserve (45 km north of Ranco, one study site, sandy-loam soil, rather stoney in nature). Both sites have been subject to human disturbance in the past, though there is no current exploitation. Mean annual precipitation (over a 40 year period) at Banco is 2095 mm, and at Yapo 1739 mm. Precipitation is mainly concentrated in two rainy seasons, from March to September and — of lesser importance — from September to November. Inventories of the two study areas have been made, and the structure and composition of the vegetation analyzed. Leaf area index is between 10 and 12. The above ground biomass of trees was estimated to be 465 t/ha at Banco and 425 t/ha at Yapo. More detailed studies at Banco indicated that the total mean biomass of producers was in the order of 562 t/ha, made up as follows : trunks and main branches of trees, 360 t/ha ; twigs and small branches, 105 t/ha ; stems and branches of bushes, 15 t/ha ; stems and branches of lianas, 25 t/ha ; leaves, 8 t/ha ; roots, 49 t/ha. Estimates of primary productivity were based on measures of tree increment and litter fall. Increase in basal area is in the order of 0.16-0.37 m2/ha/yr (0.4-0.9 %). Estimates of increase in above ground biomass range from 3.0-4.6 t/ha/yr (0. 8-1.2 %). Total litter production is between 9.0 and 11.9 t/ha/yr. Of this, 6.2-8.2 t/ha/yr is in the form of leaves, leaf fall reaching a maximum in the main dry season. Annual leaf production was estimated to be 8.1-10.6 t/ha. The total net primary production cf trees is in the order of 17 t/ha/yr at Banco and 15.5 t/ha/yr at Yapo. Photosynthetic efficiency is about 1.11 % at Banco and 1.02 % at Yapo. The quantity of soil litter varies between about 1 t/ha in the main rainy season, and 3-4 t/ha during the main dry season. Estimates of organic material in the soil at different sites range between 70 and 170 t/ha, of which a third to a half is found in the top 10 cm of soil. The period for total litter decomposition is in the order of 5-9 months. The role of the fauna and micro flora in the process of decomposition has not been determined quantitatively, though estimates of the populations of earthworms, termites and soil micro-arthropods have been made. The biogeochemical cycle and distribution of nutrient elements are similar to that recorded in other tropical forest systems. Thus, most of the stock of nutrients is stored in the plant biomass. Nutrient levels in the litter and soil are low. Turnover rates are high. For example, estimates of the annual flux of elements between the above ground living biomass and the soil surface, as a function of the nutrient stock in the above-ground tree biomass, are 15-20 % for N, 10-20 % for P, up to 50 % for K, 18-22 % for Mg, 7-10 % for Ca.Potassium is thus the most mobile element, calcium the least mobile. Indirect measures of absorp tion rates of different elements have been made. Seasonal variation in climatic factors has an important influence on the functioning of the forest ecosystems in terms of water balance (soil water reserves, evapo-transpiration), wood increment, litter fall and decomposition rates, nutrient transfers, etc. Comparison of the results obtained in the three main study sites (two in Banco, one in Yapo) illustrates the importance of soil type and topography on such indices of ecosystem condition as primary production and cycling of biogeochemical elements

Randomized clinical trial to evaluate the effect of fecal microbiota transplant for initial Clostridium difficile infection in intestinal microbiome

Objective The aim of this study was to evaluate the impact of fecal donor-unrelated donor mix (FMT-FURM) transplantation as first-line therapy for C. difficile infection (CDI) in intestinal microbiome. Methods We designed an open, two-arm pilot study with oral vancomycin (250mg every 6 h for 10–14 days) or FMT-FURM as treatments for the first CDI episode in hospitalized adult patients in Hospital Universitario “Dr. Jose Eleuterio Gonzalez”. Patients were randomized by a closed envelope method in a 1: 1 ratio to either oral vancomycin or FMT-FURM. CDI resolution was considered when there was a reduction on the Bristol scale of at least 2 points, a reduction of at least 50% in the number of bowel movements, absence of fever, and resolution of abdominal pain (at least two criteria). From each patient, a fecal sample was obtained at days 0, 3, and 7 after treatment. Specimens were cultured to isolate C. difficile, and isolates were characterized by PCR. Susceptibility testing of isolates was performed using the agar dilution method. Fecal samples and FMT-FURM were analyzed by 16S rRNA sequencing. Results We included 19 patients; 10 in the vancomycin arm and 9 in the FMT-FURM arm. However, one of the patients in the vancomycin arm and two patients in the FMT-FURM arm were eliminated. Symptoms resolved in 8/9 patients (88.9%) in the vancomycin group, while symptoms resolved in 4/7 patients (57.1%) after the first FMT-FURM dose (P = 0.26) and in 5/7 patients (71.4%) after the second dose (P = 0.55). During the study, no adverse effects attributable to FMT-FURM were observed in patients. Twelve isolates were recovered, most isolates carried tcdB, tcdA, cdtA, and cdtB, with an 18-bp deletion in tcdC. All isolates were resistant to ciprofloxacin and moxifloxacin but susceptible to metronidazole, linezolid, fidaxomicin, and tetracycline. In the FMT-FURM group, the bacterial composition was dominated by Firmicutes, Bacteroidetes, and Proteobacteria at all-time points and the microbiota were remarkably stable over time. The vancomycin group showed a very different pattern of the microbial composition when comparing to the FMT-FURM group over time. Conclusion The results of this preliminary study showed that FMT-FURM for initial CDI is associated with specific bacterial communities that do not resemble the donors’ sample.Peer reviewedFinal Published versio

Characterization of Clostridium difficile isolates using capillary gel electrophoresis-based PCR ribotyping

We have developed a Clostridium difficile PCR ribotyping method based on capillary gel electrophoresis and have compared it with conventional PCR ribotyping. A total of 146 C. difficile isolates were studied: five isolates were reference strains (PCR ribotypes 001, 014, 017, 027 and 053); 141 were clinical isolates comprising 39 Austrian PCR ribotypes collected in the period 2006–2007 at 25 Austrian healthcare facilities. Capillary gel electrophoresis yielded up to 11 fragments per isolate and 47 ribotype patterns. All but one of the five PCR ribotypes of reference strains were clearly reflected in the chromatograms of capillary-based typing. Capillary gel electrophoresis divided 24 isolates belonging to PCR ribotype type 014 into seven subgroups, whereas subtyping the same isolates using multiple-locus variable-number tandem-repeat analysis yielded three unrelated subgroups, without obvious correlation to sr subgroups. Using a web-based software program (http://webribo.ages.at), we were able to correctly identify these 014 isolates by simply allocating the seven subgroup patterns to one ribotype, i.e. to PCR ribotype 014. We consider capillary gel electrophoresis-based PCR ribotyping to be a way of overcoming the problems associated with inter-laboratory comparisons of typing results, while at the same time substantially diminishing the hands-on time for PCR ribotyping

Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease

Background: Clostridium difficile infections (CDI) are a significant health problem to humans and food animals. Clostridial toxins ToxA and ToxB encoded by genes tcdA and tcdB are located on a pathogenicity locus known as the PaLoc and are the major virulence factors of C. difficile. While toxin-negative strains of C. difficile are often isolated from faeces of animals and patients suffering from CDI, they are not considered to play a role in disease. Toxin-negative strains of C. difficile have been used successfully to treat recurring CDI but their propensity to acquire the PaLoc via lateral gene transfer and express clinically relevant levels of toxins has reinforced the need to characterise them genetically. In addition, further studies that examine the pathogenic potential of toxin-negative strains of C. difficile and the frequency by which toxin-negative strains may acquire the PaLoc are needed. Results: We undertook a comparative genomic analysis of five Australian toxin-negative isolates of C. difficile that lack tcdA, tcdB and both binary toxin genes cdtA and cdtB that were recovered from humans and farm animals with symptoms of gastrointestinal disease. Our analyses show that the five C. difficile isolates cluster closely with virulent toxigenic strains of C. difficile belonging to the same sequence type (ST) and have virulence gene profiles akin to those in toxigenic strains. Furthermore, phage acquisition appears to have played a key role in the evolution of C. difficile. Conclusions: Our results are consistent with the C. difficile global population structure comprising six clades each containing both toxin-positive and toxin-negative strains. Our data also suggests that toxin-negative strains of C. difficile encode a repertoire of putative virulence factors that are similar to those found in toxigenic strains of C. difficile, raising the possibility that acquisition of PaLoc by toxin-negative strains poses a threat to human health. Studies in appropriate animal models are needed to examine the pathogenic potential of toxin-negative strains of C. difficile and to determine the frequency by which toxin-negative strains may acquire the PaLoc

The Clostridium difficile Cell Wall Protein CwpV is Antigenically Variable between Strains, but Exhibits Conserved Aggregation-Promoting Function

Clostridium difficile is the main cause of antibiotic-associated diarrhea, leading to significant morbidity and mortality and putting considerable economic pressure on healthcare systems. Current knowledge of the molecular basis of pathogenesis is limited primarily to the activities and regulation of two major toxins. In contrast, little is known of mechanisms used in colonization of the enteric system. C. difficile expresses a proteinaceous array on its cell surface known as the S-layer, consisting primarily of the major S-layer protein SlpA and a family of SlpA homologues, the cell wall protein (CWP) family. CwpV is the largest member of this family and is expressed in a phase variable manner. Here we show CwpV promotes C. difficile aggregation, mediated by the C-terminal repetitive domain. This domain varies markedly between strains; five distinct repeat types were identified and were shown to be antigenically distinct. Other aspects of CwpV are, however, conserved. All CwpV types are expressed in a phase variable manner. Using targeted gene knock-out, we show that a single site-specific recombinase RecV is required for CwpV phase variation. CwpV is post-translationally cleaved at a conserved site leading to formation of a complex of cleavage products. The highly conserved N-terminus anchors the CwpV complex to the cell surface. Therefore CwpV function, regulation and processing are highly conserved across C. difficile strains, whilst the functional domain exists in at least five antigenically distinct forms. This hints at a complex evolutionary history for CwpV

Allele Intersection Analysis: A Novel Tool for Multi Locus Sequence Assignment in Multiply Infected Hosts

Wolbachia are wide-spread, endogenous α-Proteobacteria of arthropods and filarial nematodes. 15–75% of all insect species are infected with these endosymbionts that alter their host's reproduction to facilitate their spread. In recent years, many insect species infected with multiple Wolbachia strains have been identified. As the endosymbionts are not cultivable outside living cells, strain typing relies on molecular methods. A Multi Locus Sequence Typing (MLST) system was established for standardizing Wolbachia strain identification. However, MLST requires hosts to harbour individual and not multiple strains of supergroups without recombination. This study revisits the applicability of the current MLST protocols and introduces Allele Intersection Analysis (AIA) as a novel approach. AIA utilizes natural variations in infection patterns and allows correct strain assignment of MLST alleles in multiply infected host species without the need of artificial strain segregation. AIA identifies pairs of multiply infected individuals that share Wolbachia and differ in only one strain. In such pairs, the shared MLST sequences can be used to assign alleles to distinct strains. Furthermore, AIA is a powerful tool to detect recombination events. The underlying principle of AIA may easily be adopted for MLST approaches in other uncultivable bacterial genera that occur as multiple strain infections and the concept may find application in metagenomic high-throughput parallel sequencing projects

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population