RESUMO
Free-living amoebae (FLA) such as Acanthamoeba, Balamuthia mandrillaris, Naegleria fowleri and Sappinia pedata are naturally widespread in freshwater, causing rare but fatal and debilitating infections in humans. Although recent studies have shown an increase in infection rates, there is a paucity of epidemiological studies regarding the presence of these emerging pathogens in water. Herein, we studied the diversity and relative abundance of thermophilic FLA in different recreational baths in a tropical climate for 5 years. From 2018 to 2022, a total of 96 water samples were collected from 7 recreational baths (natural, tiled, regularly cleaned or not, and with temperatures ranging from 27 to 40 °C). DNA was extracted from FLA cultivated at 37 °C to detect thermophilic culturable FLA. Metabarcoding studies were conducted through FLA 18S rRNA gene amplicons sequencing; amplicon sequence variants (ASV) were extracted from each sample and taxonomy assigned against PR2 database using dada2 and phyloseq tools. We also searched for Naegleria sp. and N. fowleri using PCR targeting ITS and NFITS genes (respectively) and we quantified them using an optimized most probable number (MPN) method for FLA. Our results showed that differences in FLA diversity and abundance were observed amongst the 7 baths, but without a clear seasonal distribution. Naegleria, Vermamoeba and Stenamoeba were the most represented genera, while the genera Acanthamoeba and Vahlkampfia were mainly found in 2 baths. The MPN values for Naegleria sp. (NT/l) increased between 2018 and 2022, but the MPN values for N. fowleri (NF/l) seemed to decrease. Globally, our results showed that since we cannot establish a seasonal distribution of FLA, the regular presence of FLA (namely Naegleria and Acanthamoeba) in recreational waters can pose a potential threat in terms of neuroinfections as well as Acanthamoeba keratitis. It is thus imperious to perform the regular control of these baths as a preventive health measure.
Assuntos
Amoeba , Guadalupe/epidemiologia , Monitoramento Ambiental , Água Doce , PraiasRESUMO
Summary: Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a 'one health' approach, for a better comprehension and surveillance of humans, plants or animals' health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to 'omics' data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated 'Galaxy KaruBioNet' platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html. Contact: dcouvin@pasteur-guadeloupe.fr. Supplementary information: Supplementary data are available at Bioinformatics Advances online.
RESUMO
Free-living amoebae (FLA) are ubiquitous protists. Pathogenic FLA such as N. fowleri can be found in hot springs in Guadeloupe, soil being the origin of this contamination. Herein, we analyzed the diversity and distribution of FLA in soil using a targeted metataxonomic analysis. Soil samples (n = 107) were collected from 40 sites. DNA was extracted directly from soil samples or from FLA cultivated at different temperatures (30, 37 and 44 °C). Metabarcoding studies were then conducted through FLA 18SrDNA amplicons sequencing; amplicon sequence variants (ASV) were extracted from each sample and taxonomy assigned against SILVA database using QIIME2 and SHAMAN pipelines. Vermamoeba were detected in DNA extracted directly from the soil, but to detect other FLA an amoebal enrichment step was necessary. V. vermiformis was by far the most represented species of FLA, being detected throughout the islands. Although Naegleria were mainly found in Basse-Terre region, N. fowleri was also detected in Grand Terre and Les Saintes Islands. Acanthamoeba were mainly found in areas where temperature is approx. 30 °C. Vannella and Vahlkampfia were randomly found in Guadeloupe islands. FLA detected in Guadeloupe include both pathogenic genera and genera that can putatively harbor microbial pathogens, therefore posing a potential threat to human health.
RESUMO
Ehrlichia ruminantium (ER) is the causative agent of Heartwater, one of the most common tick-borne diseases affecting ruminants in African countries and West Indies. Although ER can be used as an inactivated vaccine for wild and domestic animals, there are currently no easy and reliable methods for the quantification of this obligate intracellular bacterium. This report describes the development of a SYBR Green I based real time PCR protocol for the quantification of ER for vaccine production purposes. The method was validated for four ER strains. The external-standard-based PCR protocol developed has a large dynamic quantitative range allowing accurate ER measurement in samples containing from 10(2) to 10(8) gene copies; the method is also reproducible and precise, with intra- and inter-assay coefficients below 5%. The detection limits were validated for samples collected from bovine aortic endothelial cell culture bulks, which are commonly used to produce the ER vaccine. In contrast to the methods based upon protein content, no interference from the host cells in ER quantification was observed. Furthermore, the extended applicability of the new technique was demonstrated by monitoring ER production in cell culture thus rendering it a valuable tool to ensure consistency between vaccine lots and to evaluate optimal vaccine dosage.