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1.
Microbiome ; 9(1): 18, 2021 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-33478588

RESUMO

BACKGROUND: As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens. RESULTS: This study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006-2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations. CONCLUSIONS: These results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia. Video abstract.

2.
Artigo em Inglês | MEDLINE | ID: mdl-33515096

RESUMO

Candida auris is an emerging multiresistant pathogen causing nosocomial fungal infection. Specific detection and identification are necessary. Our goal is to develop a new qPCR system that enables rapid detection of C. auris, based on a GPI (glycosyl-phosphatidylinositol) protein-encoding gene. This system is reproducible and sensitive with a limit of detection of 13 C. auris CFU/qPCR reaction. The 100% specificity of this system is confirmed on 2073 clinical and environmental samples, 50 different bacterial species, and 9 Candida spp. (70 strains). This system is suitable to correctly identify C. auris infections and to trace its source.

3.
PLoS One ; 16(1): e0245250, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33507909

RESUMO

This Southeast Asia-Europe research project will use a One Health approach to identify the major parameters responsible for the presence of animal-associated antimicrobial resistant bacteria in animal production facilities in Thailand and the risk of their transmission from animals to humans. We will focus on traditional, small, extensive pig and poultry farms where information on antibiotic use is scarce and animals live in close contact with humans. This cross-sectional study will be based on the epidemiological analysis of the antimicrobial resistance (AMR) present in fecal samples from animals and humans. Extended spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) and Enterobacteriaceae resistant to colistin will be actively searched in the feces of farm animals (pigs and poultry), small wild rodents and farmers. Phenotypic (selective plating) and genotypic (multilocus seuquence typing and sequencing) methods will be used for the detection of AMR, the identification of antibiotic resistance genes (ARGs) and the characterization of strains carrying resistance genes. Questionnaires will be administered to investigate the effects of antibiotic use, farm characteristics and biosecurity measures on the occurrence of AMR in animals. Subsequently, the fecal carriage of AMR and ARGs in farmers will be compared to a control population with no occupational contacts with animals, thus enabling an estimation of the risk of transmission of AMR/ARGs from animals to farmers.

5.
Parasite ; 27: 55, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33141658

RESUMO

This article considers a broad perspective of "One Health" that includes local and animal knowledge. Drawing from various colonial efforts to link human, animal, and environmental health, it first shows that the current "One Health" initiative has its roots in colonial engagement and coincides with a need to secure the health of administrators (controlling that of local populations), while pursing use of resources. In our contemporary period of repeated epidemic outbreaks, we then discuss the need for greater inclusion of social science knowledge for a better understanding of complex socio-ecological systems. We show how considering anthropology and allied sub-disciplines (anthropology of nature, medical anthropology, and human-animal studies) highlights local knowledge on biodiversity as well as the way social scientists investigate diversity in relation to other forms of knowledge. Acknowledging recent approaches, specifically multispecies ethnography, the article then aims to include not only local knowledge but also non-human knowledge for a better prevention of epidemic outbreaks. Finally, the conclusion stresses the need to adopt the same symmetrical approach to scientific and profane knowledge as a way to decolonize One Health, as well as to engage in a more-than-human approach including non-human animals as objects-subjects of research.

6.
Sci Rep ; 10(1): 18909, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33144595

RESUMO

While the epidemic of SARS-CoV-2 has spread worldwide, there is much concern over the mortality rate that the infection induces. Available data suggest that COVID-19 case fatality rate had varied temporally (as the epidemic has progressed) and spatially (among countries). Here, we attempted to identify key factors possibly explaining the variability in case fatality rate across countries. We used data on the temporal trajectory of case fatality rate provided by the European Center for Disease Prevention and Control, and country-specific data on different metrics describing the incidence of known comorbidity factors associated with an increased risk of COVID-19 mortality at the individual level. We also compiled data on demography, economy and political regimes for each country. We found that temporal trajectories of case fatality rate greatly vary among countries. We found several factors associated with temporal changes in case fatality rate both among variables describing comorbidity risk and demographic, economic and political variables. In particular, countries with the highest values of DALYs lost to cardiovascular, cancer and chronic respiratory diseases had the highest values of COVID-19 CFR. CFR was also positively associated with the death rate due to smoking in people over 70 years. Interestingly, CFR was negatively associated with share of death due to lower respiratory infections. Among the demographic, economic and political variables, CFR was positively associated with share of the population over 70, GDP per capita, and level of democracy, while it was negatively associated with number of hospital beds ×1000. Overall, these results emphasize the role of comorbidity and socio-economic factors as possible drivers of COVID-19 case fatality rate at the population level.


Assuntos
Infecções por Coronavirus/mortalidade , Pneumonia Viral/mortalidade , Canadá , Infecções por Coronavirus/epidemiologia , Interpretação Estatística de Dados , Demografia/estatística & dados numéricos , Europa (Continente) , Humanos , Mortalidade/tendências , Pandemias , Pneumonia Viral/epidemiologia , Sistemas Políticos/estatística & dados numéricos , Fatores Socioeconômicos , Estados Unidos
7.
Parasitol Res ; 119(11): 3675-3690, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33001253

RESUMO

In 2018, extensive field studies of diversity and prevalence of helminth infection in synanthropic rodents and non-rodent small mammals from public parks and citified areas in the Bangkok Metropolitan were conducted. Rattus rattus complex was the dominant small mammal in public parks. Of the 197 animals, 147 individuals were infected with one or more species of helminths, yielding an infection prevalence of 74.6%. Twenty-five species of helminths were recovered during necropsy. Pterygodermatites tani was the most prevalent (36.2%); other encountered species included Raillietina celebensis, Hydatigera taeniaformis (metacestode in liver tissue), Gongylonema neoplasticum and Hymenolepis diminuta. Different helminth assemblages infected three different host taxa, i.e. synanthropic Rattus spp., Tupaia belangeri (Northern treeshrew) and Suncus murinus (Asian house shrew). Nine species of possible zoonotic helminths were identified. The focus on synanthropic rats influenced the findings of helminth diversity by either host intrinsic or extrinsic factors. A significant positive correlation was found between host body mass and helminth species richness. Greater helminth species richness was found in rats from public parks compared with animals from citified areas (e.g. inside buildings or offices). Also, helminth species richness was negatively correlated with the proportion of post-flooding/rain-fed land. These results provide essential information for assessing the incidence of potential zoonotic health threats in Bangkok and updating research in parasite ecology.


Assuntos
Biota , Helmintíase Animal/parasitologia , Helmintos/classificação , Doenças dos Roedores/parasitologia , Roedores/parasitologia , Animais , Cidades , Inundações , Helmintíase Animal/epidemiologia , Helmintos/isolamento & purificação , Humanos , Parques Recreativos , Prevalência , Ratos , Doenças dos Roedores/epidemiologia , Musaranhos/parasitologia , Tailândia/epidemiologia
8.
Ecol Lett ; 23(11): 1557-1560, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32869489

RESUMO

Concerns about the prospect of a global pandemic have been triggered many times during the last two decades. These have been realised through the current COVID-19 pandemic, due to a new coronavirus SARS-CoV2, which has impacted almost every country on Earth. Here, we show how considering the pandemic through the lenses of the evolutionary ecology of pathogens can help better understand the root causes and devise solutions to prevent the emergence of future pandemics. We call for better integration of these approaches into transdisciplinary research and invite scientists working on the evolutionary ecology of pathogens to contribute to a more "solution-oriented" agenda with practical applications, emulating similar movements in the field of economics in recent decades.

10.
Biol Conserv ; 248: 108707, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32834060

RESUMO

Infectious diseases, biodiversity loss and livestock expansion are increasing globally, and examining patterns that link them is important for both public health and conservation. This study is a first attempt to analysis globally these patterns using General additive modelling and Structural equation modelling. A positive association between the number of infectious and parasitic diseases recorded in humans and the total number of animal species between nations was observed. A similar positive association between the number of outbreaks of human infectious diseases, corrected for the number of surveys, and the number of threatened animal species, corrected for the number of animal species, suggests that outbreaks of human infectious diseases are linked with threatened biodiversity. Results of the analyses over the longest period of the dataset (2000-2019) showed a positive correlation between the increasing number of cattle and the number of threatened species, a positive correlation between the increasing number of cattle and the number of outbreaks of human diseases, and a lack of correlation between the number of outbreaks and the number of threatened animal species. As a result, the growing importance of livestock on the planet, while threatening biodiversity, increasingly puts human and animal health at risk. This study calls for further analyses on the consequences of livestock expansion, which depends on several factors that vary by country, namely the growth of human population, changes in diet linked to the westernization of habits, agricultural industrialization and the integration into the world trade, but also the cultural values of livestock.

12.
Int J Parasitol ; 50(10-11): 771-786, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32687912

RESUMO

Cypriniformes, which exhibit a wide geographical distribution, are the most species-rich group of freshwater fishes. Despite considerable research on their parasites, no reliable estimates of their parasite diversity on a large geographical scale are available. In the present review, we analyse species richness of two parasitic flatworm groups (monogeneans and tapeworms) reported from cypriniform fishes in the two most intensively studied parts of the Holarctic region, Europe and North America. We also review knowledge on parasite speciation and host-parasite coevolution, and emphasise the risk of parasite co-introduction resulting from transfers of cypriniforms among different continents. As parasite diversity in European cypriniforms has been more intensively explored, we predicted a lower level of knowledge on parasite diversity in North American fishes, despite North America having a higher diversity of cypriniforms than Europe. Our data revealed a higher mean species richness of monogeneans and tapeworms per cypriniform species in Europe compared with North America. We showed that species richness of both parasite taxa in both continents is strongly affected by sample size, but that fish traits also play an important role in determining monogenean and tapeworm species richness in European cyprinoids. We recorded higher host specificity for cypriniform parasites in North America, even within parasite genera shared by cypriniforms on both continents. The host range of monogeneans parasitising cyprinoids on both continents was affected by phylogeny, indicating an effect of parasite life history on host specificity. The difference in parasite host range between the two continents could potentially be explained by either the low overall level of sampling activity in North America or an underestimation of parasite diversity in Europe. We suggest that future research efforts be focussed on cypriniforms in order to obtain reliable data for robust assessments of parasite species richness and phylogenies, to assess host-parasite coevolution and to reveal fish biogeography.

13.
Parasit Vectors ; 13(1): 364, 2020 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-32690073

RESUMO

BACKGROUND: Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics. METHODS: To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms. RESULTS: The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers. CONCLUSIONS: This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

14.
PLoS Genet ; 16(6): e1008471, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32525879

RESUMO

Viruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. We surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice: Mus caroli, M. cervicolor, and M. cookii. The presence of flanking repeats suggested it arose by LINE-mediated retroduplication within their most recent common ancestor. A high degree of natural variation was observed in both Fv1 and Fv7 and, on top of positive selection at certain residues, insertions and deletions were present that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes, with activities directed against gamma-, spuma-, and lentiviruses. It seems likely, at least in the case of M. caroli, that the observed gene duplication may expand the breadth of restriction beyond the capacity of Fv1 alone and that one or more such viruses have recently driven or continue to drive the evolution of the Fv1 and Fv7 genes.


Assuntos
Evolução Molecular , Duplicação Gênica , Camundongos/genética , Proteínas/genética , Infecções por Retroviridae/genética , Animais , Resistência à Doença/genética , Camundongos/virologia , Retroviridae/patogenicidade , Infecções por Retroviridae/imunologia , Infecções por Retroviridae/virologia
15.
Infect Genet Evol ; 84: 104384, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32473976

RESUMO

In less than five months, COVID-19 has spread from a small focus in Wuhan, China, to more than 5 million people in almost every country in the world, dominating the concern of most governments and public health systems. The social and political distresses caused by this epidemic will certainly impact our world for a long time to come. Here, we synthesize lessons from a range of scientific perspectives rooted in epidemiology, virology, genetics, ecology and evolutionary biology so as to provide perspective on how this pandemic started, how it is developing, and how best we can stop it.


Assuntos
Betacoronavirus/patogenicidade , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/transmissão , Surtos de Doenças , Interações Hospedeiro-Patógeno/genética , Peptidil Dipeptidase A/genética , Pneumonia Viral/epidemiologia , Pneumonia Viral/transmissão , Glicoproteína da Espícula de Coronavírus/genética , Animais , Ásia/epidemiologia , Betacoronavirus/classificação , Betacoronavirus/genética , Coevolução Biológica , Quirópteros/virologia , Infecções por Coronavirus/diagnóstico , Europa (Continente)/epidemiologia , Eutérios/virologia , Expressão Gênica , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Interações Hospedeiro-Patógeno/imunologia , Humanos , Imunidade Inata , América do Norte/epidemiologia , Pandemias , Peptidil Dipeptidase A/imunologia , Filogenia , Pneumonia Viral/diagnóstico , Índice de Gravidade de Doença , Glicoproteína da Espícula de Coronavírus/antagonistas & inibidores , Glicoproteína da Espícula de Coronavírus/imunologia
16.
Parasitology ; 147(9): 1038-1047, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32364099

RESUMO

Chigger mites (Trombiculidae) are temporary habitat-specific ectoparasites that often occur on rodents. Little ecological data are available on chiggers associated with rodents in South Africa. The study aims were to (1) record the chigger species associated with rodents in the savanna, (2) assess if chigger species display parasitope preference on the rodent body and (3) compare the distribution of chigger species in natural, agricultural and urban habitats. Rodents (n = 314) belonging to eight genera were trapped in the savanna biome during 2014 and 2015. Twelve chigger species, of which five are recently described species, were recorded from 161 rodent hosts. The data include three new country locality records. Microtrombicula mastomyia was the most prevalent species across sampling seasons and habitat types. Significant parasitope preference was recorded for two species, with the ear, face and tail base some of the preferred attachment sites. Sampling season and habitat type had a significant effect on chigger communities with summer and agricultural habitats recording the highest species richness, while the highest species diversity was recorded in natural habitats. The study contributes to our current knowledge regarding rodent-associated chigger diversity and distribution in South Africa and further highlights the importance of environmental characteristics in shaping chigger communities.

17.
Parasitology ; 147(9): 972-984, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32364103

RESUMO

Gastrointestinal helminth infection likely affects the gut microbiome, in turn affecting host health. To investigate the effect of intestinal parasite status on the gut microbiome, parasitic infection surveys were conducted in communities in Nan Province, Thailand. In total, 1047 participants submitted stool samples for intestinal parasite examination, and 391 parasite-positive cases were identified, equating to an infection prevalence of 37.3%. Intestinal protozoan species were less prevalent (4.6%) than helminth species. The most prevalent parasite was the minute intestinal fluke Haplorchis taichui (35.9%). Amplicon sequencing of 16S rRNA was conducted to investigate the gut microbiome profiles of H. taichui-infected participants compared with those of parasite-free participants. Prevotella copri was the dominant bacterial operational taxonomic unit (OTU) in the study population. The relative abundance of three bacterial taxa, Ruminococcus, Roseburia faecis and Veillonella parvula, was significantly increased in the H. taichui-infected group. Parasite-negative group had higher bacterial diversity (α diversity) than the H. taichui-positive group. In addition, a significant difference in bacterial community composition (ß diversity) was found between the two groups. The results suggest that H. taichui infection impacts the gut microbiome profile by reducing bacterial diversity and altering bacterial community structure in the gastrointestinal tract.

18.
Trop Med Infect Dis ; 5(2)2020 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-32349270

RESUMO

We present an approach to assess the disease ecology of rickettsial species by investigating open databases and by using data science methodologies. First, we explored the epidemiological trend and changes of human rickettsial disease epidemics over the years and compared this trend with knowledge on emerging rickettsial diseases given by published reviews. Second, we investigated the global diversity of rickettsial species recorded in humans, domestic animals and wild mammals, using the Enhanced Infectious Disease Database (EID2) and employing a network analysis approach to represent and quantify transmission ecology of rickettsial species among their carriers, arthropod vectors or mammal reservoirs and humans. Our results confirmed previous studies that emphasized the increasing incidence in rickettsial diseases at the onset of 1970. Using the Global Infectious Diseases and Epidemiology Online Network (GIDEON) database, it was even possible to date the start of this increase of global outbreaks in rickettsial diseases in 1971. Network analysis showed the importance of domestic animals and peridomestic mammals in sharing rickettsial diseases with humans and other wild animals, acting as important hubs or connectors for rickettsial transmission.

19.
Parasitol Int ; 77: 102128, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32330535

RESUMO

The whipworm Trichuris muris is known to be associated with various rodent species in the northern hemisphere, but the species identity of whipworm infecting rodents in the Oriental region remains largely unknown. We collected Trichuris of Muridae rodents in mainland and insular Southeast Asia between 2008 and 2015 and used molecular and morphological approaches to identify the systematic position of new specimens. We discovered two new species that were clearly distinct from T. muris, both in terms of molecular phylogenetic clustering and morphological features, with one species found in Thailand and another one in Borneo. We named the new species from Thailand as Trichuris cossoni and the species from Borneo as Trichuris arrizabalagai. Molecular phylogeny using internal transcribed spacer region (ITS1-5.8S-ITS2) showed a divergence between T. arrizabalagai n. sp., T. cossoni n. sp. and T. muris. Our findings of phylogeographically distinct Trichuris species despite some globally distributed host species requires further research into the distribution of different species, previously assumed to belong to T. muris, which has particular relevance for using these species as laboratory model organisms.

20.
Glob Ecol Biogeogr ; 29(3): 470-481, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32336945

RESUMO

Aim: Emerging infectious diseases arising from pathogen spillover from mammals to humans constitute a substantial health threat. Tracing virus origin and predicting the most likely host species for future spillover events are major objectives in One Health disciplines.We assessed patterns of virus sharing among a large diversity of mammals, including humans and domestic species. Location: Global. Time period: Current. Major taxa studied: Mammals and associated viruses. Methods: We used network centrality analysis and trait-based Bayesian hierarchical models to explore patterns of virus sharing among mammals. We analysed a global database that compiled the associations between 1,785 virus species and 725 mammalian host species as sourced from automatic screening of meta-data accompanying published nucleotide sequences between 1950 and 2019. Results: We show that based on current evidence, domesticated mammals hold the most central positions in networks of known mammal-virus associations. Among entire host-virus networks, Carnivora and Chiroptera hold central positions for mainly sharing RNA viruses, whereas ungulates hold central positions for sharing both RNA and DNA viruses with other host species. We revealed strong evidence that DNA viruses were phylogenetically more host specific than RNA viruses. RNA viruses exhibited low functional host specificity despite an overall tendency to infect phylogenetically related species, signifying high potential to shift across hosts with different ecological niches. The frequencies of sharing viruses among hosts and the proportion of zoonotic viruses in hosts were larger for RNA than for DNA viruses. Main conclusions: Acknowledging the role of domestic species in addition to host and virus traits in patterns of virus sharing is necessary to improve our understanding of virus spread and spillover in times of global change. Understanding multi-host virus-sharing pathways adds focus to curtail disease spread.

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