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Advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs
DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption–ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue ‘Advances and challenges in the barcoding of parasites, vectors and reservoirs’ illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.
Journal Article
Dental Shape Variation and Phylogenetic Signal in the Rattini Tribe Species of Mainland Southeast Asia
The Rattini tribe comprises some of the most specious genera in the mammalian kingdom. Many of these species are also highly morphologically conserved. As a result, identifying Rattini tribe animals, particularly those of the
Rattus
genus, to species level is extremely difficult. Problems with identification of conservative morphologies, particularly of the skeleton, have led to difficulties in understanding the fossil remains and as a result the systematics of this group. Here, we apply geometric morphometrics to the first lower molar of 14 species of the Rattini tribe. We find that the morphological data present a strong phylogenetic signal. However, within
Rattus,
this signal is rather complex and possibly hints at rapid evolutionary shape and size changes. In modern species, it is possible to identify specimens to species level with a good degree of confidence. We find that using both size and shape together affords further confidence with identification. However, we caution against the over-reliance on size in environments with unknown species composition and climate, particularly in archaeological contexts. This approach should prove to be a useful tool for identifying fossil and sub-fossil remains, particularly where biomolecular markers are absent in circumstances of poor preservation.
Journal Article
Gastrointestinal helminth fauna of rodents from Cambodia: emphasizing the community ecology of host–parasite associations
Extensive field surveys of rodents were conducted in Cambodia from 2008 to 2014 to study the diversity and ecology of helminth infection in wild rodent populations. Gastrointestinal helminths were isolated from 14 species of rodents (569 individuals) trapped from different habitats (forest, dry land, rain-fed land and human settlements) in four provinces of Cambodia (Krong Preah Sihanouk, Mondolkiri, Pursat and Steung Treng). The average prevalence of parasitic infection was 58.5% (range, 16.0–64.7%), and 19 helminth taxa were identified in total. Trichostrongylid nematodes were the most prevalent (25.8%), followed by Raillietina sp. (14.1%), Gongylonema neoplasticum (10.7%), Syphacia muris (9.8%) and Hymenolepis diminuta (9.6%). Potential rodent-borne zoonotic helminths were also identified, and the risks of helminthiasis were discussed. The status of helminth infection and species diversity in rodents from settlements were significantly lower than in rodents from forest and peri-domesticated habitats, which indicates that habitat alteration might affect helminth infection and diversity in rodent hosts. Generalized linear models revealed that host attributes (host species and maturity) and environmental factors (habitat and geographical location) were explanatory variables for helminth infection in these rodents. Using network analyses, we showed that the oriental house rat, Rattus tanezumi, was the most central host in the rodent–helminth assemblage, based on the number of helminth taxa it shared with other rodent species. Therefore, R. tanezumi could play an important role in rodent–helminth interactions and helminth transmission to other rodent hosts.
Journal Article
Distribution of the newly invasive New Guinea flatworm Platydemus manokwari (Platyhelminthes: Geoplanidae) in Thailand and its potential role as a paratenic host carrying Angiostrongylus malaysiensis larvae
Invasive species constitute one of the most serious threats to biodiversity and ecosystems, and they potentially cause economic problems and impact human health. The globally invasive New Guinea flatworm, Platydemus manokwari (Platyhelminthes: Geoplanidae), has been identified as a threat to terrestrial biodiversity, particularly soil-dwelling native species (e.g. molluscs, annelids and other land planarians), and is listed among 100 of the world's worst invasive alien species. We report here, for the first time, P. manokwari occurrences in many locations throughout Thailand, using voluntary digital public participation from the social network portals associated with the Thailand Biodiversity Conservation Group and collections of living flatworm specimens. Mitochondrial cytochrome c oxidase subunit I (COI) sequences confirmed that all collected flatworms were P. manokwari and placed them in the “world haplotype” clade alongside other previously reported specimens from France, Florida (USA), Puerto Rico, Singapore, French Polynesia, New Caledonia, and the Solomon Islands. In addition, infective stage larvae (L3) of the nematode Angiostrongylus malaysiensis were found in the flatworm specimens, with a 12.4% infection rate (15/121 specimens examined). Platydemus manokwari occurrence in Thailand and its capacity to carry L3 of Angiostrongylus should be of concern to biodiversity conservation and human health practitioners, because this invasive flatworm species may be involved in the life cycle of angiostrongylid worms in Thailand.
Journal Article
The Diversity of Parasites
Parasitism is one of the most successful modes of life displayed by living organisms, as measured by how often it evolved and how many parasitic species are presently in existence. Studying the diversity of parasites is particularly relevant because sympatric diversification may be important in some parasite taxa, and because of the opportunity for independent tests of evolutionary hypotheses in the many separate lineages in which parasitism evolved. Our incomplete knowledge of existing parasite species-the result of a range of phenomena that includes inadequate sampling effort or the lumping of different cryptic species under one name-is not always a major obstacle for the study of parasite diversity. Patterns in the diversity of parasites may be associated with either host or parasite characteristics. The distribution of parasite diversity among host taxa does not simply reflect the species diversity of the host taxa themselves; life history and ecological traits of hosts appear to play important roles. These may determine the likelihood that hosts are colonized by parasite species over evolutionary time. It is not yet clear whether some host traits also favor intrahost speciation and diversification of parasites, and the formation of new parasite species. Certain features of parasites may also be associated with speciation and diversification. Only parasite body size has received much attention; the patterns observed are not greatly different from those of free-living species, with small-bodied parasite taxa being more speciose than related large-bodied taxa. Epidemiological parameters such as the basic reproductive rate of parasites, or R0, can also generate predictions regarding the distribution or evolution of parasite diversity. For instance, parasite taxa characterized by high R0 values may be more speciose than related taxa with lower values of R0; such predictions remain untested. Large-scale biogeographical patterns of diversity have only been well studied for metazoan parasites of marine fish; for these parasites, latitudinal patterns can be explained by effects of temperature on speciation rates and epidemiological variables, though other causes are possible. The emphasis for future research must shift from pattern description to the elucidation of the processes responsible for the structure and diversity of parasite faunas. A better integration of ecological and historical (or phylogenetic) approaches to the study of parasite diversity should make this objective possible.
Journal Article
A parasite reveals cryptic phylogeographic history of its host
This study compares the continental phylogeographic patterns of two wild European species linked by a host-parasite relationship: the field mouse Apodemus sylvaticus and one of its specific parasites, the nematode Heligmosomoides polygyrus. A total of 740 base pairs (bp) of the mitochondrial cytochrome b (cyt b) gene were sequenced in 122 specimens of H. polygyrus and compared with 94 cyt b gene sequences (974 bp) previously acquired for A. sylvaticus. The results reveal partial spatial and temporal congruences in the differentiation of both species' lineages: the parasite and its host present three similar genetic and geographical lineages, i.e. Western European, Italian and Sicilian, and both species recolonized northwestern Europe from the Iberian refuge at the end of the Pleistocene. However, H. polygyrus presents three particular differentiation events. The relative rate of molecular evolution of the cyt b gene was estimated to be 1.5-fold higher in the parasite than in its host. Therefore, the use of H. polygyrus as a biological magnifying glass is discussed as this parasite may highlight previously undetected historical events of its host. The results show how incorporating phylogeographic information of an obligate associate can help to better understand the phylogeographic pattern of its host.
Journal Article
Environmental factors and public health policy associated with human and rodent infection by leptospirosis: a land cover-based study in Nan province, Thailand
Leptospirosis incidence has increased markedly since 1995 in Thailand, with the eastern and northern parts being the most affected regions, particularly during flooding events. Here, we attempt to overview the evolution of human prevalence during the past decade and identify the environmental factors that correlate with the incidence of leptospirosis and the clinical incidence in humans. We used an extensive survey of Leptospira infection in rodents conducted in 2008 and 2009 and the human incidence of the disease from 2003 to 2012 in 168 villages of two districts of Nan province in Northern Thailand. Using an ad-hoc developed land-use cover implemented in a geographical information system we showed that humans and rodents were not infected in the same environment/habitat in the land-use cover. High village prevalence was observed in open habitat near rivers for the whole decade, or in 2008–2009 mostly in rice fields prone to flooding, whereas infected rodents (2008–2009) were observed in patchy habitat with high forest cover, mostly situated on sloping ground areas. We also investigated the potential effects of public health campaigns conducted after the dramatic flood event of 2006. We showed that, before 2006, human incidence in villages was explained by the population size of the village according to the environmental source of infection of this disease, while as a result of the campaigns, human incidence in villages after 2006 appeared independent of their population size. This study confirms the role of the environment and particularly land use, in the transmission of bacteria, emphasized by the effects of the provincial public health campaigns on the epidemiological pattern of incidence, and questions the role of rodents as reservoirs.
Journal Article