Pathogens and disease vectors/hosts monitoring in aquatic environments: Potential of using eDNA/eRNA based approach

Amarasiri, Mohan; Furukawa, Takashi; Nakajima, Fumiyuki; Sei, Kazunari

doi:10.1016/j.scitotenv.2021.148810

Cited by 29 publications

(18 citation statements)

References 121 publications

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“…In addition to the sea turtle species‐specific research possible with the methodologies established in this study, it is also possible to extend these genetic analysis tools further to include the investigation and monitoring of threats to these vulnerable animals (Amarasiri et al, 2021; Diaz‐Ferguson & Moyer, 2014; Farrell, Yetsko, et al, 2021; Huver et al, 2015; Miaud et al, 2019; Sengupta et al, 2019). Given that eDNA extraction recovered DNA from all organisms/pathogens present (shed DNA or microbes themselves) there is significant potential to simultaneously monitor wildlife and their pathogens from the same eDNA sample (Alfaro‐Nunez et al, 2014; Amarasiri et al, 2021; Duffy & Martindale, 2019; Duffy et al, 2018; Farrell, Whitmore, et al, 2021; Patricio et al, 2012). Indeed, some of the rehabilitation water and sand eDNA samples utilized for sea turtle detection in the present study, were also simultaneously utilized to quantify a viral pathogen of sea turtles (Farrell, Whitmore, et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…Sand eDNA also benefits from being more straightforward than conventional invasive sampling approaches, enabling samples to be collected by networks of citizen-scientists/nesting patrol members, as utilized for this study. In addition to the sea turtle species-specific research possible with the methodologies established in this study, it is also possible to extend these genetic analysis tools further to include the investigation and monitoring of threats to these vulnerable animals (Amarasiri et al, 2021;Diaz-Ferguson & Moyer, 2014;Farrell, Yetsko, et al, 2021;Huver et al, 2015;Miaud et al, 2019;Sengupta et al, 2019) Duffy et al, 2018;Farrell, Whitmore, et al, 2021;Patricio et al, 2012). Indeed, some of the rehabilitation water and sand eDNA samples utilized for sea turtle detection in the present study, were also simultaneously utilized to quantify a viral pathogen of sea turtles (Farrell, Whitmore, et al, 2021).…”

Section: Edna Approaches To Sea Turtle Population Geneticsmentioning

confidence: 98%

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Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water

Farrell

Whitmore

Mashkour

et al. 2022

Molecular Ecology Resources

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Elusive aquatic wildlife, such as endangered sea turtles, are difficult to monitor and conserve. As novel molecular and genetic technologies develop, it is possible to adapt and optimize them for wildlife conservation. One such technology is environmental (e)DNA -the detection of DNA shed from organisms into their surrounding environments. We developed species-specific green (Chelonia mydas) and loggerhead (Caretta caretta) sea turtle probe-based qPCR assays, which can detect and quantify sea turtle eDNA in controlled (captive tank water and sand samples) and free ranging (oceanic water samples and nesting beach sand) settings. eDNA detection complemented traditional in-water sea turtle monitoring by enabling detection even when turtles were not visually observed. Furthermore, we report that high throughput shotgun sequencing of eDNA sand samples enabled sea turtle population genetic studies and pathogen monitoring, demonstrating that noninvasive eDNA techniques are viable and efficient

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Section: Discussionmentioning

confidence: 99%

Section: Edna Approaches To Sea Turtle Population Geneticsmentioning

confidence: 98%

Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water

Farrell

Whitmore

Mashkour

et al. 2022

Molecular Ecology Resources

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“…Although the direct detection of leptospires in the urine and/or kidneys of animals is the easiest approach to identifying reservoirs, it is sometimes difficult from a practical point of view in wild environments such as that in Yaeyama. Recently, the potential of using an eDNA/eRNA-based approach has been proposed as a powerful method for monitoring disease vectors/hosts in aquatic environments and understanding the spread of infectious diseases to evaluate human health risks in a given area [ 62 ]. This study applied a previously developed eDNA metabarcoding method to analyse the Leptospira –animals correlation and identify potential reservoir animals [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of human clinical and environmental Leptospira to elucidate the eco-epidemiology of leptospirosis in Yaeyama, subtropical Japan

et al. 2022

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Background Leptospirosis, a zoonosis caused by species in the spirochete genus Leptospira, is endemic to the Yaeyama region in Okinawa, subtropical Japan. Species of the P1 subclade “virulent” group, within the genus Leptospira, are the main etiological agents of leptospirosis in Okinawa. However, their environmental persistence is poorly understood. This study used a combination of bacterial isolation and environmental DNA (eDNA) metabarcoding methods to understand the eco-epidemiology of leptospirosis in this endemic region. Findings Polymerase chain reaction (PCR) characterized twelve human clinical L. interrogans isolates belonging to the P1 subclade “virulent” subgroup and 11 environmental soil isolates of the P1subclade “low virulent” subgroup (genetically related to L. kmetyi, n = 1; L. alstonii, n = 4; L. barantonii, n = 6) from the Yaeyama region targeting four virulence-related genes (lipL32, ligA, ligB and lpxD1). Clinical isolates were PCR positive for at least three targeted genes, while all environmental isolates were positive only for lipL32. Analysis of infected renal epithelial cells with selected clinical and environmental strains, revealed the disassembly of cell-cell junctions for the Hebdomadis clinical strain serogroup. Comparison of leptospiral eDNA during winter and summer identified operational taxonomic units corresponding to the species isolated from soil samples (L. kmetyi and L. barantonii) and additional P2 subclade species (L. licerasiae, L. wolffii-related, among others) that were not detected by soil cultivation. Total Leptospira read counts were higher in summer than in winter and the analysis of leptospiral/animal eDNA relationship suggested Rattus spp. as a potential reservoir animal. Conclusion Our study demonstrated high environmental Leptospira diversity in the Yaeyama region, particularly during summer, when most of the leptospirosis cases are reported. In addition, several Leptospira species with pathogenic potential were identified that have not yet been reported in Yaeyama; however, the environmental persistence of P1 subclade species previously isolated from human clinical cases in this region was absent, suggesting the need of further methodology development and surveillance.

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“…Whereas analysis of feces is usually not practical for aquatic parasites, the water itself provides a useful medium for detecting parasites simply through filtration. Hence, surveillance in aquatic systems has been deployed for detection of several human and wildlife pathogens, including parasites (Berger & Aubin-Horth 2018; Sieber et al 2020; Amarasiri et al 2021). Notably, such have been developed for detecting common water-born human parasites, such as Cryptosporidium spp.…”

Section: Introductionmentioning

confidence: 99%

Multi-state occupancy model estimates probability of detection of an aquatic parasite using environmental DNA: Pseudoloma neurophilia in zebrafish aquaria

Schuster¹,

Kent

Peterson

et al. 2022

Preprint

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Detecting the presence of important parasites within a host and its environment is critical to understanding the dynamics that influence a pathogens ability to persist, while accurate detection is also essential for implementation of effective control strategies. Pseudoloma neurophilia is the most common pathogen reported in zebrafish (Danio rerio) research facilities. The only assays currently available for P. neurophilia, are through lethal sampling, often requiring euthanasia of the entire population for accurate estimates of prevalence in small populations. We present a non-lethal screening method to detect Pseudoloma neurophilia in tank water based on detection of environmental DNA (eDNA) from this microsporidum, using a previously developed qPCR assay that was adapted to the digital PCR (dPCR) platform. Using the generated dPCR data, a multi-state occupancy model was also implemented to predict the probability of detection in tank water under different flow regimes and pathogen prevalence. The occupancy model revealed that samples collected in static conditions were more informative than samples collected from flow-through conditions, with a probability of detection at 80% and 47%, respectively. There was also a positive correlation with the prevalence of infection in water and prevalence in fish based on qPCR.

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Pathogens and disease vectors/hosts monitoring in aquatic environments: Potential of using eDNA/eRNA based approach

Cited by 29 publications

References 121 publications

Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water

Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water

Analysis of human clinical and environmental Leptospira to elucidate the eco-epidemiology of leptospirosis in Yaeyama, subtropical Japan

Multi-state occupancy model estimates probability of detection of an aquatic parasite using environmental DNA: Pseudoloma neurophilia in zebrafish aquaria

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