High-Throughput Sequencing for Understanding the Ecology of Emerging Infectious Diseases at the Wildlife-Human Interface

Abstract

Rising rates of emerging infectious diseases (EIDs) demand creative, efficient, and integrative investigations to understand their transmission, ecological contingencies, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies provide enormous potential to unravel these contingencies to improve our understanding, but their potential is only just starting to be realized. While recent work has largely focused on novel pathogen discovery at likely interfaces, high-throughput methods can also allow disease ecologists to better explore the critical effects of climate, seasonality, and land-use changes on EIDs. HTS can facilitate the creation of entire host-pathogen networks, integrate important microbiome and co-infection data, and even pinpoint important exposure routes at interfaces through environmental media. Here we highlight studies at the frontier of HTS and disease ecology research, identify current limitations, and outline promising future applications for EIDs.

Can we manage fisheries with the inherent uncertainty from eDNA?

“…Such is the case for eDNA detection of species of conservation concern such as chinook salmon ( Oncorhynchus tshawytscha (Walbaum 1892) (Laramie et al ., 2015), largetooth sawfish Pristis pristis (L. 1758) (Simpfendorfer et al ., 2016), green sturgeon Acipenser medirostris Ayres 1854 (Bergman et al ., 2016), European weather loach Misgurnus fossilis (L. 1758) (Brys et al ., 2021) and spotted gar Lepisosteus oculatus Winchell 1864 (Boothroyd et al ., 2016). More broadly applicable to fisheries management, there are many applications for eDNA related to delimiting species distributions (Dorazio & Erickson, 2018) for the purposes of testing ecological theory (Yoccoz, 2012), monitoring biodiversity trends (Lodge et al ., 2012), connecting interactions between wildlife and emerging infectious diseases (Titcomb et al ., 2019) and pathogens (Mahon et al ., 2018), across diverse taxa (Rees et al ., 2014) and in aquatic and terrestrial environments (Epp et al ., 2012). The broader research agenda of eDNA will move forward irrespective of fisheries management use and there are numerous avenues for improved fisheries management that do not require a fish in hand.…”

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

“…As an alternative, a targeted amplicon-based high-throughput sequencing, known as metabarcoding, has become an essential tool for monitoring biodiversity [ 19 , 20 ] and also increasingly used for understanding parasite diversity in host tissues and environmental samples [e.g. 21 , 22 ]. Community metabarcoding is a sensitive technique that allows detection of rare and cryptic species and species associations [ 23 , 24 ] as well as analyses of within species genetic variability and population structuring [ 25 ].…”

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

“…This means that by using untargeted sequencing of the host transcriptome it is rarely possible to obtain enough power for pathogen community composition analyses. As an alternative to sequencing of whole transcriptomes and genomes, a targeted amplicon-based high-throughput sequencing, known as metabarcoding, has become essential tool for monitoring biodiversity [19,20] and also increasingly used for understandingparasite diversity in host tissues and environmental samples [e.g., 21,22]. Community metabarcoding is a sensitive technique that allows detection of rare and cryptic species and species associations [23,24] as well as analyses of within species genetic variability and population structuring [25].…”