Wastewater sequencing as a powerful tool to reveal SARS-CoV-2 variant introduction and spread in French Guiana, South America.

The origin of introduction of a new pathogen in a country, the evolutionary dynamics of an epidemic within a country, and the role of cross-border areas on pathogen dynamics remain complex to disentangle and are often poorly understood. For instance, cross-border areas represent the ideal location for the sharing of viral variants between countries, with international air travel, land travel and waterways playing an important role in the cross-border spread of infectious diseases. Unfortunately, monitoring the point of entry and the evolutionary dynamics of viruses in space and time within local populations remain challenging. Here we tested the efficiency of wastewater-based epidemiology and genotyping in monitoring Covid-19 epidemiology and SARS-CoV-2 variant dynamics in French Guiana, a tropical country located in South America. Our results suggest that wastewater-based epidemiology and genotyping are powerful tools to monitor variant introduction and disease evolution within a tropical country but the inclusion of both clinical and wastewater samples could still improve our understanding of genetic diversity co-circulating. Wastewater sequencing also revealed the cryptic transmission of SARS-CoV-2 variants within the country. Interestingly, we found some amino acid changes specific to the variants co-circulating in French Guiana, suggesting a local evolution of the SARS-CoV-2 variants after their introduction. More importantly, our results showed that the proximity to bordering countries was not the origin of the emergence of the French Guianese B.1.160.25 variant, but rather that this variant emerged from an ancestor B.1.160 variant introduced by European air plane travelers, suggesting thus that air travel remains a significant risk for cross-border spread of infectious diseases. Overall, we suggest that wastewater-based epidemiology and genotyping provides a cost effective and non-invasive approach for pathogen monitoring and an early-warning tool for disease emergence and spread within a tropical country.

What about Current Diversity of Mycolactone-Producing Mycobacteria? Implication for the Diagnosis and Treatment of Buruli Ulcer.

The identification of an emerging pathogen in humans can remain difficult by conventional methods such as enrichment culture assays that remain highly selective, require appropriate medium and cannot avoid misidentifications, or serological tests that use surrogate antigens and are often hampered by the level of detectable antibodies. Although not originally designed for this purpose, the implementation of polymerase-chain-reaction (PCR) has resulted in an increasing number of diagnostic tests for many diseases. However, the design of specific molecular assays relies on the availability and reliability of published genetic sequences for the target pathogens as well as enough knowledge on the genetic diversity of species and/or variants giving rise to the same disease symptoms. Usually designed for clinical isolates, molecular tests are often not suitable for environmental samples in which the target DNA is mixed with a mixture of environmental DNA. A key challenge of such molecular assays is thus to ensure high specificity of the target genetic markers when focusing on clinical and environmental samples in order to follow the dynamics of disease transmission and emergence in humans. Here we focus on the Buruli ulcer (BU), a human necrotizing skin disease mainly affecting tropical and subtropical areas, commonly admitted to be caused by Mycobacterium ulcerans worldwide although other mycolactone-producing mycobacteria and even mycobacterium species were found associated with BU or BU-like cases. By revisiting the literature, we show that many studies have used non-specific molecular markers (IS2404, IS2606, KR-B) to identify M. ulcerans from clinical and environmental samples and propose that all mycolactone-producing mycobacteria should be definitively considered as variants from the same group rather than different species. Importantly, we provide evidence that the diversity of mycolactone-producing mycobacteria variants as well as mycobacterium species potentially involved in BU or BU-like skin ulcerations might have been underestimated. We also suggest that the specific variants/species involved in each BU or BU-like case should be carefully identified during the diagnosis phase, either via the key to genetic identification proposed here or by broader metabarcoding approaches, in order to guide the medical community in the choice for the most appropriate antibiotic therapy.

Emergence of the Fungal Rosette Agent in the World: Current Risk to Fish Biodiversity and Aquaculture.

The emergence of pathogenic fungi is a major and rapidly growing problem (7% increase) that affects human and animal health, ecosystems, food security, and the economy worldwide. The Dermocystida group in particular has emerged relatively recently and includes species that affect both humans and animals. Within this group, one species in particular, Sphareothecum destruens, also known as the rosette agent, represents a major risk to global aquatic biodiversity and aquaculture, and has caused severe declines in wild fish populations in Europe and large losses in salmon farms in the USA. It is a species that has been associated with a healthy carrier for millions of years, but in recent decades, the host has managed to invade parts of Southeast Asia, Central Asia, Europe, and North Africa. In order to better understand the emergence of this new disease, for the first time, we have synthesized current knowledge on the distribution, detection, and prevalence of S. destruens, as well as the associated mortality curves, and the potential economic impact in countries where the healthy carrier has been introduced. Finally, we propose solutions and perspectives to manage and mitigate the emergence of this fungus in countries where it has been introduced.

Impact of Global Warming on the Severity of Viral Diseases: A Potentially Alarming Threat to Sustainable Aquaculture Worldwide.

With an ever-increasing human population, food security remains a central issue for the coming years. The magnitude of the environmental impacts of food production has motivated the assessment of the environmental and health benefits of shifting diets, from meat to fish and seafood. One of the main concerns for the sustainable development of aquaculture is the emergence and spread of infectious animal diseases in a warming climate. We conducted a meta-analysis to investigate the influence of global warming on mortality due to viral infections in farmed aquatic animals. We found a positive trend between increasing temperature and increasing viral virulence, with an increase in water temperature of 1 °C resulting in an increase in mortality of 1.47-8.33% in OsHV-1 infected oysters, 2.55-6.98% in carps infected with CyHV-3 and 2.18-5.37% in fishes infected with NVVs. We suggest that global warming is going to pose a risk of viral disease outbreaks in aquaculture and could compromise global food security.

Human-Altered Landscapes and Climate to Predict Human Infectious Disease Hotspots.

BACKGROUND: Zoonotic diseases account for more than 70% of emerging infectious diseases (EIDs). Due to their increasing incidence and impact on global health and the economy, the emergence of zoonoses is a major public health challenge. Here, we use a biogeographic approach to predict future hotspots and determine the factors influencing disease emergence. We have focused on the following three viral disease groups of concern: Filoviridae, Coronaviridae, and Henipaviruses. METHODS: We modelled presence-absence data in spatially explicit binomial and zero-inflation binomial logistic regressions with and without autoregression. Presence data were extracted from published studies for the three EID groups. Various environmental and demographical rasters were used to explain the distribution of the EIDs. True Skill Statistic and deviance parameters were used to compare the accuracy of the different models. RESULTS: For each group of viruses, we were able to identify and map areas at high risk of disease emergence based on the spatial distribution of the disease reservoirs and hosts of the three viral groups. Common influencing factors of disease emergence were climatic covariates (minimum temperature and rainfall) and human-induced land modifications. CONCLUSIONS: Using topographical, climatic, and previous disease outbreak reports, we can identify and predict future high-risk areas for disease emergence and their specific underlying human and environmental drivers. We suggest that such a predictive approach to EIDs should be carefully considered in the development of active surveillance systems for pathogen emergence and epidemics at local and global scales.

Biological invasion costs reveal insufficient proactive management worldwide.

The global increase in biological invasions is placing growing pressure on the management of ecological and economic systems. However, the effectiveness of current management expenditure is difficult to assess due to a lack of standardised measurement across spatial, taxonomic and temporal scales. Furthermore, there is no quantification of the spending difference between pre-invasion (e.g. prevention) and post-invasion (e.g. control) stages, although preventative measures are considered to be the most cost-effective. Here, we use a comprehensive database of invasive alien species economic costs (InvaCost) to synthesise and model the global management costs of biological invasions, in order to provide a better understanding of the stage at which these expenditures occur. Since 1960, reported management expenditures have totalled at least US$95.3 billion (in 2017 values), considering only highly reliable and actually observed costs - 12-times less than damage costs from invasions ($1130.6 billion). Pre-invasion management spending ($2.8 billion) was over 25-times lower than post-invasion expenditure ($72.7 billion). Management costs were heavily geographically skewed towards North America (54%) and Oceania (30%). The largest shares of expenditures were directed towards invasive alien invertebrates in terrestrial environments. Spending on invasive alien species management has grown by two orders of magnitude since 1960, reaching an estimated $4.2 billion per year globally (in 2017 values) in the 2010s, but remains 1-2 orders of magnitude lower than damages. National management spending increased with incurred damage costs, with management actions delayed on average by 11 years globally following damage reporting. These management delays on the global level have caused an additional invasion cost of approximately $1.2 trillion, compared to scenarios with immediate management. Our results indicate insufficient management - particularly pre-invasion - and urge better investment to prevent future invasions and to control established alien species. Recommendations to improve reported management cost comprehensiveness, resolution and terminology are also made.

ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants.

MOTIVATION: Amplicon-based nanopore sequencing is increasingly used for molecular surveillance during epidemics (e.g. ZIKA, EBOLA) or pandemics (e.g. SARS-CoV-2). However, there is still a lack of versatile and easy-to-use tools that allow users with minimal bioinformatics skills to perform the main steps of downstream analysis, from quality testing to SNPs effect to phylogenetic analysis. RESULTS: Here, we present ONTdeCIPHER, an amplicon-based Oxford Nanopore Technology sequencing pipeline to analyze the genetic diversity of SARS-CoV-2 and other pathogens. Our pipeline integrates 13 bioinformatics tools. With a single command line and a simple configuration file, users can pre-process their data and obtain the sequencing statistics, reconstruct the consensus genome, identify variants and their effects for each viral isolate, infer lineage and, finally perform multi-sequence alignments and phylogenetic analyses. AVAILABILITY AND IMPLEMENTATION: ONTdeCIPHER is available at https://github.com/emiracherif/ONTdeCIPHER. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Identifying economic costs and knowledge gaps of invasive aquatic crustaceans.

Despite voluminous literature identifying the impacts of invasive species, summaries of monetary costs for some taxonomic groups remain limited. Invasive alien crustaceans often have profound impacts on recipient ecosystems, but there may be great unknowns related to their economic costs. Using the InvaCost database, we quantify and analyse reported costs associated with invasive crustaceans globally across taxonomic, spatial, and temporal descriptors. Specifically, we quantify the costs of prominent aquatic crustaceans - crayfish, crabs, amphipods, and lobsters. Between 2000 and 2020, crayfish caused US$ 120.5 million in reported costs; the vast majority (99%) being attributed to representatives of Astacidae and Cambaridae. Crayfish-related costs were unevenly distributed across countries, with a strong bias towards European economies (US$ 116.4 million; mainly due to the signal crayfish in Sweden), followed by costs reported from North America and Asia. The costs were also largely predicted or extrapolated, and thus not based on empirical observations. Despite these limitations, the costs of invasive crayfish have increased considerably over the past two decades, averaging US$ 5.7 million per year. Invasive crabs have caused costs of US$ 150.2 million since 1960 and the ratios were again uneven (57% in North America and 42% in Europe). Damage-related costs dominated for both crayfish (80%) and crabs (99%), with management costs lacking or even more under-reported. Reported costs for invasive amphipods (US$ 178.8 thousand) and lobsters (US$ 44.6 thousand) were considerably lower, suggesting a lack of effort in reporting costs for these groups or effects that are largely non-monetised. Despite the well-known damage caused by invasive crustaceans, we identify data limitations that prevent a full accounting of the economic costs of these invasive groups, while highlighting the increasing costs at several scales based on the available literature. Further cost reports are needed to better assess the true magnitude of monetary costs caused by invasive aquatic crustaceans.

Towards unravelling the Rosette agent enigma: Spread and emergence of the co-invasive host-pathogen complex, Pseudorasbora parva-Sphaerothecum destruens.

The emergence of non-native fungal pathogens is a growing threat to global health, biodiversity, conservation biology, food security and the global economy. Moreover, a thorough understanding of the spread and emergence of pathogens among invasive and native host populations, as well as genetic analysis of the structure of co-invasive host populations, is crucial in terms of conservation biology and management strategies. Here we combined extensive catchment sampling, molecular detection tools and genomic signatures to i) assess the prevalence of the rosette agent Sphaerothecum destruens in invasive and native fish populations in contrasting french regions, and ii) characterize the genetic diversity and population structure of its co-invasive and asymptomatic carrier Pseudorasbora parva. Although S. destruens was not detected in all the fish collected its presence in contrasting freshwater ecosystems suggests that the disease may already be widespread in France. Furthermore, our results show that the detection of S. destruens DNA in its asymptomatic carrier P. parva is still limited. Finally, we found that P. parva populations show a homogeneous genetic and geographical structuring, which raises the possibility of the occurrence of successive introduction events in France from their native and invasive range.

Knowledge gaps in economic costs of invasive alien fish worldwide.

Invasive alien fishes have had pernicious ecological and economic impacts on both aquatic ecosystems and human societies. However, a comprehensive and collective assessment of their monetary costs is still lacking. In this study, we collected and reviewed reported data on the economic impacts of invasive alien fishes using InvaCost, the most comprehensive global database of invasion costs. We analysed how total (i.e. both observed and potential/predicted) and observed (i.e. empirically incurred only) costs of fish invasions are distributed geographically and temporally and assessed which socioeconomic sectors are most affected. Fish invasions have potentially caused the economic loss of at least US$37.08 billion (US2017 value) globally, from just 27 reported species. North America reported the highest costs (>85% of the total economic loss), followed by Europe, Oceania and Asia, with no costs yet reported from Africa or South America. Only 6.6% of the total reported costs were from invasive alien marine fish. The costs that were observed amounted to US$2.28 billion (6.1% of total costs), indicating that the costs of damage caused by invasive alien fishes are often extrapolated and/or difficult to quantify. Most of the observed costs were related to damage and resource losses (89%). Observed costs mainly affected public and social welfare (63%), with the remainder borne by fisheries, authorities and stakeholders through management actions, environmental, and mixed sectors. Total costs related to fish invasions have increased significantly over time, from

Spatial variations in Leishmaniasis: A biogeographic approach to mapping the distribution of Leishmania species.

Cutaneous Leishmaniasis (CL) is the most prevalent form of Leishmaniasis and is widely endemic in the Americas. Several species of Leishmania are responsible for CL, a severely neglected tropical disease and the treatment of CL vary according to the different species of Leishmania. We proposed to map the distribution of the Leishmania species reported in French Guiana (FG) using a biogeographic approach based on environmental predictors. We also measured species endemism i.e., the uniqueness of species to a defined geographic location. Our results show that the distribution patterns varied between Leishmania spp. and were spatially dependent on climatic covariates. The species distribution modelling of the eco-epidemiological spatial patterns of Leishmania spp. is the first to measure endemism based on bioclimatic factors in FG. The study also emphasizes the impact of tree cover loss and climate on the increasing distribution of L. (Viannia) braziliensis in the most anthropized regions. Detection of high-risk regions for the different between Leishmania spp. is essential for monitoring and active surveillance of the vector. As climate plays a major role in the spatial distribution of the vector and reservoir and the survival of the pathogen, climatic covariates should be included in the analysis and mapping of vector-borne diseases. This study underscores the significance of local land management and the urgency of considering the impact of climate change in the development of vector-borne disease management strategies at the global scale.

High and rising economic costs of biological invasions worldwide.

Biological invasions are responsible for substantial biodiversity declines as well as high economic losses to society and monetary expenditures associated with the management of these invasions1,2. The InvaCost database has enabled the generation of a reliable, comprehensive, standardized and easily updatable synthesis of the monetary costs of biological invasions worldwide3. Here we found that the total reported costs of invasions reached a minimum of US$1.288 trillion (2017 US dollars) over the past few decades (1970-2017), with an annual mean cost of US$26.8 billion. Moreover, we estimate that the annual mean cost could reach US$162.7 billion in 2017. These costs remain strongly underestimated and do not show any sign of slowing down, exhibiting a consistent threefold increase per decade. We show that the documented costs are widely distributed and have strong gaps at regional and taxonomic scales, with damage costs being an order of magnitude higher than management expenditures. Research approaches that document the costs of biological invasions need to be further improved. Nonetheless, our findings call for the implementation of consistent management actions and international policy agreements that aim to reduce the burden of invasive alien species.

Global economic costs of aquatic invasive alien species.

Much research effort has been invested in understanding ecological impacts of invasive alien species (IAS) across ecosystems and taxonomic groups, but empirical studies about economic effects lack synthesis. Using a comprehensive global database, we determine patterns and trends in economic costs of aquatic IAS by examining: (i) the distribution of these costs across taxa, geographic regions and cost types; (ii) the temporal dynamics of global costs; and (iii) knowledge gaps, especially compared to terrestrial IAS. Based on the costs recorded from the existing literature, the global cost of aquatic IAS conservatively summed to US$345 billion, with the majority attributed to invertebrates (62%), followed by vertebrates (28%), then plants (6%). The largest costs were reported in North America (48%) and Asia (13%), and were principally a result of resource damages (74%); only 6% of recorded costs were from management. The magnitude and number of reported costs were highest in the United States of America and for semi-aquatic taxa. Many countries and known aquatic alien species had no reported costs, especially in Africa and Asia. Accordingly, a network analysis revealed limited connectivity among countries, indicating disparate cost reporting. Aquatic IAS costs have increased in recent decades by several orders of magnitude, reaching at least US$23 billion in 2020. Costs are likely considerably underrepresented compared to terrestrial IAS; only 5% of reported costs were from aquatic species, despite 26% of known invaders being aquatic. Additionally, only 1% of aquatic invasion costs were from marine species. Costs of aquatic IAS are thus substantial, but likely underreported. Costs have increased over time and are expected to continue rising with future invasions. We urge increased and improved cost reporting by managers, practitioners and researchers to reduce knowledge gaps. Few costs are proactive investments; increased management spending is urgently needed to prevent and limit current and future aquatic IAS damages.

Native drivers of fish life history traits are lost during the invasion process.

Rapid adaptation to global change can counter vulnerability of species to population declines and extinction. Theoretically, under such circumstances both genetic variation and phenotypic plasticity can maintain population fitness, but empirical support for this is currently limited. Here, we aim to characterize the role of environmental and genetic diversity, and their prior evolutionary history (via haplogroup profiles) in shaping patterns of life history traits during biological invasion. Data were derived from both genetic and life history traits including a morphological analysis of 29 native and invasive populations of topmouth gudgeon Pseudorasbora parva coupled with climatic variables from each location. General additive models were constructed to explain distribution of somatic growth rate (SGR) data across native and invasive ranges, with model selection performed using Akaike's information criteria. Genetic and environmental drivers that structured the life history of populations in their native range were less influential in their invasive populations. For some vertebrates at least, fitness-related trait shifts do not seem to be dependent on the level of genetic diversity or haplogroup makeup of the initial introduced propagule, nor of the availability of local environmental conditions being similar to those experienced in their native range. As long as local conditions are not beyond the species physiological threshold, its local establishment and invasive potential are likely to be determined by local drivers, such as density-dependent effects linked to resource availability or to local biotic resistance.

Aquaculture at the crossroads of global warming and antimicrobial resistance.

In many developing countries, aquaculture is key to ensuring food security for millions of people. It is thus important to measure the full implications of environmental changes on the sustainability of aquaculture. We conduct a double meta-analysis (460 articles) to explore how global warming and antimicrobial resistance (AMR) impact aquaculture. We calculate a Multi-Antibiotic Resistance index (MAR) of aquaculture-related bacteria (11,274 isolates) for 40 countries, of which mostly low- and middle-income countries present high AMR levels. Here we show that aquaculture MAR indices correlate with MAR indices from human clinical bacteria, temperature and countries' climate vulnerability. We also find that infected aquatic animals present higher mortalities at warmer temperatures. Countries most vulnerable to climate change will probably face the highest AMR risks, impacting human health beyond the aquaculture sector, highlighting the need for urgent action. Sustainable solutions to minimise antibiotic use and increase system resilience are therefore needed.

Patterns of fish communities and water quality in impounded lakes of China's south-to-north water diversion project.

Understanding the ecological impacts of large-scale hydraulic projects is critical for maintaining ecosystem health while meeting human water needs. It is, however, currently hindered by a lack of direct evidence on ecological impacts associated with this type of project particularly on water quality and fish communities. Here, we characterized patterns and variations of fish communities and water quality in five impounded lakes of the Chinese South-to-North Water Diversion Project (SNWDP), with the aim of better understanding potential ecological impacts of inter-basin water transfers. We found that 1) the impacts of water transfer on water quality in the impounded lakes was generally characterized by hydrological parameters (e.g. total suspended solids, turbidity, transparency, chlorophyll a, dissolved oxygen, conductivity and total hardness) in an upstream-downstream direction; 2) increased hydrological connectivity may have favored biological invasion (e.g. Tridentiger bifasciatus) and promoted a potential biotic homogenization among the impounded lakes; and 3) there was a pattern of decreased fish abundance and biomass from the upstream to downstream lakes with fish communities strongly driven by changing water quality patterns across the impounded lakes. These findings improve our understanding of ecological impacts of large-scale hydraulic projects and provide a significant basis for water agencies with similar water transfer systems to optimize their water transfer management in order to minimize ecological impacts.

Overlapping niches between two co-occurring invasive fish: the topmouth gudgeon Pseudorasbora parva and the common bleak Alburnus alburnus.

Invasive fish species impact aquatic ecosystems and modify native communities, often leading to a decline in local species. These ecological impacts include the transmission of pathogens, predation, competition as well as hybridization. Two invasive fish species, the common bleak Alburnus alburnus and the topmouth gudgeon Pseudorabora parva, have both been recently found co-occurring in several regions of southern Europe, such as the Italian Arno River. Nonetheless, the trophic relationships among invasive fish species, especially cyprinids, remain poorly understood, and no studies have reported the trophic interaction between these two species. This study compared length-weight relationship and used stomach content and stable isotope analysis of two co-occurring populations in the Arno River to characterize the growth and overlap of potential trophic niches. It also found similar allometric growth in both species, a wider generalist trophic niche for P. parva and a more specialized niche for A. alburnus. A considerable niche overlap was found, suggesting that feeding competition can occur if resources were to be limited. Moreover, the niche of P. parva was more likely to overlap with that of A. alburnus than vice versa, suggesting that P. parva can be considered as a potential over competitor. Nonetheless, the authors found in the overlapping populations no evidence of realized competition, probably avoided through a combination of fine-scale mechanisms. They also highlighted that these two invasive species can co-exist and share resources, at least in an open ecosystem like a river, thus potentially doubling up their trophic impact on local communities.

Genomic footprints of a biological invasion: Introduction from Asia and dispersal in Europe of the topmouth gudgeon (Pseudorasbora parva).

Facilitated by the intensification of global trading, the introduction and dispersal of species to areas in which they are historically non-native is nowadays common. From an evolutionary standpoint, invasions are paradoxical: not only non-native environments could be different from native ones for which introduced individuals would be ill-adapted, but also small founding population size should be associated with reduced adaptive potential. As such, biological invasions are considered valuable real-time evolutionary experiments. Here, we investigated the population structure and adaptive potential of the highly invasive topmouth gudgeon (Pseudorasbora parva) across Europe and East Asia. We RAD-sequenced 301 specimens from sixteen populations and three distinct within-catchment invaded regions as well as two locations in the native range. With 13,785 single nucleotide polymorphisms, we provide conclusive evidence for a genome-wide signature of two distinct invasion events, in Slovakia and Turkey, each originating from a specific area in the native range. A third invaded area, in France, appears to be the result of dispersal within the invasive range. Few loci showed signs of selection, the vast majority of which being identified in the Slovakian region. Functional annotation suggests that faster early stage development, resistance to pollution and immunocompetence contribute to the invasion success of the local habitats. By showing that populations in the invasive range have different evolutionary histories, our study reinforces the idea that populations, rather than species, are the units to consider in invasion biology.