Realising a global One Health disease surveillance approach: insights from wastewater and beyond.

One Health is a recognition of the shared environment inhabited by humans, animals and plants, and the impact of their interactions on the health of all organisms. The COVID-19 pandemic highlighted the need for a framework of pathogen surveillance in a tractable One Health paradigm to allow timely detection and response to threats to human and animal health. We present case studies centered around the recent global approach to tackle antimicrobial resistance and the current interest in wastewater testing, with the concept of "one sample many analyses" to be further explored as the most appropriate means of initiating this endeavor.

Drivers of arthropod biodiversity in an urban ecosystem.

Our world is becoming increasingly urbanized with a growing human population concentrated around cities. The expansion of urban areas has important consequences for biodiversity, yet the abiotic drivers of biodiversity in urban ecosystems have not been well characterized for the most diverse group of animals on the planet, arthropods. Given their great diversity, comparatively small home ranges, and ability to disperse, arthropods make an excellent model for studying which factors can most accurately predict urban biodiversity. We assessed the effects of (i) topography (distance to natural areas and to ocean) (ii) abiotic factors (mean annual temperature and diurnal range), and (iii) anthropogenic drivers (land value and amount of impervious surface) on the occurrence of six arthropod groups represented in Malaise trap collections run by the BioSCAN project across the Greater Los Angeles Area. We found striking heterogeneity in responses to all factors both within and between taxonomic groups. Diurnal temperature range had a consistently negative effect on occupancy but this effect was only significant in Phoridae. Anthropogenic drivers had mixed though mostly insignificant effects, as some groups and species were most diverse in highly urbanized areas, while other groups showed suppressed diversity. Only Phoridae was significantly affected by land value, where most species were more likely to occur in areas with lower land value. Los Angeles can support high regional arthropod diversity, but spatial community composition is highly dependent on the taxonomic group.

The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps.

Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.

Metabarcoding of Hepatitis E Virus Genotype 3 and Norovirus GII from Wastewater Samples in England Using Nanopore Sequencing.

Norovirus is one of the largest causes of gastroenteritis worldwide, and Hepatitis E virus (HEV) is an emerging pathogen that has become the most dominant cause of acute viral hepatitis in recent years. The presence of norovirus and HEV has been reported within wastewater in many countries previously. Here we used amplicon deep sequencing (metabarcoding) to identify norovirus and HEV strains in wastewater samples from England collected in 2019 and 2020. For HEV, we sequenced a fragment of the RNA-dependent RNA polymerase (RdRp) gene targeting genotype three strains. For norovirus, we sequenced the 5' portion of the major capsid protein gene (VP1) of genogroup II strains. Sequencing of the wastewater samples revealed eight different genotypes of norovirus GII (GII.2, GII.3, GII.4, GII.6, GII.7, GII.9, GII.13 and GII.17). Genotypes GII.3 and GII.4 were the most commonly found. The HEV metabarcoding assay was able to identify HEV genotype 3 strains in some samples with a very low viral concentration determined by RT-qPCR. Analysis showed that most HEV strains found in influent wastewater were typed as G3c and G3e and were likely to have originated from humans or swine. However, the small size of the HEV nested PCR amplicon could cause issues with typing, and so this method is more appropriate for samples with high CTs where methods targeting longer genomic regions are unlikely to be successful. This is the first report of HEV RNA in wastewater in England. This study demonstrates the utility of wastewater sequencing and the need for wider surveillance of norovirus and HEV within host species and environments.

Sea temperature influences accumulation of tetrodotoxin in British bivalve shellfish.

Tetrodotoxin (TTX), a potent neurotoxin mostly associated with pufferfish poisoning, is also found in bivalve shellfish. Recent studies into this emerging food safety threat reported TTX in a few, mainly estuarine, shellfish production areas in some European countries, including the United Kingdom. A pattern in occurrences has started to emerge, however the role of temperature on TTX has not been investigated in detail. Therefore, we conducted a large systematic TTX screening study, encompassing over 3500 bivalve samples collected throughout 2016 from 155 shellfish monitoring sites along the coast of Great Britain. Overall, we found that only 1.1 % of tested samples contained TTX above the reporting limit of 2 µg/kg whole shellfish flesh and these samples all originated from ten shellfish production sites in southern England. Subsequent continuous monitoring of selected areas over a five-year period showed a potential seasonal TTX accumulation in bivalves, starting in June when water temperatures reached around 15 °C. For the first time, satellite-derived data were also applied to investigate temperature differences between sites with and without confirmed presence of TTX in 2016. Although average annual temperatures were similar in both groups, daily mean values were higher in summer and lower in winter at sites where TTX was found. Here, temperature also increased significantly faster during late spring and early summer, the critical period for TTX. Our study supports the hypothesis that temperature is one of the key triggers of events leading to TTX accumulation in European bivalves. However, other factors are also likely to play an important role, including the presence or absence of a de novo biological source, which remains elusive.

Minimalist revision of Mesochorus Gravenhorst, 1829 (Hymenoptera: Ichneumonidae: Mesochorinae) from Área de Conservación Guanacaste, Costa Rica, with 158 new species and host records for 129 species / Revisión minimalista de Mesochorus Gravenhorst, 1829 (Hymenoptera: Ichneumonidae: Mesochorinae) del Área de Conservación Guanacaste, Costa Rica, con 158 especies nuevas y registros de hospedantes para 129 especies

Introduction: Species of Mesochorus are found worldwide and members of this genus are primarily hyperparasitoids of Ichneumonoidea and Tachinidae. Objectives: To describe species of Costa Rican Mesochorus reared from caterpillars and to a lesser extent Malaise-trapped. Methods: The species are diagnosed by COI mtDNA barcodes, morphological inspection, and host data. A suite of images and host data (plant, caterpillar, and primary parasitoid) are provided for each species. Results: A total of 158 new species of Mesochorus. Sharkey is the taxonomic authority for all. Conclusions: This demonstrates a practical application of DNA barcoding that can be applied to the masses of undescribed neotropical insect species in hyperdiverse groups.

Introducción: Las especies de Mesochorus se encuentran en todo el mundo y los miembros de este género son principalmente hiperparasitoides de las familias Ichneumonoidea y Tachinidae. Objetivos: Describir las especies de Mesochorus costarricenses obtenidas de orugas y en menor medida por trampas Malaise. Métodos: Las especies se diagnosticaron mediante el uso de código de barra molecular por COI del ADNmt, inspección morfológica y datos del huésped. Se proporciona un conjunto de imágenes y datos de los huéspedes (planta, oruga y parasitoide primario) para cada especie. Resultados: Se encontró un total de 158 nuevas especies de Mesochorus. Sharkey es la autoridad taxonómica para todas las especies. Conclusiones: Se demuestra una aplicación práctica del código de barras de ADN que se puede aplicar a grandes cantidades de especies de insectos neotropicales no descritas para grupos hiperdiversos.

Climate warming and increasing Vibrio vulnificus infections in North America.

Vibrio vulnificus is an opportunistic bacterial pathogen, occurring in warm low-salinity waters. V. vulnificus wound infections due to seawater exposure are infrequent but mortality rates are high (~ 18%). Seawater bacterial concentrations are increasing but changing disease pattern assessments or climate change projections are rare. Here, using a 30-year database of V. vulnificus cases for the Eastern USA, changing disease distribution was assessed. An ecological niche model was developed, trained and validated to identify links to oceanographic and climate data. This model was used to predict future disease distribution using data simulated by seven Global Climate Models (GCMs) which belong to the newest Coupled Model Intercomparison Project (CMIP6). Risk was estimated by calculating the total population within 200 km of the disease distribution. Predictions were generated for different "pathways" of global socioeconomic development which incorporate projections of greenhouse gas emissions and demographic change. In Eastern USA between 1988 and 2018, V. vulnificus wound infections increased eightfold (10-80 cases p.a.) and the northern case limit shifted northwards 48 km p.a. By 2041-2060, V. vulnificus infections may expand their current range to encompass major population centres around New York (40.7°N). Combined with a growing and increasingly elderly population, annual case numbers may double. By 2081-2100 V. vulnificus infections may be present in every Eastern USA State under medium-to-high future emissions and warming. The projected expansion of V. vulnificus wound infections stresses the need for increased individual and public health awareness in these areas.

An integrated eco-evolutionary framework to predict population-level responses of climate-sensitive pathogens.

It is critical to gain insight into how climate change impacts evolutionary responses within climate-sensitive pathogen populations, such as increased resilience, opportunistic responses and the emergence of dominant variants from highly variable genomic backgrounds and subsequent global dispersal. This review proposes a framework to support such analysis, by combining genomic evolutionary analysis with climate time-series data in a novel spatiotemporal dataframe for use within machine learning applications, to understand past and future evolutionary pathogen responses to climate change. Recommendations are presented to increase the feasibility of interdisciplinary applications, including the importance of robust spatiotemporal metadata accompanying genome submission to databases. Such workflows will inform accessible public health tools and early-warning systems, to aid decision-making and mitigate future human health threats.

Postoperative Chyle Leak Rate Following Neck Dissection for Squamous Cell Carcinoma Versus Papillary Thyroid Cancer.

OBJECTIVES: Compare the rates of post-operative chyle leak following therapeutic lateral neck dissection during treatment of papillary thyroid carcinoma (PTC) versus squamous cell carcinoma (SCC) of the head and neck. METHODS: A retrospective analysis of 226 consecutive neck dissections in 201 patients who underwent therapeutic neck dissection involving at least levels II-IV with a final pathologic diagnosis of mucosal SCC of the head and neck or PTC from 2010 to 2020. Specific cases of chyle leak were reviewed. Surgical factors associated with chyle leak were analyzed using logistic regression analysis. Duration of chyle leak was assessed by the Kaplan-Meier curve, and time-to-resolution was analyzed by Cox proportional hazard analysis. RESULTS: Postoperative chyle leak was encountered in 15 (6.6%) neck dissections, eight (12.3%) in PTC, and seven (4.3%) in SCC. High-volume chyle leak and chyle leak requiring operative intervention were only encountered in neck dissections performed for PTC. Chyle leak was significantly associated with PTC on univariable analysis (OR 3.08, p = 0.037), but not on multivariable analysis (OR 1.35, p = 0.711). High-volume chyle leak and the need for operative intervention were associated only with PTC patients (OR 23.6, p = 0.006; OR 18.09, p = 0.023 respectively). Median duration of chyle leak was 12.1 days among patients with SCC, and 20.5 days among patients with PTC (p = 0.089). CONCLUSIONS: Among 201 patients undergoing therapeutic neck dissection, chyle leak was associated with PTC pathology on univariable but not multivariable analysis. However, high-volume leaks and leaks requiring operative intervention only occurred among patients with PTC. LEVEL OF EVIDENCE: level III Laryngoscope, 133:2959-2964, 2023.

Methodological advances in the detection of biotoxins and pathogens affecting production and consumption of bivalve molluscs in a changing environment.

The production, harvesting and safe consumption of bivalve molluscs can be disrupted by biological hazards that can be divided into three categories: (1) biotoxins produced by naturally occurring phytoplankton that are bioaccumulated by bivalves during filter-feeding, (2) human pathogens also bioaccumulated by bivalves and (3) bivalve pathogens responsible for disease outbreaks. Environmental changes caused by human activities, such as climate change, can further aggravate these challenges. Early detection and accurate quantification of these hazards are key to implementing measures to mitigate their impact on production and safeguard consumers. This review summarises the methods currently used and the technological advances in the detection of biological hazards affecting bivalves, for the screening of known hazards and discovery of new ones.

What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios.

When the first microbial genome sequences were published just 20 years ago, our understanding regarding the microbial world changed dramatically. The genomes of the first pathogenic vibrios sequenced, including Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus revealed a functional and phylogenetic diversity previously unimagined as well as a genome structure indelibly shaped by horizontal gene transfer. The initial glimpses into these organisms also revealed a genomic plasticity that allowed these bacteria to thrive in challenging and varied aquatic and marine environments, but critically also a suite of pathogenicity attributes. In this review we outline how our understanding of vibrios has changed over the last two decades with the advent of genomics and advances in bioinformatic and data analysis techniques, it has become possible to provide a more cohesive understanding regarding these bacteria: how these pathogens have evolved and emerged from environmental sources, their evolutionary routes through time and space, how they interact with other bacteria and the human host, as well as initiate disease. We outline novel approaches to the use of whole genome sequencing for this important group of bacteria and how new sequencing technologies may be applied to study these organisms in future studies.

Establishing a marine monitoring programme to assess antibiotic resistance: A case study from the Gulf Cooperation Council (GCC) region.

The World Health Organization considers antimicrobial resistance as one of the most pressing global issues which poses a fundamental threat to human health, development, and security. Due to demographic and environmental factors, the marine environment of the Gulf Cooperation Council (GCC) region may be particularly susceptible to the threat of antimicrobial resistance. However, there is currently little information on the presence of AMR in the GCC marine environment to inform the design of appropriate targeted surveillance activities. The objective of this study was to develop, implement and conduct a rapid regional baseline monitoring survey of the presence of AMR in the GCC marine environment, through the analysis of seawater collected from high-risk areas across four GCC states: (Bahrain, Oman, Kuwait, and the United Arab Emirates). 560 Escherichia coli strains were analysed as part of this monitoring programme between December 2018 and May 2019. Multi-drug resistance (resistance to three or more structural classes of antimicrobials) was observed in 32.5% of tested isolates. High levels of reduced susceptibility to ampicillin (29.6%), nalidixic acid (27.9%), tetracycline (27.5%), sulfamethoxazole (22.5%) and trimethoprim (22.5%) were observed. Reduced susceptibility to the high priority critically important antimicrobials: azithromycin (9.3%), ceftazidime (12.7%), cefotaxime (12.7%), ciprofloxacin (44.6%), gentamicin (2.7%) and tigecycline (0.5%), was also noted. A subset of 173 isolates was whole genome sequenced, and high carriage rates of qnrS1 (60/173) and bla CTX-M-15 (45/173) were observed, correlating with reduced susceptibility to the fluoroquinolones and third generation cephalosporins, respectively. This study is important because of the resistance patterns observed, the demonstrated utility in applying genomic-based approaches to routine microbiological monitoring, and the overall establishment of a transnational AMR surveillance framework focussed on coastal and marine environments.

Pathogens transported by plastic debris: does this vector pose a risk to aquatic organisms?

Microplastics are small (<5 mm) plastic particles of varying shapes and polymer types that are now widespread global contaminants of marine and freshwater ecosystems. Various estimates suggest that several trillions of microplastic particles are present in our global oceanic system, and that these are readily ingested by a wide range of marine and freshwater species across feeding modes and ecological niches. Here, we present some of the key and pressing issues associated with these globally important contaminants from a microbiological perspective. We discuss the potential mechanisms of pathogen attachment to plastic surfaces. We then describe the ability of pathogens (both human and animal) to form biofilms on microplastics, as well as dispersal of these bacteria, which might lead to their uptake into aquatic species ingesting microplastic particles. Finally, we discuss the role of a changing oceanic system on the potential of microplastic-associated pathogens to cause various disease outcomes using numerous case studies. We set out some key and imperative research questions regarding this globally important issue and present a methodological framework to study how and why plastic-associated pathogens should be addressed.

A seafood risk tool for assessing and mitigating chemical and pathogen hazards in the aquaculture supply chain.

Intricate links between aquatic animals and their environment expose them to chemical and pathogenic hazards, which can disrupt seafood supply. Here we outline a risk schema for assessing potential impacts of chemical and microbial hazards on discrete subsectors of aquaculture-and control measures that may protect supply. As national governments develop strategies to achieve volumetric expansion in seafood production from aquaculture to meet increasing demand, we propose an urgent need for simultaneous focus on controlling those hazards that limit its production, harvesting, processing, trade and safe consumption. Policies aligning national and international water quality control measures for minimizing interaction with, and impact of, hazards on seafood supply will be critical as consumers increasingly rely on the aquaculture sector to supply safe, nutritious and healthy diets.

Description of Chilearinus Sharkey gen. nov. and status of Nearctic Earinus Wesmael, 1837 (Braconidae, Agathidinae) with the description of new species.

The Neotropical members formerly included in Earinus Wesmael, 1837 are transferred to a new genus, Chilearinus Sharkey gen. nov. Presently three Nearctic species of Earinus are recognized, i.e., Earinuserythropoda Cameron, 1887, Earinuslimitaris Say,1835, and Earinuszeirapherae Walley, 1935, and these are retained in Earinus. Earinuschubuquensis Berta, 2000 and Earinusscitus Enderlein, 1920 are transferred to Chilearinus, i.e., C.chubuquensis, and C.scitus, comb. nov. One other species is transferred to Chilearinus, i.e., Microgasterrubricollis Spinola, 1851, Chilearinusrubricollis, comb. nov. Two other Neotropical species, Earinushubrechtae Braet, 2002 and Earinusbourguignoni Braet, 2002 were described under the genus Earinus but are here transferred to Lytopylus, L.hubrechtae, and L.bourguignoni comb. nov. Two new species of Chilearinus are described, C.covidchronos and C.janbert spp. nov. The status of Agathislaevithorax Spinola,1851, Agathisrubricata Spinola,1851, and Agathisareolata Spinola, 1851 is discussed. A neotype is designated for Earinuslimitaris (Say, 1835) and diagnosed with a COI barcode. Earinusaustinbakeri and Earinuswalleyi spp. nov. are described. The status of both Earinus and Chilearinus in the Americas is discussed. A revised key to the genera of Agathidinae of the Americas is presented.

More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021.

This is a response to a preprint version of "A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science", https://www.biorxiv.org/content/10.1101/2021.04.28.441626v2. Meier et al. strongly criticized Sharkey et al.'s publication in which 403 new species were deliberately minimally described, based primarily on COI barcode sequence data. Here we respond to these criticisms. The following points are made: 1) Sharkey et al. did not equate BINs with species, as demonstrated in several examples in which multiple species were found to be in single BINs. 2) We reiterate that BINs were used as a preliminary sorting tool, just as preliminary morphological identification commonly sorts specimens based on color and size into unit trays; despite BINs and species concepts matching well over 90% of species, this matching does not equate to equality. 3) Consensus barcodes were used only to provide a diagnosis to conform to the rules of the International Code of Zoological Nomenclature just as consensus morphological diagnoses are. The barcode of a holotype is definitive and simply part of its cellular morphology. 4) Minimalist revisions will facilitate and accelerate future taxonomic research, not hinder it. 5) We refute the claim that the BOLD sequences of Plesiocoelusvanachterbergi are pseudogenes and demonstrate that they simply represent a frameshift mutation. 6) We reassert our observation that morphological evidence alone is insufficient to recognize species within species-rich higher taxa and that its usefulness lies in character states that are congruent with molecular data. 7) We show that in the cases in which COI barcodes code for the same amino acids in different putative species, data from morphology, host specificity, and other ecological traits reaffirm their utility as indicators of genetically distinct lineages.

Response to Zamani et al. (2020): The omission of critical data in the pursuit of "revolutionary" methods to accelerate the description of species.

Here we respond to the criticisms leveled against a proposal that suggested an efficient solution to the taxonomic impediment. We clarify some of our objectives and demonstrate that many of the criticisms apply more to traditional approaches to taxonomy rather than to our minimalist approach.

The Foodborne Transmission of Hepatitis E Virus to Humans.

Globally, Hepatitis E virus (HEV) causes over 20 million cases worldwide. HEV is an emerging and endemic pathogen within economically developed countries, chiefly resulting from infections with genotype 3 (G3) HEV. G3 HEV is known to be a zoonotic pathogen, with a broad host range. The primary source of HEV within more economically developed countries is considered to be pigs, and consumption of pork products is a significant risk factor and known transmission route for the virus to humans. However, other foods have also been implicated in the transmission of HEV to humans. This review consolidates the information available regarding transmission of HEV and looks to identify gaps where further research is required to better understand how HEV is transmitted to humans through food.

Distribution of Tetrodotoxin in Pacific Oysters (Crassostrea gigas).

A potent and heat-stable tetrodotoxin (TTX) has been found to accumulate in various marine bivalve species, including Pacific oysters (Crassostrea gigas), raising a food safety concern. While several studies on geographical occurrence of TTX have been conducted, there is a lack of knowledge about the distribution of the toxin within and between bivalves. We, therefore, measured TTX in the whole flesh, mantle, gills, labial palps, digestive gland, adductor muscle and intravalvular fluid of C. gigas using liquid chromatography-tandem mass spectrometry. Weekly monitoring during summer months revealed the highest TTX concentrations in the digestive gland (up to 242 µg/kg), significantly higher than in other oyster tissues. Intra-population variability of TTX, measured in the whole flesh of each of twenty animals, reached 46% and 32% in the two separate batches, respectively. In addition, an inter-population study was conducted to compare TTX levels at four locations within the oyster production area. TTX concentrations in the whole flesh varied significantly between some of these locations, which was unexplained by the differences in weight of flesh. This is the first study examining TTX distribution in C. gigas and the first confirmation of the preferential accumulation of TTX in oyster digestive gland.