Detection of Emerging Zoonotic Pathogens: An Integrated One Health Approach

Leptospira spp. and Rickettsia spp. as pathogens with zoonotic potential causing acute undifferentiated febrile illness in a central-eastern region of Peru

OBJETIVE

this study was to determine the relationship between acute febrile illness and bacterial pathogens with zoonotic potential that cause emerging and re-emerging diseases in a central-eastern region of Peru.

RESULTS

Out of the 279 samples analyzed, 23 (8.2%) tested positive for infection by Rickettsia spp., while a total of 15 (5.4%) tested positive for Leptospira spp. Women had a higher frequency of infection by Rickettsia spp., with 13 cases (53.3%), while men had a higher frequency of infection by Leptospira spp., with 10 cases (66.7%). The most frequently reported general symptom was headache, with 100.0% (n = 23) of patients with Rickettsia (+) and 86.7% (n = 13) of patients with Leptospira (+) experiencing it. Arthralgia was the second most frequent symptom, reported by 95.6% (n = 22) and 60% (n = 9) of patients with Rickettsia (+) and Leptospira (+), respectively. Myalgia was reported by 91.3% (n = 21) and 66.7% (n = 10) of patients with Rickettsia (+) and Leptospira (+), respectively. Retroocular pain, low back pain, and skin rash were also present, but less frequently. Among the positives, no manifestation of bleeding was recorded, although only one positive case for Leptospira spp. presented a decrease in the number of platelets.

Exploring viral diversity and metagenomics in livestock: insights into disease emergence and spillover risks in cattle

Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.

The application of the One Health approach in the management of five major zoonotic diseases using the World Bank domains: A scoping review

The international authorities, such as the Food and Agriculture Organization of the United Nations, World Health Organization, World Organization for Animal Health, United Nations Environment Programme, and World Bank, have endorsed the One Health concept as an effective approach to optimize the health of people, animals, and the environment. The One Health concept is considered as an integrated and unifying approach with the objective of sustainably balancing and optimizing the health of people, animals, and ecosystems. Despite variations in its definitions, the underlying principle remains consistent - recognizing the interconnected and interdependent health of humans, animals, and the environment, necessitating interdisciplinary collaboration to optimize health outcomes. The One Health approach has been applied in numerous countries for detecting, managing, and controlling diseases. Moreover, the concept has found application in various areas, including antimicrobial resistance, food safety, and ecotoxicology, with a growing demand. There is a growing consensus that the One Health concept and the United Nations Sustainable Development Goals mutually reinforce each other. The World Bank has recommended five domains as foundational building blocks for operationalising the One Health approach, which includes: i) One Health stakeholders, roles, and responsibilities; ii) financial and personal resources; iii) communication and information; iv) technical infrastructure; and v) governance. The domains provide a generalised overview of the One Health concept and guide to its application. We conducted a scoping review following the five-staged Arksey and O'Malley's framework. The objective of the review was to map and synthesise available evidence of application of the One Health approach to five major zoonotic diseases using the World Bank domains. Publications from the year 2004, marking the inception of the term 'One Health,' to 2022 were included. Information was charted and categorised against the World Bank domains identified as a priori. We included 1132 records obtained from three databases: Embase, Medline, and Global Health; as well as other sources. After excluding duplicates, screening for titles and abstracts, and full text screening, 20 articles that contained descriptions of 29 studies that implemented the One Health approach were selected for the review. We found that included studies varied in the extent to which the five domains were utilised. Less than half the total studies (45%) used all the five domains and none of the studies used all the sub-domains. The environmental sector showed an underrepresentation in the application of the One Health approach to zoonotic diseases as 14 (48%) studies in 10 articles did not mention it as a stakeholder. Sixty two percent of the studies mentioned receiving support from international partners in implementing the One Health approach and 76% of the studies were supported by international donors to conduct the studies. The review identified disparate funding mechanisms employed in the implementation of the One Health approach. However, there were limited discussions on plans for continuity and viability of these funding mechanisms in the future.

Integrated Antigenic and Nucleic Acid Detection in Single Virions and Extracellular Vesicles with Viral Content

Virion-mediated outbreaks are imminent and despite rapid responses, continue to cause adverse symptoms and death. Therefore, tunable, sensitive, high-throughput assays are needed to help diagnose future virion-mediated outbreaks. Herein, it is developed a tunable in situ assay to selectively enrich virions and extracellular vesicles (EVs) and simultaneously detect antigens and nucleic acids at a single-particle resolution. The Biochip Antigen and RNA Assay (BARA) enhanced sensitivities compared to quantitative reverse-transcription polymerase chain reaction (qRT-PCR), enabling the detection of virions in asymptomatic patients, genetic mutations in single virions, and enabling the continued long-term expression of viral RNA in the EV-enriched subpopulation in the plasma of patients with post-acute sequelae of the coronavirus disease of 2019 (COVID-19). BARA revealed highly accurate diagnoses of COVID-19 by simultaneously detecting the spike glycoprotein and nucleocapsid-encoding RNA in saliva and nasopharyngeal swab samples. Altogether, the single-particle detection of antigens and viral RNA provides a tunable framework for the diagnosis, monitoring, and mutation screening of current and future outbreaks.

Advances in Detecting Cystic Echinococcosis in Intermediate Hosts and New Diagnostic Tools: A Literature Review

Cystic echinococcosis (CE) is a zoonotic disease affecting humans and animals. Despite a lack of clarity about many details of parasite-intermediate host interactions, the nature of the immune responses triggered by hydatid infection has revealed new perspectives. This study discusses the latest advances in elucidating the immunologic mechanism of echinococcosis and its detection and potential approaches to enhance serodiagnosis accuracy. Moreover, nanobiosensors have been evaluated according to their potential to improve treatment efficiency and aid in an early diagnosis of cystic echinococcosis. The serum of an intermediate host can diagnose CE by analyzing antibodies induced by Echinococcus granulosus. Among the most notable features of this method are its noninvasive ability and high sensitivity, both of which make it an excellent tool for clinical diagnosis. Several serological tests, including ELISAs and immunoblotting, can detect these antibodies to assess the disease's state and determine the treatment outcome. A thorough understanding of what cross-reactivity means and the stage of the disease are crucial to interpreting serological results. Nanobiosensors have also proven better than conventional biosensors in detecting hydatid cysts. Additionally, they are highly sensitive and versatile when detecting specific biomarkers, improving diagnostic accuracy. These immunomodulatory molecules, induced by E. granulosus, are a good candidate for diagnosing cystic echinococcosis because they alter intermediate host immune responses. Hydatid cyst detection is also enhanced through nanobiosensors, which provide better accuracy.

Association between anthropization and rodent reservoirs of zoonotic pathogens in Northwestern Mexico

The world is facing a major pulse of ecological and social changes that may favor the risk of zoonotic outbreaks. Such risk facilitation may occur through the modification of the host's community diversity and structure, leading to an increase in pathogen reservoirs and the contact rate between these reservoirs and humans. Here, we examined whether anthropization alters the relative abundance and richness of zoonotic reservoir and non-reservoir rodents in three Socio-Ecological Systems. We hypothesized that anthropization increases the relative abundance and richness of rodent reservoirs while decreasing non-reservoir species. We first developed an Anthropization index based on 15 quantitative socio-ecological variables classified into five groups: 1) Vegetation type, 2) Urbanization degree, 3) Water quality, 4) Potential contaminant sources, and 5) Others. We then monitored rodent communities in three regions of Northwestern Mexico (Baja California, Chihuahua, and Sonora). A total of 683 rodents of 14 genera and 27 species were captured, nine of which have been identified as reservoirs of zoonotic pathogens (359 individuals, 53%). In all regions, we found that as anthropization increased, the relative abundance of reservoir rodents increased; in contrast, the relative abundance of non-reservoir rodents decreased. In Sonora, reservoir richness increased with increasing anthropization, while in Baja California and Chihuahua non-reservoir richness decreased as anthropization increased. We also found a significant positive relationship between the anthropization degree and the abundance of house mice (Mus musculus) and deer mice (Peromyscus maniculatus), the most abundant reservoir species in the study. These findings support the hypothesis that reservoir species of zoonotic pathogens increase their abundance in disturbed environments, which may increase the risk of pathogen exposure to humans, while anthropization creates an environmental filtering that promotes the local extinction of non-reservoir species.

Emerging Microbes, Infections, and Spillovers: Charting a Path Forward

In an age defined by rapid globalization and unprecedented technological advancements, the field of infectious diseases stands at the intersection of complex challenges and promising opportunities [...].

Are rabid raccoons (Procyon lotor) ready for the rapture? Determining the geographic origin of rabies virus-infected raccoons using RADcapture and microhaplotypes

North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management of RV is accomplished through vaccination targeting mesocarnivore reservoir populations, such as the raccoon (Procyon lotor) in Eastern North America. Raccoons are a common generalist species, and populations may reach high densities in developed areas, which can result in contact with humans and pets with potential exposures to the raccoon variant of RV throughout the eastern United States. Understanding the spatial movement of RV by raccoon populations is important for monitoring and refining strategies supporting the landscape-level control and local elimination of this lethal zoonosis. We developed a high-throughput genotyping panel for raccoons based on hundreds of microhaplotypes to identify population structure and genetic diversity relevant to rabies management programs. Throughout the eastern United States, we identified hierarchical population genetic structure with clusters that were connected through isolation-by-distance. We also illustrate that this genotyping approach can be used to support real-time management priorities by identifying the geographic origin of a rabid raccoon that was collected in an area of the United States that had been raccoon RV-free for 8 years. The results from this study and the utility of the microhaplotype panel and genotyping method will provide managers with information on raccoon ecology that can be incorporated into future management decisions.

Rapid detection of Salmonella enterica in primary production samples by eliminating DNA amplification inhibitors using an improved sample pre-treatment method

Sensitive detection of pathogens in livestock farms is an integral part of the One Health Action Plan of the European Union (EU). Ensuring this requires on-site testing devices that are compatible with complex matrices such as primary production samples. Among all, faeces are considered the most challenging matrix type that makes it difficult to identify pathogens because of complexity in sample preparation for molecular testing. We have developed a loop-mediated isothermal amplification (LAMP) based veterinary point-of-care (POC) device (VETPOD) and adapted it to detect Salmonella enterica in primary production samples. Three different sampling methods (semi-wet chicken faeces, boot socks collection and dust samples from poultry shed) were iteratively tested to assess their nature of complexity and possibility for adapting them as suitable sampling methods for on-site testing. During the study, the sample preparation method that included a two-step centrifugation combined with washing of the enriched Salmonella cells was found crucial in eliminating amplification inhibitors originating from the faecal matrices. A total of 90 samples were tested that included 60 samples for sensitivity study and 30 samples for relative level of detection (RLOD, a level of detection in comparison to ISO 6579:1 reference method). Overall, the VETPOD had a sensitivity of 90%, 84.62% and 81.82% for boot sock, faecal and dust samples, respectively. The RLOD was 2.23 CFU/25 g which was found to be 1.33 times higher than the ISO 6579:1. Performing with an excellent agreement with ISO 6579:1, the VETPOD proved as a promising alternative to detect Salmonella spp. in primary production and animal husbandry samples.

Validation of Point-of-Care Device for Rapid Detection of Salmonella enterica in Meat Products

Accurate and rapid detection of pathogens in foods of animal origin has been a critical part of the One Health Action Plan of the European Union (EU). Biosensors have the potential in bringing required technologies to accomplish this on the field, wherein loop-mediated isothermal amplification (LAMP) and lab-on-a-chip have proven to be ideal. We have developed a LAMP-based point-of-care (POC) device, the VETPOD, as a solution to the contemporary challenges in the rapid detection of Salmonella spp. The core technology in the VETPOD is a ready-to-use cartridge that included an injection-molded polymer chip with pyramid-shaped optical structures embedded within the chip. These pyramid-shaped optical structures direct the incident light, due to total internal reflection (TIR), through the reaction chambers to the phototransistor. The VETPOD was validated against the ISO 6579-1 reference method. A total of 310 samples were tested that included 180 Salmonella spiked samples in 6 different meat categories and 130 strains to determine the specificity. The overall results were satisfactory, wherein the VETPOD had an acceptable sensitivity (96.51%) compared to the reference (98.81%) and near perfect agreement with ISO 6579-1 with an overall Cohen's kappa of 0.94. The relative level of detection (RLOD) for the VETPOD was 1.38 CFU/25 g that was found to be 1.17 times higher than the reference. The VETPOD showed 98% precision for inclusivity and 100% precision for the exclusivity samples. The VETPOD proved as a useful alternative to detect Salmonella spp. that can be adaptable to a broader spectrum of pathogens in future.

Evaluation of the Effect of Pb Pollution on Avian Influenza Virus-Specific Antibody Production in Black-Headed Gulls (Chroicocephalus ridibundus)

Lead (Pb), an environmental pollutant, has been widely reported to have contaminated mammals, including humans and birds. This study focuses on the effects of Pb pollution on avian influenza virus (AIV) antibody production. A total of 170 black-headed gulls (Chroicocephalus ridibundus) were captured in Tokyo Bay (TBP) from January 2019 to April 2020 and in Mikawa Bay (MBP) from November 2019 to April 2021. The gulls were weighed, subjected to blood sampling, and released with a ring band on their tarsus. The samples were used to measure blood Pb levels (BLL) and AIV-specific antibodies. The BLL were compared using the Wilcoxon two-sample test between the period when black-headed gulls arrived and the wintering period, defined by the number of gulls counted in each area. A significant increase was found in the TBP. A decrease in BLL significantly increased antibody titer during wintering in TBP and MBP. Pb pollution had a negative effect on the production of AIV antibodies. These findings suggest that wild birds that were contaminated by Pb in the environment may facilitate the spread of zoonotic diseases, further increasing the possibility that environmental pollutants may threaten human health.

Lactiplantibacillus plantarum Lac16 Attenuates Enterohemorrhagic Escherichia coli O157:H7 Infection by Inhibiting Virulence Traits and Improving Intestinal Epithelial Barrier Function

Large-scale use of antimicrobials in agriculture and medicine contributes to antibiotic residues in raw foods, the spread of antimicrobial resistance (AMR) and drug pollution, which seriously threatens human health and imposes significant economic burdens on society, suggesting the need for novel therapeutic options that prevent or control zoonoses. In this study, four probiotics were selected to assess their capability to alleviate pathogen-induced damage. Results showed that a simulated gastrointestinal juice and bile tolerated L. plantarum Lac16 with high lactic acid secretion can significantly inhibit the growth of multiple zoonotic pathogens. Lac16 also significantly inhibited the biofilm formation and mRNA expression of virulence traits (genes related to virulence, toxins, flagella biogenesis and motility, antibiotic resistance, biofilm formation and AI-2 quorum sensing) of enterohemorrhagic E. coli O157:H7 (EHEC). Furthermore, Lac16 and Lac26 significantly protected C. elegans against zoonotic pathogen-induced (EHEC, S. typhimurium, C. perfringens) deaths. Moreover, Lac16 significantly promoted epithelial repair and ameliorated lipopolysaccharide (LPS)-induced intestinal epithelial apoptosis and barrier dysfunction by activating the Wnt/β-catenin signaling pathway, and markedly reduced LPS-induced inflammatory responses by inhibiting the TLR4/MyD88 signaling pathway. The present results indicate that Lac16 attenuates enterohemorrhagic E. coli infection-induced damage by inhibiting key virulence traits of E. coli, promoting epithelial repair and improving intestinal epithelial barrier function, which may be mediated by the activated Wnt/β-catenin signaling pathway and the inhibited TLR4/MyD88 signaling pathway of the intestinal epithelium.

Interactions of Equine Viruses with the Host Kinase Machinery and Implications for One Health and Human Disease

Zoonotic pathogens that are vector-transmitted have and continue to contribute to several emerging infections globally. In recent years, spillover events of such zoonotic pathogens have increased in frequency as a result of direct contact with livestock, wildlife, and urbanization, forcing animals from their natural habitats. Equines serve as reservoir hosts for vector-transmitted zoonotic viruses that are also capable of infecting humans and causing disease. From a One Health perspective, equine viruses, therefore, pose major concerns for periodic outbreaks globally. Several equine viruses have spread out of their indigenous regions, such as West Nile virus (WNV) and equine encephalitis viruses (EEVs), making them of paramount concern to public health. Viruses have evolved many mechanisms to support the establishment of productive infection and to avoid host defense mechanisms, including promoting or decreasing inflammatory responses and regulating host machinery for protein synthesis. Viral interactions with the host enzymatic machinery, specifically kinases, can support the viral infectious process and downplay innate immune mechanisms, cumulatively leading to a more severe course of the disease. In this review, we will focus on how select equine viruses interact with host kinases to support viral multiplication.

Prevalence Estimation, Antimicrobial Susceptibility, and Serotyping of Salmonella enterica Recovered from New World Non-Human Primates (Platyrrhini), Feed, and Environmental Surfaces from Wildlife Centers in Costa Rica

Concern about zoonoses and wildlife has increased. Few studies described the role of wild mammals and environments in the epidemiology of Salmonella. Antimicrobial resistance is a growing problem associated with Salmonella that threatens global health, food security, the economy, and development in the 21st century. The aim of this study is to estimate the prevalence and identify antibiotic susceptibility profiles and serotypes of non-typhoidal Salmonella enterica recovered from non-human primate feces, feed offered, and surfaces in wildlife centers in Costa Rica. A total of 180 fecal samples, 133 environmental, and 43 feed samples from 10 wildlife centers were evaluated. We recovered Salmonella from 13.9% of feces samples, 11.3% of environmental, and 2.3% of feed samples. Non-susceptibility profiles included six isolates from feces (14.6%): four non-susceptible isolates (9.8%) to ciprofloxacin, one (2.4%) to nitrofurantoin, and one to both ciprofloxacin and nitrofurantoin (2.4%). Regarding the environmental samples, one profile was non-susceptible to ciprofloxacin (2.4%) and two to nitrofurantoin (4.8%). The serotypes identified included Typhimurium/I4,[5],12:i:-, S. Braenderup/Ohio, S. Newport, S. Anatum/Saintpaul, and S. Westhampton. The epidemiological surveillance of Salmonella and antimicrobial resistance can serve in the creation of strategies for the prevention of the disease and its dissemination throughout the One Health approach.

AutoPLP: A Padlock Probe Design Pipeline for Zoonotic Pathogens

Emergence of novel zoonotic infections among the human population has increased the burden on global healthcare systems to curb their spread. To meet the evolutionary agility of pathogens, it is essential to revamp the existing diagnostic methods for early detection and characterization of the pathogens at the molecular level. Padlock probes (PLPs), which can leverage the power of isothermal nucleic acid amplification techniques (NAAT) such as rolling circle amplification (RCA), are known for their high sensitivity and specificity in detecting a diverse pathogen panel of interest. However, due to the complexity involved in deciding the target regions for PLP design and the need for optimization of multiple experimental parameters, the applicability of RCA has been limited in point-of-care testing for pathogen detection. To address this gap, we have developed a novel and integrated PLP design pipeline named AutoPLP, which can automate the probe design process for a diverse pathogen panel of interest. The pipeline is composed of three modules which can perform sequence data curation, multiple sequence alignment, conservation analysis, filtration based on experimental parameters (T_m, GC content, and secondary structure formation), and in silico probe validation via potential cross-hybridization check with host genome. The modules can also take into account the backbone and restriction site information, appropriate combinations of which are incorporated along with the probe arms to design a complete probe sequence. The potential applications of AutoPLP are showcased through the design of PLPs for the detection of rabies virus and drug-resistant strains of Mycobacterium tuberculosis.

A systematic review to describe patterns of animal and human viral research in Rwanda

Rwanda is located in the Central East African region where several viral pathogens with global importance were originally described, including human immunodeficiency virus (HIV), Ebola, Zika, Rift Valley Fever (RVF), dengue and a long list of other neglected tropical viral pathogens. Due to many factors, this region has the potential to become a global hotspot for viral emergence. In Rwanda, viral diseases are underreported and the question is whether this is due to the absence of these viruses or a lack of investigation. Like many developing countries, capabilities in Rwanda need improvement despite research efforts throughout the years. This review describes the status of human and animal virus research in Rwanda and identifies relevant research and operational gaps. A comprehensive search was conducted in PubMed for virus research in Rwanda: 233 primary studies on viruses/viral diseases are indexed with connection to Rwanda. From 1958 to 2020, yearly publications generally increased and HIV/acquired immunodeficiency syndrome is the most studied virus. Compared with human viruses, few studies focus on animal and/or zoonotic viruses. The occurrence of the current severe acute respiratory syndrome coronavirus 2 pandemic shows strengthening warning and surveillance systems is critical to efficient preparedness and response. We recommend investment in human capacity, laboratory facilities and research to inform policy for viral surveillance in Rwanda.

A global analysis of One Health Networks and the proliferation of One Health collaborations

There has been a renewed focus on threats to the human-animal-environment interface as a result of the COVID-19 pandemic, and investments in One Health collaborations are expected to increase. Efforts to monitor the development of One Health Networks (OHNs) are essential to avoid duplication or misalignment of investments. This Series paper shows the global distribution of existing OHNs and assesses their collective characteristics to identify potential deficits in the ways OHNs have formed and to help increase the effectiveness of investments. We searched PubMed, Google, Google Scholar, and relevant conference websites for potential OHNs and identified 184 worldwide for further analysis. We developed four case studies to show important findings from our research and exemplify best practices in One Health operationalisation. Our findings show that, although more OHNs were formed in the past 10 years than in the preceding decade, investment in OHNs has not been equitably distributed; more OHNs are formed and headquartered in Europe than in any other region, and emerging infections and novel pathogens were the priority focus area for most OHNs, with fewer OHNs focusing on other important hazards and pressing threats to health security. We found substantial deficits in the OHNs collaboration model regarding the diversity of stakeholder and sector representation, which we argue impedes effective and equitable OHN formation and contributes to other imbalances in OHN distribution and priorities. These findings are supported by previous evidence that shows the skewed investment in One Health thus far. The increased attention to One Health after the COVID-19 pandemic is an opportunity to focus efforts and resources to areas that need them most. Analyses, such as this Series paper, should be used to establish databases and repositories of OHNs worldwide. Increased attention should then be given to understanding existing resource allocation and distribution patterns, establish more egalitarian networks that encompass the breadth of One Health issues, and serve communities most affected by emerging, re-emerging, or endemic threats at the human-animal-environment interface.

Rapid culture-independent loop-mediated isothermal amplification detection of antimicrobial resistance markers from environmental water samples

Environmental water is considered one of the main vehicles for the transmission of antimicrobial resistance (AMR), posing an increasing threat to humans and animals health. Continuous efforts are being made to eliminate AMR; however, the detection of AMR pathogens from water samples often requires at least one culture step, which is time-consuming and can limit sensitivity. In this study, we employed comparative genomics to identify the prevalence of AMR genes within among: Escherichia coli, Klebsiella, Salmonella enterica and Acinetobacter, using publicly available genomes. The mcr-1, blaKPC (KPC-1 to KPC-4 alleles), blaOXA-48, blaOXA-23 and blaVIM (VIM-1 and VIM-2 alleles) genes are of great medical and veterinary significance, thus were selected as targets for the development of isothermal loop-mediated amplification (LAMP) detection assays. We also developed a rapid and sensitive sample preparation method for an integrated culture-independent LAMP-based detection from water samples. The developed assays successfully detected the five AMR gene markers from pond water within 1 h and were 100% sensitive and specific with a detection limit of 0.0625 μg/mL and 10 cfu/mL for genomic DNA and spiked bacterial cells, respectively. The integrated detection can be easily implemented in resource-limited areas to enhance One Health AMR surveillances and improve diagnostics.

MBPD: A multiple bacterial pathogen detection pipeline for One Health practices

Bacterial pathogens are one of the major threats to biosafety and environmental health, and advanced assessment is a prerequisite to combating bacterial pathogens. Currently, 16S rRNA gene sequencing is efficient in the open-view detection of bacterial pathogens. However, the taxonomic resolution and applicability of this method are limited by the domain-specific pathogen database, taxonomic profiling method, and sequencing target of 16S variable regions. Here, we present a pipeline of multiple bacterial pathogen detection (MBPD) to identify the animal, plant, and zoonotic pathogens. MBPD is based on a large, curated database of the full-length 16S genes of 1986 reported bacterial pathogen species covering 72,685 sequences. In silico comparison allowed MBPD to provide the appropriate similarity threshold for both full-length and variable-region sequencing platforms, while the subregion of V3-V4 (mean: 88.37%, accuracy rate compared to V1-V9) outperformed other variable regions in pathogen identification compared to full-length sequencing. Benchmarking on real data sets suggested the superiority of MBPD in a broader range of pathogen detections compared with other methods, including 16SPIP and MIP. Beyond detecting the known causal agent of animal, human, and plant diseases, MBPD is capable of identifying cocontaminating pathogens from biological and environmental samples. Overall, we provide a MBPD pipeline for agricultural, veterinary, medical, and environmental monitoring to achieve One Health.

Monkeypox outbreak: Wastewater and environmental surveillance perspective

Monkeypox disease (MPXD), a viral disease caused by the monkeypox virus (MPXV), is an emerging zoonotic disease endemic in some countries of Central and Western Africa but seldom reported outside the affected region. Since May 2022, MPXD has been reported at least in 74 countries globally, prompting the World Health Organization to declare the MPXD outbreak a Public Health Emergency of International Concern. As of July 24, 2022; 92 % (68/74) of the countries with reported MPXD cases had no historical MPXD case reports. From the One Health perspective, the spread of MPXV in the environment poses a risk not only to humans but also to small mammals and may, ultimately, spread to potent novel host populations. Wastewater-based surveillance (WBS) has been extensively utilized to monitor communicable diseases, particularly during the ongoing COVID-19 pandemic. It helped in monitoring infectious disease caseloads as well as specific viral variants circulating in communities. The detection of MPXV DNA in lesion materials (e.g. skin, vesicle fluid, crusts), skin rashes, and various body fluids, including respiratory and nasal secretions, saliva, urine, feces, and semen of infected individuals, supports the possibility of using WBS as an early proxy for the detection of MPXV infections. WBS of MPXV DNA can be used to monitor MPXV activity/trends in sewerage network areas even before detecting laboratory-confirmed clinical cases within a community. However, several factors affect the detection of MPXV in wastewater including, but not limited to, routes and duration time of virus shedding by infected individuals, infection rates in the relevant affected population, environmental persistence, the processes and analytical sensitivity of the used methods. Further research is needed to identify the key factors that impact the detection of MPXV biomarkers in wastewater and improve the utility of WBS of MPXV as an early warning and monitoring tool for safeguarding human health. In this review, we shortly summarize aspects of the MPXV outbreak relevant to wastewater monitoring and discuss the challenges associated with WBS.

Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius

BACKGROUND

The striped field mouse Apodemus agrarius is a wild rodent commonly found in fields in Korea. It is a known carrier of various pathogens. Amplicon-based next-generation sequencing (NGS) targeting the 16S ribosomal RNA (rRNA) gene is the most common technique used to analyze the bacterial microbiome. Although many bacterial microbiome analyses have been attempted using feces of wild animals, only a few studies have used NGS to screen for parasites. This study aimed to rapidly detect bacterial, fungal and parasitic pathogens in the guts of A. agrarius using NGS-based metabarcoding analysis.

METHODS

We conducted 18S/16S rDNA-targeted high-throughput sequencing on cecal samples collected from A. agrarius (n = 48) trapped in May and October 2017. Taxa of protozoa, fungi, helminths and bacteria in the cecal content were then identified.

RESULTS

Among the protozoa identified, the most prevalent was Tritrichomonas sp., found in all of the cecal samples, followed by Monocercomonas sp. (95.8% prevalence; in 46/48 samples) and Giardia sp. (75% prevalence; in 36/48 samples). For helminths, Heligmosomoides sp. was the most common, found in 85.4% (41/48) of samples, followed by Hymenolepis sp. (10.4%; 5/48) and Syphacia sp. (25%; 12/48). The 16S rRNA gene analysis showed that the microbial composition of the cecal samples changed by season (P = 0.005), with the linear discriminant analysis effect size showing that in the spring Escherichia coli and Lactobacillus murinus were more abundant and Helicobacter rodentium was less abundant. Helicobacter japonicus was more abundant and Prevotella_uc was less abundant in males. The microbial composition changed based on the Heligmosomoides sp. infection status (P = 0.019); specifically, Lactobacillus gasseri and Lactobacillus intestinalis were more abundant in the Heligmosomoides sp.-positive group than in the Heligmosomoides sp.-negative group.

CONCLUSIONS

This study demonstrated that bacterial abundance changed based on the season and specific parasitic infection status of the trapped mice. These results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs.

Immunohistochemical Characterization of Immune System Cells in Lymphoid Organs from Roe and Fallow Deer

Simple Summary

Diseases emerging from wildlife represent a growing public health issue. Cervids share many pathogens with domestic species and humans, representing useful spontaneous models to evaluate host-pathogen balance. Histology and immunohistochemistry can help in fully understanding the pathogenesis of infection in these species, but few studies have been conducted to characterize immune cell markers. This study highlights that lymphocytes and macrophagic subsets in roe and fallow deer lymphoid tissue can be identified by a panel of commercial antibodies developed against humans. A description of the main immune cell distribution was provided. These results may support future investigations on immune cell response and pathogenesis in roe and fallow deer diseases.

Abstract

Roe and Fallow deer are common wild ruminants widely distributed in Italy. Infectious diseases of these species can potentially pose health risks to domestic animals and humans. However, few studies have been conducted in which immune system cells in these species were phenotyped. The aims of this study were to determine the cross-reactivity of a wide anti-human panel of commercial antibodies on formalin-fixed and paraffin-embedded (FFPE) samples and to describe the distribution of roe and fallow deer main immune cell subsets in the lymph nodes and spleen. Twenty retromandibular lymph nodes (RLNs) and spleen samples were collected from 10 roe deer and 10 fallow deer and were tested by a panel of 12 commercial anti-human antibodies. The CD79a, CD20, CD3, Iba-1, MAC387, and AM-3K antibodies were successfully labeled cells in cervine tissue, while the Foxp3 and the CD68 did not show suitable immunostaining. This study supplies the first immunohistochemical description of immune cell subpopulations in non-pathological spleen and RLNs from roe and fallow deer and provides an easily repeatable manual IHC protocol to immunolocalize cervine B-, T-cells, and macrophages subsets in FFPE tissue samples.

Screen the unforeseen: Microbiome-profiling for detection of zoonotic pathogens in wild rats

Wild rats can host various zoonotic pathogens. Detection of these pathogens is commonly performed using molecular techniques targeting one or a few specific pathogens. However, this specific way of surveillance could lead to (emerging) zoonotic pathogens staying unnoticed. This problem may be overcome by using broader microbiome-profiling techniques, which enable broad screening of a sample's bacterial or viral composition. In this study, we investigated if 16S rRNA gene amplicon sequencing would be a suitable tool for the detection of zoonotic bacteria in wild rats. Moreover, we used virome-enriched (VirCapSeq) sequencing to detect zoonotic viruses. DNA from kidney samples of 147 wild brown rats (Rattus norvegicus) and 42 black rats (Rattus rattus) was used for 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. Blocking primers were developed to reduce the amplification of rat host DNA. The kidney bacterial composition was studied using alpha- and beta-diversity metrics and statistically assessed using PERMANOVA and SIMPER analyses. From the sequencing data, 14 potentially zoonotic bacterial genera were identified from which the presence of zoonotic Leptospira spp. and Bartonella tribocorum was confirmed by (q)PCR or Sanger sequencing. In addition, more than 65% of all samples were dominated (>50% reads) by one of three bacterial taxa: Streptococcus (n = 59), Mycoplasma (n = 39) and Leptospira (n = 25). These taxa also showed the highest contribution to the observed differences in beta diversity. VirCapSeq sequencing in rat liver samples detected the potentially zoonotic rat hepatitis E virus in three rats. Although 16S rRNA gene amplicon sequencing was limited in its capacity for species level identifications and can be more difficult to interpret due to the influence of contaminating sequences in these low microbial biomass samples, we believe it has potential to be a suitable pre-screening method in the future to get a better overview of potentially zoonotic bacteria that are circulating in wildlife.

Dynamic antimicrobial resistant patterns of Escherichia coli from healthy poultry and swine over 10 years in Chongming Island, Shanghai

Background

Antimicrobial resistance (AMR) is one of the greatest threats to animal and public health. Here, we conducted a dynamic surveillance of Escherichia coli on Chongming Island in Shanghai during 2009–2021 to identify the characteristics and trends of Chongming’s AMR pandemic.

Methods

Rectal (cloaca) swabs from four poultry and nine swine farms (Chongming Island, 2009–2021) were collected for E. coli strains acquisition. The micro-broth dilution method was used to test antimicrobial susceptibility of E. coli isolates against 10 antimicrobial classes including 15 antimicrobials. Utilizing generalized linear mixed models (GLMMs) and co-occurrence analyses, we further explored the multiple-drug-resistance (MDR) combinations and dynamic patterns of E. coli over 10 years in two food animals.

Results

Total of 863 MDR isolates were found among 945 collected E. coli isolates, 337 from poultry and 608 from swine. Both isolates exhibited high resistant rates (> 70%) to tetracyclines, phenicols, sulfonamides, penicillins, and aminoglycosides (only in swine). The resistant rates of swine isolates to penicillins, aminoglycosides, tetracyclines, phenicols, and polymyxins were significantly higher than those of poultry isolates, whereas resistance to fluoroquinolones was reversed. Resistance to polymyxins decreased similarly in swine (42.4% in 2009 to 0.0% in 2021) and poultry isolates (from 16.5% to 0.0%). However, resistance to other seven antimicrobial classes (excluding carbapenems and penicillins) declined dramatically in swine isolates, particularly fluoroquinolones (from 80.5% to 14.4%), and tendencies of resistance to the seven classes showed markedly divergent patterns in poultry isolates. Using Poisson GLMMs, the AMR carriage since 2016 was significantly lower than that of 2009 (odds ratio < 1), indicating a decline in the risk of MDR emergence. Furthermore, despite the highly diverse MDR profiles, co-occurrence analysis identified two prominent MDR clusters of penicillins-phenicols-fluoroquinolones in poultry and aminoglycosides-tetracyclines-sulfonamides-phenicols in swine.

Conclusions

Our study uncovered vastly distinct AMR patterns and dynamic tendencies of poultry and swine E. coli isolates from Chongming. Meanwhile, Chongming’s AMR status has ameliorated, as indicated by the decline in antimicrobials prevalence (particularly in swine), lower likelihood of MDR emergence and low carbapenem-, cephalosporin-, and polymyxin resistance. Importantly, this surveillance results are the vital basis for future policy development in Chongming and Shanghai.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-022-01025-4.

Texas professionals are employing a one health approach to protect the United States against biosecurity threats

Texas is a geographically large state with large human and livestock populations, many farms, a long coastal region, and extreme fluctuations in weather. During the last 15 years, the state of Texas has frequently suffered disasters or catastrophes causing extensive morbidity and economic loss. These disasters often have complicated consequences requiring multi-faceted responses. Recently, an interdisciplinary network of professionals from multiple academic institutions has emerged to collaborate in protecting Texas and the USA using a One Health approach. These experts are training the next generation of scientists in biopreparedness; increasing understanding of pathogens that cause repetitive harm; developing new therapeutics and vaccines against them; and developing novel surveillance approaches so that emerging pathogens will be detected early and thwarted before they can cause disastrous human and economic losses. These academic One Health partnerships strengthen our ability to protect human and animal health against future catastrophes that may impact the diverse ecoregions of Texas and the world.

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Texas has suffered from numerous disasters or catastrophes, often more than other US states.

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These disasters have caused tremendous morbidity, mortality, and economic loss.

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Texas professionals are partnering in One Health ways to mitigate such catastrophes.

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These numerous collaborations are important to Texas, the USA, and abroad.

Understanding and strengthening wildlife and zoonotic disease policy processes: A research imperative

The COVID-19 pandemic highlights the urgency and importance of monitoring, managing and addressing zoonotic diseases, and the acute challenges of doing so with sufficient inter-jurisdictional coordination in a dynamic global context. Although wildlife pathogens are well-studied clinically and ecologically, there is very little systematic scholarship on their management or on policy implications. The current global pandemic therefore presents a unique social science research imperative: to understand how decisions are made about preventing and responding to wildlife diseases, especially zoonoses, and how those policy processes can be improved as part of early warning systems, preparedness and rapid response. To meet these challenges, we recommend intensified research efforts towards: (i) generating functional insights about wildlife and zoonotic disease policy processes, (ii) enabling social and organizational learning to mobilize those insights, (iii) understanding epistemic instability to address populist anti-science and (iv) anticipating evolving and new zoonotic emergences, especially their human dimensions. Since policy processes for zoonoses can be acutely challenged during the early stages of an epidemic or pandemic, such insights can provide a pragmatic, empirically-based roadmap for enhancing their robustness and efficacy, and benefiting long-term decision-making efforts.

When might host heterogeneity drive the evolution of asymptomatic, pandemic coronaviruses?

Controlling many infectious diseases, including SARS-Coronavirus-2 (SARS-CoV-2), requires surveillance followed by isolation, contact-tracing and quarantining. These interventions often begin by identifying symptomatic individuals. However, actively removing pathogen strains causing symptomatic infections may inadvertently select for strains less likely to cause symptomatic infections. Moreover, a pathogen's fitness landscape is structured around a heterogeneous host pool; uneven surveillance efforts and distinct transmission risks across host classes can meaningfully alter selection pressures. Here, we explore this interplay between evolution caused by disease control efforts and the evolutionary consequences of host heterogeneity. Using an evolutionary epidemiology model parameterized for coronaviruses, we show that intense symptoms-driven disease control selects for asymptomatic strains, particularly when these efforts are applied unevenly across host groups. Under these conditions, increasing quarantine efforts have diverging effects. If isolation alone cannot eradicate, intensive quarantine efforts combined with uneven detections of asymptomatic infections (e.g., via neglect of some host classes) can favor the evolution of asymptomatic strains. We further show how, when intervention intensity depends on the prevalence of symptomatic infections, higher removal efforts (and isolating symptomatic cases in particular) more readily select for asymptomatic strains than when these efforts do not depend on prevalence. The selection pressures on pathogens caused by isolation and quarantining likely lie between the extremes of no intervention and thoroughly successful eradication. Thus, analyzing how different public health responses can select for asymptomatic pathogen strains is critical for identifying disease suppression efforts that can effectively manage emerging infectious diseases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11071-022-07548-7.

Major bat-borne zoonotic viral epidemics in Asia and Africa: A systematic review and meta-analysis

Bats are the natural reservoir host for many pathogenic and non‐pathogenic viruses, potentially spilling over to humans and domestic animals directly or via an intermediate host. The ongoing COVID‐19 pandemic is the continuation of virus spillover events that have taken place over the last few decades, particularly in Asia and Africa. Therefore, these bat‐associated epidemics provide a significant number of hints, including respiratory cellular tropism, more intense susceptibility to these cell types, and overall likely to become a pandemic for the next spillover. In this systematic review, we analysed data to insight, through bat‐originated spillover in Asia and Africa. We used STATA/IC‐13 software for descriptive statistics and meta‐analysis. The random effect of meta‐analysis showed that the pooled estimates of case fatality rates of bat‐originated viral zoonotic diseases were higher in Africa (61.06%, 95%CI: 50.26 to 71.85, l²% = 97.3, p < 0.001). Moreover, estimates of case fatality rates were higher in Ebola (61.06%; 95%CI: 50.26 to 71.85, l²% = 97.3, p < 0.001) followed by Nipah (55.19%; 95%CI: 39.29 to 71.09, l²% = 94.2, p < 0.001), MERS (18.49%; 95%CI: 8.19 to 28.76, l²% = 95.4, p < 0.001) and SARS (10.86%; 95%CI: 6.02 to 15.71, l²% = 85.7, p < 0.001) with the overall case fatality rates of 29.86 (95%CI: 29.97 to 48.58, l²% = 99.0, p < 0.001). Bat‐originated viruses have caused several outbreaks of deadly diseases, including Nipah, Ebola, SARS and MERS in Asia and Africa in a sequential fashion. Nipah virus emerged first in Malaysia, but later, periodic outbreaks were noticed in Bangladesh and India. Similarly, the Ebola virus was detected in the African continent with neurological disorders in humans, like Nipah, seen in the Asian region. Two important coronaviruses, MERS and SARS, were introduced, both with the potential to infect respiratory passages. This paper explores the dimension of spillover events within and/or between bat–human and the epidemiological risk factors, which may lead to another pandemic occurring. Further, these processes enhance the bat‐originated virus, which utilises an intermediate host to jump into human species.

Understanding the changing role of global public health in biodiversity conservation

Zoonotic disease emergence has become a core concern of biodiversity conservation amid the ongoing impacts of the COVID-19 pandemic. Major international conservation groups now comprehensively center larger human-nature imbalances not only as problems of global public health but as a core challenge of the conservation movement, alongside habitat destruction, biodiversity loss and climate change. There is, however, little consideration of how new biosecurity concerns might alter conservation practice with unexpected and potential harmful impacts on human communities, particularly in developing nations with significant human-wildlife interfaces. Reviewing emerging policy positions from key conservation organizations, this article argues that the proposed responses to the COVID-19 pandemic hold the potential to (a) amplify existing people-park conflicts, and (b) generate new tensions by integrating global systems of viral surveillance into biodiversity conservation. I conclude that the close integration of biosecurity concerns into conservation policies requires greater acknowledgment of the unique challenges for human communities.

Zoonoses and global epidemics

PURPOSE OF REVIEW

The purpose of the review is to summarize recent advances in understanding the origins, drivers and clinical context of zoonotic disease epidemics and pandemics. In addition, we aimed to highlight the role of clinicians in identifying sentinel cases of zoonotic disease outbreaks.

RECENT FINDINGS

The majority of emerging infectious disease events over recent decades, including the COVID-19 pandemic, have been caused by zoonotic viruses and bacteria. In particular, coronaviruses, haemorrhagic fever viruses, arboviruses and influenza A viruses have caused significant epidemics globally. There have been recent advances in understanding the origins and drivers of zoonotic epidemics, yet there are gaps in diagnostic capacity and clinical training about zoonoses.

SUMMARY

Identifying the origins of zoonotic pathogens, understanding factors influencing disease transmission and improving the diagnostic capacity of clinicians will be crucial to early detection and prevention of further epidemics of zoonoses.

Analytical and Early Detection System of Infectious Diseases and Animal Health Status in Kuwait

This study aimed at the development of an analytic web-based system for the assessment of animal health in Kuwait. The data sources were based on the World Organization for Animal Health (OIE) and the World Animal Health Information System (WAHIS) repository with data gathered for the period (2005–2020). An on-line web-based system using TABLEAU Creator was developed for monitoring and surveillance of animal disease outbreaks. Five animal diseases were identified in Kuwait; namely, HPAI, FMD, glanders, LSD and MERS-CoV. The highest numbers of outbreaks were recorded for HPAI, followed by FMD. Examples of spatio-temporal visualizations of the web based mappings are presented and include disease cases, number of outbreaks and farm locations, among other features. The web-based system can serve as a monitoring tool to easily display the status of animal health in Kuwait. It can also serve to quickly identify and track disease outbreaks and monitor the spread patterns of new or emerging animal diseases between neighboring countries.

Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation†

Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.

Detection and distribution of zoonotic pathogens in wild Norway rats (Rattus norvegicus) from Tehran, Iran

This is the first study on the prevalence of vector-borne zoonotic pathogens found in Rattus norvegicus (R. norvegicus) in urban areas of Tehran, Iran. Serological tests were used to detect IgG antibodies against Coxiella burnetii (C. burnetii) and Rickettsia spp. using a commercial qualitative rat ELISA kit. The frequency of Streptobacillus moniliformis (S. moniliformis) and Bartonella spp. was determined using a conventional PCR method. Molecular detection and characterization of Leptospira spp. were conducted using TaqMan real-time PCR based on lipL32 gene and SecY typing methods. A total of 100 R. norvegicus rats were collected from five regions in Tehran, Iran, and investigated to determine their zoonotic pathogens. S. moniliformis and Bartonella spp. were detected in 23 of 100 (23%) and 17 of 100 (17%) R. norvegicus populations, respectively. The highest prevalence of S. moniliformis and Bartonella spp. with similar frequency rates (n = 6/20; 30%) was seen among the R. norvegicus rats captured from the northern and southern parts of Tehran, respectively. Seroreactivity against C. burnetii and Rickettsia spp. was detected in 4% and 1% of R. norvegicus, respectively. C. burnetii. was identified only in one rat captured from the eastern part of Tehran. Results showed that Leptospira spp. was detected only in two rats, collected from the southern part (n = 2/20; 10%) of Tehran. The secY typing method identified two different Leptospira species including L. interrogans and L. kirschneri. The results showed that urban rats might play an important role in transmission of zoonotic pathogens to humans.

Implications of Zoonoses From Hunting and Use of Wildlife in North American Arctic and Boreal Biomes: Pandemic Potential, Monitoring, and Mitigation

The COVID-19 pandemic has re-focused attention on mechanisms that lead to zoonotic disease spillover and spread. Commercial wildlife trade, and associated markets, are recognized mechanisms for zoonotic disease emergence, resulting in a growing global conversation around reducing human disease risks from spillover associated with hunting, trade, and consumption of wild animals. These discussions are especially relevant to people who rely on harvesting wildlife to meet nutritional, and cultural needs, including those in Arctic and boreal regions. Global policies around wildlife use and trade can impact food sovereignty and security, especially of Indigenous Peoples. We reviewed known zoonotic pathogens and current risks of transmission from wildlife (including fish) to humans in North American Arctic and boreal biomes, and evaluated the epidemic and pandemic potential of these zoonoses. We discuss future concerns, and consider monitoring and mitigation measures in these changing socio-ecological systems. While multiple zoonotic pathogens circulate in these systems, risks to humans are mostly limited to individual illness or local community outbreaks. These regions are relatively remote, subject to very cold temperatures, have relatively low wildlife, domestic animal, and pathogen diversity, and in many cases low density, including of humans. Hence, favorable conditions for emergence of novel diseases or major amplification of a spillover event are currently not present. The greatest risk to northern communities from pathogens of pandemic potential is via introduction with humans visiting from other areas. However, Arctic and boreal ecosystems are undergoing rapid changes through climate warming, habitat encroachment, and development; all of which can change host and pathogen relationships, thereby affecting the probability of the emergence of new (and re-emergence of old) zoonoses. Indigenous leadership and engagement in disease monitoring, prevention and response, is vital from the outset, and would increase the success of such efforts, as well as ensure the protection of Indigenous rights as outlined in the United Nations Declaration on the Rights of Indigenous Peoples. Partnering with northern communities and including Indigenous Knowledge Systems would improve the timeliness, and likelihood, of detecting emerging zoonotic risks, and contextualize risk assessments to the unique human-wildlife relationships present in northern biomes.

The Berlin principles on one health - Bridging global health and conservation

For over 15-years, proponents of the One Health approach have worked to consistently interweave components that should never have been separated and now more than ever need to be re-connected: the health of humans, non-human animals, and ecosystems. We have failed to heed the warning signs. A One Health approach is paramount in directing our future health in this acutely and irrevocably changed world. COVID-19 has shown us the exorbitant cost of inaction. The time to act is now.

Mitigating Future Respiratory Virus Pandemics: New Threats and Approaches to Consider

Despite many recent efforts to predict and control emerging infectious disease threats to humans, we failed to anticipate the zoonotic viruses which led to pandemics in 2009 and 2020. The morbidity, mortality, and economic costs of these pandemics have been staggering. We desperately need a more targeted, cost-efficient, and sustainable strategy to detect and mitigate future zoonotic respiratory virus threats. Evidence suggests that the transition from an animal virus to a human pathogen is incremental and requires a considerable number of spillover events and considerable time before a pandemic variant emerges. This evolutionary view argues for the refocusing of public health resources on novel respiratory virus surveillance at human-animal interfaces in geographical hotspots for emerging infectious diseases. Where human-animal interface surveillance is not possible, a secondary high-yield, cost-efficient strategy is to conduct novel respiratory virus surveillance among pneumonia patients in these same hotspots. When novel pathogens are discovered, they must be quickly assessed for their human risk and, if indicated, mitigation strategies initiated. In this review, we discuss the most common respiratory virus threats, current efforts at early emerging pathogen detection, and propose and defend new molecular pathogen discovery strategies with the goal of preempting future pandemics.

Emergency preparedness for public health threats, surveillance, modelling & forecasting

In the interconnected world, safeguarding global health security is vital for maintaining public health and economic upliftment of any nation. Emergency preparedness is considered as the key to control the emerging public health challenges at both national as well as international levels. Further, the predictive information systems based on routine surveillance, disease modelling and forecasting play a pivotal role in both policy building and community participation to detect, prevent and respond to potential health threats. Therefore, reliable and timely forecasts of these untoward events could mobilize swift and effective public health responses and mitigation efforts. The present review focuses on the various aspects of emergency preparedness with special emphasis on public health surveillance, epidemiological modelling and capacity building approaches. Global coordination and capacity building, funding and commitment at the national and international levels, under the One Health framework, are crucial in combating global public health threats in a holistic manner.

Neurologic Manifestations of the World Health Organization's List of Pandemic and Epidemic Diseases

The World Health Organization (WHO) monitors the spread of diseases globally and maintains a list of diseases with epidemic or pandemic potential. Currently listed diseases include Chikungunya, cholera, Crimean-Congo hemorrhagic fever, Ebola virus disease, Hendra virus infection, influenza, Lassa fever, Marburg virus disease, Neisseria meningitis, MERS-CoV, monkeypox, Nipah virus infection, novel coronavirus (COVID-19), plague, Rift Valley fever, SARS, smallpox, tularemia, yellow fever, and Zika virus disease. The associated pathogens are increasingly important on the global stage. The majority of these diseases have neurological manifestations. Those with less frequent neurological manifestations may also have important consequences. This is highlighted now in particular through the ongoing COVID-19 pandemic and reinforces that pathogens with the potential to spread rapidly and widely, in spite of concerted global efforts, may affect the nervous system. We searched the scientific literature, dating from 1934 to August 2020, to compile data on the cause, epidemiology, clinical presentation, neuroimaging features, and treatment of each of the diseases of epidemic or pandemic potential as viewed through a neurologist's lens. We included articles with an abstract or full text in English in this topical and scoping review. Diseases with epidemic and pandemic potential can be spread directly from human to human, animal to human, via mosquitoes or other insects, or via environmental contamination. Manifestations include central neurologic conditions (meningitis, encephalitis, intraparenchymal hemorrhage, seizures), peripheral and cranial nerve syndromes (sensory neuropathy, sensorineural hearing loss, ophthalmoplegia), post-infectious syndromes (acute inflammatory polyneuropathy), and congenital syndromes (fetal microcephaly), among others. Some diseases have not been well-characterized from a neurological standpoint, but all have at least scattered case reports of neurological features. Some of the diseases have curative treatments available while in other cases, supportive care remains the only management option. Regardless of the pathogen, prompt, and aggressive measures to control the spread of these agents are the most important factors in lowering the overall morbidity and mortality they can cause.

A descriptive study of zoonotic disease risk at the human-wildlife interface in a biodiversity hot spot in South Western Uganda

Zoonotic diseases pose a significant health challenge at the human-wildlife interface, especially in Sub-Saharan Africa where ecosystem services contribute significantly to local livelihoods and individual well-being. In Uganda, the fragmented forests of Hoima district, form part of a "biodiversity and emerging infectious disease hotspot" composed of communities with high dependency on these wildlife protected areas, unaware of the associated health risks. We conducted a cross-sectional mixed methods study from March to May 2017 and interviewed 370 respondents, using a semi-structured questionnaire from eight villages neighbouring forest fragments in Hoima District, Uganda. Additionally, a total of ten (10) focus group discussions (FGDs) consisting of 6-10 men or women were conducted to further explore the drivers of hunting and perception of zoonotic disease risks at community level. Qualitative and quantitative data were analysed using content analysis and STATA version 12 respectively. We found twenty-nine percent (29.0%, CI: 24.4-33.9) of respondents were engaged in hunting of wildlife such as chimpanzee (Pan troglodytes) and 45.8% (CI: 40.6-51.0), cane rats (Thryonomyidae spp). Acquisition of animal protein was among the main reasons why communities hunt (55.3%, CI: 50.1-60.4), followed by "cultural" and "medicinal" uses of wildlife and or its parts (22.7%, CI: 18.6-27.4). Results further revealed that hunting and bushmeat consumption is persistent for other perceived reasons like; bushmeat strengthens the body, helps mothers recover faster after delivery, boosts one's immunity and hunting is exercise for the body. However, respondents reported falling sick after consumption of bushmeat at least once (7.9%, CI: 5.3-11.1), with 5.3% (CI: 2.60-9.60) reporting similar symptoms among some family members. Generally, few respondents (37.0%, CI: 32.1-42.2) were aware of diseases transmissible from wildlife to humans, although 88.7% (CI: 85.0-92.0) had heard of Ebola or Marburg without context. Hunting non-human primate poses a health risk compared to edible rats (cane rats) and wild ruminants (cOR = 0.4, 95% CI = 0.1-0.9) and (cOR = 0.7, 95% CI = 0.2-2.1) respectively. Study suggests some of the pathways for zoonotic disease spillover to humans exist at interface areas driven by livelihoods, nutrition and cultural needs. This study offers opportunities for a comprehensive risk communication and health education strategy for communities living at the interface of wildlife and human interactions.

Here, There, and Everywhere: The Wide Host Range and Geographic Distribution of Zoonotic Orthopoxviruses

The global emergence of zoonotic viruses, including poxviruses, poses one of the greatest threats to human and animal health. Forty years after the eradication of smallpox, emerging zoonotic orthopoxviruses, such as monkeypox, cowpox, and vaccinia viruses continue to infect humans as well as wild and domestic animals. Currently, the geographical distribution of poxviruses in a broad range of hosts worldwide raises concerns regarding the possibility of outbreaks or viral dissemination to new geographical regions. Here, we review the global host ranges and current epidemiological understanding of zoonotic orthopoxviruses while focusing on orthopoxviruses with epidemic potential, including monkeypox, cowpox, and vaccinia viruses.

Reasons for and barriers to biosafety and biosecurity training in health-related organizations in Africa, Middle East and Central Asia: findings from GIBACHT training needs assessments 2018-2019

Introduction

the Global-Partnership-Initiated-Biosecurity-Academia for Controlling Health Threats (GIBACHT) consortium conducts a biosafety and biosecurity training for fellows from Africa, the Middle East and Asia. To achieve a multiplier effect, fellows conduct trainings in their own organizations. It was during such trainings that training needs assessments were done assessing reasons for and barriers to biosafety and biosecurity training.

Methods

this was a cross sectional assessment. Trainings were conducted from April to July 2018 and April to June 2019. In 2018, training needs were explored using a structured tool. Responses were coded using manifest content analysis and key issues identified. In 2019, respondents quantified the identified key issues using a Likert scale. Proportions of those who strongly agreed, agreed, neither agreed nor disagreed, disagreed or strongly disagreed were calculated and results presented in tables and charts.

Results

in 2018 and 2019, there were 183 and 191 respondents respectively. About 96% of respondents in 2018 supported training in biosafety and biosecurity citing individual, community and global benefits. Barriers highlighted included governance, financial, human resource, information and infrastructure challenges. In 2019, majority of respondents indicated inadequate guidelines dissemination, lack of financial resources, inadequate personnel, lack of equipped laboratories and lack of instructional materials among major barriers.

Conclusion

support for biosafety and biosecurity training was high though systemic barriers exist. Improving human resource capacity and provision of instructional materials can be achieved through training programs. However, systemic assessments need to be done before each training as different organizations have different barriers.

LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa

High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.

A Comparative Study of Associated Microbiota Between Pig Farm and Pig Slaughterhouse in Guangdong, China

The goal of this study was to compare the microbiota in different pig-present settings in China. Bioaerosol samples from pig farms and slaughterhouses and nasal samples from pig farmers and slaughterhouse workers were collected in Guangdong, southern China. The bacterial genomic DNA was isolated and subjected to 16S sequencing. The data were analyzed using QIIME2 with the DADA2 pipeline. A total of 14,923,551 clean reads and 2785 operational taxonomic units (OTUs) were obtained, which were mostly grouped into 4 phyla (Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria) and 220 families. The microbiota richness of nasal samples in pig-present workers was higher than that of bioaerosols collected in the vicinity of the pig enclosures. There were 31.7% (620/1954) shared OTUs between pig farm bioaerosols and pig farmers which was higher than that between pig slaughterhouses and slaughterhouse workers (23.4%, 364/1553) (p < 0.001). Acinetobacter and Pseudomonas were the most abundant in pig-present bioaerosols, and Staphylococcus, Pseudomonas, and Corynebacterium were dominant bacterial genus in pig farmers. The bacterial patterns are also specific to the location of sample collected. The results suggest that bioaerosol microbiota interact with human nasal microbes in the vicinity of the pig farm enclosures, providing the basis for further analysis of microbial transmission across hosts in pig-present settings.

Self-disseminating vaccines to suppress zoonoses

The SARS-CoV-2 epidemic is merely the most recent demonstration that our current approach to emerging zoonotic infectious disease is ineffective. SARS, MERS, Ebola, Nipah and an array of arenavirus infections sporadically spillover into human populations and are often contained only as a result of their poor transmission in human hosts, coupled with intense public health control efforts in the early stages of an emerging epidemic. It is now more apparent than ever that we need a better and more proactive approach. One possibility is to eliminate the threat of spillover before it occurs using vaccines capable of autonomously spreading through wild animal reservoirs. We are now poised to begin developing self-disseminating vaccines targeting a wide range of human pathogens, but important decisions remain about how they can be most effectively designed and used to target pathogens with a high risk of spillover and/or emergence. In this Perspective, we first review the basic epidemiological theory establishing the feasibility and utility of self-disseminating vaccines. We then outline a road map for overcoming remaining technical challenges: identifying high-risk pathogens before they emerge, optimizing vaccine design with an eye to evolution, behaviour and epidemiology, and minimizing the risk of unintended consequences.

Evidence for SARS-CoV-2 Infection of Animal Hosts

COVID-19 is the first known pandemic caused by a coronavirus, SARS-CoV-2, which is the third virus in the family Coronaviridae to cause fatal infections in humans after SARS-CoV and MERS-CoV. Animals are involved in the COVID-19 pandemic. This review summarizes the role of animals as reservoirs, natural hosts and experimental models. SARS-CoV-2 originated from animal reservoir, most likely bats and/or pangolins. Anthroponotic transmission has been reported in cats, dogs, tigers, lions and minks. As of now, there is no a strong evidence for natural animal-to-human transmission or sustained animal-to-animal transmission of SARS-CoV-2. Experimental infections conducted by several research groups have shown that monkeys, hamsters, ferrets, cats, tree shrews, transgenic mice and fruit bats were permissive, while dogs, pigs and poultry were resistant. There is an urgent need to understand the zoonotic potential of different viruses in animals, particularly in bats, before they transmit to humans. Vaccines or antivirals against SARS-CoV-2 should be evaluated not only for humans, but also for the protection of companion animals (particularly cats) and susceptible zoo and farm animals.

Fair J, Smith W, Martinez Torres T, Lucas J, Monagin C, Winegar R, Fletcher J. Assessing Climate Change Impact on Ecosystems and Infectious Disease: Important Roles for Genomic Sequencing and a One Health Perspective

Changes in the Earth's climate and weather continue to impact the planet's ecosystems, including the interface of infectious disease agents with their hosts and vectors. Environmental disasters, natural and human-made activities raise risk factors that indirectly facilitate infectious disease outbreaks. Subsequently, changes in habitat, displaced populations, and environmental stresses that affect the survival of species are amplified over time. The recurrence and spread of vector-borne (e.g., mosquito, tick, aphid) human, animal, and plant pathogens to new geographic locations are also influenced by climate change. The distribution and range of humans, agricultural animals and plants, wildlife and native plants, as well as vectors, parasites, and microbes that cause neglected diseases of the tropics as well as other global regions are also impacted. In addition, genomic sequencing can now be applied to detect signatures of infectious pathogens as they move into new regions. Molecular detection assays complement metagenomic sequencing to help us understand the microbial community found within the microbiomes of hosts and vectors, and help us uncover mechanistic relationships between climate variability and pathogen transmission. Our understanding of, and responses to, such complex dynamics and their impacts can be enhanced through effective, multi-sectoral One Health engagement coupled with applications of both traditional and novel technologies. Concerted efforts are needed to further harness and leverage technology that can identify and track these impacts of climate changes in order to mitigate and adapt to their effects.