Epidemiology. Infectious diseases: preparing for the future

LAMP Reaction in Plant Disease Surveillance: Applications, Challenges, and Future Perspectives

Movements of plant pathogenic microorganisms in uncontaminated areas occur today at an alarming rate, driven mainly by global trade and climate change. These invaders can trigger new disease outbreaks able to impact the biodiversity and economies of vast territories and affect a variety of ecosystem services. National and supranational regulatory deficiencies, such as inadequate quarantine measures and ineffective early pathogen detection at ports of entry, exacerbate the issue. Thus, there is an urgent need for accurate and rapid diagnostic tools to intercept invasive and nonindigenous plant pathogens. The LAMP (Loop-mediated isothermal AMPlification) technique is a robust, flexible tool representing a significant advance in point-of-care (POC) diagnostics. Its user-friendliness and sensitivity offer a breakthrough in phytosanitary checks at points of entry (harbors and airports), for disease and pest surveillance at vulnerable sites (e.g., nurseries and wood-processing and storage facilities), and for territorial monitoring of new disease outbreaks. This review highlights the strengths and weaknesses of LAMP, emphasizing its potential to revolutionize modern plant disease diagnostics.

The Role of Collective Group Orientation and Social Norms on Physical Distancing Behaviors for Disease Prevention

To reduce the impact of communicable diseases like COVID-19, collective action is required and likely to be susceptible to normative influence as well as whether people are more or less collectively oriented. We extend the theory of normative social behavior (TNSB) to account for group orientation and predict the relationships between social norms and physical distancing behaviors. Using a rolling cross-sectional design during 17 weeks of the pandemic, a national sample of US residents from 20 states (N = 8,778) participated in the study. The findings show that perceived descriptive norms, injunctive norms, and group orientation are significantly associated with physical distancing. The descriptive norm-behavior relationship and injunctive norm-behavior relationship are moderated by group orientation and the other predicted moderators in the TNSB. The findings extend the TNSB and highlight the need to understand social norms and group orientation in formative research for health communication campaigns designed to promote prevention behaviors.

Computational design, docking, and molecular dynamics simulation study of RNA helicase inhibitors of dengue virus

BACKGROUND OBJECTIVES

RNA viruses are complex pathogens in terms of their genetic makeup, mutation frequency, and transmission modes. They contain the RNA helicase enzyme, which plays a crucial role in the viral genome replication process. This work aims to develop and screen a potential molecule that could function as a dengue virus (DENV) RNA helicase inhibitor.

METHODS

The present study was performed by taking 26 potential derivatives of gedunin phytochemicals from the PubChem database as ligands. The binding of the compounds was analyzed by in silico docking considering DENV RNA helicase enzyme as the receptor.

RESULTS

After a thorough analysis of the docking scores, toxicity, and physicochemical properties, the compound tetrahydrogedunin was obtained as the best. Based on tetrahydrogedunin molecular structure, 100 drug-like molecules were designed using the Data Warrior tool. After screening for drug-likeness and ADMET properties, derivative number 42 was considered as promising. Further comparative docking of derivative 42 and a standard inhibitor molecule ST-610 with DENV RNA helicase enzyme showed binding affinity of 10.0 kcal/mol and -9.6 kcal/mol, respectively. The favorable interaction between DENV RNA helicase and derivative 42 was further validated by 50 nanoseconds molecular dynamics simulation and MM-GBSA analysis.

INTERPRETATION CONCLUSION

Since the antiviral activity of derivative 42 has not been reported till date, the compound was predicted as a novel therapeutic molecule that can act against the dengue virus (DENV) RNA helicase enzyme.

Prevalence and predictors of self-medication with antibiotics in Ethiopia: a systematic review and meta-analysis

INTRODUCTION

Antibiotic self-medication is a global public health concern contributing to antibiotic resistance. This systematic review and meta-analysis aim to assess the prevalence of antibiotic self-medication and its associated factors in Ethiopia.

METHODS

A comprehensive search of electronic databases was conducted from MEDLINE (PubMed), Scopus, Google Scholar and Web of Science to identify relevant studies published between 2000 and 2024. Adult households, undergraduate university students and health care professionals who had taken antibiotics without a prescription in the household setting were included in this review. The primary outcome of this review is antibiotic self- medication. The random-effects model was used to estimate pooled prevalence rates. The outcome measure was analyzed with STATA version 17 software.

RESULTS

A total of nine studies were included in the Meta-analysis, comprising a sample size of 5908 participants. The pooled prevalence of antibiotic self-medication among Ethiopians was found to be 46.14 with 95% Confidence Interval [35.71, 56.57]. The most frequently used classes of self-medicated antibiotics were penicillins, followed by tetracyclines. Community pharmacies were the source of information that individuals utilized. The most common reported reasons for antibiotic self-medication include previous experience of treating a similar illness, to save cost, lack of time and avoiding waiting time for medical services. Participants having less than high school educational level was the most commonly reported factor associated with self-medication antibiotics.

CONCLUSION

Antibiotic self-medication is a prevalent practice in Ethiopia. This underscores the need for targeted interventions such as educating people about the risks associated with using antibiotics without medical guidance, which results in a reduction in antibiotic resistance.

An Analytical Approach for Temporal Infection Mapping and Composite Index Development

Significant and composite indices for infectious disease can have implications for developing interventions and public health. This paper presents an investment for developing access to further analysis of the incidence of individual and multiple diseases. This research mainly comprises two steps: first, an automatic and reproducible procedure based on functional data analysis techniques was proposed for analyzing the dynamic properties of each disease; second, orthogonal transformation was adopted for the development of composite indices. Between 2000 and 2019, nineteen class B notifiable diseases in China were collected for this study from the National Bureau of Statistics of China. The study facilitates the probing of underlying information about the dynamics from discrete incidence rates of each disease through the procedure, and it is also possible to obtain similarities and differences about diseases in detail by combining the derivative features. There has been great success in intervening in the majority of notifiable diseases in China, like bacterial or amebic dysentery and epidemic cerebrospinal meningitis, while more efforts are required for some diseases, like AIDS and virus hepatitis. The composite indices were able to reflect a more complex concept by combining individual incidences into a single value, providing a simultaneous reflection for multiple objects, and facilitating disease comparisons accordingly. For the notifiable diseases included in this study, there was superior management of gastro-intestinal infectious diseases and respiratory infectious diseases from the perspective of composite indices. This study developed a methodology for exploring the prevalent properties of infectious diseases. The development of effective and reliable analytical methods provides special insight into infectious diseases’ common dynamics and properties and has implications for the effective intervention of infectious diseases.

Characterising Biosecurity Initiatives Globally to Support the Development of a Progressive Management Pathway for Terrestrial Animals: A Scoping Review

While biosecurity is of increasing importance globally, there is still limited evidence of the factors or elements that support the progressive and sustainable scaling up of biosecurity along the value chains from the local to the global level. To gain insight into the current body of literature on biosecurity, a mixed-methods approach was used based on a scoping literature review and an online survey with subject matter experts. Six databases were searched for published literature, and textual information from titles and abstracts of all included records (n = 266) were analysed through inductive content analysis to build biosecurity-relevant categories and identify strengths, weaknesses, opportunities, and threats (SWOT) of existing biosecurity systems or initiatives (such as projects or programs). Most records focused on initiatives in high-income countries, traditional livestock species (pigs, poultry, and large ruminants), and the production stage and had a disease-specific focus. No records described a comprehensive or global framework to progressively scale up biosecurity. Overall, the findings highlight the need for initiatives such as the FAO Progressive Management Pathway for Terrestrial Animal Biosecurity (FAO-PMP-TAB), which is a stepwise approach for strengthening biosecurity management along value chains to enhance the health, resilience, and sustainability of animal sectors. The findings highlight important elements and provide recommendations useful for developing approaches or a global framework to progressively improve biosecurity management.

Nutritional Profile Changes in an Insect-Fungus Complex of Antheraea pernyi Pupa Infected by Samsoniella hepiali

Historically, some edible insects have been processed into a complex of insect and fungus, such as Antherea pernyi and Samsoniella hepiali. Until now, the dynamics of the nutritional changes due to this infection were unclear. This study reveals the dynamic changes in nutritional components of Antherea pernyi pupa after infection with Samsoniella hepiali at post-infection time points of 0 d, 10 d, 20 d, and 30 d. The dynamic analysis of the components at different post-infection times showed that the content of polysaccharides and cordycepin increased with time while the content of fats and chitin decreased. The content of proteins showed a trend of decreasing at the beginning and then increasing. The essential amino acids (EAAs) decreased at the beginning and then increased, and non-essential amino acids (NEAA) changed similarly. The essential amino acid index showed a slight continuous decrease. Although the crude fat decreased dramatically due to the infection, from a value of 30.75% to 7.2%, the infection of S. hepiali produced five new fatty acids (14-methyl-pentadecanoic acid, docosanoic acid, succinic acid, arachidonic acid, and myristic acid) while the content of the seven fatty acids was greatly reduced after infection. Therefore, after being infected by S. hepiali and combined with it, the nutritional profile of A pernyi pupa was changed significantly and there were different characteristics at different infection stages. The above findings provide scientifically fundamental data to understand the nutritional value of the insect-fungus complex as human food and animal feed.

Pharmacy-based immunization: a systematic review

Background

The coronavirus disease 2019 pandemic has prompted the exploration of new response strategies for such health contingencies in the near future. Over the last 15 years, several pharmacy-based immunization (PBI) strategies have emerged seeking to exploit the potential of pharmacies as immunization, medication sale, and rapid test centers. However, the participation of pharmacies during the last pandemic was very uneven from one country to another, suggesting a lack of consensus on the definition of their roles and gaps between the literature and practice.

Purpose

This study aimed to consolidate the current state of the literature on PBI, document its progress over time, and identify the gaps not yet addressed. Moreover, this study seeks to (i) provide new researchers with an overview of the studies on PBI and (ii) to inform both public health and private organization managers on the range of possible immunization models and strategies.

Methodology

A systematic review of scientific qualitative and quantitative studies on the most important scientific databases was conducted. The Preferred Reporting Items for Systematic Reviews and Meta-analyzes guidelines were followed. Finally, this study discusses the trends, challenges, and limitations on the existing literature on PBI.

Findings

Must studies concluded that PBI is a beneficial strategy for the population, particularly in terms of accessibility and territorial equity. However, the effectiveness of PBI is affected by the economic, political, and/or social context of the region. The collaboration between the public (government and health departments) and private (various pharmacy chains) sectors contributes to PBI's success.

Originality

Unlike previous literature reviews on PBI that compiled qualitative and statistical studies, this study reviewed studies proposing mathematical optimization methods to approach PBI.

Nutritional aspects and dietary benefits of "Silkworms": Current scenario and future outlook

In the current scenario, it is estimated that by 2050, there will be an additional 2.5 billion people and a 70% increase in food demand. Crop yields are not increasing fast enough to support global needs, and world agriculture is facing several serious challenges. Therefore, insects can be a nutritious alternative to meet the ever-increasing food demand in the present and future. The majority of insect consumption occurs in developing countries, with approximately 1,900 insect species consumed worldwide. Food and feed derived from them are of high quality, have a high feed conversion ratio and emit a low level of greenhouse gases. Among insects silkworms are beneficial to humans, not only because of their high nutritional value, but also because of their several pharmacological properties. Silkworm eggs, larvae, and pupae contains high amount of proteins, oils, minerals, vitamins, and several other beneficial components which are nutritious as well as have positive effect on human health. Studies have shown that silkworm pupae protect the liver, enhance immunity, inhibit apoptosis, inhibit cancer, inhibit tumor growth, inhibit microbial growth, regulate blood glucose and blood lipids, and lower blood pressure. This review paper summerized the nutritional value of different life stages of silkworm, nutritional comparison of silkworm with the major human foods, and the effects of silkworm consumption on human health, thus ittargets to generate interest toward in sericulture and improve human health by using silkworm as a nutritious food and attain sustainability in food and nutritional security.

Ultraminiature optical fiber-tip directly-printed plasmonic biosensors for label-free biodetection

Miniaturization of biosensors has become an imperative demand because of its great potential in in vivo biomarker detection and disease diagnostics as well as the point-of-care testing for coping with public health crisis, such as the coronavirus disease 2019 pandemic. Here, we present an ultraminiature optical fiber-tip biosensor based on the plasmonic gold nanoparticles (AuNPs) directly printed upon the end face of a standard multimode optical fiber at visible light range. An in-situ precision photoreduction technology is developed to additively print the micropatterns of size-controlled AuNPs. The AuNPs reveal distinct localized surface plasmon resonance, whose peak wavelength provides an ideal spectral signal for label-free biodetection. The fabricated optical fiber-tip plasmonic biosensor can not only detect antibody, but also test SARS-CoV-2 mimetic DNA sequence at the concentration level of 0.8 pM. Such an ultraminiature fiber-tip plasmonic biosensor offers a cost-effective biodetection technology for a myriad of applications ranging from point-of-care testing to in vivo diagnosis of stubborn diseases.

How are large-scale One Health initiatives targeting infectious diseases and antimicrobial resistance evaluated? A scoping review

While One Health initiatives are gaining in popularity, it is unclear if and how they are evaluated when implementation at scale is intended. The main purpose of this scoping review was to describe how One Health initiatives targeting infectious diseases and antimicrobial resistance at a large scale are evaluated. Secondary objectives included identifying the main facilitators and barriers to the implementation and success of these initiatives, and how their impacts were assessed. Twenty-three studies evaluating One Health initiatives were eligible. Most studies included the human (n = 22) and animal (n = 15) sectors; only four included the environment sector. The types of evaluated initiative (non-exclusive) included governance (n = 5), knowledge (n = 6), protection (n = 17), promotion (n = 16), prevention (n = 9), care (n = 8), advocacy (n = 10) and capacity (n = 10). Studies used normative (n = 4) and evaluative (n = 20) approaches to assess the One Health initiatives, the latter including impact (n = 19), implementation (n = 8), and performance (n = 7) analyses. Structural and economic, social, political, communication and coordination-related factors, as well as ontological factors, were identified as both facilitators and barriers for successful One Health initiatives. These results identified a wide range of evaluation methods and indicators used to demonstrate One Health's added values, strengths, and limitations: the inherent complexity of the One Health approach leads to the use of multiple types of evaluation. The strengths and remaining gaps in the evaluation of such initiative highlight the relevance of comprehensive, mixed-method, context-sensitive evaluation frameworks to inform and support the implementation of One Health initiatives by stakeholders in different governance settings.

Tracing the connections between international business and communicable diseases

We posit that international business and the emergence and spread of communicable diseases are intrinsically connected. To support our arguments, we first start with a historical timeline that traces the connections between international business and communicable diseases back to the sixth century. Second, following the epidemiology of communicable diseases, we identify two crucial transitions related to international business: the emergence of epidemics within a host country and the shift from epidemics to global pandemics. Third, we highlight international business contextual factors (host country regulatory quality, urbanization, trade barriers, global migration) and multinationals' activities (foreign direct investment, corporate political activity, global supply chain management, international travel) that could accelerate each transition. Finally, building on public health insights, we suggest research implications for business scholars on how to integrate human health challenges into their studies and practical implications for global managers on how to help prevent the emergence and spread of communicable diseases.

Dual Host and Pathogen RNA-Seq Analysis Unravels Chicken Genes Potentially Involved in Resistance to Highly Pathogenic Avian Influenza Virus Infection

Highly pathogenic avian influenza viruses (HPAIVs) cause severe systemic disease and high mortality rates in chickens, leading to a huge economic impact in the poultry sector. However, some chickens are resistant to the disease. This study aimed at evaluating the mechanisms behind HPAIV disease resistance. Chickens of different breeds were challenged with H7N1 HPAIV or clade 2.3.4.4b H5N8 HPAIV, euthanized at 3 days post-inoculation (dpi), and classified as resistant or susceptible depending on the following criteria: chickens that presented i) clinical signs, ii) histopathological lesions, and iii) presence of HPAIV antigen in tissues were classified as susceptible, while chickens lacking all these criteria were classified as resistant. Once classified, we performed RNA-Seq from lung and spleen samples in order to compare the transcriptomic signatures between resistant and susceptible chickens. We identified minor transcriptomic changes in resistant chickens in contrast with huge alterations observed in susceptible chickens. Interestingly, six differentially expressed genes were downregulated in resistant birds and upregulated in susceptible birds. Some of these genes belong to the NF-kappa B and/or mitogen-activated protein kinase signaling pathways. Among these six genes, the serine protease-encoding gene PLAU was of particular interest, being the most significantly downregulated gene in resistant chickens. Expression levels of this protease were further validated by RT-qPCR in a larger number of experimentally infected chickens. Furthermore, HPAIV quasi-species populations were constructed using 3 dpi oral swabs. No substantial changes were found in the viral segments that interact with the innate immune response and with the host cell receptors, reinforcing the role of the immune system of the host in the clinical outcome. Altogether, our results suggest that an early inactivation of important host genes could prevent an exaggerated immune response and/or viral replication, conferring resistance to HPAIV in chickens.

From concept to action: a united, holistic and One Health approach to respond to the climate change crisis

It is unequivocal that human influence has warmed the planet, which is seriously affecting the planetary health including human health. Adapting climate change should not only be a slogan, but requires a united, holistic action and a paradigm shift from crisis response to an ambitious and integrated approach immediately. Recognizing the urgent needs to tackle the risk connection between climate change and One Health, the four key messages and recommendations that with the intent to guide further research and to promote international cooperation to achieve a more climate-resilient world are provided.

High-Throughput Sequencing of Environmental DNA as a Tool for Monitoring Eukaryotic Communities and Potential Pathogens in a Coastal Upwelling Ecosystem

The marine environment includes diverse microeukaryotic organisms that play important functional roles in the ecosystem. With molecular approaches, eukaryotic taxonomy has been improved, complementing classical analysis. In this study, DNA metabarcoding was performed to describe putative pathogenic eukaryotic microorganisms in sediment and marine water fractions collected in Galicia (NW Spain) from 2016 to 2018. The composition of eukaryotic communities was distinct between sediment and water fractions. Protists were the most diverse group, with the clade TSAR (Stramenopiles, Alveolata, Rhizaria, and Telonemida) as the primary representative organisms in the environment. Harmful algae and invasive species were frequently detected. Potential pathogens, invasive pathogenic organisms as well as the causative agents of harmful phytoplanktonic blooms were identified in this marine ecosystem. Most of the identified pathogens have a crucial impact on the aquacultural sector or affect to relevant species in the marine ecosystem, such as diatoms. Moreover, pathogens with medical and veterinary importance worldwide were also found, as well as pathogens that affect diatoms. The evaluation of the health of a marine ecosystem that directly affects the aquacultural sector with a zoonotic concern was performed with the metabarcoding assay.

Pirahy virus: Identification of a new and potential emerging arbovirus in South Brazil

Genomic and epidemiological surveillance are paramount for the discovery of new viruses with the potential to cross species barriers. Here, we present a new member of the genus Alphavirus found in Trichoprosopon and Wyeomia mosquitoes, tentatively named Pirahy virus (PIRAV). PIRAV was isolated from mosquito pools collected in a rural area of Piraí do Sul, South Brazil. In vitro assays revealed that PIRAV replicates and causes cytopathic effects in vertebrate cell lines such as Vero E6, SH-SY5Y, BHK-21 and UMNSAH/DF-1. Genomic signature analysis supports these results showing a dinucleotide and codon usage balance compatible with several hosts. Phylogenetic analyses placed PIRAV basal to the Venezuelan equine encephalitis complex. Genome analyses, electron microscopy, and biological characterization show findings that may alert for the emergence of a new arbovirus in South America.

Outside the Box: Working With Wildlife in Biocontainment

Research with captive wildlife in Animal Biosafety Level 2 (ABSL2) and 3 (ABSL3) facilities is becoming increasingly necessary as emerging and re-emerging diseases involving wildlife have increasing impacts on human, animal, and environmental health. Utilizing wildlife species in a research facility often requires outside the box thinking with specialized knowledge, practices, facilities, and equipment. The USGS National Wildlife Health Center (NWHC) houses an ABSL3 facility dedicated to understanding wildlife diseases and developing tools to mitigate their impacts on animal and human health. This review presents considerations for utilizing captive wildlife for infectious disease studies, including, husbandry, animal welfare, veterinary care, and biosafety. Examples are drawn from primary literature review and collective 40-year experience of the NWHC. Working with wildlife in ABSL2 and ABSL3 facilities differs from laboratory animals in that typical laboratory housing systems, husbandry practices, and biosafety practices are not designed for work with wildlife. This requires thoughtful adaptation of standard equipment and practices, invention of customized solutions and development of appropriate enrichment plans using the natural history of the species and the microbiological characteristics of introduced and native pathogens. Ultimately, this task requires critical risk assessment, understanding of the physical and psychological needs of diverse species, creativity, innovation, and flexibility. Finally, continual reassessment and improvement are imperative in this constantly changing specialty area of infectious disease and environmental hazard research.

Genome Editing Technologies as Cellular Defense Against Viral Pathogens

Viral infectious diseases are significant threats to the welfare of world populations. Besides the widespread acute viral infections (e.g., dengue fever) and chronic infections [e.g., those by the human immunodeficiency virus (HIV) and hepatitis B virus (HBV)], emerging viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), pose great challenges to the world. Genome editing technologies, including clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) proteins, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), have played essential roles in the study of new treatment for viral infectious diseases in cell lines, animal models, and clinical trials. Genome editing tools have been used to eliminate latent infections and provide resistance to new infections. Increasing evidence has shown that genome editing-based antiviral strategy is simple to design and can be quickly adapted to combat infections by a wide spectrum of viral pathogens, including the emerging coronaviruses. Here we review the development and applications of genome editing technologies for preventing or eliminating infections caused by HIV, HBV, HPV, HSV, and SARS-CoV-2, and discuss how the latest advances could enlighten further development of genome editing into a novel therapy for viral infectious diseases.

Comparative assessment of the prevalence, practices and factors associated with self-medication with antibiotics in Africa

OBJECTIVE

To evaluate and compare the prevalence, reasons, sources and factors associated with self-medication with antibiotics (SMA) within Africa.

METHODS

Systematic review and meta-analysis. An electronic search of PubMed and Google Scholar databases was performed for observational studies conducted between January 2005 and February 2020. Two reviewers independently screened abstracts and full texts using the PRISMA flowchart and performed quality assessment of eligible studies. Both qualitative and quantitative syntheses were carried out.

RESULTS

Forty studies from 19 countries were eligible for qualitative synthesis. The prevalence of SMA in Africa ranged from 12.1% to 93.9% with a median prevalence of 55.7% (IQR 41-75%). Western Africa was the sub-region with the highest reported prevalence of 70.1% (IQR 48.3-82.1%), followed by Northern Africa with 48.1% (IQR 41.1-64.3%). We identified 27 antibiotics used for self-medication from 13 different antibiotic classes. Most frequently used antibiotics were penicillins (31 studies), tetracyclines (25 studies) and fluoroquinolones (23 studies). 41% of these antibiotics belong to the WHO Watch Group. The most frequent indications for SMA were upper respiratory tract infections (27 studies), gastrointestinal tract symptoms (25 studies) and febrile illnesses (18 studies). Common sources of antibiotics used for self-medication were community pharmacies (31 studies), family/friends (20 studies), leftover antibiotics (19 studies) and patent medicine stores (18 studies). The most frequently reported factor associated with SMA was no education/low educational status (nine studies).

CONCLUSIONS

The prevalence of SMA is high in Africa and varies across sub-regions with the highest prevalence reported in Western Africa. Drivers of SMA are complex, comprising of socio-economic factors and insufficient access to health care coupled with poorly implemented policies regulating antibiotic sales.

Taking a lesson from the COVID-19 pandemic: Preventing the future outbreaks of viral zoonoses through a multi-faceted approach

The pandemic of the novel coronavirus disease 2019 (COVID-19) has caused a significant burden to healthcare systems, economic crisis, and public fears. It is also a lesson to be learned and a call-to-action to minimize the risk of future viral pandemics and their associated challenges. The present paper outlines selected measures (i.e., monitoring and identification of novel viral agents in animals, limitations to wildlife trade, decreasing hunting activities, changes to mink farming and meat production), the implementation of which would decrease such a risk. The role of viral surveillance systems and research exploring the virus strains associated with different animal hosts is emphasized along with the need for stricter wild trade regulations and changes to hunting activities. Finally, the paper suggests modifications to the meat production system, particularly through the introduction of cultured meat that would not only decrease the risk of exposure to novel human viral pathogens but also strengthen food security and decrease the environmental impacts of food production.

Community engagement in public health: a bibliometric mapping of global research

Background

Community engagement (CE) has been regarded as a critical element of successful health programs to achieve “the health for all” goals. Numerous studies have shown that it plays a significant role in reducing inequalities, improving social justice, enhancing benefits, and sharing responsibility towards public health. Despite this, the extant literature of community engagement in public health (CEPH) has topic-focused boundaries and is scattered across disciplinary. Large-scale studies are needed to systematically identify current status, hotspots, knowledge structure, dynamic trends, and future developments in this field.

Methods

The bibliometric techniques were applied in the analysis of publications on CEPH in Web of Science Core Collection from Thomson Reuters. One thousand one hundred two papers out of 70.8 million publications over the period of 1980 to 2020 and their 15,116 references were retrieved as the sample set. First, basic characteristics of publications, including distributions of geography, journals and categories, productive authors and frequently cited articles, etc. were obtained. Then, four bibliometric methods, i.e. social network analysis, co-citation analysis, co-occurrence clustering, and burst detection, were further conducted to sketch the contours of the structure and evolution of CEPH.

Results

Between Jan 1, 1980, and Apr 25, 2020, CEPH has attracted a sharp increase in interest all over the world. Total 117 countries or regions have participated in the field of CEPH and the contributions are geographically and institutionally distinct. The United States is the key region performing such research, which accounts for more than half of the total number of publications. Developing countries, such as South Africa, India, Brazil and China also contributed a lot. The advancements of CEPH are marked by historically momentous public health events and evolved from macroscopic strategies to mesoscopic and microscopic actions. Based on keyword clustering and co-citation clustering, we propose a 4O (i.e. orientation, object, operation, and outcome) framework of CEPH to facilitate a better understanding of the current global achievements and an elaborate structuring of developments in the future.

Conclusion

This study draws an outline of the global review on the contemporary and cross-disciplinary research of CEPH which might present an opportunity to take stock and understand the march of knowledge as well as the logical venation underlying research activities which are fundamental to inform policy making.

The Evolutionary Significance of Generalist Viruses with Special Emphasis on Plant Viruses and their Hosts

The host range of a virus is defined as the number of species a virus potentially infects. The specialist virus infects one or few related species while the generalist virus infects several different species, possibly in different families. Origin of generalist viruses from their specialist nature and the expansion of the host range of the generalist virus occur with the host shift event in which the virus encounters and adapts to a new host. Host shift events have resulted in the majority of the newly emerging viral diseases. This review discusses the advantages and disadvantages of generalist over specialist viruses and the unique features of plant viruses and their hosts that result in a higher incidence of generalist viruses in plants.

A qualitative enquiry into strategic and operational responses to Covid-19 challenges in South Asia

The Covid-19 epidemic is a public health emergency of international concern. It poses a massive risk for the human race across the planet, calling for the need to take measures at the local, regional, national, and global levels. South Asian countries stand more vulnerable to the pandemic due to their dense population, poor infrastructure, and low surveillance system. This paper aims to understand the challenges from the Covid-19 pandemic for South Asia; and investigates the strategic and operational responses to this pandemic by policymakers and healthcare professionals, respectively, in South Asia. The study uses interviews and opinions of policymakers and doctors, from the South Asian region, involved in tackling the Covid-19 crisis. The qualitative analysis is performed on these interviews and opinions by using NVivo 12 software. The findings indicate that policymakers and healthcare providers across South Asia have been showing efficient teamwork while dealing with this pandemic. The healthcare administrators being at the operational level, convey the challenges they face to the policymakers who then respond to them at a strategic level.

Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts

Identifying whether novel human viruses disproportionately originate from certain animal groups could inform risk-based allocations of research and surveillance effort. Whether such “special reservoirs” exist remains controversial. We show that the proportion of viruses that infect humans varies minimally across reservoir taxonomic orders. Instead, the number of human-infecting viruses increases proportionately to the total number of viruses maintained by each reservoir group, which is in turn explained by the number of animal species within each group. This supports a host-neutral explanation for observed variation in the number of zoonoses among animal groups, such that traits of animal orders are unlikely to produce viruses that disproportionately threaten humans. These findings refine strategies to identify high-risk viruses prior to their emergence.

The notion that certain animal groups disproportionately maintain and transmit viruses to humans due to broad-scale differences in ecology, life history, and physiology currently influences global health surveillance and research in disease ecology, virology, and immunology. To directly test whether such “special reservoirs” of zoonoses exist, we used literature searches to construct the largest existing dataset of virus–reservoir relationships, consisting of the avian and mammalian reservoir hosts of 415 RNA and DNA viruses along with their histories of human infection. Reservoir host effects on the propensity of viruses to have been reported as infecting humans were rare and when present were restricted to one or two viral families. The data instead support a largely host-neutral explanation for the distribution of human-infecting viruses across the animal orders studied. After controlling for higher baseline viral richness in mammals versus birds, the observed number of zoonoses per animal order increased as a function of their species richness. Animal orders of established importance as zoonotic reservoirs including bats and rodents were unexceptional, maintaining numbers of zoonoses that closely matched expectations for mammalian groups of their size. Our findings show that variation in the frequency of zoonoses among animal orders can be explained without invoking special ecological or immunological relationships between hosts and viruses, pointing to a need to reconsider current approaches aimed at finding and predicting novel zoonoses.

Implications of mixed viral infections on plant disease ecology and evolution

Mixed viral infections occur more commonly than would be expected by chance in nature. Virus-virus interactions may affect viral traits and leave a genetic signature in the population, and thus influence the prevalence and emergence of viral diseases. Understanding about how the interactions between viruses within a host shape the evolutionary dynamics of the viral populations is needed for viral disease prevention and management. Here, we first synthesize concepts implied in the occurrence of virus-virus interactions. Second, we consider the role of the within-host interactions of virus-virus and virus-other pathogenic microbes, on the composition and structure of viral populations. Third, we contemplate whether mixed viral infections can create opportunities for the generation and maintenance of viral genetic diversity. Fourth, we attempt to summarize the evolutionary response of viral populations to mixed infections to understand how they shape the spatio-temporal dynamics of viral populations at the individual plant and field scales. Finally, we anticipate the future research under the reconciliation of molecular epidemiology and evolutionary ecology, drawing attention to the need of adding more complexity to future research in order to gain a better understanding about the mechanisms operating in nature.

[Bushmeat, human impacts and human health in tropical rainforests: The Ebola virus case]

At a time when more than 5 million tonnes of bushmeat are harvested annually from tropical forests, and which account for a significant, but unrecorded, share of the gross domestic product of many forest countries, decision makers are encouraged, within conservation and food security policies, to understand the role that wildlife can play in the conservation of ecosystem services. In this article, we present an analysis of the problem, describing the role played by bushmeat in human diets, and the health risks linked to the consumption of bushmeat, in particular with regard to Ebola disease, to provide insights on the direction of possible strategies to manage the use of wildlife for meeting the needs of local populations and reducing risks to human health.

Victors: a web-based knowledge base of virulence factors in human and animal pathogens

Virulence factors (VFs) are molecules that allow microbial pathogens to overcome host defense mechanisms and cause disease in a host. It is critical to study VFs for better understanding microbial pathogenesis and host defense mechanisms. Victors (http://www.phidias.us/victors) is a novel, manually curated, web-based integrative knowledge base and analysis resource for VFs of pathogens that cause infectious diseases in human and animals. Currently, Victors contains 5296 VFs obtained via manual annotation from peer-reviewed publications, with 4648, 179, 105 and 364 VFs originating from 51 bacterial, 54 viral, 13 parasitic and 8 fungal species, respectively. Our data analysis identified many VF-specific patterns. Within the global VF pool, cytoplasmic proteins were more common, while adhesins were less common compared to findings on protective vaccine antigens. Many VFs showed homology with host proteins and the human proteins interacting with VFs represented the hubs of human-pathogen interactions. All Victors data are queriable with a user-friendly web interface. The VFs can also be searched by a customized BLAST sequence similarity searching program. These VFs and their interactions with the host are represented in a machine-readable Ontology of Host-Pathogen Interactions. Victors supports the 'One Health' research as a vital source of VFs in human and animal pathogens.

Dealing in deadly pathogens: Taking stock of the legal trade in live wildlife and potential risks to human health

Zoonotic diseases cause millions of deaths every year. Diseases such as Ebola, severe acute respiratory syndrome (SARS), and avian influenza cause economic losses at the global level and jeopardize diplomatic relations between countries. As wildlife are the source of at least 70% of all emerging diseases and given the on-going concerns associated with wildlife trade as a disease transmission mechanism, we provide a 'global snapshot' of the legal trade in live wild animals and take stock of the potential health risks that it poses to global human health. Our analysis showed that 11,569,796 individual live wild animals, representing 1316 different species were exported from 189 different countries between 2012 and 2016. China was the largest exporter of live mammals (with 98,979 animals representing 58.7% of global trade). Nicaragua was the largest exporter of live amphibians (with 122,592 animals representing 53.8% of global trade). South Africa was the largest exporter of live birds (with 889,607 animals representing 39.2% of global trade). Peru was the largest exporter of live reptiles (with 1,675,490 animals representing 18.8% of global trade). Our analysis showed that mostly the USA and other high-income countries, the largest importers, drive the live animal trade. High-income countries and not the countries where wildlife diseases and pathogens are more likely to occur reported almost all of the disease reports to the World Organisation for Animal Health. Based on our findings, we discuss how maximising trade bans; working on human behaviour change and improving regulatory efforts to improve surveillance will decrease the risk of future pandemics, epidemics and outbreaks.

Developing a 3D intestinal epithelium model for livestock species

The in vitro 3D culture of intestinal epithelium is a valuable resource in the study of its function. Organoid culture exploits stem cells' ability to regenerate and produce differentiated epithelium. Intestinal organoid models from rodent or human tissue are widely available whereas large animal models are not. Livestock enteric and zoonotic diseases elicit significant morbidity and mortality in animal and human populations. Therefore, livestock species-specific models may offer novel insights into host-pathogen interactions and disease responses. Bovine and porcine jejunum were obtained from an abattoir and their intestinal crypts isolated, suspended in Matrigel, cultured, cryopreserved and resuscitated. 'Rounding' of crypts occurred followed by budding and then enlargement of the organoids. Epithelial cells were characterised using immunofluorescent staining and confocal microscopy. Organoids were successfully infected with Toxoplasma gondii or Salmonella typhimurium. This 3D organoid model offers a long-term, renewable resource for investigating species-specific intestinal infections with a variety of pathogens.

Traditional knowledge regarding edible insects in Burkina Faso

BACKGROUND

Insects play an important role as a diet supplement in Burkina Faso, but the preferred insect species vary according to the phytogeographical zone, ethnic groups, and gender. The present study aims at documenting indigenous knowledge on edible insects in Burkina Faso.

METHODS

A structured ethno-sociological survey was conducted with 360 informants in nine villages located in two phytogeographical zones of Burkina Faso. Identification of the insects was done according to the classification of Scholtz. Chi-square tests and principal component analysis were performed to test for significant differences in edible insect species preferences among phytogeographical zones, villages, ethnic groups, and gender.

RESULTS

Edible insects were available at different times of the year. They were collected by hand picking, digging in the soil, and luring them into water traps. The edible insects collected were consumed fried, roasted, or grilled. All species were indifferently consumed by children, women, and men without regard to their ages. A total of seven edible insect species belonging to five orders were cited in the Sudanian zone of Burkina Faso. Macrotermes subhyalinus (Rambur), Cirina butyrospermi (Vuillet, 1911), Kraussaria angulifera (Krauss, 1877), Gryllus campestris (Linnaeus, 1758), and Carbula marginella (Thunberg) (35.66-8.47% of the citations) were most cited whereas Rhynchophorus phoenicis (Fabricius, 1801) and Oryctes sp. (3.41-0.27%) were least cited. Cirina butyrospermi was most cited in the South Sudanian zone, whereas Macrotermes subhyalinus and Kraussaria angulifera were most cited in the North Sudanian zone but were cited in all nine villages. Cirina butyrospermi was preferred by Bobo, Guin, Sambla, Senoufo, and Turka ethnic groups whereas Macrotermes subhyalinus was preferred by Fulani, Mossi, and Toussian ethnic groups. Oryctes sp. was cited only by the Toussian.

CONCLUSION

A diversity of edible insects was consumed in both the South and North Sudanian zone of Burkina Faso with significant differences in species preferences according to phytogeographical zones, villages, ethnic groups, and gender.

Lyme Disease Transmission Risk: Seasonal Variation in the Built Environment

Seasonal variation in spatial distribution and pathogen prevalence of Borrelia burgdorferi in blacklegged ticks (Ixodes scapularis) influences human population risk of Lyme disease in peri-urban built environments. Parks, gardens, playgrounds, school campuses and neighborhoods represent a significant risk for Lyme disease transmission. From June 2012 through May 2014, ticks were collected using 1 m² corduroy cloths dragged over low-lying vegetation parallel to walkways with high human foot traffic. DNA was extracted from ticks, purified and presence of B. burgdorferi assessed by polymerase chain reaction amplification. Summer is reported as the time of highest risk for Lyme disease transmission in the United States and our results indicate a higher tick density of 26.0/1000 m² in summer vs. 0.2/1000 m² to 10.5/1000 m² in spring and fall. However, our findings suggest that tick infection rate is proportionally higher during the fall and spring than summer (30.0–54.7% in fall and 36.8–65.6% in spring vs. 20.0–28.2% in summer). Seasonal variation in infected tick density has significant implications for Lyme disease transmission as people are less likely to be aware of ticks in built environments, and unaware of increased infection in ticks in spring and fall. These factors may lead to more tick bites resulting in Lyme infection.

Antiviral effects and mechanisms of Yinhuapinggan granule against H1N1 influenza virus infection in RAW264.7 cells

Yinhuapinggan granule (YHPG), a modified prescription based on Ma-Huang-Tang (MHT), is used in traditional Chinese medicine (TCM) to treat influenza, cough, and viral pneumonia. In this study, we investigated the antiviral effects of YHPG by means of pre-, post-, and co-treatment, and its underlying mechanisms on regulating the levels of inflammatory-related cytokines, modulating the mRNA expressions of interferon-stimulated genes in influenza virus-infected murine macrophage cells (RAW264.7), and evaluating the protein expressions of key effectors in the Type I IFN and pattern recognition receptor (PRRs) signaling pathways. The results showed that YHPG markedly inhibited influenza virus (IFV) replication in pre-, post- and co-treatment assay, especially in post-treatment assay. Antiviral mechanisms studies revealed that YHPG (500 and 250 μg/mL) significantly up-regulated levels of IFN-β, IFN-stimulated genes (Mx-1, ISG-15 and ISG-56) compared with the IFV control group, while the levels of IL-6 and TNF-α were significantly down-regulated. Furthermore, western blot analysis results revealed that the protein expressions of the phosphorylated forms of TBK1, IRF3, ERK1/2, P38 MAPK and NF-κB p65 were significantly down-regulated in RAW264.7 cells with the YHPG (500 and 250 μg/mL) treatment, while the expression of the phosphorylated form of STAT1 was significantly enhanced. Based on these results, YHPG had antiviral effects in IFV-infected RAW264.7 cells, which might be associated with regulation of the inflammatory cytokines production, evaluation of the levels of IFN-stimulated genes, and modulation of the protein expressions of key effectors in the Type I IFN and PRRs signaling pathways.

Conservation, development and the management of infectious disease: avian influenza in China, 2004-2012

There is growing evidence that wildlife conservation measures have mixed effects on the emergence and spread of zoonotic disease. Wildlife conservation has been found to have both positive (dilution) and negative (contagion) effects. In the case of avian influenza H5N1 in China, the focus has been on negative effects. Lakes and wetlands attracting migrating waterfowl have been argued to be disease hotspots. We consider the implications of waterfowl conservation for H5N1 infections in both poultry and humans between 2004 and 2012. We model both environmental and economic risk factors. Environmental risk factors comprise the conditions that structure interaction between wild and domesticated birds. Economic risk factors comprise the cost of disease, biosecurity measures and disease risk mitigation. We find that H5N1 outbreaks in poultry populations are indeed sensitive to the existence of wild-domesticated bird mixing zones, but not in the way we would expect from the literature. We find that risk is decreasing in protected migratory bird habitat. Since the number of human cases is increasing in the number of poultry outbreaks, as expected, the implication is that the protection of wetlands important for migratory birds offers unexpected human health benefits.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

The Zika Virus Epidemic in Brazil: From Discovery to Future Implications

The first confirmed case of Zika virus infection in the Americas was reported in Northeast Brazil in May 2015, although phylogenetic studies indicate virus introduction as early as 2013. Zika rapidly spread across Brazil and to more than 50 other countries and territories on the American continent. The Aedesaegypti mosquito is thought to be the principal vector responsible for the widespread transmission of the virus. However, sexual transmission has also been reported. The explosively emerging epidemic has had diverse impacts on population health, coinciding with cases of Guillain-Barré Syndrome and an unexpected epidemic of newborns with microcephaly and other neurological impairments. This led to Brazil declaring a national public health emergency in November 2015, followed by a similar decision by the World Health Organization three months later. While dengue virus serotypes took several decades to spread across Brazil, the Zika virus epidemic diffused within months, extending beyond the area of permanent dengue transmission, which is bound by a climatic barrier in the south and low population density areas in the north. This rapid spread was probably due to a combination of factors, including a massive susceptible population, climatic conditions conducive for the mosquito vector, alternative non-vector transmission, and a highly mobile population. The epidemic has since subsided, but many unanswered questions remain. In this article, we provide an overview of the discovery of Zika virus in Brazil, including its emergence and spread, epidemiological surveillance, vector and non-vector transmission routes, clinical complications, and socio-economic impacts. We discuss gaps in the knowledge and the challenges ahead to anticipate, prevent, and control emerging and re-emerging epidemics of arboviruses in Brazil and worldwide.

The promise of marine molecules as cosmetic active ingredients

The marine environment represents an underexploited resource for the discovery of novel products, despite its high level of biological and chemical diversity. With increasing awareness of the harmful effects of chronic ultraviolet exposure, and a universal desire to improve cosmetic appearance, the market for new cosmetic ingredients is growing, and current trends have generated a greater demand for products sourced from the environment. A growing number of novel molecules from marine flora and fauna exhibit potent and effective dermatological activities. Secondary metabolites isolated from macroalgae, including carotenoids and polyphenols, have demonstrated antioxidant, anti-ageing and anti-inflammatory activities. In addition, marine extremophilic bacteria have recently been shown to produce bioactive exopolymeric molecules, some of which have been commercialized. Available data on their activities show significant antioxidant, moisturizing and anti-ageing activities, but a more focussed investigation into their mechanisms and applications is required. This review surveys the reported biological activities of an emerging and growing portfolio of marine molecules that show promise in the treatment of cosmetic skin problems including ultraviolet damage, ageing and cutaneous dryness.

Chimpanzee adenoviral vectors as vaccines for outbreak pathogens

The 2014-15 Ebola outbreak in West Africa highlighted the potential for large disease outbreaks caused by emerging pathogens and has generated considerable focus on preparedness for future epidemics. Here we discuss drivers, strategies and practical considerations for developing vaccines against outbreak pathogens. Chimpanzee adenoviral (ChAd) vectors have been developed as vaccine candidates for multiple infectious diseases and prostate cancer. ChAd vectors are safe and induce antigen-specific cellular and humoral immunity in all age groups, as well as circumventing the problem of pre-existing immunity encountered with human Ad vectors. For these reasons, such viral vectors provide an attractive platform for stockpiling vaccines for emergency deployment in response to a threatened outbreak of an emerging pathogen. Work is already underway to develop vaccines against a number of other outbreak pathogens and we will also review progress on these approaches here, particularly for Lassa fever, Nipah and MERS.

Bank vole immunoheterogeneity may limit Nephropatia Epidemica emergence in a French non-endemic region

Ecoevolutionary processes affecting hosts, vectors and pathogens are important drivers of zoonotic disease emergence. In this study, we focused on nephropathia epidemica (NE), which is caused by Puumala hantavirus (PUUV) whose natural reservoir is the bank vole, Myodes glareolus. We questioned the possibility of NE emergence in a French region that is considered to be NE-free but that is adjacent to a NE-endemic region. We first confirmed the epidemiology of these two regions and we demonstrated the absence of spatial barriers that could have limited dispersal, and consequently, the spread of PUUV into the NE-free region. We next tested whether regional immunoheterogeneity could impact PUUV chances to circulate and persist in the NE-free region. We showed that bank voles from the NE-free region were sensitive to experimental PUUV infection. We observed high levels of immunoheterogeneity between individuals and also between regions. Antiviral gene expression (Tnf and Mx2) reached higher levels in bank voles from the NE-free region. During experimental infections, anti-PUUV antibody production was higher in bank voles from the NE-endemic region. These results indicated a lower susceptibility to PUUV for bank voles from this NE-free region, which might limit PUUV persistence and therefore, the risk of NE.

Optimization of human, animal, and environmental health by using the One Health approach

Emerging diseases are increasing burdens on public health, negatively affecting the world economy, causing extinction of species, and disrupting ecological integrity. One Health recognizes that human, domestic animal, and wildlife health are interconnected within ecosystem health and provides a framework for the development of multidisciplinary solutions to global health challenges. To date, most health-promoting interventions have focused largely on single-sector outcomes. For example, risk for transmission of zoonotic pathogens from bush-meat hunting is primarily focused on human hygiene and personal protection. However, bush-meat hunting is a complex issue promoting the need for holistic strategies to reduce transmission of zoonotic disease while addressing food security and wildlife conservation issues. Temporal and spatial separation of humans and wildlife, risk communication, and other preventative strategies should allow wildlife and humans to co-exist. Upstream surveillance, vaccination, and other tools to prevent pathogen spillover are also needed. Clear multi-sector outcomes should be defined, and a systems-based approach is needed to develop interventions that reduce risks and balance the needs of humans, wildlife, and the environment. The ultimate goal is long-term action to reduce forces driving emerging diseases and provide interdisciplinary scientific approaches to management of risks, thereby achieving optimal outcomes for human, animal, and environmental health.

Tunable and label-free virus enrichment for ultrasensitive virus detection using carbon nanotube arrays

Viral infectious diseases can erupt unpredictably, spread rapidly, and ravage mass populations. Although established methods, such as polymerase chain reaction, virus isolation, and next-generation sequencing have been used to detect viruses, field samples with low virus count pose major challenges in virus surveillance and discovery. We report a unique carbon nanotube size-tunable enrichment microdevice (CNT-STEM) that efficiently enriches and concentrates viruses collected from field samples. The channel sidewall in the microdevice was made by growing arrays of vertically aligned nitrogen-doped multiwalled CNTs, where the intertubular distance between CNTs could be engineered in the range of 17 to 325 nm to accurately match the size of different viruses. The CNT-STEM significantly improves detection limits and virus isolation rates by at least 100 times. Using this device, we successfully identified an emerging avian influenza virus strain [A/duck/PA/02099/2012(H11N9)] and a novel virus strain (IBDV/turkey/PA/00924/14). Our unique method demonstrates the early detection of emerging viruses and the discovery of new viruses directly from field samples, thus creating a universal platform for effectively remediating viral infectious diseases.

Observed and projected drivers of emerging infectious diseases in Europe

Emerging infectious diseases are of international concern because of the potential for, and impact of, pandemics; however, they are difficult to predict. To identify the drivers of disease emergence, we analyzed infectious disease threat events (IDTEs) detected through epidemic intelligence collected at the European Centre for Disease Prevention and Control (ECDC) between 2008 and 2013, and compared the observed results with a 2008 ECDC foresight study of projected drivers of future IDTEs in Europe. Among 10 categories of IDTEs, foodborne and waterborne IDTEs were the most common, vaccine-preventable IDTEs caused the highest number of cases, and airborne IDTEs caused the most deaths. Observed drivers for each IDTE were sorted into three main groups: globalization and environmental drivers contributed to 61% of all IDTEs, public health system drivers contributed to 21%, and social and demographic drivers to 18%. A multiple logistic regression analysis showed that four of the top five drivers for observed IDTEs were in the globalization and environment group. In the observational study, the globalization and environment group was related to all IDTE categories, but only to five of eight categories in the foresight study. Directly targeting these drivers with public health interventions may diminish the chances of IDTE occurrence from the outset.

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these biases and of their consequences, and we propose a comprehensive trimming strategy for managing these biases. We demonstrated the application of this strategy using 711 commensal rodents, including 208 Mus musculus domesticus, 189 Rattus rattus, 93 Mastomys natalensis, and 221 Mastomys erythroleucus, collected from 24 villages in Senegal. Seven major genera of pathogenic bacteria were detected in their spleens: Borrelia, Bartonella, Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia. Mycoplasma, Ehrlichia, Rickettsia, Streptobacillus, and Orientia have never before been detected in West African rodents. Bacterial prevalence ranged from 0% to 90% of individuals per site, depending on the bacterial taxon, rodent species, and site considered, and 26% of rodents displayed coinfection. The 16S rRNA amplicon sequencing strategy presented here has the advantage over other molecular surveillance tools of dealing with a large spectrum of bacterial pathogens without requiring assumptions about their presence in the samples. This approach is therefore particularly suitable to continuous pathogen surveillance in the context of disease-monitoring programs. IMPORTANCE Several recent public health crises have shown that the surveillance of zoonotic agents in wildlife is important to prevent pandemic risks. High-throughput sequencing (HTS) technologies are potentially useful for this surveillance, but rigorous experimental processes are required for the use of these effective tools in such epidemiological contexts. In particular, HTS introduces biases into the raw data set that might lead to incorrect interpretations. We describe here a procedure for cleaning data before estimating reliable biological parameters, such as positivity, prevalence, and coinfection, using 16S rRNA amplicon sequencing on an Illumina MiSeq platform. This procedure, applied to 711 rodents collected in West Africa, detected several zoonotic bacterial species, including some at high prevalence, despite their never before having been reported for West Africa. In the future, this approach could be adapted for the monitoring of other microbes such as protists, fungi, and even viruses.

Antibiotic resistance genes and human bacterial pathogens: Co-occurrence, removal, and enrichment in municipal sewage sludge digesters

Understanding which/how antibiotic resistance genes (ARGs) contribute to increased acquisition of resistance by pathogens in aquatic environments are challenges of profound significance. We explored the co-occurrence and removal versus enrichment of ARGs and human bacterial pathogens (HBPs) in municipal sewage sludge digesters. We combined metagenomic detection of a wide spectrum of 323 ARGs and 83 HBPs with a correlation-based statistical approach and charted a network of their co-occurrence relationships. The results indicate that most ARGs and a minor proportion of HBPs (mainly Collinsella aerofaciens, Streptococcus salivarius and Gordonia bronchialis) could not be removed by anaerobic digestion, revealing a biological risk of post-digestion sludge in disseminating antibiotic resistance and pathogenicity. Moreover, preferential co-occurrence patterns were evident within one ARG type (e.g., multidrug, beta-lactam, and aminoglycoside) and between two different ARG types (i.e., aminoglycoside and beta-lactam), possibly implicating co-effects of antibiotic selection pressure and co-resistance on shaping antibiotic resistome in sewage sludge. Unlike beta-lactam resistance genes, ARGs of multidrug and macrolide-lincosamide-streptogramin tended to co-occur more with HBPs. Strikingly, we presented evidence that the most straightforward biological origin of an ARG-species co-occurring event is a hosting relationship. Furthermore, a significant and robust HBP-species co-occurrence correlation provides a proper scenario for nominating HBP indicators (e.g., Bifidobacterium spp. are perfect indicators of C. aerofaciens; r = 0.92-0.99 and P-values < 0.01). Combined, this study demonstrates a creative and effective network-based metagenomic approach for exploring ARG hosts and HBP indicators and assessing ARGs acquisition by HBPs in human-impacted environments where ARGs and HBPs may co-thrive.

A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics

The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC's ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC's performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings.

RNA Viruses: A Case Study of the Biology of Emerging Infectious Diseases

There are 180 currently recognized species of RNA virus that can infect humans, and on average, 2 new species are added every year. RNA viruses are routinely exchanged between humans and other hosts (particularly other mammals and sometimes birds) over both epidemiological and evolutionary time: 89% of human-infective species are considered zoonotic and many of the remainder have zoonotic origins. Some viruses that have crossed the species barrier into humans have persisted and become human-adapted viruses, as exemplified by the emergence of HIV-1. Most, however, have remained as zoonoses, and a substantial number have apparently disappeared again. We still know relatively little about what determines whether a virus is able to infect, transmit from, and cause disease in humans, but there is evidence that factors such as host range, cell receptor usage, tissue tropisms, and transmission route all play a role. Although systematic surveillance for potential new human viruses in nonhuman hosts would be enormously challenging, we can reasonably aspire to much better knowledge of the diversity of mammalian and avian RNA viruses than exists at present.