The challenge of emerging and re-emerging infectious diseases

The Bioarchaeology of Health Crisis: Infectious Disease in the Past

Beginning some 10,000 years ago, humans began a dramatic alteration in living conditions relating especially to the shift in lifeway from foraging to farming. In addition to the initiation of and increasing focus on the production and consumption of domesticated plant carbohydrates, this revolutionary transformation in diet occasioned a decline in mobility and an increased size and agglomeration of populations in semipermanent or permanent settlements. These changes in life conditions presented an opportunity for increased transmission of pathogenic microbes from host to host, such as those that cause major health threats affecting most of the 7.5 billion members of our species today. This article discusses the bioarchaeology of infectious disease, focusing on tuberculosis, treponematosis, dental caries, and periodontitis, all of which continue to contribute to high levels of morbidity and mortality among the world's populations today.

Adherence to Universal Travel Screening in the Emergency Department During Epidemic Ebola Virus Disease

Background

During the 2014 West African Ebola Virus Disease (EVD) outbreak, the U.S. Centers for Disease Control and Prevention recommended that all emergency department (ED) patients undergo travel screening for risk factors of importing EVD.

Objectives

We sought to determine the overall adherence rate to the recommended travel screening protocol and to identify factors associated with nonadherence to the protocol.

Methods

We conducted a multicenter, retrospective analysis of adherence to the travel screening program in an academic hospital and three affiliated community hospitals. A regression model identified patient and hospital factors associated with nonadherence.

Results

Of the 147,062 patients included for analysis, 93.7% (n = 137,834) had travel screenings completed. We identified several characteristics of patients that were most likely to be missed by the screening protocol—patients with low English proficiency, patients who arrive via ambulance or helicopter, and patients with more severe illness or injury based on initial triage acuity.

Conclusions

These findings should be used to improve adherence to the travel screening protocol for future emerging infectious disease threats.

High juvenile mortality in amphibians during overwintering related to fungal pathogen exposure

The result of pathogen exposures may depend upon trade-offs in energetic demands for immune responses against host growth and survival. Environmental conditions may influence these trade-offs by affecting host size, or trade-offs may change across seasons, altering impacts of pathogens. We exposed northern leopard frog Lithobates pipiens tadpoles to different larval environments (low leaf litter, high density of conspecifics, atrazine, caged fish, or controls) that influenced size at metamorphosis. Subsequently, we exposed metamorphs to Batrachochytrium dendrobatidis (Bd), a fungal pathogen, just after metamorphosis and/or prior to overwintering 12 wk later. Bd exposure dramatically reduced survival during overwintering, with the strongest effects when hosts were exposed at both time points. Larval environments resulted in differences in host size. Those exposed to caged fish were 2.5 times larger than the smallest (those exposed to high density of conspecifics), but larval environment did not influence Bd effects on growth and survival. The largest frogs exposed to caged fish had greater survival through overwintering, but in the absence of Bd. We built stage-structured models to evaluate if overwinter mortality from Bd is capable of having effects on host populations. Our models suggest that Bd exposure after metamorphosis or before overwintering can reduce population growth rates. Our study demonstrates that hosts suffer little effects of Bd exposures following metamorphosis and that small body size did not hamper growth and survival. Instead, we provide evidence that winter mortality from Bd exposure is capable of reducing population sizes, providing a plausible mechanism for amphibian declines in temperate regions.

Point-of-care microfluidic devices for pathogen detection

The rapid diagnosis of pathogens is crucial in the early stages of treatment of diseases where the choice of the correct drug can be critical. Although conventional cell culture-based techniques have been widely utilized in clinical applications, newly introduced optical-based, microfluidic chips are becoming attractive. The advantages of the novel methods compared to the conventional techniques comprise more rapid diagnosis, lower consumption of patient sample and valuable reagents, easy application, and high reproducibility in the detection of pathogens. The miniaturized channels used in microfluidic systems simulate interactions between cells and reagents in microchannel structures, and evaluate the interactions between biological moieties to enable diagnosis of microorganisms. The overarching goal of this review is to provide a summary of the development of microfluidic biochips and to comprehensively discuss different applications of microfluidic biochips in the detection of pathogens. New types of microfluidic systems and novel techniques for viral pathogen detection (e.g. HIV, HVB, ZIKV) are covered. Next generation techniques relying on high sensitivity, specificity, lower consumption of precious reagents, suggest that rapid generation of results can be achieved via optical based detection of bacterial cells. The introduction of smartphones to replace microscope based observation has substantially improved cell detection, and allows facile data processing and transfer for presentation purposes.

Overexpressed recombinant quorum quenching lactonase reduces the virulence, motility and biofilm formation of multidrug-resistant Pseudomonas aeruginosa clinical isolates

The increasing occurrence of resistance among Pseudomonas aeruginosa clinical isolates necessitates finding alternatives to antibiotics for controlling the infection of such pathogenic bacteria. In this study, lactonase gene ahl-1 from Bacillus weihenstephanensis isolate-P65 was successfully cloned and expressed in Escherichia coli BL21 (DE3) under the control of T7 promoter for utilizing its quorum quenching activity against three multidrug-resistant (MDR) P. aeruginosa clinical isolates. The biological activity of the overexpressed lactonase enzyme (Ahl-1), tested using a synthetic signal and Chromobacterium violaceum CV026 as a biosensor, displayed good catalytic activity using hexanoyl homoserine lactone (HHL) as a substrate and Chromobacterium violaceum (CV026) as a biosensor (77.2 and 133 nm min^-1 for the crude and the purified Ahl-lactonase enzymes, respectively). Upon challenging its ability to inhibit the virulence of three MDR P. aeruginosa clinical isolates, recombinant Ahl-1 successfully prevented the accumulation of acylhomoserine lactone signals resulting in a significant reduction in the investigated virulence determinants; protease (from 40 up to 75.5%), pyocyanin (48-75.9%), and rhamnolipids (52.7-63.4%) (P value < 0.05). Ahl-1 also displayed significant inhibitory activities on the swarming motility and biofilm formation of the three tested MDR P. aeruginosa clinical isolates (P value < 0.05). Consequently, Ahl-1 lactonase enzyme in this study is considered a promising therapeutic agent to inhibit P. aeruginosa pathogenicity with no fear of emergence of resistance.

Factors in the emergence of serious human infections associated with highly pathogenic strains of shiga toxin-producing Escherichia coli

The appearance of highly pathogenic strains of Shiga toxin (Stx)-producingEscherichia. coli (STEC) has owed largely to the acquisition of Stx-encoding prophages by strains of E. coli that have pre-existing potential as enteric pathogens, such as atypical enteropathogenic E. coli (aEPEC) and enteroaggregative E. coli (EAEC). However, while high pathogenic potential is necessary, it is not sufficient for such strains to have a serious public health impact (i.e., large outbreaks, many cases of HUS, or both). To do so requires susceptible hosts and additional elements related to transmission, such as, socio-economic, societal, and lifestyle, factors. Two examples are discussed to illustrate this. The factors involved in the emergence of serious disease associated with E. coli O157:H7 in the 1980s probably included a massive increase in population exposure to this pathogen, likely as a result of the introduction of factory farming of cattle in the 1960s, and the development and wide patronage of fast food hamburger restaurants, and, potentially, waning immunity to intimin as a result of the reduction of incidence of enteropathogenic E. coli (EPEC) infection. In the devastating outbreak of Stx2-positiveEAEC O104:H4 in 2011, the wide distribution of the proposed vehicle of transmission, imported fenugreek seeds, was decisive in the exposure of a large population in Central Europe to this pathogen. Contributing factors likely included a preference for eating raw sprouts as a healthy food choice by the affected cases, many of whom were women. Low population levels of immunity to Stx2 probably contributed to the severe clinical outcome. A better understanding of the factors responsible for the emergence of potentially dangerous STEC pathogens as well as of extensive and serious disease associated with them can enhance public health strategies to respond to them.

A Comparison of Optical, Electrochemical, Magnetic, and Colorimetric Point-of-Care Biosensors for Infectious Disease Diagnosis

Each year, infectious diseases are responsible for millions of deaths, most of which occur in the rural areas of developing countries. Many of the infectious disease diagnostic tools used today require a great deal of time, a laboratory setting, and trained personnel. Due to this, the need for effective point-of-care (POC) diagnostic tools is greatly increasing with an emphasis on affordability, portability, sensitivity, specificity, timeliness, and ease of use. In this Review, we discuss the various diagnostic modalities that have been utilized toward this end and are being further developed to create POC diagnostic technologies, and we focus on potential effectiveness in resource-limited settings. The main modalities discussed herein are optical-, electrochemical-, magnetic-, and colorimetric-based modalities utilized in diagnostic technologies for infectious diseases. Each of these modalities feature pros and cons when considering application in POC settings but, overall, reveal a promising outlook for the future of this field of technological development.

Rapid Diagnostic for Point-of-Care Malaria Screening

Despite significant success in therapeutic development, malaria remains a widespread and deadly infectious disease in the developing world. Given the nearly 100% efficacy of current malaria therapeutics, the primary barrier to eradication is lack of early diagnosis of the infected population. However, there are multiple strains of malaria. Although significant efforts and resources have been invested in developing antibody-based diagnostic methods for Plasmodium falciparum, a rapid and easy to use screening method capable of detecting all malaria strains has not been realized. Yet, until the entire malaria-infected population receives treatment, the disease will continue to impact society. Here, we report the development of a portable, magneto-optic technology for early stage malaria diagnosis based on the detection of the malaria pigment, hemozoin. Using β-hematin, a hemozoin mimic, we demonstrate detection limits of <0.0081 μg/mL in 500 μL of whole rabbit blood with no additional reagents required. This level corresponds to <26 parasites/μL, a full order of magnitude below clinical relevance and comparable to or less than existing technologies.

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.

Factors Influencing Mitigation of Risk of Waterborne Disease in Vietnam Among Small Scale Integrated Livestock Farmers

The integrated livestock, crops, and fish (VAC) model of integrated small scale agriculture has been important to economic and ecological sustainability in Vietnam for many centuries. Recently, emerging waterborne diseases including avian influenza as well as the potential for zoonotic disease arising from small scale farms have jeopardized the VAC model. In order to promote mitigation of the risk of waterborne and other diseases in the VAC system, there needs to be recognition of the significant predictors of such behavior, particularly with respect to water sources including well and rain water. We report primarily quantitative results of research generated from 300 farms in each of North and South Vietnam that indicate the small scale farmers who are more likely to engage in mitigation of waterborne disease are those who raise pigs, perceive themselves to be more at risk of HPAI infection from well water, report they are good livestock managers, value the advice of health care workers, and where a female household member is the decision maker for family health. These results bear importance to water and health policy formulators in rural Vietnam. (JEL I130, I180, O130, Q180, Q570).

JEL CLASSIFICATIONS:

I130: Health and economic development

I180: Public health

O130: Economic Development: Agriculture; Environment

Q180: Agricultural policy; Food policy

Q570: Ecological economics: biodiversity conservation

Exploring spatial patterns of cardiovascular disease in Sweden between 2000 and 2010

AIMS

Cardiovascular disease (CVD) is one of the leading causes of mortality and morbidity worldwide, including in Sweden. The main aim of this study was to explore the temporal trends and spatial patterns of CVD in Sweden using spatial autocorrelation analyses.

METHODS

The CVD admission rates between 2000 and 2010 throughout Sweden were entered as the input disease data for the analytic processes performed for the Swedish capital, Stockholm, and also for the whole of Sweden. Age-adjusted admission rates were calculated using a direct standardisation approach for men and women, and temporal trends analysis were performed on the standardised rates. Global Moran's I was used to explore the structure of patterns and Anselin's local Moran's I, together with Kulldorff's scan statistic were applied to explore the geographical patterns of admission rates.

RESULTS

The rates followed a spatially clustered pattern in Sweden with differences occurring between sexes. Accordingly, hot spots were identified in northern Sweden, with higher intensity identified for men, together with clusters in central Sweden. Cold spots were identified in the adjacency of the three major Swedish cities of Stockholm, Gothenburg and Malmö.

CONCLUSIONS

The findings of this study can serve as a basis for distribution of health-care resources, preventive measures and exploration of aetiological factors.

Evaluation of Allplex Respiratory Panel 1/2/3 Multiplex Real-Time PCR Assays for the Detection of Respiratory Viruses with Influenza A Virus subtyping

The Allplex Respiratory Panel 1/2/3 (All16) is a multiplex PCR assay for detecting 16 respiratory viruses with influenza A virus (FluA) subtyping, and the first clinical assay based on multiple detection temperatures. We compared the results between All16 and Anyplex II RV16 (Any16) in 426 clinical samples. Samples showing discrepancies between the two tests were further tested using monoplex PCR. FluA subtyping based on the hemagglutinin type results of All16, which yielded H1, H3, and non-H1/H3, was compared with the results of the BioFire FilmArray respiratory panel. The positive and negative percent agreements and kappa value for each virus between All16 and Any16 ranged from 54.5-100.0%, 84.7-100.0%, and 0.57-1.00, respectively. FluA subtype results from All16 for 26 samples were consistent with those from FilmArray. Good agreement was observed between the two methods, except when analyzing human enterovirus (kappa value 0.70), and the All16 showed reliable FluA subtyping results. For parainfluenza virus 3, the All16 was more sensitive than Any16. When testing 28 samples simultaneously, the mean test time and hands-on time were 4.3 and 0.5 hours, respectively in All16. In conclusion, All16 showed reliable performance, but further studies are needed regarding human enterovirus analysis.

Pertussis Outbreak in a Primary School in China: Infection and Transmission of the Macrolide-resistant Bordetella pertussis

BACKGROUND

A pertussis outbreak was studied in a primary school in Xi'an, China, in March 2016. The school consisted of 536 pupils 6-12 years of age who were divided into 12 classes of 6 grades (2 classes for each grade). The identified index case was an 11-year-old girl at class 2 of grade 5.

METHODS

Interview was conducted and nasopharyngeal swabs were taken from all pupils (N = 94) in the 2 classes of grade 5. Nasopharyngeal swabs were tested by both culture and polymerase chain reaction (PCR).

RESULTS

Four culture- and 17 PCR-positive cases were identified in 94 pupils. Infection rate was significantly higher in class 2 compared with that in class 1 [37.0% (17/46) vs. 14.6% (7/48), χ(2) = 4.26, P < 0.05]. All Bordetella pertussis isolates were macrolide-resistant, harbored prn1/ptxP1/fim3-1 as previously reported and belonged to multilocus variable tandem repeat analysis type MLVA 195. Of the 17 DNAs positive for diagnostic PCR, 12 were also positive for 23S ribosomal RNA PCR. All the 12 DNAs had the A2047G mutation of 23S rRNA gene of B. pertussis.

CONCLUSIONS

This study described a pertussis outbreak caused by macrolide-resistant B. pertussis in a primary school and indicated that close contact of index case causes the bacterial transmission.

The Economic Case for a Pandemic Fund

The rapid urban spread of Ebola virus in West Africa in 2014 and consequent breakdown of control measures led to a significant economic impact as well as the burden on public health and wellbeing. The US government appropriated $5.4 Billion for FY2015 and WHO proposed a $100 Million emergency fund largely to curtail the threat of future outbreaks. Using epidemiological analyses and economic modeling, we propose that the best use of these and similar funds would be to serve as global insurance against the continued threat of emerging infectious diseases. An effective strategy would involve the initial investment in strengthening mobile and adaptable capacity to deal with the threat and reality of disease emergence, coupled with repeated investment to maintain what is effectively a 'national guard' for pandemic prevention and response. This investment would create a capital stock that could also provide access to safe treatment during and between crises in developing countries, lowering risk to developed countries.

Anticipating epidemic transitions with imperfect data

Epidemic transitions are an important feature of infectious disease systems. As the transmissibility of a pathogen increases, the dynamics of disease spread shifts from limited stuttering chains of transmission to potentially large scale outbreaks. One proposed method to anticipate this transition are early-warning signals (EWS), summary statistics which undergo characteristic changes as the transition is approached. Although theoretically predicted, their mathematical basis does not take into account the nature of epidemiological data, which are typically aggregated into periodic case reports and subject to reporting error. The viability of EWS for epidemic transitions therefore remains uncertain. Here we demonstrate that most EWS can predict emergence even when calculated from imperfect data. We quantify performance using the area under the curve (AUC) statistic, a measure of how well an EWS distinguishes between numerical simulations of an emerging disease and one which is stationary. Values of the AUC statistic are compared across a range of different reporting scenarios. We find that different EWS respond to imperfect data differently. The mean, variance and first differenced variance all perform well unless reporting error is highly overdispersed. The autocorrelation, autocovariance and decay time perform well provided that the aggregation period of the data is larger than the serial interval and reporting error is not highly overdispersed. The coefficient of variation, skewness and kurtosis are found to be unreliable indicators of emergence. Overall, we find that seven of ten EWS considered perform well for most realistic reporting scenarios. We conclude that imperfect epidemiological data is not a barrier to using EWS for many potentially emerging diseases.

Airborne microbial communities in the atmospheric environment of urban hospitals in China

Clinically relevant antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in bioaerosols have become a greater threat to public health. However, few reports have shown that ARB and ARGs were found in the atmosphere. High-throughput sequencing applied to environmental sciences has enhanced the exploration of microbial populations in atmospheric samples. Thus, five nosocomial bioaerosols were collected, and the dominant microbial and pathogenic microorganisms were identified by high-throughput sequencing in this study. The results suggested that the dominant microorganisms at the genus level were Massilia, Sphingomonas, Methylobacterium, Methylophilus, Micrococcineae, and Corynebacterineae. The most abundant pathogenic microorganisms were Staphylococcus saprophyticus, Corynebacterium minutissimum, Streptococcus pneumoniae, Escherichia coli, Arcobacter butzleri, Aeromonas veronii, Pseudomonas aeruginosa, and Bacillus cereus. The relationship between microbial communities and environmental factors was evaluated with canonical correspondence analysis (CCA). Meanwhile, differences in the pathogenic bacteria between bioaerosols and dust in a typical hospital was investigated. Furthermore, cultivable Staphylococcus isolates with multi-drug resistance phenotype (>3 antibiotics) in the inpatient departments were much higher than those in the transfusion area and out-patient departments, possibly attributed to the dense usage of antibiotics in inpatient departments. The results of this study might be helpful for scientifically air quality control in hospitals.

Epidemic as a natural process

Mathematical epidemiology is a well-recognized discipline to model infectious diseases. It also provides guidance for public health officials to limit outbreaks. Nevertheless, epidemics take societies by surprise every now and then, for example, when the Ebola virus epidemic raged seemingly unrestrained in Western Africa. We provide insight to this capricious character of nature by describing the epidemic as a natural process, i.e., a phenomenon governed by thermodynamics. Our account, based on statistical mechanics of open systems, clarifies that it is impossible to predict accurately epidemic courses because everything depends on everything else. Nonetheless, the thermodynamic theory yields a comprehensive and analytical view of the epidemic. The tenet subsumes various processes in a scale-free manner from the molecular to the societal levels. The holistic view accentuates overarching procedures in arresting and eradicating epidemics.

Bioenergetic theory predicts infection dynamics of human schistosomes in intermediate host snails across ecological gradients

Epidemiological dynamics depend on the traits of hosts and parasites, but hosts and parasites are heterogeneous entities that exist in dynamic environments. Resource availability is a particularly dynamic and potent environmental driver of within-host infection dynamics (temporal patterns of growth, reproduction, parasite production and survival). We developed, parameterised and validated a model for resource-explicit infection dynamics by incorporating a parasitism module into dynamic energy budget theory. The model mechanistically explained the dynamic multivariate responses of the human parasite Schistosoma mansoni and its intermediate host snail to variation in resources and host density. At the population level, feedbacks mediated by resource competition could create a unimodal relationship between snail density and human risk of exposure to schistosomes. Consequently, weak snail control could backfire if reductions in snail density release remaining hosts from resource competition. If resource competition is strong and relevant to schistosome production in nature, it could inform control strategies.

Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of in vitro human cells by viral infection

Human cell lines have been used in a variety of research fields as an in vitro model. These cells are all derived from human tissue samples, thus there is a possibility of virus infection. Virus tests are routinely performed in clinical practice, but are limited in cell lines. In this study, we investigated 15 kinds of viruses in 844 human cell lines registered at the Japanese Collection of Research Bioresources (JCRB) Cell Bank. Our real-time PCR analysis revealed that six viruses, EBV, HTLV-1, HBV, B19V, HHV-6 and HHV-7, were detected in 43 cell lines. Of them, 20 cell lines were transformed by intentional infection in vitro with EBV or HTLV-1. Viruses in the other 23 cell lines and one EBV transformed cell line are derived from an in vivo infection, including five de novo identifications of EBV, B19V or HHV-7 carriers. Among them, 17 cell lines were established from patients diagnosed with virus-associated diseases. However, the other seven cell lines originated from in vivo cells unrelated to disease or cellular tropism. Our approach to screen for a set of 15 viruses in each cell line has worked efficiently to identify these rare cases. Virus tests in cell lines contribute not only to safety assessments but also to investigation of in vivo viral infection which can be a characteristic feature of cell lines.

Urbanization prolongs hantavirus epidemics in cities

Urbanization reduces exposure risk to many wildlife parasites and in general, improves overall health. However, our study importantly shows the complicated relationship between the diffusion of zoonotic pathogens and urbanization. Here, we reveal an unexpected relationship between hemorrhagic fever with renal syndrome incidence caused by a severe rodent-borne zoonotic pathogen worldwide and the process of urbanization in developing China. Our findings show that the number of urban immigrants is highly correlated with human incidence over time and also explain how the endemic turning points are associated with economic growth during the urbanization process. Our study shows that urbanizing regions of the developing world should focus their attention on zoonotic diseases.

Urbanization and rural–urban migration are two factors driving global patterns of disease and mortality. There is significant concern about their potential impact on disease burden and the effectiveness of current control approaches. Few attempts have been made to increase our understanding of the relationship between urbanization and disease dynamics, although it is generally believed that urban living has contributed to reductions in communicable disease burden in industrialized countries. To investigate this relationship, we carried out spatiotemporal analyses using a 48-year-long dataset of hemorrhagic fever with renal syndrome incidence (HFRS; mainly caused by two serotypes of hantavirus in China: Hantaan virus and Seoul virus) and population movements in an important endemic area of south China during the period 1963–2010. Our findings indicate that epidemics coincide with urbanization, geographic expansion, and migrant movement over time. We found a biphasic inverted U-shaped relationship between HFRS incidence and urbanization, with various endemic turning points associated with economic growth rates in cities. Our results revealed the interrelatedness of urbanization, migration, and hantavirus epidemiology, potentially explaining why urbanizing cities with high economic growth exhibit extended epidemics. Our results also highlight contrasting effects of urbanization on zoonotic disease outbreaks during periods of economic development in China.

Temperature Variability and Gastrointestinal Infections: A Review of Impacts and Future Perspectives

The objectives of this research are to review and assess the current state of knowledge of the association between environmental temperature and gastrointestinal (GI) infections. A review of the published literature was undertaken using standard approaches. Initially, four electronic databases including Embase, Medline, Scopus, and Web of Science were chosen to retrieve studies published from 1 January 2006 to 31 December 2017 based on selected keywords used in the primary search. After the elimination of duplicates, the titles were reviewed for relevance to the principal research question. Secondly, the abstracts of titles deemed to be relevant were reviewed for significance and finally the articles were reviewed in their entirety to identify their contribution to the principal research question. Initially, 8201 articles were identified, and eight studies finally met the inclusion criteria. A secondary phase involving scrutiny of the references of key identified articles found three further studies. Consequently, 11 papers were selected for the final review. Current literature confirms a significant association between temperature and infectious gastroenteritis worldwide. Also, a most-likely non-linear correlation between rainfall and GI infections has been identified in that the rate of such infections can be increased with either high or low precipitation. Finally, some studies suggest high relative humidity may not increase the rate of GI infections and some have found it may decrease it. These findings help inform predictions of risk, particularly under future climate change scenarios.

Use of gasotransmitters for the controlled release of polymer-based nitric oxide carriers in medical applications

Nitric Oxide (NO) is a small molecule gasotransmitter synthesized by nitric oxide synthase in almost all types of mammalian cells. NO is synthesized by NO synthase by conversion of l-arginine to l-citrulline in the human body. NO then stimulates soluble guanylate cyclase, from which various physiological functions are mediated in a concentration-dependent manner. High concentrations of NO induce apoptosis or antibacterial responses whereas low NO circulation leads to angiogenesis. The bidirectional effect of NO has attracted considerable attention, and efforts to deliver NO in a controlled manner, especially through polymeric carriers, has been the topic of much research. This naturally produced signaling molecule has stood out as a potentially more potent therapeutic agent compared to exogenously synthesized drugs. In this review, we will focus on past efforts of using the controlled release of NO via polymer-based materials to derive specific therapeutic results. We have also added studies and our future suggestions on co-delivery methods with other gasotransmitters as a step towards developing multifunctional carriers.

Nucleic acid aptamer-based methods for diagnosis of infections

Infectious diseases are a serious global problem, which not only take an enormous human toll but also incur tremendous economic losses. In combating infectious diseases, rapid and accurate diagnostic tests are required for pathogen identification at the point of care (POC). In this review, investigations of diagnostic strategies for infectious diseases that are based on aptamers, especially nucleic acid aptamers, oligonucleotides that have high affinities and specificities toward their targets, are described. Owing to their unique features including low cost of production, easy chemical modification, high chemical stability, reproducibility, and low levels of immunogenicity and toxicity, aptamers have been widely utilized as bio-recognition elements (bio-receptors) for the development of infection diagnostic systems. We discuss nucleic acid aptamer-based methods that have been developed for diagnosis of infections using a format that organizes discussion according to the target pathogenic analytes including toxins or proteins, whole cells and nucleic acids. Also included is, a summary of recent advances made in the sensitive detection of pathogenic bacteria utilizing the isothermal nucleic acid amplification method. Lastly, a nucleic acid aptamer-based POC system is described and future directions of studies in this area are discussed.

Dopamine coated Fe3O4 nanoparticles as enzyme mimics for the sensitive detection of bacteria

We report a simple and economical colorimetric bacterial sensing strategy with catalytic amplification using dopamine-capped iron oxide (Dop-Fe₃O₄) nanoparticles. These nanoparticles catalyse the oxidation of a chromogenic substrate in the presence of H₂O₂ into a green colored product. The catalytic activity of the nanoparticles is inhibited in the presence of bacteria, providing naked eye detection of bacteria at 10⁴ cfu mL^-1 and by spectrophotometric detection down to 10² cfu mL^-1.

Rapid Viral Diagnosis of Orthopoxviruses by Electron Microscopy: Optional or a Must?

Diagnostic electron microscopy (DEM) was an essential component of viral diagnosis until the development of highly sensitive nucleic acid amplification techniques (NAT). The simple negative staining technique of DEM was applied widely to smallpox diagnosis until the world-wide eradication of the human-specific pathogen in 1980. Since then, the threat of smallpox re-emerging through laboratory escape, molecular manipulation, synthetic biology or bioterrorism has not totally disappeared and would be a major problem in an unvaccinated population. Other animal poxviruses may also emerge as human pathogens. With its rapid results (only a few minutes after arrival of the specimen), no requirement for specific reagents and its "open view", DEM remains an important component of virus diagnosis, particularly because it can easily and reliably distinguish smallpox virus or any other member of the orthopoxvirus (OPV) genus from parapoxviruses (PPV) and the far more common and less serious herpesviruses (herpes simplex and varicella zoster). Preparation, enrichment, examination, internal standards and suitable organisations are discussed to make clear its continuing value as a diagnostic technique.

Xenosurveillance reflects traditional sampling techniques for the identification of human pathogens: A comparative study in West Africa

Background

Novel surveillance strategies are needed to detect the rapid and continuous emergence of infectious disease agents. Ideally, new sampling strategies should be simple to implement, technologically uncomplicated, and applicable to areas where emergence events are known to occur. To this end, xenosurveillance is a technique that makes use of blood collected by hematophagous arthropods to monitor and identify vertebrate pathogens. Mosquitoes are largely ubiquitous animals that often exist in sizable populations. As well, many domestic or peridomestic species of mosquitoes will preferentially take blood-meals from humans, making them a unique and largely untapped reservoir to collect human blood.

Methodology/Principal findings

We sought to take advantage of this phenomenon by systematically collecting blood-fed mosquitoes during a field trail in Northern Liberia to determine whether pathogen sequences from blood engorged mosquitoes accurately mirror those obtained directly from humans. Specifically, blood was collected from humans via finger-stick and by aspirating bloodfed mosquitoes from the inside of houses. Shotgun metagenomic sequencing of RNA and DNA derived from these specimens was performed to detect pathogen sequences. Samples obtained from xenosurveillance and from finger-stick blood collection produced a similar number and quality of reads aligning to two human viruses, GB virus C and hepatitis B virus.

Conclusions/Significance

This study represents the first systematic comparison between xenosurveillance and more traditional sampling methodologies, while also demonstrating the viability of xenosurveillance as a tool to sample human blood for circulating pathogens.

Infectious diseases continue to be a burden on mankind, particularly in the developing countries of the tropics. Recognition of pathogen transmission in humans is a crucial step to thwarting epidemics of these pathogens. However, sampling human blood or tissue is invasive and logistically difficult. Xenosurveillance takes advantage of the blood-feeding behavior of mosquitoes to sample human blood for the presence of infectious disease agents. In this study, we aimed to compare xenosurveillance to a more traditional sampling method to assess the usefulness of this technique in field settings where it could potentially be beneficial. DNA and RNA next generation sequencing followed by an in-house bioinformatic pipeline identified viruses and parasites of human origin in blood collected by either mosquitoes or finger-stick. Xenosurveillance produces samples of comparable quality to finger-stick blood collections while alleviating many of the difficulties of direct human sampling. This study suggests xenosurveillance can be a complimentary strategy for infectious disease surveillance in low-resource areas.

A One Health Evaluation of the Southern African Centre for Infectious Disease Surveillance

Rooted in the recognition that emerging infectious diseases occur at the interface of human, animal, and ecosystem health, the Southern African Centre for Infectious Disease Surveillance (SACIDS) initiative aims to promote a trans-sectoral approach to address better infectious disease risk management in five countries of the Southern African Development Community. Nine years after SACIDS’ inception, this study aimed to evaluate the program by applying a One Health (OH) evaluation framework developed by the Network for Evaluation of One Health (NEOH). The evaluation included a description of the context and the initiative, illustration of the theory of change, identification of outputs and outcomes, and assessment of the One Healthness. The latter is the sum of characteristics that defines an integrated approach and includes OH thinking, OH planning, OH working, sharing infrastructure, learning infrastructure, and systemic organization. The protocols made available by NEOH were used to develop data collection protocols and identify the study design. The framework relies on a mixed methods approach by combining a descriptive and qualitative assessment with a semi-quantitative evaluation (scoring). Data for the analysis were gathered during a document review, in group and individual interviews and in an online survey. Operational aspects (i.e., OH thinking, planning, and working) were found to be balanced overall with the highest score in the planning dimension, whereas the infrastructure (learning infrastructure, systemic organization, and sharing infrastructure) was high for the first two dimensions, but low for sharing. The OH index calculated was 0.359, and the OH ratio calculated was 1.495. The program was praised for its great innovative energy in a difficult landscape dominated by poor infrastructure and its ability to create awareness for OH and enthuse people for the concept; training of people and networking. Shortcomings were identified regarding the balance of contributions, funds and activities across member countries in the South, lack of data sharing, unequal allocation of resources, top-down management structures, and limited horizontal collaboration. Despite these challenges, SACIDS is perceived to be an effective agent in tackling infectious diseases in an integrated manner.

Synthesis, Bioassays and Field Evaluation of Hydroxycoumarins and their Alkyl Derivatives as Repellents or Kairomones for Aedes albopictus Skuse (Diptera: Culicidae)

In recent years, a significant increase in mosquito-borne diseases has been recorded worldwide. Faced with the limitations of existing methods for controlling the vector mosquito population, the development of attractants to bait traps and repellents to limit host-vector contacts could be promising and environmentally-friendly control strategies. The purpose of this study was to evaluate the effect of hydroxycoumarins and their alkyls derivatives against Aedes albopictus, the main vector of several arboviruses. Synthesis, bioassays and field trials were carried out in Madagascar. The results showed that 3, 4 and 6-hydroxycoumarins are attractive to this mosquito, 4-hydroxycoumarin being the most effective both in the laboratory and under field conditions. In addition, a good synergistic effect was found with octenol to attract mosquitoes and especially Ae. albopictus in comparison to other mosquito species living in sympatry. On the contrary, the 4-s-butoxycoumarin and 4-s-pentoxycoumarin derivatives had a repellent effect with the former showing the most significant effect. Further optimization of the dose and structure of these products will be carried out in order to maximize their utility for the control of Ae. albopictus and other mosquitoes.

The utility of LASSO-based models for real time forecasts of endemic infectious diseases: A cross country comparison

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A LASSO based forecast model for endemic infectious diseases is proposed.

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Predictions at 4 weeks achieve desirable accuracy.

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Models predict outbreaks but may struggle to predict outbreak size.

Introduction

Accurate and timely prediction for endemic infectious diseases is vital for public health agencies to plan and carry out any control methods at an early stage of disease outbreaks. Climatic variables has been identified as important predictors in models for infectious disease forecasts. Various approaches have been proposed in the literature to produce accurate and timely predictions and potentially improve public health response.

Methods

We assessed how the machine learning LASSO method may be useful in providing useful forecasts for different pathogens in countries with different climates. Separate LASSO models were constructed for different disease/country/forecast window with different model complexity by including different sets of predictors to assess the importance of different predictors under various conditions.

Results

There was a more apparent cyclicity for both climatic variables and incidence in regions further away from the equator. For most diseases, predictions made beyond 4 weeks ahead were increasingly discrepant from the actual scenario. Prediction models were more accurate in capturing the outbreak but less sensitive to predict the outbreak size. In different situations, climatic variables have different levels of importance in prediction accuracy.

Conclusions

For LASSO models used for prediction, including different sets of predictors has varying effect in different situations. Short term predictions generally perform better than longer term predictions, suggesting public health agencies may need the capacity to respond at short-notice to early warnings.

Endemic and emerging acute virus infections in Indonesia: an overview of the past decade and implications for the future

Being the largest archipelago country in the world, with a tropical climate and a unique flora and fauna, Indonesia habitats one of the most diverse biome in the world. These characteristics make Indonesia a popular travel destination, with tourism numbers increasing yearly. These characteristics also facilitate the transmission of zoonosis and provide ideal living and breading circumstances for arthropods, known vectors for viral diseases. A review of the past 10 years of literature, reports of the Ministry of Health, Republic of Indonesia and ProMED-mail shows a significant increase in dengue infection incidence. Furthermore, chikungunya, Japanese encephalitis and rabies are proven to be endemic in Indonesia. The combination of cohort studies, governmental data and ProMED-mail reveals an integrated overview for those working in travel medicine and public health, focusing on both endemic and emerging acute virus infections. This review summarizes the epidemiology of acute virus infections in Indonesia, including outbreak reports, as well as public health response measurements and their potential or efficacy. Knowledge about human behaviour, animal reservoirs, climate factors, environment and their role in emerging virus infection are discussed. We aim to support public health authorities and health care policy makers in a One Health approach.

Applications of gold nanoparticles in virus detection

Viruses are the smallest known microbes, yet they cause the most significant losses in human health. Most of the time, the best-known cure for viruses is the innate immunological defense system of the host; otherwise, the initial prevention of viral infection is the only alternative. Therefore, diagnosis is the primary strategy toward the overarching goal of virus control and elimination. The introduction of a new class of nanoscale materials with multiple unique properties and functions has sparked a series of breakthrough applications. Gold nanoparticles (AuNPs) are widely reported to guide an impressive resurgence in biomedical and diagnostic applications. Here, we review the applications of AuNPs in virus testing and detection. The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. We pay particular attention to highlighting the functional role and activity of each core Au nanostructure and the resultant detection improvements in terms of sensitivity, detection range, and time. In addition, we provide a general summary of the contributions of AuNPs to the mainstream methods of virus detection, technical measures, and recommendations required in guidance toward commercial in-field applications.

Implementation and Initial Analysis of a Laboratory-Based Weekly Biosurveillance System, Provence-Alpes-Côte d'Azur, France

We describe the implementation of an automated infectious disease surveillance system that uses data collected from 210 microbiologic laboratories throughout the Provence-Alpes-Côte d’Azur region in France. Each week, these facilities report bacterial species that have been isolated from patients in their area. An alarm is triggered whenever the case count for a bacterial species infection exceeds 2 SDs of the historical mean for that species at the participating laboratory. At its inception in July 2013, the system monitored 611 bacterial species. During July 1, 2013–March 20, 2016, weekly analyses of incoming surveillance data generated 34 alarms signaling possible infectious disease outbreaks; after investigation, 14 (41%) of these alarms resulted in health alerts declared by the regional health authority. We are currently improving the system by developing an Internet-based surveillance platform and extending our surveillance to include more laboratories in the region.

Infectious pathogens meet point-of-care diagnostics

The field of point-of-care (POC) diagnostics provides the rapid diagnosis of infectious diseases which is essential and critical for improving the general public health in resource-limited settings. POC platforms offer many advantages for detection of various pathogens including portability, automation, speed, cost, and efficiency. In this review, we provide an overview of the recent trends for POC diagnostics of infectious diseases with focus on portable platforms. We review here the present status of POC platforms, emphasizing in period of the past three years, then extrapolate their advance into the future applications for diagnosis of infectious pathogens.

Synergistic Interactions in Microbial Biofilms Facilitate the Establishment of Opportunistic Pathogenic Fungi in Household Dishwashers

Biofilms formed on rubber seals in dishwashers harbor diverse microbiota. In this study, we focussed on the microbial composition of bacteria and fungi, isolated from a defined area of one square centimeter of rubber from four domestic dishwashers and assessed their abilities to in vitro multispecies biofilm formation. A total of 80 isolates (64 bacterial and 16 fungal) were analyzed. Multiple combinations of bacterial isolates from each dishwasher were screened for synergistic interactions. 32 out of 140 tested (23%) four-species bacterial combinations displayed consistent synergism leading to an overall increase in biomass, in all experimental trails. Bacterial isolates from two of the four dishwashers generated a high number of synergistically interacting four-species consortia. Network based correlation analyses also showed higher co-occurrence patterns observed between bacterial members in the same two dishwasher samples, indicating cooperative effects. Furthermore, two synergistic four-species bacterial consortia were tested for their abilities to incorporate an opportunistic fungal pathogen, Exophiala dermatitidis and their establishment as biofilms on sterile ethylene propylene diene monomer M-class (EPDM) rubber and polypropylene (PP) surfaces. When the bacterial consortia included E. dermatitidis, the overall cell numbers of both bacteria and fungi increased and a substantial increase in biofilm biomass was observed. These results indicate a novel phenomenon of cross kingdom synergy in biofilm formation and these observations could have potential implications for human health.

Generalized herd effects and vaccine evaluation: impact of live influenza vaccine on off-target bacterial colonisation

Interactions between pathogens and commensal microbes are major contributors to health and disease. Infectious diseases however are most often considered independent, viewed within a one-host one-pathogen paradigm and, by extension, the interventions used to treat and prevent them are measured and evaluated within this same paradigm. Vaccines, especially live vaccines, by stimulating immune responses or directly interacting with other microbes can alter the environment in which they act, with effects that span across pathogen species. Live attenuated infl uenza vaccines for example, while safe, increase upper respiratory tract bacterial carriage density of important human commensal pathogens like Streptococcus pneumoniae and Staphylococcus aureus. Further, by altering the ecological niche and dynamics of phylogenetically distinct microbes within the host, vaccines may unintentionally affect transmission of non-vaccine targeted pathogens. Thus, vaccine effects may span across species and across scales, from the individual to the population level. In keeping with traditional vaccine herd-effects that indirectly protect even unvaccinated individuals by reducing population prevalence of vaccine-targeted pathogens, we call these cross-species cross-scale effects "generalized herd-effects". As opposed to traditional herd-effects, "generalized" relaxes the assumption that the effect occurs at the level of the vaccine-target pathogen and "herd effect" implies, as usual, that the effects indirectly impact the population at large, including unvaccinated bystanders. Unlike traditional herd-effects that decrease population prevalence of the vaccine-target, generalized herd-effects may decrease or increase prevalence and disease by the off-target pathogen. LAIV, for example, by increasing pneumococcal density in the upper respiratory tract of vaccine recipients, especially children, may increase pneumococcal transmission and prevalence, leading to excess pneumococcal invasive disease in the population, especially among the elderly and others most susceptible to pneumococcal disease. However, these effects may also be beneficial, for example the large reductions in all-cause mortality noted following measles vaccines. Here we discuss evidence for these novel vaccine effects and suggest that vaccine monitoring and evaluation programs should consider generalized herd effects to appreciate the full impacts of vaccines, beneficial or detrimental, across species and scales that are inevitably hiding in plain sight, affecting human health and disease.

Recommendations on diagnostic tools for Batrachochytrium salamandrivorans

Batrachochytrium salamandrivorans (Bsal) poses a major threat to amphibian, and more specifically caudata, diversity. Bsal is currently spreading through Europe, and mitigation measures aimed at stopping its spread and preventing its introduction into naïve environments are urgently needed. Screening for presence of Bsal and diagnosis of Bsal-induced disease in amphibians are essential core components of effective mitigation plans. Therefore, the aim of this study was to present an overview of all Bsal diagnostic tools together with their limitations and to suggest guidelines to allow uniform interpretation. Here, we investigate the use of different diagnostic tools in post-mortem detection of Bsal and whether competition between Bd and Bsal occurs in the species-specific Bd and Bsal duplex real-time PCR. We also investigate the diagnostic sensitivity, diagnostic specificity and reproducibility of the Bsal real-time PCR and show the use of immunohistochemistry in diagnosis of Bsal-induced chytridiomycosis in amphibian samples stored in formaldehyde. Additionally, we have drawn up guidelines for the use and interpretation of the different diagnostic tools for Bsal currently available, to facilitate standardization of execution and interpretation.

Ecological distribution and population dynamics of Rift Valley fever virus mosquito vectors (Diptera, Culicidae) in Senegal

Background

Many zoonotic infectious diseases have emerged and re-emerged over the last two decades. There has been a significant increase in vector-borne diseases due to climate variations that lead to environmental changes favoring the development and adaptation of vectors. This study was carried out to improve knowledge of the ecology of mosquito vectors involved in the transmission of Rift Valley fever virus (RVFV) in Senegal.

Methods

An entomological survey was conducted in three Senegalese agro-systems, Senegal River Delta (SRD), Senegal River Valley (SRV) and Ferlo, during the rainy season (July to November) of 2014 and 2015. Mosquitoes were trapped using CDC light traps set at ten sites for two consecutive nights during each month of the rainy season, for a total of 200 night-traps. Ecological indices were calculated to characterize the different populations of RVFV mosquito vectors. Generalized linear models with mixed effects were used to assess the influence of climatic conditions on the abundance of RVFV mosquito vectors.

Results

A total of 355,408 mosquitoes belonging to 7 genera and 35 species were captured in 200 night-traps. RVFV vectors represented 89.02% of the total, broken down as follows: Ae. vexans arabiensis (31.29%), Cx. poicilipes (0.6%), Cx. tritaeniorhynchus (33.09%) and Ma. uniformis (24.04%). Comparison of meteorological indices (rainfall, temperature, relative humidity), abundances and species diversity indicated that there were no significant differences between SRD and SRV (P = 0.36) while Ferlo showed significant differences with both (P < 0.001). Mosquito collection increased significantly with temperature for Ae. vexans arabiensis (P < 0.001), Cx. tritaeniorhynchus (P = 0.04) and Ma. uniformis (P = 0.01), while Cx. poicilipes decreased (P = 0.003). Relative humidity was positively and significantly associated with the abundances of Ae. vexans arabiensis (P < 0.001), Cx. poicilipes (P = 0.01) and Cx. tritaeniorhynchus (P = 0.007). Rainfall had a positive and significant effect on the abundances of Ae. vexans arabiensis (P = 0.005). The type of biotope (temporary ponds, river or lake) around the trap points had a significant effect on the mosquito abundances (P < 0.001).

Conclusions

In terms of species diversity, the SRD and SRV ecosystems are similar to each other and different from that of Ferlo. Meteorological indices and the type of biotope (river, lake or temporary pond) have significant effects on the abundance of RVFV mosquito vectors.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2591-9) contains supplementary material, which is available to authorized users.

Sensitive and specific detection of clinical bacteria via vancomycin-modified Fe3O4@Au nanoparticles and aptamer-functionalized SERS tags

A sensitive SERS platform for the simultaneous detection of S. aureus and E. coli on the basis of dual recognition by vancomycin and aptamers is reported.