Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks.

Next-generation sequencing technologies, exponential increases in the availability of virus genomic data, and ongoing advances in phylogenomic methods have made genomic epidemiology an increasingly powerful tool for public health response to a range of mosquito-borne virus outbreaks. In this review, we offer a brief primer on the scope and methods of phylogenomic analyses that can answer key epidemiological questions during mosquito-borne virus public health emergencies. We then focus on case examples of outbreaks, including those caused by dengue, Zika, yellow fever, West Nile, and chikungunya viruses, to demonstrate the utility of genomic epidemiology to support the prevention and control of mosquito-borne virus threats. We extend these case studies with operational perspectives on how to best incorporate genomic epidemiology into structured surveillance and response programs for mosquito-borne virus control. Many tools for genomic epidemiology already exist, but so do technical and nontechnical challenges to advancing their use. Frameworks to support the rapid sharing of multidimensional data and increased cross-sector partnerships, networks, and collaborations can support advancement on all scales, from research and development to implementation by public health agencies.

Childhood allergy is preceded by an absence of gut lactobacilli species and higher levels of atopy-related plasma chemokines.

Alterations in the composition and reduced diversity of the infant microbiome are associated with allergic disease in children. Further, an altered microbiota is linked to immune dysregulation, including skewing of different T helper (Th) subsets, which is also seen in atopic individuals. The aim of this study was, therefore, to investigate the associations between gut lactobacilli and Th-related plasma factors in allergy development during childhood. A total of 194 children with known allergy status at 1 year of age were followed to 10 years of age. We used real-time polymerase chain reaction (PCR) to investigate the presence of three lactobacilli species (Lactobacillus casei, L. paracasei, L. rhamnosus) in infant fecal samples (collected between 1 week and 2 months of age) from a subgroup of children. Plasma chemokines and cytokines were quantified at 6 months and at 1, 2, 5 and 10 years of age with Luminex or enzyme-linked immunosorbent assay (ELISA). Fractional exhaled nitrogen oxide (FeNO) was measured and spirometry performed at 10 years of age. The data were analysed by non-parametric testing and a logistic regression model adjusted for parental allergy. An absence of these lactobacilli and higher levels of the chemokines BCA-1/CXCL13, CCL17/TARC, MIP-3α/CCL20 and MDC/CCL22 in plasma at 6 months of age preceded allergy development. The presence of lactobacilli associated with lower levels of atopy-related chemokines during infancy, together with higher levels of interferon (IFN)-γ and lower FeNO during later childhood. The results indicate that the presence of certain lactobacilli species in the infant gut may influence allergy-related parameters in the peripheral immune system, and thereby contribute to allergy protection.

Global distribution and environmental suitability for chikungunya virus, 1952 to 2015.

Chikungunya fever is an acute febrile illness caused by the chikungunya virus (CHIKV), which is transmitted to humans by Aedes mosquitoes. Although chikungunya fever is rarely fatal, patients can experience debilitating symptoms that last from months to years. Here we comprehensively assess the global distribution of chikungunya and produce high-resolution maps, using an established modelling framework that combines a comprehensive occurrence database with bespoke environmental correlates, including up-to-date Aedes distribution maps. This enables estimation of the current total population-at-risk of CHIKV transmission and identification of areas where the virus may spread to in the future. We identified 94 countries with good evidence for current CHIKV presence and a set of countries in the New and Old World with potential for future CHIKV establishment, demonstrated by high environmental suitability for transmission and in some cases previous sporadic reports. Aedes aegypti presence was identified as one of the major contributing factors to CHIKV transmission but significant geographical heterogeneity exists. We estimated 1.3 billion people are living in areas at-risk of CHIKV transmission. These maps provide a baseline for identifying areas where prevention and control efforts should be prioritised and can be used to guide estimation of the global burden of CHIKV.

Maternal country of origin, breast milk characteristics and potential influences on immunity in offspring.

Breast milk contains pro- and anti-inflammatory cytokines and chemokines with potential to influence immunological maturation in the child. We have shown previously that country of birth is associated with the cytokine/chemokine profile of breast milk. In this study we have investigated how these differences in breast milk affect the cellular response of cord blood mononuclear cells (CBMCs) and intestinal epithelial cells (IECs, cell line HT-29) to microbial challenge. Ninety-five women were included: 30 from Mali in West Africa, 32 Swedish immigrants and 33 native Swedish women. CBMCs or IECs were stimulated in vitro with breast milk, alone or in combination with lipopolysaccharide (LPS) or peptidoglycan (PGN). Breast milk in general abrogated the LPS-induced down-regulation of surface CD14 and Toll-like receptor (TLR)-4 expression on CB monocytes, while inhibiting the PGN-induced TLR-2 up-regulation. However, breast milk from immigrant women together with LPS induced a lower CBMC release of interleukin (IL)-6 (P = 0·034) and CXCL-8/IL-8 (P = 0·037) compared with breast milk from Swedish women, while breast milk from Swedish women and Mali women tended to increase the response. The same pattern of CXCL-8/IL-8 release could be seen after stimulation of IECs (HT-29). The lower CBMC and IEC (HT-29) responses to microbial compounds by breast milk from immigrant women could be explained by the fact that breast milk from the immigrant group showed a divergent pro- and anti-inflammatory content for CXCL-8/IL-8, transforming growth factor-ß1 and soluble CD14, compared to the other two groups of women. This may have implications for maturation of their children's immune responses.

Characterization of mutagenic activity in instant hot beverage powders.

Extracts of several grain-based coffee-substitute blends and instant coffees were mutagenic in the Ames/Salmonella test using TA98, YG1024, and YG1029 with metabolic activation. The beverage powders induced 150 to 500 TA98 and 1,150 to 4,050 YG1024 revertant colonies/g, respectively. Increased sensitivity was achieved using strain YG1024. No mutagenic activity was found in instant hot cocoa products. The mutagenic activity in the beverage powders was shown to be stable to heat and the products varied in resistance to acid nitrite treatment. Differential bacterial strain specificity, and a requirement for metabolic activation suggest that aromatic amines are present. Characterization of the mutagenic activity, using HPLC and the Ames test of the collected fractions, showed the coffee-substitute blends and instant coffees contain several mutagenic compounds. Known heterocyclic amines are not responsible for the major part of the mutagenic activity. The main mutagenic activity in grain-based coffee-substitute blends and instant coffees is due to several unidentified compounds, which are most likely aromatic amines.

Carcinogenic heterocyclic amines in model systems and cooked foods: a review on formation, occurrence and intake.

Frying or grilling of meat and fish products may generate low ppb levels of mutagenic/carcinogenic heterocyclic amines (HAs). Many heterocyclic amines are formed via the Maillard reaction from creatine, free amino acids and monosaccharides; compounds naturally occurring in protein-rich foods of animal origin. The formation and yield of HAs are dependent on physical parameters, such as cooking temperature and time, cooking technique and equipment, heat and mass transport, and on chemical parameters, especially the precursors to HAs. This paper reviews the current knowledge on the formation of HAs in cooked foods and model systems, and summarizes data on the content of HAs in various cooked foods, and estimates of the dietary intake of HAs. It should be noted that the presence of carcinogens of other types in food (e.g. nitrosamines, aromatic amines, cholesterol oxide products) and that their generation during frying and grilling are outside the scope of this review.

Influence of frying fat on the formation of heterocyclic amines in fried beefburgers and pan residues.

The influence of six frying fats (butter, margarine, margarine fat phase, liquid margarine, rapeseed oil and sunflower seed oil) on the formation of mutagenic/carcinogenic heterocyclic amines (HAs) during the frying of beefburgers was investigated. Frying was performed at 165 and 200 degrees C (i.e. under conditions that represented normal household cooking practices). The fried beefburgers and their corresponding pan residues were purified using solid-phase extraction and analysed for HAs using HPLC with photodiode array UV and fluorescence detection. The HAs 2-amino-3,8-dimethylimidazo[4,5-f]-quinoxaline (MeIQx), 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (DiMeIQx), 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 9H-pyrido[3,4-b]indole (norharman) and 1-methyl-9H-pyridol[3,4-b]indole (harman) were recovered. The amount increased with the temperature, and the content of HAs in the pan residue was much higher than in the corresponding beefburger. The amounts of MeIQx ranged from 0.2 to 1.6 ng/g in the beefburgers and from 0.8 to 4.3 ng/g in the pan residues. DiMeIQx ranged from undetectable to 0.4 ng/g in the beefburgers and from 0.4 to 1.3 ng/g in the residues. PhIP ranged from 0.08 to 1.5 ng/g in the meat and from 0.4 to 13.3 ng/g in the residues. The total amount of HAs in meat and pan residue combined was significantly lower after frying in sunflower seed oil or margarine than after frying with the other fats. The observed differences in MeIQx and DiMeIQx formation could be explained in terms of oxidation status (peroxide and anisidine value) and antioxidant content (vitamin A, vitamin E and tocopherols/tocotrienols) using partial least squares analysis.

Sensor chip preparation and assay construction for immunobiosensor determination of beta-agonists and hormones.

Immuno-sensing with optical biosensors is a new technique that is currently being exploited for detection of residues in foods. The present study explores the possibilities of obtaining fast screening assays for a number of illegal veterinary drug residues at low concentrations. Analyte specific sensor surfaces were prepared and used to construct inhibition assays with various antibody reagents. Assay sensitivities for calibration curves in buffer solutions around 0.5 ng ml(-1) in terms of IC50 (concentration of the inhibitor) values were achieved for the beta-agonist clenbuterol and the hormone analogues ethinylestradiol and trenbolone. Assay performance was optimised by evaluating factors such as sensor surface ligand density, active antibody concentration, biosensor flow rate, etc.

Occurrence of mutagenic/carcinogenic heterocyclic amines in meat and fish products, including pan residues, prepared under domestic conditions.

Some typical Swedish meat and fish products, e.g. bacon, beefburgers, meatballs, Baltic herring, salmon, smoked fish, black pudding and sausages, and their corresponding pan residues, were analysed by HPLC for their content of mutagenic/carcinogenic heterocyclic amines (HAs). The products were cooked using recommended domestic cooking conditions concerning temperature, time and frying equipment. The amount of HAs was low in most products, though the amount was higher in the pan residues, especially in the pan residue from the frying of Falun sausage, which contained 18.5 ng HAs/g cooked product. Mostly MeIQx (2-amino-3,8-dimethylimidazo[4,5-f]-quinoxaline) and 4,8-DiMeIQx (2-amino-3,4,8-trimethylimidazo[4,5-f]-quinoxaline) were found, being 0.03-2.8 ng MeIQx/g and n.d.-3.4 ng 4,8-DiMeIQx/g cooked product in the food products and 0.05-7.3 ng MeIQx/g and n.d.-2.8 ng 4,8-DiMeIQx/g cooked product in the pan residues. High levels of IQ (2-amino-3-methylimidazo[4,5-f]quinoline), 10.5 ng/g, were only found in well-done bacon and a correlation was seen between fat content and IQ formation. Low levels of MeIQ (2-amino-3,4-dimethylimidazo[4,5-f]quinoline) and PhIP (2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine) were found in the foods.

Influence of amino acids on the formation of mutagenic/carcinogenic heterocyclic amines in a model system.

Mixtures of creatinine, glucose and various single amino acids were heated at 180 degrees C for 10 min in an aqueous model system. The heated mixtures all showed mutagenic activity, ranging from 80 to 2400 TA98 revertant colonies/mumol creatinine with metabolic activation. Testing of HPLC fractions for mutagenic activity showed each mixture to contain several mutagenic components, some of which corresponded to known heterocyclic amines and others to unknown compounds. The presence of 2-amino-3-methyl-imidazo[4,5-f]quinoxaline, 2-amino-3,8-dimethylmidazo[4,5-f]quinoxaline and 2-amino-3,7,8-trimethylimidazo[4,5-f]quinoxaline in most of the samples was established using HPLC with photodiode array detection and liquid chromatography/mass spectrometry with electrospray interface and single ion monitoring. In addition, 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline, 2-amino-1-methyl-6-phenylimidazo[4,5-f]quinoxaline, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole and 3-amino-1-methyl-5H-pyrido[4,3-b]indole and the co-mutagenic compounds 9H-pyrido[3,4-b]indole and 1-methyl-9H-pyrido[3,4-b]indole were detected in some samples.

Dose-dependent milk transfer and tissue distribution of the food mutagen PhIP in rats and their suckling pups.

The transfer of the neonatal carcinogen and food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) into milk of lactating Sprague-Dawley rats and the uptake in 10 day old suckling pups were investigated. PhIP was quantified by HPLC. In dams given a single i.v. injection of PhIP (0.5 mg/kg body wt) and milked 1 h later, 0.04-0.16% of the dose per ml milk was excreted. In dams dosed i.v. with PhIP (0, 0.05, 0.5 and 5.0 mg/kg body wt) and killed 4 h later a linear dose-dependent milk excretion and uptake of PhIP in the tissues were observed (y = 76.1 chi + 1.0; r = 0.94; P < 0.001). In addition, a linear correlation was found between PhIP levels in dam's liver and milk (y = 0.61 chi + 37.4; r = 0.97; P < 0.001). Following administration of PhIP at doses of 0.05 and 0.5 mg/kg body wt, the highest level of PhIP was observed in the milk samples. Following injection of 5.0 mg PhIP/kg body wt, the highest level of PhIP was observed in the mammary gland and liver. The milk/plasma ratio was 9.3 +/- 6.8 at the highest dose at 4 h. High levels of unmetabolized PhIP were also detected in liver and blood of pups allowed to suck the PhIP-dosed dams for 3 h. Autoradiography of pups injected i.p. with [2-14C]PhIP (4.8 mg/kg body wt) showed that only a low level of radioactivity was irreversibly bound in the liver, and high levels of radioactivity were found in stomach milk, intestinal contents and in the urine, 1 h and 4 h following injection. In addition, radioactivity was present in the skin, liver and kidney. Since milk is the major dietary source for nursing infants, the milk transfer of PhIP is of great concern.