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LIAO, C. M., S. C. YANG, C. P. CHIO, and S. C. CHEN. "Understanding influenza virus-specific epidemiological properties by analysis of experimental human infections." Epidemiology and Infection 138, no. 6 (2009): 825–35. http://dx.doi.org/10.1017/s0950268809991178.
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SUMMARYThis study aimed to estimate the natural history and transmission parameters based on experimental viral shedding and symptom dynamics in order to understand the key epidemiological factors that characterize influenza (sub)type epidemics. A simple statistical algorithm was developed by combining a well-defined mathematical scheme of epidemiological determinants and experimental human influenza infection. Here we showed that (i) the observed viral shedding dynamics mapped successfully the estimated time-profile of infectiousness and (ii) the profile of asymptomatic probability was obtained based on observed temporal variation of symptom scores. Our derived estimates permitted evaluation of relationships between various model-derived and data-based estimations, allowing evaluation of trends proposed previously but not tested fully. As well as providing insights into the dynamics of viral shedding and symptom scores, a more profound understanding of influenza epidemiological parameters and determinants could enhance the viral kinetic studies of influenza during infection in the respiratory tracts of experimentally infected individuals.
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Grant, Andrew J., Gemma L. Foster, Trevelyan J. McKinley, et al. "Bacterial Growth Rate and Host Factors as Determinants of Intracellular Bacterial Distributions in Systemic Salmonella enterica Infections." Infection and Immunity 77, no. 12 (2009): 5608–11. http://dx.doi.org/10.1128/iai.00827-09.
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ABSTRACT Bacteria of the species Salmonella enterica cause a range of life-threatening diseases in humans and animals worldwide. The within-host quantitative, spatial, and temporal dynamics of S. enterica interactions are key to understanding how immunity acts on these infections and how bacteria evade immune surveillance. In this study, we test hypotheses generated from mathematical models of in vivo dynamics of Salmonella infections with experimental observation of bacteria at the single-cell level in infected mouse organs to improve our understanding of the dynamic interactions between host and bacterial mechanisms that determine net growth rates of S. enterica within the host. We show that both bacterial and host factors determine the numerical distributions of bacteria within host cells and thus the level of dispersiveness of the infection.
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Fibriansah, Guntur, Xin-Ni Lim, and Shee-Mei Lok. "Morphological Diversity and Dynamics of Dengue Virus Affecting Antigenicity." Viruses 13, no. 8 (2021): 1446. http://dx.doi.org/10.3390/v13081446.
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The four serotypes of the mature dengue virus can display different morphologies, including the compact spherical, the bumpy spherical and the non-spherical clubshape morphologies. In addition, the maturation process of dengue virus is inefficient and therefore some partially immature dengue virus particles have been observed and they are infectious. All these viral particles have different antigenicity profiles and thus may affect the type of the elicited antibodies during an immune response. Understanding the molecular determinants and environmental conditions (e.g., temperature) in inducing morphological changes in the virus and how potent antibodies interact with these particles is important for designing effective therapeutics or vaccines. Several techniques, including cryoEM, site-directed mutagenesis, hydrogen-deuterium exchange mass spectrometry, time-resolve fluorescence resonance energy transfer, and molecular dynamic simulation, have been performed to investigate the structural changes. This review describes all known morphological variants of DENV discovered thus far, their surface protein dynamics and the key residues or interactions that play important roles in the structural changes.
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Quaglia, Agustin I., Erik M. Blosser, Bethany L. McGregor, et al. "Tracking Community Timing: Pattern and Determinants of Seasonality in Culicoides (Diptera: Ceratopogonidae) in Northern Florida." Viruses 12, no. 9 (2020): 931. http://dx.doi.org/10.3390/v12090931.
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Community dynamics are embedded in hierarchical spatial–temporal scales that connect environmental drivers with species assembly processes. Culicoides species are hematophagous arthropod vectors of orbiviruses that impact wild and domestic ruminants. A better sense of Culicoides dynamics over time is important because sympatric species can lengthen the seasonality of virus transmission. We tested a putative departure from the four seasons calendar in the phenology of Culicoides and the vector subassemblage in the Florida panhandle. Two years of weekly abundance data, temporal scales, persistence and environmental thresholds were analyzed using a tripartite Culicoides β-diversity based modeling approach. Culicoides phenology followed a two-season regime and was explained by stream flow and temperature, but not rainfall. Species richness fit a nested pattern where the species recruitment was maximized during spring months. Midges were active year-round, and two suspected vectors species, Culicoides venustus and Culicoides stellifer, were able to sustain and connect the seasonal modules. Persistence suggests that Orbivirus maintenance does not rely on overwintering and that viruses are maintained year-round, with the seasonal dynamics resembling subtropical Culicoides communities with temporal-overlapping between multivoltine species. Viewing Culicoides-borne orbiviruses as a time-sensitive community-based issue, our results help to recommend when management operations should be delivered.
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METCALF, C. J. E., O. N. BJØRNSTAD, M. J. FERRARI, et al. "The epidemiology of rubella in Mexico: seasonality, stochasticity and regional variation." Epidemiology and Infection 139, no. 7 (2010): 1029–38. http://dx.doi.org/10.1017/s0950268810002165.
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SUMMARYThe factors underlying the temporal dynamics of rubella outside of Europe and North America are not well known. Here we used 20 years of incidence reports from Mexico to identify variation in seasonal forcing and magnitude of transmission across the country and to explore determinants of inter-annual variability in epidemic magnitude in rubella. We found considerable regional variation in both magnitude of transmission and amplitude of seasonal variation in transmission. Several lines of evidence pointed to stochastic dynamics as an important driver of multi-annual cycles. Since average age of infection increased with the relative importance of stochastic dynamics, this conclusion has implications for the burden of congenital rubella syndrome. We discuss factors underlying regional variation, and implications of the importance of stochasticity for vaccination implementation.
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Chukwuma Sr, Chrysanthus. "Features of the Emergence and Re-Emergence of Infectious Diseases, Geopolitics and Gain-of-Function Research." International Journal of Coronaviruses 3, no. 4 (2022): 10–18. http://dx.doi.org/10.14302/issn.2692-1537.ijcv-21-4044.
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This paper attempts to present the dissemination and transmission dynamics of emerging and reemerging infectious diseases and the underlying features of gain-of-function research and geopolitics in the ambient within and across borders. Research and publication are relevant from perspectives in the management of local and global health because disease is perspicuously a geopolitical issue ostensibly linked to gain-of-function research where health diplomacy undergirds present and future global functionalities regarding the emergence and reemergence of infectious diseases. These have generated vehement reactions with propensity for extreme geopolitics and gain-of-function natural and anthropogenic activities. Geopolitical parameters and gain-of-function issues impact on the social determinants of health and vice versa. The convening and convergence of countries for unprecented epidemic or pandemic treaty settings or other formulations to confront emerging and reemerging infectious diseases will afford considerable opportunities concerning challenges in action, preparedness and response. Provisions are pertinent for legal instruments, effective and efficient systems to curb future threats and outbreaks of infectious diseases.
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Chrysanthus, Chukwuma Sr. "Geopolitical issues in health and biosecurity concerning gain-of-function research, emergence and re-emergence of infectious diseases." International Journal of Clinical Virology 6, no. 1 (2022): 011–16. http://dx.doi.org/10.29328/journal.ijcv.1001043.
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There are global concerns in the dissemination and transmission dynamics of emerging and reemerging infectious diseases and the underlying features of gain-of-function research and geopolitics within and across borders. These concerns have become pertinent in the management of local and global health because the disease is perspicuously a geopolitical issue ostensibly linked to gain-of-function research where health diplomacy focuses on the present and future global emergence and re-emergence of infectious diseases, pandemics, and microbiome variants. These have generated vehement reactions with a propensity for extreme geopolitics and gain-of-function natural and anthropogenic activities. Geopolitical parameters and gain-of-function issues impact the social determinants of health and vice versa. The convening and convergence of countries for unprecedented epidemic or pandemic treaty settings or other formulations to confront emerging and reemerging infectious diseases will afford considerable opportunities concerning challenges in action, preparedness, and response. Provisions are pertinent for legal instruments, effective and efficient systems to curb future threats and outbreaks of infectious diseases.
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Sr, Dr Chrysanthus Chukwuma. "Perspectives in the Emergence and Re-Emergence of Infectious Diseases, Geopolitics and Gain-of-Function Research." Scholars International Journal of Biochemistry 5, no. 1 (2022): 1–7. http://dx.doi.org/10.36348/sijb.2022.v05i01.001.
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This paper attempts to present the dissemination and transmission dynamics of emerging and reemerging infectious diseases and the underlying features of gain-of-function research and geopolitics in the ambient within and across borders. Research and publication are relevant from perspectives in the management of local and global health because disease is perspicuously a geopolitical issue ostensibly linked to gain-of-function research where health diplomacy undergirds present and future global functionalities regarding the emergence and reemergence of infectious diseases. These have generated vehement reactions with propensity for extreme geopolitics and gain-of-function natural and anthropogenic activities. Geopolitical parameters and gain-of-function issues impact on the social determinants of health and vice versa. The convening and convergence of countries for unprecented epidemic or pandemic treaty settings or other formulations to confront emerging and reemerging infectious diseases will afford considerable opportunities concerning challenges in action, preparedness and response. Provisions are pertinent for legal instruments, effective and efficient systems to curb future threats and outbreaks of infectious diseases.
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Myall, A., I. Venkatachalam, C. Philip, et al. "SPATIAL-TEMPORAL DETERMINANTS OF MDRO TRANSMISSION DYNAMICS: IMPLICATIONS FOR INFECTION CONTROL." International Journal of Infectious Diseases 130 (May 2023): S31. http://dx.doi.org/10.1016/j.ijid.2023.04.071.
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Verkade, Erwin, Birgit van Benthem, Marjolein Kluytmans-van den Bergh, et al. "Dynamics and Determinants of Staphylococcus aureus Carriage in Livestock Veterinarians: A Prospective Cohort Study." Clinical Infectious Diseases 57, no. 2 (2013): e11-e17. http://dx.doi.org/10.1093/cid/cit228.
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Pereira, Felicidade Mota, Aline Salomão de Araujo, Ana Catarina Martins Reis, et al. "Dynamics and Determinants of SARS-CoV-2 RT-PCR Testing on Symptomatic Individuals Attending Healthcare Centers during 2020 in Bahia, Brazil." Viruses 14, no. 7 (2022): 1549. http://dx.doi.org/10.3390/v14071549.
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RT-PCR testing data provides opportunities to explore regional and individual determinants of test positivity and surveillance infrastructure. Using Generalized Additive Models, we explored 222,515 tests of a random sample of individuals with COVID-19 compatible symptoms in the Brazilian state of Bahia during 2020. We found that age and male gender were the most significant determinants of test positivity. There was evidence of an unequal impact among socio-demographic strata, with higher positivity among those living in areas with low education levels during the first epidemic wave, followed by those living in areas with higher education levels in the second wave. Our estimated probability of testing positive after symptom onset corroborates previous reports that the probability decreases with time, more than halving by about two weeks and converging to zero by three weeks. Test positivity rates generally followed state-level reported cases, and while a single laboratory performed ~90% of tests covering ~99% of the state’s area, test turn-around time generally remained below four days. This testing effort is a testimony to the Bahian surveillance capacity during public health emergencies, as previously witnessed during the recent Zika and Yellow Fever outbreaks.
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Lambrechts, Louis, Robert C. Reiner, M. Veronica Briesemeister, et al. "Direct mosquito feedings on dengue-2 virus-infected people reveal dynamics of human infectiousness." PLOS Neglected Tropical Diseases 17, no. 9 (2023): e0011593. http://dx.doi.org/10.1371/journal.pntd.0011593.
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Dengue virus (DENV) transmission from humans to mosquitoes is a poorly documented, but critical component of DENV epidemiology. Magnitude of viremia is the primary determinant of successful human-to-mosquito DENV transmission. People with the same level of viremia, however, can vary in their infectiousness to mosquitoes as a function of other factors that remain to be elucidated. Here, we report on a field-based study in the city of Iquitos, Peru, where we conducted direct mosquito feedings on people naturally infected with DENV and that experienced mild illness. We also enrolled people naturally infected with Zika virus (ZIKV) after the introduction of ZIKV in Iquitos during the study period. Of the 54 study participants involved in direct mosquito feedings, 43 were infected with DENV-2, two with DENV-3, and nine with ZIKV. Our analysis excluded participants whose viremia was detectable at enrollment but undetectable at the time of mosquito feeding, which was the case for all participants with DENV-3 and ZIKV infections. We analyzed the probability of onward transmission during 50 feeding events involving 27 participants infected with DENV-2 based on the presence of infectious virus in mosquito saliva 7–16 days post blood meal. Transmission probability was positively associated with the level of viremia and duration of extrinsic incubation in the mosquito. In addition, transmission probability was influenced by the day of illness in a non-monotonic fashion; i.e., transmission probability increased until 2 days after symptom onset and decreased thereafter. We conclude that mildly ill DENV-infected humans with similar levels of viremia during the first two days after symptom onset will be most infectious to mosquitoes on the second day of their illness. Quantifying variation within and between people in their contribution to DENV transmission is essential to better understand the biological determinants of human infectiousness, parametrize epidemiological models, and improve disease surveillance and prevention strategies.
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Boyd, Patricia S., Janae B. Brown, Joshua D. Brown, et al. "NMR Studies of Retroviral Genome Packaging." Viruses 12, no. 10 (2020): 1115. http://dx.doi.org/10.3390/v12101115.
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Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
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DE MELKER, H. E., and M. A. E. CONYN-VAN SPAENDONCK. "Immunosurveillance and the evaluation of national immunization programmes: a population-based approach." Epidemiology and Infection 121, no. 3 (1998): 637–43. http://dx.doi.org/10.1017/s0950268898001587.
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Mass vaccination can change the epidemiological dynamics of infectious diseases. It may result in a limited persistence of natural and vaccine-induced immunity and a higher mean age of infection, which may lead to a greater risk of complications. The epidemiological situation should be monitored and immunosurveillance based on the assessment of specific antibodies against vaccine-preventable diseases in human serum is one of the tools. In order to estimate the immunity of the Dutch population reliably, a large-scale, population-based, collection of serum samples was established (8359 sera in a nation-wide sampling and 1589 sera from municipalities with low vaccine coverage). In contrast to collecting residual sera from laboratories, this approach gains extensive information by means of a questionnaire regarding the determinants of the immune status and the risk factors for the transmission of infectious diseases in general. The population-based approach gives a better guarantee that the data are representative than collecting sera from laboratories does.
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Ntajal, Joshua, Timo Falkenberg, Thomas Kistemann, and Mariele Evers. "Influences of Land-Use Dynamics and Surface Water Systems Interactions on Water-Related Infectious Diseases—A Systematic Review." Water 12, no. 3 (2020): 631. http://dx.doi.org/10.3390/w12030631.
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Human interactions with surface water systems, through land-use dynamics, can influence the transmission of infectious water-related diseases. As a result, the aim of our study was to explore and examine the state of scientific evidence on the influences of these interactions on water-related infectious disease outcomes from a global perspective. A systematic review was conducted, using 54 peer-reviewed research articles published between 1995 and August 2019. The study revealed that there has been an increase in the number of publications since 2009; however, few of these publications (n = 6) made explicit linkages to the topic. It was found that urban and agricultural land-use changes had relatively high adverse impacts on water quality, due to high concentrations of fecal matter, heavy metals, and nutrients in surface water systems. Water systems were found as the common “vehicle” for infectious disease transmission, which in turn had linkages to sanitation and hygiene conditions. The study found explicit linkages between human–surface water interaction patterns and the transmission of water-based disease. However, weak and complex linkages were found between land-use change and the transmission of water-borne disease, due to multiple pathways and the dynamics of the other determinants of the disease. Therefore, further research studies, using interdisciplinary and transdisciplinary approaches to investigate and enhance a deeper understanding of these complexities and linkages among land use, surface water quality, and water-related infectious diseases, is crucial in developing integrated measures for sustainable water quality monitoring and diseases prevention.
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Charuni, T. M. J. "Narrative review on the spectrum of diseases prevalent among substance-addicted populations and their interconnected health dynamics." Journal of Science of the University of Kelaniya 17, no. 1 (2024): 57–63. http://dx.doi.org/10.4038/josuk.v17i1.8107.
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Substance addiction is a complex phenomenon characterized by the dysfunction of the brain's reward system and neuroplasticity, leading individuals to lose control over their behaviour. This review explores the diverse health implications of addiction, including its impact on liver diseases, cardiovascular conditions, respiratory issues, cancers, infectious diseases, gastrointestinal problems, and mental disorders. Heavy alcohol consumption, tobacco use, illicit drug abuse, and prescription drug misuse contribute significantly to these health burdens, affecting various organs and systems in the body. Respiratory issues arise from tobacco smoking, inhalation of illicit drugs, and volatile chemicals, causing chronic obstructive pulmonary disease, lung cancers, and bronchial asthma. Substance addiction is also linked to various cancers, particularly lung cancer from tobacco, oral cancers from tobacco and alcohol, and oesophageal cancers from alcohol and prescription drugs. Furthermore, addictive substances impair immunity, making individuals more susceptible to infectious diseases like pneumonia, tuberculosis, and HIV/AIDS, especially among injection drug users. The interconnected nature of substance addiction with mental health disorders, genetic factors, environmental influences, and social determinants underscores the need for comprehensive public health strategies. These strategies should encompass education, prevention programs, access to treatment and support services, harm reduction approaches, and destigmatization efforts to address substance addiction comprehensively and improve overall health outcomes for individuals and communities.
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CHANG, M., S. L. GROSECLOSE, A. A. ZAIDI, and C. R. BRADEN. "An ecological analysis of sociodemographic factors associated with the incidence of salmonellosis, shigellosis, and E. coli O157:H7 infections in US counties." Epidemiology and Infection 137, no. 6 (2008): 810–20. http://dx.doi.org/10.1017/s0950268808001477.
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SUMMARYIdentifying county-level sociodemographic and economic factors associated with the incidence of enteric disease may provide new insights concerning the dynamics of community transmission of these diseases as well as opportunities for prevention. We used data from the National Notifiable Diseases Surveillance System, the U.S. Census Bureau, and the Health Resources and Services Administration to conduct an ecological analysis of 26 sociodemographic and economic factors associated with the incidence of salmonellosis, shigellosis, and E. coli O157:H7 infections in US counties for the period 1993 to 2002. Our study indicates that race, ethnicity, place of residence, age, educational attainment, and poverty may affect the risk of acquiring one of these enteric bacterial diseases. The lack of specificity of information regarding salmonellae and shigellae serotypes may have led to less specific associations between community-level determinants and reported incidence of those diseases. Future ecological analyses should use serotype-specific data on incidence, which may be available from laboratory-based surveillance systems.
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Hounkonnou, Cornélia P. A., Valérie Briand, Nadine Fievet, et al. "Dynamics of Submicroscopic Plasmodium falciparum Infections Throughout Pregnancy: A Preconception Cohort Study in Benin." Clinical Infectious Diseases 71, no. 1 (2019): 166–74. http://dx.doi.org/10.1093/cid/ciz748.
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Abstract Background In the context of global malaria elimination efforts, special attention is being paid to submicroscopic Plasmodium falciparum infections. In pregnant, sub-Saharan African women, such infections are more prevalent than microscopic infections, and are thought to have adverse effects on both mothers’ and newborns’ health. However, no study has studied the dynamics and determinants of these infections throughout pregnancy. Retard de Croissance Intra-uterin et Paludisme (RECIPAL), a preconception cohort study carried out in Benin between 2014 and 2017, represented a unique opportunity to assess this issue. Methods We used data from 273 pregnant Beninese women who were followed-up from preconception to delivery. We studied the dynamics of and factors influencing submicroscopic (and microscopic) P. falciparum infections during the 3 trimesters of pregnancy, using an ordinal logistic mixed model. Results The incidence rate of submicroscopic P. falciparum infections during pregnancy was 12.7 per 100 person-months (95% confidence interval [CI] 10.8–14.9), compared to 6.7 per 100 person-months (95% CI 5.5–8.1) for microscopic infections. The prevalences were highest in the first trimester for both submicroscopic and microscopic infections. After adjustment for potential confounding factors, we found that those of young age and those with a submicroscopic P. falciparum infection prior to pregnancy were at significantly higher risks of submicroscopic and microscopic infections throughout pregnancy, with a more pronounced effect in the first trimester of pregnancy. Conclusions The first trimester of pregnancy is a particularly high-risk period for P. falciparum infection during pregnancy, especially for the youngest women. Malaria prevention tools covering the preconception period and early pregnancy are urgently needed to better protect pregnant women and their newborns.
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Mironova, L. V., A. S. Ponomareva, E. A. Basov та ін. "Assessing the Efciency of Detection of Vibrio cholerae Genetic Determinants Through Waterbody Vibrioflora Monitoring System". Problems of Particularly Dangerous Infections, № 3 (23 жовтня 2021): 89–97. http://dx.doi.org/10.21055/0370-1069-2021-3-89-97.
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Objective of the study was to assess the effectiveness of PCR screening of Vibrio cholerae genetic determinants in samples from surface water reservoirs for optimization of the cholera microbiological monitoring system.Materials and methods. The study was carried out as a part of the vibrioflora monitoring in surface water bodies in Irkutsk city. The study design included: 1) PCR screening of V. cholerae genetic determinants in nutrient-enriched (1 % peptone water) samples from surface water reservoirs during the monitoring period (824 samples); 2) studying of the V. cholerae DNA accumulation dynamics applying PCR assay of the samples from surface water reservoirs during cultivation on the enriched media (16 samples in dynamics); 3) experimental study of the detected V. cholerae concentrations in samples from surface water reservoirs. Species-specifc (hlyA, toxR) and serogroup-specifc (wbeT, wbfR) V. cholerae determinants were indicated in PCR with hybridization-fluorescent and electrophoretic detection.Results and discussion. At the frst stage it was found that the proportion of the positive samples through PCR screening (33.9 %) exceeded the percentage of the positive samples in bacteriological examination (19.3 %) (t=6.6; p<0,01). In the assessment of DNA accumulation dynamics, a decrease in the threshold cycle (Ct) by 1.2–5.2 times was recorded, indicating an increase in the V. cholerae concentration and proving the detection of genetic determinants of viable forms during PCR screening. An extended study of PCR-positive but bacteriologically negative samples made it possible to additionally isolate 4 V. cholerae cultures. However, there were no differences in the sensitivity of PCR screening and bacteriological analysis in the experiment with water samples artifcially contaminated with V. cholerae unlike the analysis of the enriched native samples. It can be determined by the metabolism and adaptation peculiarities of the microorganism in different environmental conditions. The results of the integrated study indicate the epidemiological effectiveness of PCR screening which gives grounds to recommend its application in monitoring studies of vibrioflora from environment after preliminary enrichment on liquid nutrient media in the work of federal, territorial, and regional laboratories.
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Lourenço, José, and Mario Recker. "Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes." PLoS Neglected Tropical Diseases 4, no. 11 (2010): e894. http://dx.doi.org/10.1371/journal.pntd.0000894.
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Ding, Wandi, Yun Kang, and Anuj Mubayi. "Special Issue: Mathematical modeling and analysis of social and ecological determinants for the dynamics of infectious diseases and public health policies." Mathematical Biosciences and Engineering 18, no. 6 (2021): 8535–37. http://dx.doi.org/10.3934/mbe.2021422.
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Snyman, Albert, Ralph Eric Thijl Vanstreels, Chandré Nell, et al. "Determinants of external and blood parasite load in African penguins (Spheniscus demersus) admitted for rehabilitation." Parasitology 147, no. 5 (2020): 577–83. http://dx.doi.org/10.1017/s0031182020000141.
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AbstractWe investigate the factors associated with the occurrence and abundance of external and blood parasites in African penguins (Spheniscus demersus), an endangered seabird that breeds exclusively on the coasts of Namibia and South Africa. External parasites were collected using the dust-ruffling method from 171 African Penguins admitted at a rehabilitation facility in the Western Cape, South Africa. Additionally, blood smears were obtained upon admission and weekly during rehabilitation and examined for blood parasites. Fleas Parapsyllus longicornis humboldti, ticks Ornithodoros capensis and lice Austrogoniodes demersus were recovered from 93, 63 and 40%, respectively, of the penguins upon admission to the centre. Rescue location and age group were identified as significant determinants of flea abundance, whereas month of admission was a significant determinant of tick abundance. Blood parasites were also common on admission, with Babesia being the most frequent (46% prevalence) whereas Borrelia was recorded sporadically (1.2%) and Plasmodium was recorded once. The prevalence and abundance of ticks on admission was positively associated with Babesia infection on admission. Our findings demonstrate the variability and contributing factor of parasite infections in an endangered species of penguin, and highlight the need for additional research on the parasite–host dynamics involving these potential disease vectors.
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Fabre, Frédéric, Claude Bruchou, Alain Palloix, and Benoît Moury. "Key determinants of resistance durability to plant viruses: Insights from a model linking within- and between-host dynamics." Virus Research 141, no. 2 (2009): 140–49. http://dx.doi.org/10.1016/j.virusres.2008.11.021.
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Segundo Salej Higgins, Sílvio, Adrian Pablo Hinojosa Luna, Reinaldo Onofre dos Santos, Andreia Maria Pinto Rabelo, Maíra Soalheiro, and Vanessa Cardoso Ferreira. "A study on social contact rates relevant for the spread of infectious diseases in a Brazilian slum." Revista Brasileira de Estudos de População 40 (August 11, 2023): 1–20. http://dx.doi.org/10.20947/s0102-3098a0241.
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Inspired by the POLYMOD study, an epidemiological survey was conducted in June 2021 in one of the most densely populated and socially vulnerable sectors of Belo Horizonte (Brazil). A sample of 1000 individuals allowed us to identify, within a 24-hour period, the rates of social contacts by age groups, the size and frequency of clique in which respondents participated, as well as other associated sociodemographic factors (number of household residents, location of contact, use of public transportation, among others). Data were analyzed in two phases. In the first one, results between two SIR models that simulated an eight-day pandemic process were compared. One included parameters adjusted from observed contact rates, the other operated with parameters adjusted from projected rates for Brazil. In the second phase, by means of a log-lin regression, we modeled the main social determinants of contact rates, using clique density as a proxy variable. The data analysis showed that family size, age, and social circles are the main covariates influencing the formation of cliques. It also demonstrated that compartmentalized epidemiological models, combined with social contact rates, have a better capacity to describe the epidemiological dynamics, providing a better basis for mitigation and control measures for diseases that cause acute respiratory syndromes.
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Al-Neama, Raed Taha, Kevin J. Bown, Damer P. Blake, and Richard J. Birtles. "Determinants of Eimeria and Campylobacter infection dynamics in UK domestic sheep: the role of co-infection." Parasitology 148, no. 5 (2021): 623–29. http://dx.doi.org/10.1017/s0031182021000044.
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Bernhauerová, Veronika, Veronica V. Rezelj, and Marco Vignuzzi. "Modelling Degradation and Replication Kinetics of the Zika Virus In Vitro Infection." Viruses 12, no. 5 (2020): 547. http://dx.doi.org/10.3390/v12050547.
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Mathematical models of in vitro viral kinetics help us understand and quantify the main determinants underlying the virus–host cell interactions. We aimed to provide a numerical characterization of the Zika virus (ZIKV) in vitro infection kinetics, an arthropod-borne emerging virus that has gained public recognition due to its association with microcephaly in newborns. The mathematical model of in vitro viral infection typically assumes that degradation of extracellular infectious virus proceeds in an exponential manner, that is, each viral particle has the same probability of losing infectivity at any given time. We incubated ZIKV stock in the cell culture media and sampled with high frequency for quantification over the course of 96 h. The data showed a delay in the virus degradation in the first 24 h followed by a decline, which could not be captured by the model with exponentially distributed decay time of infectious virus. Thus, we proposed a model, in which inactivation of infectious ZIKV is gamma distributed and fit the model to the temporal measurements of infectious virus remaining in the media. The model was able to reproduce the data well and yielded the decay time of infectious ZIKV to be 40 h. We studied the in vitro ZIKV infection kinetics by conducting cell infection at two distinct multiplicity of infection and measuring viral loads over time. We fit the mathematical model of in vitro viral infection with gamma distributed degradation time of infectious virus to the viral growth data and identified the timespans and rates involved within the ZIKV-host cell interplay. Our mathematical analysis combined with the data provides a well-described example of non-exponential viral decay dynamics and presents numerical characterization of in vitro infection with ZIKV.
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Churakov, Mikhail, Christian J. Villabona-Arenas, Moritz U. G. Kraemer, Henrik Salje, and Simon Cauchemez. "Spatio-temporal dynamics of dengue in Brazil: Seasonal travelling waves and determinants of regional synchrony." PLOS Neglected Tropical Diseases 13, no. 4 (2019): e0007012. http://dx.doi.org/10.1371/journal.pntd.0007012.
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Farooq, Tahir, Muhammad Dilshad Hussain, Muhammad Taimoor Shakeel, et al. "Deploying Viruses against Phytobacteria: Potential Use of Phage Cocktails as a Multifaceted Approach to Combat Resistant Bacterial Plant Pathogens." Viruses 14, no. 2 (2022): 171. http://dx.doi.org/10.3390/v14020171.
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Plants in nature are under the persistent intimidation of severe microbial diseases, threatening a sustainable food production system. Plant-bacterial pathogens are a major concern in the contemporary era, resulting in reduced plant growth and productivity. Plant antibiotics and chemical-based bactericides have been extensively used to evade plant bacterial diseases. To counteract this pressure, bacteria have evolved an array of resistance mechanisms, including innate and adaptive immune systems. The emergence of resistant bacteria and detrimental consequences of antimicrobial compounds on the environment and human health, accentuates the development of an alternative disease evacuation strategy. The phage cocktail therapy is a multidimensional approach effectively employed for the biocontrol of diverse resistant bacterial infections without affecting the fauna and flora. Phages engage a diverse set of counter defense strategies to undermine wide-ranging anti-phage defense mechanisms of bacterial pathogens. Microbial ecology, evolution, and dynamics of the interactions between phage and plant-bacterial pathogens lead to the engineering of robust phage cocktail therapeutics for the mitigation of devastating phytobacterial diseases. In this review, we highlight the concrete and fundamental determinants in the development and application of phage cocktails and their underlying mechanism, combating resistant plant-bacterial pathogens. Additionally, we provide recent advances in the use of phage cocktail therapy against phytobacteria for the biocontrol of devastating plant diseases.
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Luz, Saturnino, and Masood Masoodian. "Exploring Environmental and Geographical Factors Influencing the Spread of Infectious Diseases with Interactive Maps." Sustainability 14, no. 16 (2022): 9990. http://dx.doi.org/10.3390/su14169990.
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Environmental problems due to human activities such as deforestation, urbanisation, and large scale intensive farming are some of the major factors behind the rapid spread of many infectious diseases. This in turn poses significant challenges not only in as regards providing adequate healthcare, but also in supporting healthcare workers, medical researchers, policy makers, and others involved in managing infectious diseases. These challenges include surveillance, tracking of infections, communication of public health knowledge and promotion of behavioural change. Behind these challenges lies a complex set of factors which include not only biomedical and population health determinants but also environmental, climatic, geographic, and socioeconomic variables. While there is broad agreement that these factors are best understood when considered in conjunction, aggregating and presenting diverse information sources requires effective information systems, software tools, and data visualisation. In this article, we argue that interactive maps, which couple geographical information systems and advanced information visualisation techniques, provide a suitable unifying framework for coordinating these tasks. Therefore, we examine how interactive maps can support spatial epidemiological visualisation and modelling involving distributed and dynamic data sources and incorporating temporal aspects of disease spread. Combining spatial and temporal aspects can be crucial in such applications. We discuss these issues in the context of support for disease surveillance in remote regions, utilising tools that facilitate distributed data collection and enable multidisciplinary collaboration, while also providing support for simulation and data analysis. We show that interactive maps deployed on a combination of mobile devices and large screens can provide effective means for collection, sharing, and analysis of health data.
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Wang, Zhe, Lu Liu, Liang Shi, et al. "Identifying the Determinants of Distribution of Oncomelania hupensis Based on Geographically and Temporally Weighted Regression Model along the Yangtze River in China." Pathogens 11, no. 9 (2022): 970. http://dx.doi.org/10.3390/pathogens11090970.
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Background: As the unique intermediate host of Schistosoma japonicum, the geographical distribution of Oncomelania hupensis (O. hupensis) is an important index in the schistosomiasis surveillance system. This study comprehensively analyzed the pattern of snail distribution along the Yangtze River in Jiangsu Province and identified the dynamic determinants of the distribution of O. hupensis. Methods: Snail data from 2017 to 2021 in three cities (Nanjing, Zhenjiang, and Yangzhou) along the Yangtze River were obtained from the annual cross-sectional survey produced by the Jiangsu Institute of Parasitic Diseases. Spatial autocorrelation and hot-spot analysis were implemented to detect the spatio–temporal dynamics of O. hupensis distribution. Furthermore, 12 factors were used as independent variables to construct an ordinary least squares (OLS) model, a geographically weighted regression (GWR) model, and a geographically and temporally weighted regression (GTWR) model to identify the determinants of the distribution of O. hupensis. The adjusted coefficients of determination (adjusted R2, AICc, RSS) were used to evaluate the performance of the models. Results: In general, the distribution of O. hupensis had significant spatial aggregation in the past five years, and the density of O. hupensis increased eastwards in the Jiangsu section of the lower reaches of the Yangtze River. Relatively speaking, the distribution of O. hupensis wase spatially clustered from 2017 to 2021, that is, it was found that the border between Yangzhou and Zhenjiang was the high density agglomeration area of O. hupensis snails. According to the GTWR model, the density of O. hupensis was related to the normalized difference vegetation index, wetness, dryness, land surface temperature, elevation, slope, and distance to nearest river, which had a good explanatory power for the snail data in Yangzhou City (adjusted R2 = 0.7039, AICc = 29.10, RSS = 6.81). Conclusions: The distribution of O. hupensis and the environmental factors in the Jiangsu section of the lower reaches of the Yangtze River had significant spatial aggregation. In different areas, the determinants affecting the distribution of O. hupensis were different, which could provide a scientific basis for precise prevention and control of O. hupensis. A GTWR model was prepared and used to identify the dynamic determinants for the distribution of O. hupensis and contribute to the national programs of control of schistosomiasis and other snail-borne diseases.
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Davis, E. L., J. Prada, L. J. Reimer, and T. D. Hollingsworth. "Modelling the Impact of Vector Control on Lymphatic Filariasis Programs: Current Approaches and Limitations." Clinical Infectious Diseases 72, Supplement_3 (2021): S152—S157. http://dx.doi.org/10.1093/cid/ciab191.
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Abstract Vector control is widely considered an important tool for lymphatic filariasis (LF) elimination but is not usually included in program budgets and has often been secondary to other policy questions in modelling studies. Evidence from the field demonstrates that vector control can have a large impact on program outcomes and even halt transmission entirely, but implementation is expensive. Models of LF have the potential to inform where and when resources should be focused, but often simplify vector dynamics and focus on capturing human prevalence trends, making them comparatively ill-designed for direct analysis of vector control measures. We review the recent modelling literature and present additional results using a well-established model, highlighting areas of agreement between model predictions and field evidence, and discussing the possible determinants of existing disagreements. We conclude that there are likely to be long-term benefits of vector control, both on accelerating programs and preventing resurgence.
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Chen, Huanhuan, Guangshuo Zhang, Guiling Ding, et al. "Interspecific Host Variation and Biotic Interactions Drive Pathogen Community Assembly in Chinese Bumblebees." Insects 14, no. 11 (2023): 887. http://dx.doi.org/10.3390/insects14110887.
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Bumblebees have been considered one of the most important pollinators on the planet. However, recent reports of bumblebee decline have raised concern about a significant threat to ecosystem stability. Infectious diseases caused by multiple pathogen infections have been increasingly recognized as an important mechanism behind this decline worldwide. Understanding the determining factors that influence the assembly and composition of pathogen communities among bumblebees can provide important implications for predicting infectious disease dynamics and making effective conservation policies. Here, we study the relative importance of biotic interactions versus interspecific host resistance in shaping the pathogen community composition of bumblebees in China. We first conducted a comprehensive survey of 13 pathogens from 22 bumblebee species across China. We then applied joint species distribution modeling to assess the determinants of pathogen community composition and examine the presence and strength of pathogen–pathogen associations. We found that host species explained most of the variations in pathogen occurrences and composition, suggesting that host specificity was the most important variable in predicting pathogen occurrences and community composition in bumblebees. Moreover, we detected both positive and negative associations among pathogens, indicating the role of competition and facilitation among pathogens in determining pathogen community assembly. Our research demonstrates the power of a pluralistic framework integrating field survey of bumblebee pathogens with community ecology frameworks to understand the underlying mechanisms of pathogen community assembly.
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Pikuła, Anna, Anna Lisowska, and Katarzyna Domańska-Blicharz. "Epidemiology of Infectious Bursal Disease Virus in Poland during 2016–2022." Viruses 15, no. 2 (2023): 289. http://dx.doi.org/10.3390/v15020289.
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Infectious bursal disease virus is an immunosuppressive ubiquitous pathogen that causes serious economic losses in poultry production. The virus is prone to genetic changes through mutations and reassortment, which drive the emergence of new variants and lead to a change in the epidemiological situation in a field. Such a situation is currently being reported due to a large wave of IBDV A3B1 reassortant infections in northwestern Europe. On the other hand, in Poland, which is the largest producer of chicken meat in the EU, the IBDVs of genotypes A3B2 and A3B4 were circulating just before the emergence of A3B1 reassortants. The purpose of the presented study was to update the IBDV epidemiological situation. The performed molecular survey based on the sequence of both genome segments showed the presence of very virulent strains (A3B2) and reassortants of genotypes A3B4 and A3B1; moreover, two of these genotypes are newly introduced IBDV lineages. In addition, a number of amino acid substitutions were demonstrated, including within antigenic epitopes and virulence determinants. In conclusion, the results obtained indicated a dynamic epidemiological situation in Poland, which highlights the need for further monitoring studies in the region and verification of protection conferred by the vaccines used against infection with detected IBDV.
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Lamouroux, David, Jan Nagler, Theo Geisel, and Stephan Eule. "Paradoxical effects of coupling infectious livestock populations and imposing transport restrictions." Proceedings of the Royal Society B: Biological Sciences 282, no. 1800 (2015): 20142805. http://dx.doi.org/10.1098/rspb.2014.2805.
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Spatial heterogeneity of a host population of mobile agents has been shown to be a crucial determinant of many aspects of disease dynamics, ranging from the proliferation of diseases to their persistence and to vaccination strategies. In addition, the importance of regional and structural differences grows in our modern world. Little is known, though, about the consequences when traits of a disease vary regionally. In this paper, we study the effect of a spatially varying per capita infection rate on the behaviour of livestock diseases. We show that the prevalence of an infectious livestock disease in a community of animals can paradoxically decrease owing to transport connections to other communities in which the risk of infection is higher. We study the consequences for the design of livestock transportation restriction measures and establish exact criteria to discriminate those connections that increase the level of infection in the community from those that decrease it.
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OGDEN, N. H., M. BIGRAS-POULIN, C. J. O'CALLAGHAN, et al. "Vector seasonality, host infection dynamics and fitness of pathogens transmitted by the tickIxodes scapularis." Parasitology 134, no. 2 (2006): 209–27. http://dx.doi.org/10.1017/s0031182006001417.
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Fitness of tick-borne pathogens may be determined by the degree to which their infection dynamics in vertebrate hosts permits transmission cycles if infective and uninfected tick stages are active at different times of the year. To investigate this hypothesis we developed a simulation model that integrates the transmission pattern imposed by seasonally asynchronous nymphal and larvalIxodes scapularisticks in northeastern North America, with a model of infection in white-footed mice (Peromyscus leucopus) reservoir hosts, using the bacteriaBorrelia burgdorferiandAnaplasma phagocytophilumas examples. In simulations, survival of microparasites, their sensitivity to reduced rodent and tick abundance, and to ‘dilution’ by a reservoir-incompetent host depended on traits that allowed (i) highly efficient transmission from acutely-infected hosts, (ii) long-lived acute or ‘carrier’ host infections, and/or (iii) transmission amongst co-feeding ticks. Minimum values for transmission efficiency to ticks, and duration of host infectivity, necessary for microparasite persistence, were always higher when nymphal and larval ticks were seasonally asynchronous than when these instars were synchronous. Thus, traits influencing duration of host infectivity, transmission efficiency to ticks and co-feeding transmission are likely to be dominant determinants of fitness inI. scapularis-borne microparasites in northeastern North America due to abiotic forcings influencingI. scapularisseasonality.
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Hancke, Diego, and Olga Virginia Suárez. "Factors Affecting Helminth Abundances in Synanthropic Rodents of an Urban Environment." Open Parasitology Journal 6, no. 1 (2018): 87–95. http://dx.doi.org/10.2174/1874421401806010087.
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Background: Current levels of urbanization cause changes in the ecology of hosts, the pathogens, or both, promoting the proliferation of zoonotic diseases. Rodents are a good biological model for the development of pathogen transmission models because it presence is often related to a none-adequate environmental management. Objective: The main goal of this paper was to study the changes in the abundance of helminth populations in synanthropic rodents of an urban landscape. Methods: A total of 92 R. norvegicus and 65 M. musculus were captured in the City of Buenos Aires (Argentina) and were screened for parasites. The variations in helminth abundances were studied at host population scale to determine the factors, such as the type of environment, meteorological conditions and demographic parameters of the hosts, which have an effect on helminth infection rates. Results: Parasites with intermediate hosts or free living larval stages in their life cycle were the most affected. It was found how rodents’ use of the habitats in the different urban environments has an effect on the helminth infection levels. Besides, the importance of season on helminth abundance was determined, suggesting that climatic conditions are crucial for parasite survival and transmission. Conclusion: This information is relevant because it not only allows us to deepen the ecological dynamics of parasites in urban rodents, but also shows that environmental conditions are determinants for the persistence of helminth populations in a city.
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Mohanty, Pratap C., and Kamal Sharma. "Households’ responses on medical pluralism: Dynamics and determinants of access to traditional medicines in India." Clinical Epidemiology and Global Health 12 (October 2021): 100880. http://dx.doi.org/10.1016/j.cegh.2021.100880.
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Fawzy, Mohamed, and Yosra A. Helmy. "The One Health Approach is Necessary for the Control of Rift Valley Fever Infections in Egypt: A Comprehensive Review." Viruses 11, no. 2 (2019): 139. http://dx.doi.org/10.3390/v11020139.
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Rift Valley fever (RVF) is an emerging transboundary, mosquito-borne, zoonotic viral disease caused high morbidity and mortality in both human and ruminant populations. It is considered an important threat to both agriculture and public health in African and the Middle Eastern countries including Egypt. Five major RVF epidemics have been reported in Egypt (1977, 1993, 1994, 1997, and 2003). The virus is transmitted in Egypt by different mosquito's genera such as Aedes, Culex, Anopheles, and Mansonia, leading to abortions in susceptible animal hosts especially sheep, goat, cattle, and buffaloes. Recurrent RVF outbreaks in Egypt have been attributed in part to the lack of routine surveillance for the virus. These periodic epizootics have resulted in severe economic losses. We posit that there is a critical need for new approaches to RVF control that will prevent or at least reduce future morbidity and economic stress. One Health is an integrated approach for the understanding and management of animal, human, and environmental determinants of complex problems such as RVF. Employing the One Health approach, one might engage local communities in surveillance and control of RVF efforts, rather than continuing their current status as passive victims of the periodic RVF incursions. This review focuses upon endemic and epidemic status of RVF in Egypt, the virus vectors and their ecology, transmission dynamics, risk factors, and the ecology of the RVF at the animal/human interface, prevention, and control measures, and the use of environmental and climate data in surveillance systems to predict disease outbreaks.
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Sun, Qinfang, Avik Biswas, Dmitry Lyumkis, Ronald Levy, and Nanjie Deng. "Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization." Viruses 16, no. 1 (2024): 76. http://dx.doi.org/10.3390/v16010076.
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The first- and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffolds, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding with intasomes from HIV-1 and the closely related prototype foamy virus (PFV) despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we applied a novel molecular dynamics-based free energy method that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between the two bound conformations of ligand 4f within the crowded environments of the INSTI binding pockets in these intasomes. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode, and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.
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Bbosa, Nicholas, Deogratius Ssemwanga, Rebecca N. Nsubuga, et al. "Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control." Viruses 13, no. 6 (2021): 970. http://dx.doi.org/10.3390/v13060970.
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Phylogenetic inference is useful in characterising HIV transmission networks and assessing where prevention is likely to have the greatest impact. However, estimating parameters that influence the network structure is still scarce, but important in evaluating determinants of HIV spread. We analyzed 2017 HIV pol sequences (728 Lake Victoria fisherfolk communities (FFCs), 592 female sex workers (FSWs) and 697 general population (GP)) to identify transmission networks on Maximum Likelihood (ML) phylogenetic trees and refined them using time-resolved phylogenies. Network generative models were fitted to the observed degree distributions and network parameters, and corrected Akaike Information Criteria and Bayesian Information Criteria values were estimated. 347 (17.2%) HIV sequences were linked on ML trees (maximum genetic distance ≤4.5%, ≥95% bootstrap support) and, of these, 303 (86.7%) that consisted of pure A1 (n = 168) and D (n = 135) subtypes were analyzed in BEAST v1.8.4. The majority of networks (at least 40%) were found at a time depth of ≤5 years. The waring and yule models fitted best networks of FFCs and FSWs respectively while the negative binomial model fitted best networks in the GP. The network structure in the HIV-hyperendemic FFCs is likely to be scale-free and shaped by preferential attachment, in contrast to the GP. The findings support the targeting of interventions for FFCs in a timely manner for effective epidemic control. Interventions ought to be tailored according to the dynamics of the HIV epidemic in the target population and understanding the network structure is critical in ensuring the success of HIV prevention programs.
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Cruz-Alegría, Ingrid Yazmin, Nancy Gabriela Santos-Hernández, Christian Ruiz-Castillejos, et al. "Ecoepidemiology of Chagas Disease in a Biological Corridor in Southeastern Mexico: A Promising Approach to Understand the Risk of Chagas Disease." Journal of Parasitology Research 2024 (March 8, 2024): 1–9. http://dx.doi.org/10.1155/2024/4775361.
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Ecoepidemiology is an emerging field that attempts to explain how biotic, environmental, and even social factors influence the dynamics of infectious diseases. Particularly in vector-borne diseases, the study under this approach offers us an overview of the pathogens, vectors, and hosts that coexist in a given region and their ecological determinants. As a result of this, risk predictions can be established in a changing environment and how it may impact human populations. This paper is aimed at evaluating some ecoepidemiological characteristics of Chagas disease in a natural reserve in southeastern Mexico that borders human settlements. We carry out a cross-sectional study in 2022 where we search insects manually and with light traps. We set traps for small mammals and bats and conducted interviews with the inhabitants living around the study site. We identified the presence of Triatoma dimidiata and T. huehuetenanguensis species with a percentage of TcI T. cruzi infection of 68.4% (95% CI: 66.9-69.9). Temperature and humidity were not determining factors for the probability of insect capture. Of the 108 wild mammals (Chiroptera, Rodentia, and Didelphimorphia), none was infected with T. cruzi. Knowledge about Chagas disease in nearby inhabitants is poor, and some characteristics were found on the periphery of dwellings that could offer a refuge for insect vectors. With this information, surveillance strategies can be generated in the study area that reduce the risk of transmission of T. cruzi parasite to humans, and it is expected to motivate the use of this field in future research.
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Ranjan, Amit, Sabiha Shaik, Agnismita Mondal та ін. "Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India". Antimicrobial Agents and Chemotherapy 60, № 11 (2016): 6795–805. http://dx.doi.org/10.1128/aac.01345-16.
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ABSTRACTThe global dissemination and increasing incidence of carbapenem-resistant, Gram-negative organisms have resulted in acute public health concerns. Here, we present a retrospective multicenter study on molecular characterization of metallo-β-lactamase (MBL)-producing clinicalEscherichia coliisolates recovered from extraintestinal infections in two hospitals in Pune, India. We screened a large sample size of 510E. coliisolates for MBL production wherein we profiled their molecular determinants, antimicrobial resistance phenotypes, functional virulence properties, genomic features, and transmission dynamics. Approximately 8% of these isolates were MBL producers, the majority of which were of the NDM-1 (69%) type, followed by NDM-5 (19%), NDM-4 (5.5%), and NDM-7 (5.5%). MBL producers were resistant to all antibiotics tested except for colistin, fosfomycin, and chloramphenicol, which were effective to various extents. Plasmids were found to be an effective means of dissemination of NDM genes and other resistance traits. All MBL producers adhered to and invaded bladder epithelial (T24) cells and demonstrated significant serum resistance. Genomic analysis of MBL-producingE. coliisolates revealed higher resistance but a moderate virulence gene repertoire. A subset of NDM-1-positiveE. coliisolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. A majority of MBL-producingE. colistrains revealed unique genotypes, suggesting that they were clonally unrelated. Overall, the coexistence of virulence and carbapenem resistance in clinicalE. coliisolates is of serious concern. Moreover, the emergence of NDM-1 among the globally dominantE. coliST101 isolates warrants stringent surveillance and control measures.
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Liu, Yang, Sebastian Funk, and Stefan Flasche. "The contribution of pre-symptomatic infection to the transmission dynamics of COVID-2019." Wellcome Open Research 5 (April 1, 2020): 58. http://dx.doi.org/10.12688/wellcomeopenres.15788.1.
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Background: Pre-symptomatic transmission can be a key determinant of the effectiveness of containment and mitigation strategies for infectious diseases, particularly if interventions rely on syndromic case finding. For COVID-19, infections in the absence of apparent symptoms have been reported frequently alongside circumstantial evidence for asymptomatic or pre-symptomatic transmission. We estimated the potential contribution of pre-symptomatic cases to COVID-19 transmission. Methods: Using the probability for symptom onset on a given day inferred from the incubation period, we attributed the serial interval reported from Shenzen, China, into likely pre-symptomatic and symptomatic transmission. We used the serial interval derived for cases isolated more than 6 days after symptom onset as the no active case finding scenario and the unrestricted serial interval as the active case finding scenario. We reported the estimate assuming no correlation between the incubation period and the serial interval alongside a range indicating alternative assumptions of positive and negative correlation. Results: We estimated that 23% (range accounting for correlation: 12 – 28%) of transmissions in Shenzen may have originated from pre-symptomatic infections. Through accelerated case isolation following symptom onset, this percentage increased to 46% (21 – 46%), implying that about 35% of secondary infections among symptomatic cases have been prevented. These results were robust to using reported incubation periods and serial intervals from other settings. Conclusions: Pre-symptomatic transmission may be essential to consider for containment and mitigation strategies for COVID-19.
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Kizy, Anne E., and Melody N. Neely. "First Streptococcus pyogenes Signature-Tagged Mutagenesis Screen Identifies Novel Virulence Determinants." Infection and Immunity 77, no. 5 (2009): 1854–65. http://dx.doi.org/10.1128/iai.01306-08.
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ABSTRACT The virulence of bacterial pathogens is a complex process that requires the dynamic expression of many genes for the pathogens to invade and circumvent host defenses, as well as to proliferate in vivo. In this study, we employed a large-scale screen, signature-tagged mutagenesis (STM), to identify Streptococcus pyogenes virulence genes important for pathogenesis within the host. Approximately 1,200 STM mutants were created and screened using the zebrafish infectious disease model. The transposon insertion site was identified for 29 of the 150 mutants that were considered attenuated for virulence. Previously reported streptococcal virulence genes, such as mga, hasA, amrA, smeZ, and two genes in the sil locus, were identified, confirming the utility of the model for revealing genes important for virulence. Multiple genes not previously implicated in virulence were also identified, including genes encoding putative transporters, hypothetical cytosolic proteins, and macrolide efflux pumps. The STM mutant strains display various levels of attenuation, and multiple separate insertions were identified in either the same gene or the same locus, suggesting that these factors are important for this type of acute, invasive infection. We further examined two such genes, silB and silC of a putative quorum-sensing regulon, and determined that they are significant virulence factors in our model of necrotizing fasciitis. sil locus promoter expression was examined under various in vitro conditions, as well as in zebrafish tissues, and was found to be differentially induced. This study was a unique investigation of S. pyogenes factors required for successful invasive infection.
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Banerjee, Soumya, Alan S. Perelson, and Melanie Moses. "Modelling the effects of phylogeny and body size on within-host pathogen replication and immune response." Journal of The Royal Society Interface 14, no. 136 (2017): 20170479. http://dx.doi.org/10.1098/rsif.2017.0479.
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Understanding how quickly pathogens replicate and how quickly the immune system responds is important for predicting the epidemic spread of emerging pathogens. Host body size, through its correlation with metabolic rates, is theoretically predicted to impact pathogen replication rates and immune system response rates. Here, we use mathematical models of viral time courses from multiple species of birds infected by a generalist pathogen (West Nile Virus; WNV) to test more thoroughly how disease progression and immune response depend on mass and host phylogeny. We use hierarchical Bayesian models coupled with nonlinear dynamical models of disease dynamics to incorporate the hierarchical nature of host phylogeny. Our analysis suggests an important role for both host phylogeny and species mass in determining factors important for viral spread such as the basic reproductive number, WNV production rate, peak viraemia in blood and competency of a host to infect mosquitoes. Our model is based on a principled analysis and gives a quantitative prediction for key epidemiological determinants and how they vary with species mass and phylogeny. This leads to new hypotheses about the mechanisms that cause certain taxonomic groups to have higher viraemia. For example, our models suggest that higher viral burst sizes cause corvids to have higher levels of viraemia and that the cellular rate of virus production is lower in larger species. We derive a metric of competency of a host to infect disease vectors and thereby sustain the disease between hosts. This suggests that smaller passerine species are highly competent at spreading the disease compared with larger non-passerine species. Our models lend mechanistic insight into why some species (smaller passerine species) are pathogen reservoirs and some (larger non-passerine species) are potentially dead-end hosts for WNV. Our techniques give insights into the role of body mass and host phylogeny in the spread of WNV and potentially other zoonotic diseases. The major contribution of this work is a computational framework for infectious disease modelling at the within-host level that leverages data from multiple species. This is likely to be of interest to modellers of infectious diseases that jump species barriers and infect multiple species. Our method can be used to computationally determine the competency of a host to infect mosquitoes that will sustain WNV and other zoonotic diseases. We find that smaller passerine species are more competent in spreading the disease than larger non-passerine species. This suggests the role of host phylogeny as an important determinant of within-host pathogen replication. Ultimately, we view our work as an important step in linking within-host viral dynamics models to between-host models that determine spread of infectious disease between different hosts.
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Adams, Mark D., E. Ricky Chan, Neil D. Molyneaux, and Robert A. Bonomo. "Genomewide Analysis of Divergence of Antibiotic Resistance Determinants in Closely Related Isolates of Acinetobacter baumannii." Antimicrobial Agents and Chemotherapy 54, no. 9 (2010): 3569–77. http://dx.doi.org/10.1128/aac.00057-10.
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ABSTRACT Multidrug resistance has emerged as a significant concern with infections caused by Acinetobacter baumannii. Ample evidence supports the involvement of mobile genetic elements in the transfer of antibiotic resistance genes, but the extent of variability and the rate of genetic change associated with the acquisition of antibiotic resistance have not been studied in detail. Whole-genome sequence analysis of six closely related clinical isolates of A. baumannii, including four from the same hospital, revealed extensive divergence of the resistance genotype that correlated with observed differences in antimicrobial susceptibility. Resistance genes associated with insertion sequences, plasmids, and a chromosomal resistance gene island all showed variability. The highly dynamic resistance gene repertoire suggests rapid evolution of drug resistance.
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Sindi, Suzanne S., and Tricia R. Serio. "Prion dynamics and the quest for the genetic determinant in protein-only inheritance." Current Opinion in Microbiology 12, no. 6 (2009): 623–30. http://dx.doi.org/10.1016/j.mib.2009.09.003.
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Torres, Maria Celeste, Marcos Cesar Lima de Mendonça, Cintia Damasceno dos Santos Rodrigues, et al. "Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes." Viruses 13, no. 2 (2021): 349. http://dx.doi.org/10.3390/v13020349.
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Intrahost genetic diversity is thought to facilitate arbovirus adaptation to changing environments and hosts, and it might also be linked to viral pathogenesis. Dengue virus serotype 2 (DENV-2) has circulated in Brazil since 1990 and is associated with severe disease and explosive outbreaks. Intending to shed light on the viral determinants for severe dengue pathogenesis, we sought to analyze the DENV-2 intrahost genetic diversity in 68 patient cases clinically classified as dengue fever (n = 31), dengue with warning signs (n = 19), and severe dengue (n = 18). Unlike previous DENV intrahost diversity studies whose approaches employed PCR, here we performed viral whole-genome deep sequencing from clinical samples with an amplicon-free approach, representing the real intrahost diversity scenario. Striking differences were detected in the viral population structure between the three clinical categories, which appear to be driven mainly by different infection times and selection pressures, rather than being linked with the clinical outcome itself. Diversity in the NS2B gene, however, showed to be constrained, irrespective of clinical outcome and infection time. Finally, 385 non-synonymous intrahost single-nucleotide variants located along the viral polyprotein, plus variants located in the untranslated regions, were consistently identified among the samples. Of them, 124 were exclusively or highly detected among cases with warning signs and among severe cases. However, there was no variant that by itself appeared to characterize the cases of greater severity, either due to its low intrahost frequency or the conservative effect on amino acid substitution. Although further studies are necessary to determine their real effect on viral proteins, this heightens the possibility of epistatic interactions. The present analysis represents an initial effort to correlate DENV-2 genetic diversity to its pathogenic potential and thus contribute to understanding the virus’s dynamics within its human host.
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Kwong, Jason C., Eric P. F. Chow, Kerrie Stevens, et al. "Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study." Sexually Transmitted Infections 94, no. 2 (2017): 151–57. http://dx.doi.org/10.1136/sextrans-2017-053287.
Full textAbstract:
ObjectivesDrug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence (NG-MAST). We therefore aimed to systematically investigate the transmission of N. gonorrhoeae between men in sexual partnerships using WGS to compare isolates and their resistance to antibiotics at a genome level.Methods458 couples from a large prospective cohort of men who have sex with men (MSM) tested for gonorrhoea together between 2005 and 2014 were included, and WGS was conducted on all isolates from couples where both men were culture-positive for N. gonorrhoeae. Resistance-determining sequences were identified from genome assemblies, and comparison of isolates between and within individuals was performed by pairwise single nucleotide polymorphism and pangenome comparisons, and in silico predictions of NG-MAST and MLST.ResultsFor 33 of 34 (97%; 95% CI 85% to 100%) couples where both partners were positive for gonorrhoea, the resistance-determining genes and mutations were identical in isolates from each partner (94 isolates in total). Resistance determinants in isolates from 23 of 23 (100%; 95% CI 86% to 100%) men with multisite infections were also identical within an individual. These partner and within-host isolates were indistinguishable by NG-MAST, MLST and whole genomic comparisons.ConclusionsThese data support the transmission of antibiotic-resistant strains between sexual partners as a key driver of resistance rates in gonorrhoea among MSM. This improved understanding of the transmission dynamics of N. gonorrhoeae between sexual partners will inform treatment and prevention guidelines.
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Rozhnova, Ganna, C. Jessica E. Metcalf, and Bryan T. Grenfell. "Characterizing the dynamics of rubella relative to measles: the role of stochasticity." Journal of The Royal Society Interface 10, no. 88 (2013): 20130643. http://dx.doi.org/10.1098/rsif.2013.0643.
Full textAbstract:
Rubella is a completely immunizing and mild infection in children. Understanding its behaviour is of considerable public health importance because of congenital rubella syndrome, which results from infection with rubella during early pregnancy and may entail a variety of birth defects. The recurrent dynamics of rubella are relatively poorly resolved, and appear to show considerable diversity globally. Here, we investigate the behaviour of a stochastic seasonally forced susceptible–infected–recovered model to characterize the determinants of these dynamics and illustrate patterns by comparison with measles. We perform a systematic analysis of spectra of stochastic fluctuations around stable attractors of the corresponding deterministic model and compare them with spectra from full stochastic simulations in large populations. This approach allows us to quantify the effects of demographic stochasticity and to give a coherent picture of measles and rubella dynamics, explaining essential differences in the recurrent patterns exhibited by these diseases. We discuss the implications of our findings in the context of vaccination and changing birth rates as well as the persistence of these two childhood infections.