1
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Nazari-Vanani R, Negahdary M. Recent advances in electrochemical aptasensors and genosensors for the detection of pathogens. ENVIRONMENTAL RESEARCH 2024; 243:117850. [PMID: 38081349 DOI: 10.1016/j.envres.2023.117850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
In recent years, pathogenic microorganisms have caused significant mortality rates and antibiotic resistance and triggered exorbitant healthcare costs. These pathogens often have high transmission rates within human populations. Rapid diagnosis is crucial in controlling and reducing the spread of pathogenic infections. The diagnostic methods currently used against individuals infected with these pathogens include relying on outward symptoms, immunological-based and, some biomolecular ones, which mainly have limitations such as diagnostic errors, time-consuming processes, and high-cost platforms. Electrochemical aptasensors and genosensors have emerged as promising diagnostic tools for rapid, accurate, and cost-effective pathogen detection. These bio-electrochemical platforms have been optimized for diagnostic purposes by incorporating advanced materials (mainly nanomaterials), biomolecular technologies, and innovative designs. This review classifies electrochemical aptasensors and genosensors developed between 2021 and 2023 based on their use of different nanomaterials, such as gold-based, carbon-based, and others that employed other innovative assemblies without the use of nanomaterials. Inspecting the diagnostic features of various sensing platforms against pathogenic analytes can identify research gaps and open new avenues for exploration.
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Affiliation(s)
- Razieh Nazari-Vanani
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Negahdary
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil.
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2
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Sauters TJC, Roth C, Murray D, Sun S, Floyd Averette A, Onyishi CU, May RC, Heitman J, Magwene PM. Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis. PLoS Pathog 2023; 19:e1011763. [PMID: 37956179 PMCID: PMC10681322 DOI: 10.1371/journal.ppat.1011763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 11/27/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.
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Affiliation(s)
- Thomas J. C. Sauters
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Cullen Roth
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Debra Murray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Chinaemerem U. Onyishi
- School of Biosciences, College of Life and Environmental Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Robin C. May
- School of Biosciences, College of Life and Environmental Sciences, The University of Birmingham, Birmingham, United Kingdom
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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3
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Gamża AM, Hagenaars TJ, Koene MGJ, de Jong MCM. Combining a parsimonious mathematical model with infection data from tailor-made experiments to understand environmental transmission. Sci Rep 2023; 13:12986. [PMID: 37563156 PMCID: PMC10415373 DOI: 10.1038/s41598-023-38817-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/15/2023] [Indexed: 08/12/2023] Open
Abstract
Although most infections are transmitted through the environment, the processes underlying the environmental stage of transmission are still poorly understood for most systems. Improved understanding of the environmental transmission dynamics is important for effective non-pharmaceutical intervention strategies. To study the mechanisms underlying environmental transmission we formulated a parsimonious modelling framework including hypothesised mechanisms of pathogen dispersion and decay. To calibrate and validate the model, we conducted a series of experiments studying distance-dependent transmission of Campylobacter jejuni in broilers. We obtained informative simultaneous estimates for all three model parameters: the parameter of C. jejuni inactivation, the diffusion coefficient describing pathogen dispersion, and the transmission rate parameter. The time and distance dependence of transmission in the fitted model is quantitatively consistent with marked spatiotemporal patterns in the experimental observations. These results, for C. jejuni in broilers, show that the application of our modelling framework to suitable transmission data can provide mechanistic insight in environmental pathogen transmission.
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Affiliation(s)
- Anna M Gamża
- Quantitative Veterinary Epidemiology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
- Wageningen Bioveterinary Research, Wageningen University and Research, 8221 RA, Lelystad, The Netherlands.
| | - Thomas J Hagenaars
- Wageningen Bioveterinary Research, Wageningen University and Research, 8221 RA, Lelystad, The Netherlands.
| | - Miriam G J Koene
- Wageningen Bioveterinary Research, Wageningen University and Research, 8221 RA, Lelystad, The Netherlands
| | - Mart C M de Jong
- Quantitative Veterinary Epidemiology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
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4
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Chang Y, de Jong MCM. A novel method to jointly estimate transmission rate and decay rate parameters in environmental transmission models. Epidemics 2023; 42:100672. [PMID: 36738639 DOI: 10.1016/j.epidem.2023.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 12/23/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
In environmental transmission, pathogens transfer from one individual to another via the environment. It is a common transmission mechanism in a wide range of host-pathogen systems. Incorporating environmental transmission in dynamic transmission models is crucial for gauging the effect of interventions, as extrapolating model results to new situations is only valid when the mechanisms are modelled correctly. The challenge in environmental transmission models lies in not jointly identifiable parameters for pathogen shedding, decay, and transmission dynamics. To solve this unidentifiability issue, we present a stochastic environmental transmission model with a novel scaling method for shedding rate parameter and a novel estimation method that distinguishes transmission rate and decay rate parameters. The core of our scaling and estimation method is calculating exposure and relating exposure to infection risks. By scaling shedding rate parameter, we standardize exposure to pathogens contributed by one infectious individual present during one time interval to one. The standardized exposure leads to a standard definition of transmission rate parameter applicable to scenarios with different decay rate parameters. Hence, we unify direct transmission (large decay rate) and environmental transmission in a continuous manner. More importantly, our exposure-based estimation method can correctly estimate back the transmission rate and the decay rate parameters, while the commonly used trajectory-based method failed. The reason is that exposure-based method gives the correct weight to infection data from previous observation periods. The correct estimation from exposure-based method will lead to more reliable predictions of intervention impact. Using the effect of disinfection as an example, we show how incorrectly estimated parameters may lead to incorrect conclusions about the effectiveness of interventions. This illustrates the importance of correct estimation of transmission rate and decay rate parameters for extrapolating environmental transmission models and predicting intervention effects.
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Affiliation(s)
- You Chang
- Quantitative Veterinary Epidemiology Group, Wageningen Institute of Animal Sciences, the Netherlands.
| | - Mart C M de Jong
- Quantitative Veterinary Epidemiology Group, Wageningen Institute of Animal Sciences, the Netherlands
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5
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Davies K, Lenhart S, Day J, Lloyd AL, Lanzas C. Extensions of mean-field approximations for environmentally-transmitted pathogen networks. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:1637-1673. [PMID: 36899502 DOI: 10.3934/mbe.2023075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Many pathogens spread via environmental transmission, without requiring host-to-host direct contact. While models for environmental transmission exist, many are simply constructed intuitively with structures analogous to standard models for direct transmission. As model insights are generally sensitive to the underlying model assumptions, it is important that we are able understand the details and consequences of these assumptions. We construct a simple network model for an environmentally-transmitted pathogen and rigorously derive systems of ordinary differential equations (ODEs) based on different assumptions. We explore two key assumptions, namely homogeneity and independence, and demonstrate that relaxing these assumptions can lead to more accurate ODE approximations. We compare these ODE models to a stochastic implementation of the network model over a variety of parameters and network structures, demonstrating that with fewer restrictive assumptions we are able to achieve higher accuracy in our approximations and highlighting more precisely the errors produced by each assumption. We show that less restrictive assumptions lead to more complicated systems of ODEs and the potential for unstable solutions. Due to the rigour of our derivation, we are able to identify the reason behind these errors and propose potential resolutions.
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Affiliation(s)
- Kale Davies
- Department of Mathematics, University of Chicago, Chicago, IL, USA
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Suzanne Lenhart
- Department of Mathematics, University of Tennessee, Knoxville, TN, USA
| | - Judy Day
- Department of Mathematics, University of Tennessee, Knoxville, TN, USA
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Alun L Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC, USA
| | - Cristina Lanzas
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
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6
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Ownagh A, Etemadi N, Khademi P, Tajik H. Identification of Salmonella carriers by amplification of FimA, Stn and InvA genes and bacterial culture methods in fecal samples of buffalo. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2023; 14:21-28. [PMID: 36816862 PMCID: PMC9906613 DOI: 10.30466/vrf.2022.544308.3312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 08/29/2022] [Indexed: 02/24/2023]
Abstract
Salmonellosis is one of the most important bacterial diseases in human and animals. Rapid diagnosis and sub sequence accurate treatment of Salmonella carriers help reduce the salmonellosis in human and livestock animals. In this study, 420 fecal samples were taken during year 2019 from buffalo in the Urmia, Khoy and Piranshahr regions in west Azerbaijan province, Iran. Samplings were carried out in different seasons. Presence of Salmonella invasion genes (FimA, Stn and InvA) were evaluated by polymerase chain reaction. The bacterial culture and biochemical tests were performed on feces samples for isolation of bacterium Salmonella; however, all samples were negative in culture method. PCR findings showed that, 50 (11.90%) fecal samples were positive to the genes. The analysis of results showed that frequency of salmonellosis outbreak in different parts of west Azerbaijan province followed a similar pattern and the incidence of salmonellosis according to forecast in the warm seasons (spring and summer) was more than in cold seasons (autumn and winter). The prevalence of Salmonella in buffalo's feces based on warm and cold seasons were 32 (64.00%) and 18 (36.00%), respectively. The results showed significant difference between cold and warm season in the prevalence of salmonellosis. Therefore, the application of molecular technics is essential for the prevention and treatment of salmonellosis. The results also showed that specificity of PCR method was better than culture method for detection of Salmonella in feces sample.
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Affiliation(s)
- Abdulghaffar Ownagh
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran; ,Correspondence Abdulghaffar Ownagh. DVM, DVSc, Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran . E-mail:
| | - Navid Etemadi
- DVM Graduate, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran;
| | - Peyman Khademi
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran;
| | - Hossein Tajik
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran.
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7
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Stewart R, Erwin S, Piburn J, Nagle N, Kaufman J, Peluso A, Christian JB, Grant J, Sorokine A, Bhaduri B. Near real time monitoring and forecasting for COVID-19 situational awareness. APPLIED GEOGRAPHY (SEVENOAKS, ENGLAND) 2022; 146:102759. [PMID: 35945952 PMCID: PMC9353608 DOI: 10.1016/j.apgeog.2022.102759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 07/06/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In the opening months of the pandemic, the need for situational awareness was urgent. Forecasting models such as the Susceptible-Infectious-Recovered (SIR) model were hampered by limited testing data and key information on mobility, contact tracing, and local policy variations would not be consistently available for months. New case counts from sources like John Hopkins University and the NY Times were systematically reliable. Using these data, we developed the novel COVID County Situational Awareness Tool (CCSAT) for reliable monitoring and decision support. In CCSAT, we developed a retrospective seven-day moving window semantic map of county-level disease magnitude and acceleration that smoothed noisy daily variations. We also developed a novel Bayesian model that reliably forecasted county-level magnitude and acceleration for the upcoming week based on population and new case count data. Together these formed a robust operational update including county-level maps of new case rate changes, estimates of new cases in the upcoming week, and measures of model reliability. We found CCSAT provided stable, reliable estimates across the seven-day time window, with the greatest errors occurring in cases of anomalous, single day spikes. In this paper, we provide CCSAT details and apply it to a single week in June 2020.
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Affiliation(s)
- Robert Stewart
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
| | - Samantha Erwin
- Pacific Northwest National Laboratory (PNNL), 902 Battelle Blvd, Richland, WA, 99354, USA
| | - Jesse Piburn
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
| | - Nicholas Nagle
- University of Tennessee Geography (UT), 304C Burchfiel Geography Bldg., Knoxville, TN, 37996-0925, USA
| | - Jason Kaufman
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
| | - Alina Peluso
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
| | - J Blair Christian
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
| | - Joshua Grant
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
| | - Alexandre Sorokine
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
| | - Budhendra Bhaduri
- Oak Ridge National Laboratory (ORNL), 1 Bethel Valley RD, Bldg 5600, MS-6017, Oak Ridge, TN, 37830, USA
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8
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Lanzas C, Jara M, Tucker R, Curtis S. A review of epidemiological models of Clostridioides difficile transmission and control (2009-2021). Anaerobe 2022; 74:102541. [PMID: 35217149 DOI: 10.1016/j.anaerobe.2022.102541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/09/2022] [Accepted: 02/20/2022] [Indexed: 02/08/2023]
Abstract
Clostridioides difficile is the leading cause of infectious diarrhea and one of the most common healthcare-acquired infections worldwide. We performed a systematic search and a bibliometric analysis of mathematical and computational models for Clostridioides difficile transmission. We identified 33 publications from 2009 to 2021. Models have underscored the importance of asymptomatic colonized patients in maintaining transmission in health-care settings. Infection control, antimicrobial stewardship, active testing, and vaccination have often been evaluated in models. Despite active testing and vaccination being not currently implemented, they are the most commonly evaluated interventions. Some aspects of C. difficile transmission, such community transmission and interventions in health-care settings other than in acute-care hospitals, remained less evaluated through modeling.
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Affiliation(s)
- Cristina Lanzas
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA.
| | - Manuel Jara
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Rachel Tucker
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Savannah Curtis
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
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- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
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9
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Pandey A, Mideo N, Platt TG. Virulence Evolution of Pathogens That Can Grow in Reservoir Environments. Am Nat 2022; 199:141-158. [DOI: 10.1086/717177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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Farthing TS, Dawson DE, Sanderson MW, Seger H, Lanzas C. Combining epidemiological and ecological methods to quantify social effects on Escherichia coli transmission. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210328. [PMID: 34754493 PMCID: PMC8493196 DOI: 10.1098/rsos.210328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Enteric microparasites like Escherichia coli use multiple transmission pathways to propagate within and between host populations. Characterizing the relative transmission risk attributable to host social relationships and direct physical contact between individuals is paramount for understanding how microparasites like E. coli spread within affected communities and estimating colonization rates. To measure these effects, we carried out commensal E. coli transmission experiments in two cattle (Bos taurus) herds, wherein all individuals were equipped with real-time location tracking devices. Following transmission experiments in this model system, we derived temporally dynamic social and contact networks from location data. Estimated social affiliations and dyadic contact frequencies during transmission experiments informed pairwise accelerated failure time models that we used to quantify effects of these sociobehavioural variables on weekly E. coli colonization risk in these populations. We found that sociobehavioural variables alone were ultimately poor predictors of E. coli colonization in feedlot cattle, but can have significant effects on colonization hazard rates (p ≤ 0.05). We show, however, that observed effects were not consistent between similar populations. This work demonstrates that transmission experiments can be combined with real-time location data collection and processing procedures to create an effective framework for quantifying sociobehavioural effects on microparasite transmission.
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Affiliation(s)
- Trevor S. Farthing
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
| | - Daniel E. Dawson
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
| | - Mike W. Sanderson
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Hannah Seger
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Cristina Lanzas
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
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11
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Mushayi C, Nyabadza F, Chigidi E, Mataramvura H, Pfavayi L, Rusakaniko S, Sibanda EN. A mathematical model for the prediction of the prevalence of allergies in Zimbabwe. World Allergy Organ J 2021; 14:100555. [PMID: 34257796 PMCID: PMC8246639 DOI: 10.1016/j.waojou.2021.100555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 11/26/2022] Open
Abstract
Background The prevalence of allergies has been observed to be increasing in the past years in Zimbabwe. It is thus important to consider the long term prevalence of allergies. Our interest is in investigating the trends of allergies in the next 2 decades. Method We formulate a deterministic model with 6 compartments to predict the prevalence of allergies in Zimbabwe. The human population is divided into 4 distinct epidemiological, classes based on their exposure to 2 allergen groups (food and inhalants), represented by 2 compartments. The model is used to predict the prevalence of allergen sensitization. The number of human allergen groups in each compartment are tracked through a system of differential equations. Model parameters were obtained by fitting observed data to the model. Graphical solutions of the model were developed using Matlab and Excel. Results The rate of sensitisation to food allergen sources is found to be lower than the rate of sensitisation to inhalant allergens. The rate at which individuals develop tolerance to food allergen sources is found to be almost twice the rate of developing tolerance to inhalant allergies. The equilibrium solutions (the long-term states of the populations) of the model are found to be non-zero implying that there will never be an allergy-free population. Our results also show that the prevalence of food allergy is likely to increase in the next 2 decades while inhalant allergy prevalence is expected to decrease. Conclusion Our long-term solutions show endemicity in allergies in Zimbabwe. So, allergy will be endemic in the Zimbabwean population; hence there is a need for allergy care and management facilities to be increased. These results are critical in policy development and planning around allergies in the near future.
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Affiliation(s)
- Caroline Mushayi
- Midlands State University, Department of Mathematics, Senga Road, Gweru, Zimbabwe.,Asthma, Allergy and Immune Dysfunction Clinic, 113 Kwame Nkrumah Ave., Harare, Zimbabwe
| | - Farai Nyabadza
- University of Johannesburg, Department of Mathematics and Applied Mathematics, Auckland Park, Johannesburg, 2006, South Africa
| | - Esther Chigidi
- Midlands State University, Department of Mathematics, Senga Road, Gweru, Zimbabwe
| | - Hope Mataramvura
- Asthma, Allergy and Immune Dysfunction Clinic, 113 Kwame Nkrumah Ave., Harare, Zimbabwe.,University of Zimbabwe; College of Health Sciences, Avondale, Harare, Zimbabwe
| | - Lorraine Pfavayi
- Asthma, Allergy and Immune Dysfunction Clinic, 113 Kwame Nkrumah Ave., Harare, Zimbabwe.,National University of Science and Technology, NUST Medical School, Department of Pathology, Vera Road, Bulawayo, Zimbabwe
| | - Simbarashe Rusakaniko
- University of Zimbabwe, College of Health Sciences, Department of Community Medicine, Avondale, Harare, Zimbabwe
| | - Elopy Nimele Sibanda
- Asthma, Allergy and Immune Dysfunction Clinic, 113 Kwame Nkrumah Ave., Harare, Zimbabwe.,National University of Science and Technology, NUST Medical School, Department of Pathology, Vera Road, Bulawayo, Zimbabwe
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12
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Dawson D, Rasmussen D, Peng X, Lanzas C. Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen. J R Soc Interface 2021; 18:20210041. [PMID: 34102084 DOI: 10.1098/rsif.2021.0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Indirect (environmental) and direct (host-host) transmission pathways cannot easily be distinguished when they co-occur in epidemics, particularly when they occur on similar time scales. Phylodynamic reconstruction is a potential approach to this problem that combines epidemiological information (temporal, spatial information) with pathogen whole-genome sequencing data to infer transmission trees of epidemics. However, factors such as differences in mutation and transmission rates between host and non-host environments may obscure phylogenetic inference from these methods. In this study, we used a network-based transmission model that explicitly models pathogen evolution to simulate epidemics with both direct and indirect transmission. Epidemics were simulated according to factorial combinations of direct/indirect transmission proportions, host mutation rates and conditions of environmental pathogen growth. Transmission trees were then reconstructed using the phylodynamic approach SCOTTI (structured coalescent transmission tree inference) and evaluated. We found that although insufficient diversity sets a lower bound on when accurate phylodynamic inferences can be made, transmission routes and assumed pathogen lifestyle affected pathogen population structure and subsequently influenced both reconstruction success and the likelihood of direct versus indirect pathways being reconstructed. We conclude that prior knowledge of the likely ecology and population structure of pathogens in host and non-host environments is critical to fully using phylodynamic techniques.
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Affiliation(s)
- Daniel Dawson
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - David Rasmussen
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Xinxia Peng
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Cristina Lanzas
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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13
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Machado G, Galvis JA, Lopes FPN, Voges J, Medeiros AAR, Cárdenas NC. Quantifying the dynamics of pig movements improves targeted disease surveillance and control plans. Transbound Emerg Dis 2020; 68:1663-1675. [PMID: 32965771 DOI: 10.1111/tbed.13841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/27/2020] [Accepted: 09/12/2020] [Indexed: 12/11/2022]
Abstract
Tracking animal movements over time may fundamentally determine the success of disease control interventions. In commercial pig production growth stages determine animal transportation schedule, thus it generates time-varying contact networks showed to influence the dynamics of disease spread. In this study, we reconstructed pig networks of one Brazilian state from 2017 to 2018, comprising 351,519 movements and 48 million transported pigs. The static networks view did not capture time-respecting movement pathways. For this reason, we propose a time-dependent network approach. A susceptible-infected model was used to spread an epidemic over the pig network globally through the temporal between-farm networks, and locally by a stochastic model to account for within-farm dynamics. We propagated disease to calculate the cumulative contacts as a proxy of epidemic sizes and evaluate the impact of network-based disease control strategies in the absence of other intervention alternatives. The results show that targeting 1,000 farms ranked by degree would be sufficient and feasible to diminish disease spread considerably. Our modelling results indicated that independently from where initial infections were seeded (i.e. independent, commercial farms), the epidemic sizes and the number of farms needed to be targeted to effectively control disease spread were quite similar; indeed, this finding can be explained by the presence of contact among all pig operation types The proposed strategy limited the transmission the total number of secondarily infected farms to 29, over two simulated years. The identified 1,000 farms would benefit from enhanced biosecurity plans and improved targeted surveillance. Overall, the modelling framework provides a parsimonious solution for targeted disease surveillance when temporal movement data are available.
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Affiliation(s)
- Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Jason Ardila Galvis
- Department of Population Health and Pathobiology, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Francisco Paulo Nunes Lopes
- Departamento de Defesa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Brazil
| | - Joana Voges
- Departamento de Defesa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Brazil
| | - Antônio Augusto Rosa Medeiros
- Departamento de Defesa Agropecuária, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Brazil
| | - Nicolás Céspedes Cárdenas
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
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14
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White LA, VandeWoude S, Craft ME. A mechanistic, stigmergy model of territory formation in solitary animals: Territorial behavior can dampen disease prevalence but increase persistence. PLoS Comput Biol 2020; 16:e1007457. [PMID: 32525874 PMCID: PMC7289346 DOI: 10.1371/journal.pcbi.1007457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Although movement ecology has leveraged models of home range formation to explore the effects of spatial heterogeneity and social cues on movement behavior, disease ecology has yet to integrate these potential drivers and mechanisms of contact behavior into a generalizable disease modeling framework. Here we ask how dynamic territory formation and maintenance might contribute to disease dynamics in a territorial, solitary predator for an indirectly transmitted pathogen. We developed a mechanistic individual-based model where stigmergy—the deposition of signals into the environment (e.g., scent marking, scraping)—dictates local movement choices and long-term territory formation, but also the risk of pathogen transmission. Based on a variable importance analysis, the length of the infectious period was the single most important variable in predicting outbreak success, maximum prevalence, and outbreak duration. Host density and rate of pathogen decay were also key predictors. We found that territoriality best reduced maximum prevalence in conditions where we would otherwise expect outbreaks to be most successful: slower recovery rates (i.e., longer infectious periods) and higher conspecific densities. However, for slower pathogen decay rates, stigmergy-driven movement increased outbreak durations relative to random movement simulations. Our findings therefore support a limited version of the “territoriality benefits” hypothesis—where reduced home range overlap leads to reduced opportunities for pathogen transmission, but with the caveat that reduction in outbreak severity may increase the likelihood of pathogen persistence. For longer infectious periods and higher host densities, key trade-offs emerged between the strength of pathogen load, the strength of the stigmergy cue, and the rate at which those two quantities decayed; this finding raises interesting questions about the evolutionary nature of these competing processes and the role of possible feedbacks between parasitism and territoriality. This work also highlights the importance of considering social cues as part of the movement landscape in order to better understand the consequences of individual behaviors on population level outcomes. Making decisions about conservation and disease management relies on our understanding of what allows animal populations to be successful, which often depends on when and where animals encounter each other. However, disease ecology often focuses on the social behavior of animals without accounting for their individual movement patterns. We developed a simulation model that bridges the fields of disease and movement ecology by allowing hosts to inform their movement based on the past movements of other hosts. As hosts navigate their environment, they leave behind a scent trail while avoiding the scent trails of other individuals. We wanted to know if this means of territory formation could heighten or dampen disease spread when infectious hosts leave pathogens in their wake. We found that territoriality can inhibit disease spread under conditions that we would normally expect pathogens to be most successful: when there are many hosts on the landscape and hosts stay infectious for longer. This work points to how incorporating movement behavior into disease models can provide improved understanding of how diseases spread in wildlife populations; such understanding is particularly important in the face of combatting ongoing and emerging infectious diseases.
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Affiliation(s)
- Lauren A. White
- National Socio-Environmental Synthesis Center, University of Maryland, Annapolis, Maryland, United States of America
- * E-mail:
| | - Sue VandeWoude
- Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Meggan E. Craft
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
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15
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Garabed RB, Jolles A, Garira W, Lanzas C, Gutierrez J, Rempala G. Multi-scale dynamics of infectious diseases. Interface Focus 2019. [DOI: 10.1098/rsfs.2019.0118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To address the challenge of multiscale dynamics of infectious diseases, the Mathematical Biosciences Institute organized a workshop at The Ohio State University to bring together scientists from a variety of disciplines to share expertise gained through looking at infectious diseases across different scales. The researchers at the workshop, held in April 2018, were specifically looking at three model systems: foot-and-mouth disease, vector-borne diseases and enteric diseases. Although every multiscale model must be necessarily derived from a multiscale system, not every multiscale system has to lead to multiscale models. These three model systems seem to have produced a variety of both multiscale and integrated single-scale mechanistic models that have developed their own strengths and particular challenges. Here, we present papers from some of the workshop participants to show the breadth of the field.
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Affiliation(s)
- Rebecca B. Garabed
- College of Veterinary Medicine–Preventive Medicine, The Ohio State University, Columbus, OH, USA
| | - Anna Jolles
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
- Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Winston Garira
- Mathematics and Applied Mathematics, University of Venda, Thohoyandou, Limpopo, South Africa
| | | | - Juan Gutierrez
- Department of Mathematics, University of Texas at San Antonio, San Antonio, TX, USA
| | - Grzegorz Rempala
- College of Public Health–Biostatistics, The Ohio State University, Columbus, OH, USA
- College of Arts and Sciences–Mathematics, The Ohio State University, Columbus, OH, USA
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