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Nduba V, Njagi LN, Murithi W, Mwongera Z, Byers J, Logioia G, Peterson G, Segnitz RM, Fennelly K, Hawn TR, Horne DJ. Mycobacterium tuberculosis cough aerosol culture status associates with host characteristics and inflammatory profiles. Nat Commun 2024; 15:7604. [PMID: 39217183 PMCID: PMC11365933 DOI: 10.1038/s41467-024-52122-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
Interrupting transmission events is critical to tuberculosis control. Cough-generated aerosol cultures predict tuberculosis transmission better than microbiological or clinical markers. We hypothesize that highly infectious individuals with pulmonary tuberculosis (positive for cough aerosol cultures) have elevated inflammatory markers and unique transcriptional profiles compared to less infectious individuals. We performed a prospective, longitudinal study using cough aerosol sampling system. We enrolled 142 participants with treatment-naïve pulmonary tuberculosis in Kenya and assessed the association of clinical, microbiologic, and immunologic characteristics with Mycobacterium tuberculosis aerosolization and transmission in 129 household members. Contacts of the forty-three aerosol culture-positive participants (30%) are more likely to have a positive interferon-gamma release assay (85% vs 53%, P = 0.006) and higher median IFNγ level (P < 0.001, 4.28 IU/ml (1.77-5.91) vs. 0.71 (0.01-3.56)) compared to aerosol culture-negative individuals. We find that higher bacillary burden, younger age, larger mean upper arm circumference, and host inflammatory profiles, including elevated serum C-reactive protein and lower plasma TNF levels, associate with positive cough aerosol cultures. Notably, we find pre-treatment whole blood transcriptional profiles associate with aerosol culture status, independent of bacillary load. These findings suggest that tuberculosis infectiousness is associated with epidemiologic characteristics and inflammatory signatures and that these features may identify highly infectious persons.
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Affiliation(s)
- Videlis Nduba
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Lilian N Njagi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Wilfred Murithi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Zipporah Mwongera
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jodi Byers
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Gisella Logioia
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Glenna Peterson
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - R Max Segnitz
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kevin Fennelly
- Division of Intramural Research, National Heart, Lung and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, USA
| | - Thomas R Hawn
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - David J Horne
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
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Chua JY, Lim ZQ, Loy SQD, Koh V, Thevasagayam NM, Huan X, Linn KZ, Marimuthu K, Ng OT. Evaluation of the Xpert Carba-R assay for quantifying carbapenemase-producing bacterial load in stool samples. PLoS One 2024; 19:e0309089. [PMID: 39196974 PMCID: PMC11356397 DOI: 10.1371/journal.pone.0309089] [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: 04/21/2024] [Accepted: 08/06/2024] [Indexed: 08/30/2024] Open
Abstract
BACKGROUND The spread of Carbapenemase-producing Organisms (CPO) remains a major threat globally. Within clinical settings, the existing method of determining gene load involves traditional culture to determine bacterial load and polymerase-chain-reaction-based Xpert Carba-R Assay to determine carbapenemase gene type. However, there is a need for a fast and accurate method of quantifying CPO colonisation to study the risk of persistent CPO carriage. OBJECTIVE This study evaluated the accuracy of Xpert Carba-R Ct value in estimating carbapenamase producing bacterial loads in stool samples. METHODS Stool samples were obtained from an ongoing study investigating the household transmission of CPO in Singapore. Stool samples lacking carbapenemase producing organisms were spiked with organism carrying a single carbapenemase gene (blaKPC, blaNDM, blaVIM, blaOXA-48(-like) or blaIMP-1) and serially diluted before being subjected to Xpert Carba-R assay and traditional culture. Standard curves with regression lines showing correlation between Ct values and plate counts were generated. The standard curves were validated with stool samples collected from patients. RESULTS The limit of detection of blaNDM, blaKPC, and blaOXA-48 was approximately 103 cfu/mL, while that of blaIMP-1 and blaVIM was approximately 104 cfu/mL. Validation of the blaNDM and blaOXA-48 curves revealed average delta values of 0.56 log(cfu/mL) (95% CI 0.24-0.88) and 0.80 log(cfu/mL) (95% CI 0.53-1.07), respectively. CONCLUSIONS Our validation data for stool positive for blaNDM and blaOXA-48-type suggests that bacterial loads can be estimated within a reasonable range of error.
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Affiliation(s)
- Jie Yin Chua
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Ze Qin Lim
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Song Qi Dennis Loy
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Vanessa Koh
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Natascha May Thevasagayam
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Xiaowei Huan
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Kyaw Zaw Linn
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Oon Tek Ng
- National Centre for Infectious Diseases, Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
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Pluta A, Jaworski JP, Droscha C, VanderWeele S, Taxis TM, Valas S, Brnić D, Jungić A, Ruano MJ, Sánchez A, Murakami K, Nakamura K, Puentes R, De Brun ML, Ruiz V, Gómez MEL, Lendez P, Dolcini G, Camargos MF, Fonseca A, Barua S, Wang C, Giza A, Kuźmak J. Inter-laboratory comparison of eleven quantitative or digital PCR assays for detection of proviral bovine leukemia virus in blood samples. BMC Vet Res 2024; 20:381. [PMID: 39187880 PMCID: PMC11346035 DOI: 10.1186/s12917-024-04228-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 08/09/2024] [Indexed: 08/28/2024] Open
Abstract
Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis and causes a persistent infection that can leave cattle with no symptoms. Many countries have been able to successfully eradicate BLV through improved detection and management methods. However, with the increasing novel molecular detection methods there have been few efforts to standardize these results at global scale. This study aimed to determine the interlaboratory accuracy and agreement of 11 molecular tests in detecting BLV. Each qPCR/ddPCR method varied by target gene, primer design, DNA input and chemistries. DNA samples were extracted from blood of BLV-seropositive cattle and lyophilized to grant a better preservation during shipping to all participants around the globe. Twenty nine out of 44 samples were correctly identified by the 11 labs and all methods exhibited a diagnostic sensitivity between 74 and 100%. Agreement amongst different assays was linked to BLV copy numbers present in samples and the characteristics of each assay (i.e., BLV target sequence). Finally, the mean correlation value for all assays was within the range of strong correlation. This study highlights the importance of continuous need for standardization and harmonization amongst assays and the different participants. The results underscore the need of an international calibrator to estimate the efficiency (standard curve) of the different assays and improve quantitation accuracy. Additionally, this will inform future participants about the variability associated with emerging chemistries, methods, and technologies used to study BLV. Altogether, by improving tests performance worldwide it will positively aid in the eradication efforts.
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Affiliation(s)
- Aneta Pluta
- Department of Biochemistry, National Veterinary Research Institute, Puławy, 24-100, Poland.
- Department of Omics Analyses, National Veterinary Research Institute, 24-100, Puławy, Poland.
| | - Juan Pablo Jaworski
- Instituto de Virología E Innovaciones Tecnológicas (IVIT), Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA) - CONICET, Buenos Aires, Argentina
| | - Casey Droscha
- CentralStar Cooperative, 4200 Forest Rd, Lansing, MI, 48910, USA
| | | | - Tasia M Taxis
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Stephen Valas
- Niort Laboratory, Unit Pathology and Welfare of Ruminants, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Ploufragan-Plouzané, Niort, France
| | - Dragan Brnić
- Croatian Veterinary Institute, Savska Cesta 143, Zagreb, 10000, Croatia
| | - Andreja Jungić
- Croatian Veterinary Institute, Savska Cesta 143, Zagreb, 10000, Croatia
| | - María José Ruano
- Laboratorio Central de Veterinaria (LCV), Ministry of Agriculture, Fisheries and Food, Carretera M-106 (Km 1,4), Madrid, Algete, 28110, Spain
| | - Azucena Sánchez
- Laboratorio Central de Veterinaria (LCV), Ministry of Agriculture, Fisheries and Food, Carretera M-106 (Km 1,4), Madrid, Algete, 28110, Spain
| | - Kenji Murakami
- Department of Veterinary Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | - Kurumi Nakamura
- Department of Veterinary Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, 020-8550, Japan
| | - Rodrigo Puentes
- Departamento de Patobiología, Facultad de Veterinaria, Unidad de Microbiología, Universidad de La República, Ruta 8, Km 18, Montevideo, 13000, Uruguay
| | - MLaureana De Brun
- Departamento de Patobiología, Facultad de Veterinaria, Unidad de Microbiología, Universidad de La República, Ruta 8, Km 18, Montevideo, 13000, Uruguay
| | - Vanesa Ruiz
- Instituto de Virología E Innovaciones Tecnológicas (IVIT), Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA) - CONICET, Buenos Aires, Argentina
| | - Marla Eliana Ladera Gómez
- Laboratorio de Virología, Departamento SAMP, Centro de Investigación Veterinaria de Tandil-CIVETAN (CONICET/UNCPBA/CICPBA), Buenos Aires, Argentina
| | - Pamela Lendez
- Laboratorio de Virología, Departamento SAMP, Centro de Investigación Veterinaria de Tandil-CIVETAN (CONICET/UNCPBA/CICPBA), Buenos Aires, Argentina
| | - Guillermina Dolcini
- Laboratorio de Virología, Departamento SAMP, Centro de Investigación Veterinaria de Tandil-CIVETAN (CONICET/UNCPBA/CICPBA), Buenos Aires, Argentina
| | | | - Antônio Fonseca
- Laboratório Federal de Defesa Agropecuária de Minas Gerais, Pedro Leopoldo, Brazil
| | - Subarna Barua
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849-5519, USA
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, 36849-5519, USA
| | - Aleksandra Giza
- Department of Omics Analyses, National Veterinary Research Institute, 24-100, Puławy, Poland
| | - Jacek Kuźmak
- Department of Biochemistry, National Veterinary Research Institute, Puławy, 24-100, Poland
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Soto-López JD, Barrios-Izás MA, Vieira Lista MC, Muro A. Role of Non-Residential Larval Habitats in Aedes Spatiotemporal Egg Production. Life (Basel) 2024; 14:1013. [PMID: 39202755 PMCID: PMC11355553 DOI: 10.3390/life14081013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/22/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Aedes mosquitoes play a pivotal role as vectors of several arboviral diseases, presenting significant public health challenges worldwide. Their invasive success in tropical regions has raised substantial medical concerns. In Guatemala, Aedes mosquitoes are widely distributed and are the primary vectors of the dengue virus. Efforts to control and monitor Aedes populations have evolved over time, incorporating strategies such as spatial repellents, larvicides, genetic modifications, and targeted interventions. Previous research has shown the heterogeneous spatial-temporal distribution of these mosquitoes within each season, influenced by temperature variations and favorable environmental conditions for breeding. This study analyzed hot-spot patterns of spatiotemporal egg density in Santa Elena de la Cruz, Petén, Guatemala, from March to September 2022. The aim was to determine whether these patterns were influenced by non-residential larval habitats with plant cover that are not treated by healthcare entities, as well as the proximity between such habitats. Our findings include the collection and registration of over 16,000 Aedes eggs during the study period. Local analyses revealed hot-spot patterns in egg densities associated with non-residential larval habitats and their proximity. These insights highlight critical focal points where targeted interventions could be implemented more effectively, resulting in cost-efficient mosquito vector control.
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Affiliation(s)
- Julio D. Soto-López
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37008 Salamanca, Spain; (J.D.S.-L.); (M.C.V.L.)
- Research Institute, University Center of Zacapa, University of San Carlos of Guatemala, Zacapa 01019, Guatemala;
| | - Manuel A. Barrios-Izás
- Research Institute, University Center of Zacapa, University of San Carlos of Guatemala, Zacapa 01019, Guatemala;
| | - María Carmen Vieira Lista
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37008 Salamanca, Spain; (J.D.S.-L.); (M.C.V.L.)
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37008 Salamanca, Spain; (J.D.S.-L.); (M.C.V.L.)
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5
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Rijal S, Neuhaus P, Thorley J, Caulkett N, Kutz S, Ruckstuhl KE. Patterns of gastrointestinal parasite infections in bighorn sheep, Ovis canadensis, with respect to host sex and seasonality. Int J Parasitol Parasites Wildl 2024; 24:100950. [PMID: 38966857 PMCID: PMC11222929 DOI: 10.1016/j.ijppaw.2024.100950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 07/06/2024]
Abstract
Males and females in sexually dimorphic species show differences in their physiology and behaviour due to differences in energetic investment into reproduction and soma. This means that the two sexes may show different patterns of parasitism at different times of the year. In this study, we evaluate the abundance of fecal eggs and larvae of 5 parasite types (Strongyles, Nematodirus spp., Marshallagia marshalli., Protostrongylus spp. lungworms, and Eimeria spp.) in relation to season and sex in Rocky Mountain bighorn sheep (Ovis canadensis). We use fecal egg counts (FEC) as a proxy for infection intensity. Parasite FECs differed between male and female bighorn sheep and varied with season. We found pronounced fluctuations in fecal egg counts of various parasite species in males and females across different seasons and reproductive stages. Strongyle counts were significantly higher during late gestation and lactation/summer, and particularly pronounced in males. Nematodirus counts were highest during late gestation in females and during the rut in males. Marshallagia counts peaked during late gestation in females and during the rut in males. Protostrongylus spp. lungworm counts were highest during late gestation in females and in males during lactation/summer and the rut. Eimeria oocyst counts varied across seasons, with higher counts in males during the rut and in females during winter and late gestation. Additionally, significant differences in Strongyle counts were observed between coursing and tending rams, with tending rams exhibiting higher counts. We discuss why the sexes might differ in FECs and suggest that differences between FECs of the parasites across seasons may be due to different life cycles and cold tolerance of the parasites themselves.
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Affiliation(s)
- Samridhi Rijal
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Peter Neuhaus
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
- Department of Zoology, Cambridge University, Downing Street, Cambridge, CB2 3EJ, UK
| | - Jack Thorley
- Department of Zoology, Cambridge University, Downing Street, Cambridge, CB2 3EJ, UK
| | - Nigel Caulkett
- Faculty of Veterinary Medicine, University of Calgary, Foothills Campus, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada
| | - Susan Kutz
- Faculty of Veterinary Medicine, University of Calgary, Foothills Campus, 3280 Hospital Drive NW, Calgary, Alberta, T2N 4Z6, Canada
| | - Kathreen E. Ruckstuhl
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
- Department of Zoology, Cambridge University, Downing Street, Cambridge, CB2 3EJ, UK
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6
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Tuschhoff BM, Kennedy DA. Detecting and quantifying heterogeneity in susceptibility using contact tracing data. PLoS Comput Biol 2024; 20:e1012310. [PMID: 39074159 PMCID: PMC11309420 DOI: 10.1371/journal.pcbi.1012310] [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: 10/06/2023] [Revised: 08/08/2024] [Accepted: 07/10/2024] [Indexed: 07/31/2024] Open
Abstract
The presence of heterogeneity in susceptibility, differences between hosts in their likelihood of becoming infected, can fundamentally alter disease dynamics and public health responses, for example, by changing the final epidemic size, the duration of an epidemic, and even the vaccination threshold required to achieve herd immunity. Yet, heterogeneity in susceptibility is notoriously difficult to detect and measure, especially early in an epidemic. Here we develop a method that can be used to detect and estimate heterogeneity in susceptibility given contact by using contact tracing data, which are typically collected early in the course of an outbreak. This approach provides the capability, given sufficient data, to estimate and account for the effects of this heterogeneity before they become apparent during an epidemic. It additionally provides the capability to analyze the wealth of contact tracing data available for previous epidemics and estimate heterogeneity in susceptibility for disease systems in which it has never been estimated previously. The premise of our approach is that highly susceptible individuals become infected more often than less susceptible individuals, and so individuals not infected after appearing in contact networks should be less susceptible than average. This change in susceptibility can be detected and quantified when individuals show up in a second contact network after not being infected in the first. To develop our method, we simulated contact tracing data from artificial populations with known levels of heterogeneity in susceptibility according to underlying discrete or continuous distributions of susceptibilities. We analyzed these data to determine the parameter space under which we are able to detect heterogeneity and the accuracy with which we are able to estimate it. We found that our power to detect heterogeneity increases with larger sample sizes, greater heterogeneity, and intermediate fractions of contacts becoming infected in the discrete case or greater fractions of contacts becoming infected in the continuous case. We also found that we are able to reliably estimate heterogeneity and disease dynamics. Ultimately, this means that contact tracing data alone are sufficient to detect and quantify heterogeneity in susceptibility.
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Affiliation(s)
- Beth M. Tuschhoff
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - David A. Kennedy
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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7
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Smith LA, Fox NJ, Marion G, Booth NJ, Morris AMM, Athanasiadou S, Hutchings MR. Animal Behaviour Packs a Punch: From Parasitism to Production, Pollution and Prevention in Grazing Livestock. Animals (Basel) 2024; 14:1876. [PMID: 38997988 PMCID: PMC11240309 DOI: 10.3390/ani14131876] [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: 04/11/2024] [Revised: 06/06/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Behaviour is often the fundamental driver of disease transmission, where behaviours of individuals can be seen to scale up to epidemiological patterns seen at the population level. Here we focus on animal behaviour, and its role in parasite transmission to track its knock-on consequences for parasitism, production and pollution. Livestock face a nutrition versus parasitism trade-off in grazing environments where faeces creates both a nutritional benefit, fertilizing the surrounding sward, but also a parasite risk from infective nematode larvae contaminating the sward. The grazing decisions of ruminants depend on the perceived costs and benefits of the trade-off, which depend on the variations in both environmental (e.g., amounts of faeces) and animal factors (e.g., physiological state). Such grazing decisions determine the intake of both nutrients and parasites, affecting livestock growth rates and production efficiency. This impacts on the greenhouse gas costs of ruminant livestock production via two main mechanisms: (1) slower growth results in longer durations on-farm and (2) parasitised animals produce more methane per unit food intake. However, the sensitivity of behaviour to host parasite state offers opportunities for early detection of parasitism and control. Remote monitoring technology such as accelerometers can detect parasite-induced sickness behaviours soon after exposure, before impacts on growth, and thus may be used for targeting individuals for early treatment. We conclude that livestock host x parasite interactions are at the centre of the global challenges of food security and climate change, and that understanding livestock behaviour can contribute to solving both.
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Affiliation(s)
- Lesley A Smith
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), West Mains Road, Edinburgh EH9 3JG, UK
| | - Naomi J Fox
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), West Mains Road, Edinburgh EH9 3JG, UK
| | - Glenn Marion
- Biomathematics and Statistics Scotland (BioSS), Kings Buildings, Edinburgh EH9 3FD, UK
| | - Naomi J Booth
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), West Mains Road, Edinburgh EH9 3JG, UK
| | - Alex M M Morris
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), West Mains Road, Edinburgh EH9 3JG, UK
| | - Spiridoula Athanasiadou
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), West Mains Road, Edinburgh EH9 3JG, UK
| | - Michael R Hutchings
- Animal and Veterinary Sciences, Scotland's Rural College (SRUC), West Mains Road, Edinburgh EH9 3JG, UK
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8
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Kuo CC, Huang JL, Wang HC. Parasite infestation patterns differ between ticks and chigger mites on two rodent host species in Taiwan. EXPERIMENTAL & APPLIED ACAROLOGY 2024; 93:35-48. [PMID: 38695989 DOI: 10.1007/s10493-024-00918-3] [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] [Received: 11/26/2023] [Accepted: 04/16/2024] [Indexed: 06/18/2024]
Abstract
Parasites are typically concentrated on a few host individuals, and identifying the mechanisms underlying aggregated distribution can facilitate a more targeted control of parasites. We investigated the infestation patterns of hard ticks and chigger mites on two rodent species, the striped field mouse, Apodemus agrarius, and the lesser ricefield rat, Rattus losea, in Taiwan. We also explored abiotic and biotic factors that were important in explaining variation in the abundance of ticks and chiggers on rodent hosts. Ticks were more aggregated than chiggers on both rodent species. Factors important for the variation in parasitic loads, especially biotic factors, largely differed between ticks and chiggers. Variation partitioning analyses revealed that a larger proportion of variation in chiggers than in ticks can be explained, especially by abiotic factors. If, as proposed, the higher number of parasites in males is due to a larger range area or immunity being suppressed by testosterone, when A. agrarius males host more ticks, they are expected to also host more chiggers, given that chiggers adopt a similar host finding approach to that of ticks. Instead, the similar abundance of chiggers in male and female A. agrarius implies that a large home range or suppressed immunity does not predispose males to inevitably host more parasites. More variations were explained by abiotic than biotic factors, suggesting that controlling practices are more likely to be successful by focusing on factors related to the environment instead of host traits. Our study indicated that the extent of parasitism is rarely determined by a sole factor, but is an outcome of complex interactions among animal physiology, animal behavior, characteristics of parasites, and the environments.
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Affiliation(s)
- Chi-Chien Kuo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan.
- Department of Wildlife, Fish, and Conservation Biology, University of California, One Shields Avenue, 95616, Davis, CA, USA.
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan.
| | - Jing-Lun Huang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Biodiversity Research Center, National Taiwan University, Taipei, Taiwan
| | - Hsi-Chieh Wang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan.
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9
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Markwalter CF, Lapp Z, Abel L, Kimachas E, Omollo E, Freedman E, Chepkwony T, Amunga M, McCormick T, Bérubé S, Mangeni JN, Wesolowski A, Obala AA, Taylor SM, Prudhomme O'Meara W. Plasmodium falciparum infection in humans and mosquitoes influence natural Anopheline biting behavior and transmission. Nat Commun 2024; 15:4626. [PMID: 38816383 PMCID: PMC11139876 DOI: 10.1038/s41467-024-49080-9] [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: 02/20/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
The human infectious reservoir of Plasmodium falciparum is governed by transmission efficiency during vector-human contact and mosquito biting preferences. Understanding biting bias in a natural setting can help target interventions to interrupt transmission. In a 15-month cohort in western Kenya, we detected P. falciparum in indoor-resting Anopheles and human blood samples by qPCR and matched mosquito bloodmeals to cohort participants using short-tandem repeat genotyping. Using risk factor analyses and discrete choice models, we assessed mosquito biting behavior with respect to parasite transmission. Biting was highly unequal; 20% of people received 86% of bites. Biting rates were higher on males (biting rate ratio (BRR): 1.68; CI: 1.28-2.19), children 5-15 years (BRR: 1.49; CI: 1.13-1.98), and P. falciparum-infected individuals (BRR: 1.25; CI: 1.01-1.55). In aggregate, P. falciparum-infected school-age (5-15 years) boys accounted for 50% of bites potentially leading to onward transmission and had an entomological inoculation rate 6.4x higher than any other group. Additionally, infectious mosquitoes were nearly 3x more likely than non-infectious mosquitoes to bite P. falciparum-infected individuals (relative risk ratio 2.76, 95% CI 1.65-4.61). Thus, persistent P. falciparum transmission was characterized by disproportionate onward transmission from school-age boys and by the preference of infected mosquitoes to feed upon infected people.
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Affiliation(s)
| | - Zena Lapp
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Emmah Kimachas
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | | | - Elizabeth Freedman
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Tabitha Chepkwony
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Mark Amunga
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Tyler McCormick
- Departments of Statistics & Sociology, University of Washington, Seattle, WA, USA
| | - Sophie Bérubé
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Judith N Mangeni
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew A Obala
- School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Steve M Taylor
- Duke Global Health Institute, Duke University, Durham, NC, USA.
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.
| | - Wendy Prudhomme O'Meara
- Duke Global Health Institute, Duke University, Durham, NC, USA.
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.
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10
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Barrera R, Ruiz J, Adams LE, Marzan-Rodriguez M, Paz-Bailey G. Historical Hot Spots of Dengue and Zika Viruses to Guide Targeted Vector Control in San Juan, Puerto Rico (2010-2022). Am J Trop Med Hyg 2024; 110:731-737. [PMID: 38412550 PMCID: PMC10993837 DOI: 10.4269/ajtmh.23-0627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/24/2023] [Indexed: 02/29/2024] Open
Abstract
Dengue viruses (DENV) continue to cause large outbreaks in tropical countries, while chikungunya and Zika (ZIKV) viruses have added complexity to Aedes-borne disease prevention and control efforts. Because these viruses are transmitted by the same vectors in urban areas, it is useful to understand if sequential outbreaks caused by these viruses have commonalities, such as similar seasonal and spatial patterns, that would help anticipate and perhaps prevent future outbreaks. We explored and analyzed the heterogeneity of confirmed cases of DENV (2010-2014 and 2015-2022) and ZIKV (2016-2017) during outbreaks in the San Juan metropolitan area of Puerto Rico to explore their degree of overlap and prioritize areas for Aedes aegypti control. Deidentified, georeferenced case data were aggregated into grid cells (500 × 500 m) within a geographical information system of the study area and analyzed to calculate the degree of overlap between outbreaks. Spatial autocorrelations using local indicators of spatial associations were conducted to identify significant disease case hot spots and correlations between outbreaks. We found that 75% of cases during the three transmission periods were concentrated in 25% of the total number of grid cells covering the study area. We also found significant clustering of cases during each outbreak, enabling identification of consistent disease hot spots. Our results showed 85% spatial overlap between cases of ZIKV in 2015-2017 and DENV in 2010-2014 and 97% overlap between DENV cases in 2010-2014 and 2015-2022. These results reveal urban areas at greater risk of future arbovirus outbreaks that should be prioritized for vector control.
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Affiliation(s)
- Roberto Barrera
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Jose Ruiz
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Laura E. Adams
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | | | - Gabriela Paz-Bailey
- Dengue Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
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11
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Ortega-López LD, Betancourth MP, León R, Kohl A, Ferguson HM. Behaviour and distribution of Aedes aegypti mosquitoes and their relation to dengue incidence in two transmission hotspots in coastal Ecuador. PLoS Negl Trop Dis 2024; 18:e0010932. [PMID: 38683840 PMCID: PMC11081501 DOI: 10.1371/journal.pntd.0010932] [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: 11/04/2022] [Revised: 05/09/2024] [Accepted: 02/08/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Dengue (DENV) transmission is endemic throughout coastal Ecuador, showing heterogeneous incidence patterns in association with fine-scale variation in Aedes aegypti vector populations and other factors. Here, we investigated the impact of micro-climate and neighbourhood-level variation in urbanization on Aedes abundance, resting behaviour and associations with dengue incidence in two endemic areas. METHODOLOGY/PRINCIPAL FINDINGS Aedes aegypti were collected in Quinindé and Portoviejo, two urban cantons with hyperendemic dengue transmission in coastal Ecuador. Aedes vectors were sampled in and around houses within urban and peri-urban neighbourhoods at four time periods. We tested for variation in vector abundance and resting behaviour in relation to neighbourhood urbanization level and microclimatic factors. Aedes abundance increased towards the end of the rainy season, was significantly higher in Portoviejo than in Quinindé, and in urban than in peri-urban neighbourhoods. Aedes vectors were more likely to rest inside houses in Portoviejo but had similar abundance in indoor and outdoor resting collections in Quinindé. Over the study period, DENV incidence was lower in Quinindé than in Portoviejo. Relationships between weekly Ae. aegypti abundance and DENV incidence were highly variable between trapping methods; with positive associations being detected only between BG-sentinel and outdoor Prokopack collections. CONCLUSIONS/SIGNIFICANCE Aedes aegypti abundance was significantly higher in urban than peri-urban neighbourhoods, and their resting behaviour varied between study sites. This fine-scale spatial heterogeneity in Ae. aegypti abundance and behaviour could generate site-specific variation in human exposure and the effectiveness of indoor-based interventions. The trap-dependent nature of associations between Aedes abundance and local DENV incidence indicates further work is needed to identify robust entomological indicators of infection risk.
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Affiliation(s)
- Leonardo D. Ortega-López
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Mauro Pazmiño Betancourth
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Renato León
- Laboratorio de Entomología Médica & Medicina Tropical LEMMT, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Heather M. Ferguson
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
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12
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Zhang S, Hanjalic A, Wang H. Predicting nodal influence via local iterative metrics. Sci Rep 2024; 14:4929. [PMID: 38418506 PMCID: PMC10901818 DOI: 10.1038/s41598-024-55547-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/25/2024] [Indexed: 03/01/2024] Open
Abstract
Nodal spreading influence is the capability of a node to activate the rest of the network when it is the seed of spreading. Combining nodal properties (centrality metrics) derived from local and global topological information respectively has been shown to better predict nodal influence than using a single metric. In this work, we investigate to what extent local and global topological information around a node contributes to the prediction of nodal influence and whether relatively local information is sufficient for the prediction. We show that by leveraging the iterative process used to derive a classical nodal centrality such as eigenvector centrality, we can define an iterative metric set that progressively incorporates more global information around the node. We propose to predict nodal influence using an iterative metric set that consists of an iterative metric from order 1 to K produced in an iterative process, encoding gradually more global information as K increases. Three iterative metrics are considered, which converge to three classical node centrality metrics, respectively. In various real-world networks and synthetic networks with community structures, we find that the prediction quality of each iterative based model converges to its optimal when the metric of relatively low orders ( K ∼ 4 ) are included and increases only marginally when further increasing K. This fast convergence of prediction quality with K is further explained by analyzing the correlation between the iterative metric and nodal influence, the convergence rate of each iterative process and network properties. The prediction quality of the best performing iterative metric set with K = 4 is comparable with the benchmark method that combines seven centrality metrics: their prediction quality ratio is within the range [ 91 % , 106 % ] across all three quality measures and networks. In two spatially embedded networks with an extremely large diameter, however, iterative metric of higher orders, thus a large K, is needed to achieve comparable prediction quality with the benchmark.
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Affiliation(s)
- Shilun Zhang
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands
| | - Alan Hanjalic
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands
| | - Huijuan Wang
- Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD, Delft, The Netherlands.
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13
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Bragazzi NL, Woldegerima WA, Siri A. Economic microbiology: exploring microbes as agents in economic systems. Front Microbiol 2024; 15:1305148. [PMID: 38450162 PMCID: PMC10915239 DOI: 10.3389/fmicb.2024.1305148] [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: 09/30/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Microbial communities exhibit striking parallels with economic markets, resembling intricate ecosystems where microorganisms engage in resource exchange akin to human market transactions. This dynamic network of resource swapping mirrors economic trade in human markets, with microbes specializing in metabolic functions much like businesses specializing in goods and services. Cooperation and competition are central dynamics in microbial communities, with alliances forming for mutual benefit and species vying for dominance, similar to businesses seeking market share. The human microbiome, comprising trillions of microorganisms within and on our bodies, is not only a marker of socioeconomic status but also a critical factor contributing to persistent health inequalities. Social and economic factors shape the composition of the gut microbiota, impacting healthcare access and quality of life. Moreover, these microbes exert indirect influence over human decisions by affecting neurotransmitter production, influencing mood, behavior, and choices related to diet and emotions. Human activities significantly impact microbial communities, from dietary choices and antibiotic use to environmental changes, disrupting these ecosystems. Beyond their natural roles, humans harness microbial communities for various applications, manipulating their interactions and resource exchanges to achieve specific goals in fields like medicine, agriculture, and environmental science. In conclusion, the concept of microbial communities as biological markets offers valuable insights into their intricate functioning and adaptability. It underscores the profound interplay between microbial ecosystems and human health and behavior, with far-reaching implications for multiple disciplines. To paraphrase Alfred Marshall, "the Mecca of the economist lies in economic microbiology."
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Affiliation(s)
- Nicola Luigi Bragazzi
- Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, ON, Canada
- Department of Health Sciences (DISSAL), Postgraduate School of Public Health, University of Genoa, Genoa, Italy
- United Nations Educational, Scientific and Cultural Organization (UNESCO) Chair, Health Anthropology Biosphere and Healing Systems, University of Genoa, Genoa, Italy
| | - Woldegebriel Assefa Woldegerima
- Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, ON, Canada
| | - Anna Siri
- United Nations Educational, Scientific and Cultural Organization (UNESCO) Chair, Health Anthropology Biosphere and Healing Systems, University of Genoa, Genoa, Italy
- Department of Wellbeing, Nutrition and Sport, Pegaso University, Naples, Italy
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14
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Kamber L, Bürli C, Harbrecht H, Odermatt P, Sayasone S, Chitnis N. Modeling the persistence of Opisthorchis viverrini worm burden after mass-drug administration and education campaigns with systematic adherence. PLoS Negl Trop Dis 2024; 18:e0011362. [PMID: 38422118 DOI: 10.1371/journal.pntd.0011362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 03/12/2024] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Opisthorchis viverrini is a parasitic liver fluke contracted by consumption of raw fish, which affects over 10 million people in Southeast Asia despite sustained control efforts. Chronic infections are a risk factor for the often fatal bile duct cancer, cholangiocarcinoma. Previous modeling predicted rapid elimination of O. viverrini following yearly mass drug administration (MDA) campaigns. However, field data collected in affected populations shows persistence of infection, including heavy worm burden, after many years of repeated interventions. A plausible explanation for this observation is systematic adherence of individuals in health campaigns, such as MDA and education, with some individuals consistently missing treatment. We developed an agent-based model of O. viverrini which allows us to introduce various heterogeneities including systematic adherence to MDA and education campaigns at the individual level. We validate the agent-based model by comparing it to a previously published population-based model. We estimate the degree of systematic adherence to MDA and education campaigns indirectly, using epidemiological data collected in Lao PDR before and after 5 years of repeated MDA, education and sanitation improvement campaigns. We predict the impact of interventions deployed singly and in combination, with and without the estimated systematic adherence. We show how systematic adherence can substantially increase the time required to achieve reductions in worm burden. However, we predict that yearly MDA campaigns alone can result in a strong reduction of moderate and heavy worm burden, even under systematic adherence. We predict latrines and education campaigns to be particularly important for the reduction in overall prevalence, and therefore, ultimately, elimination. Our findings show how systematic adherence can explain the observed persistence of worm burden; while emphasizing the benefit of interventions for the entire population, even under systematic adherence. At the same time, the results highlight the substantial opportunity to further reduce worm burden if patterns of systematic adherence can be overcome.
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Affiliation(s)
- Lars Kamber
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Christine Bürli
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Helmut Harbrecht
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Peter Odermatt
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Somphou Sayasone
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Lao Tropical and Public Health Institute, Vientiane, Lao People's Democratic Republic
| | - Nakul Chitnis
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
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15
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Seidl CM, Ferreira FC, Parise KL, Paxton KL, Paxton EH, Atkinson CT, Fleischer RC, Foster JT, Marm Kilpatrick A. Linking avian malaria parasitemia estimates from quantitative PCR and microscopy reveals new infection patterns in Hawai'i. Int J Parasitol 2024; 54:123-130. [PMID: 37922977 DOI: 10.1016/j.ijpara.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/29/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Plasmodium parasites infect thousands of species and provide an exceptional system for studying host-pathogen dynamics, especially for multi-host pathogens. However, understanding these interactions requires an accurate assay of infection. Assessing Plasmodium infections using microscopy on blood smears often misses infections with low parasitemias (the fractions of cells infected), and biases in malaria prevalence estimates will differ among hosts that differ in mean parasitemias. We examined Plasmodium relictum infection and parasitemia using both microscopy of blood smears and quantitative polymerase chain reaction (qPCR) on 299 samples from multiple bird species in Hawai'i and fit models to predict parasitemias from qPCR cycle threshold (Ct) values. We used these models to quantify the extent to which microscopy underestimated infection prevalence and to more accurately estimate infection patterns for each species for a large historical study done by microscopy. We found that most qPCR-positive wild-caught birds in Hawaii had low parasitemias (Ct scores ≥35), which were rarely detected by microscopy. The fraction of infections missed by microscopy differed substantially among eight species due to differences in species' parasitemia levels. Infection prevalence was likely 4-5-fold higher than previous microscopy estimates for three introduced species, including Zosterops japonicus, Hawaii's most abundant forest bird, which had low average parasitemias. In contrast, prevalence was likely only 1.5-2.3-fold higher than previous estimates for Himatione sanguinea and Chlorodrepanis virens, two native species with high average parasitemias. Our results indicate that relative patterns of infection among species differ substantially from those observed in previous microscopy studies, and that differences depend on variation in parasitemias among species. Although microscopy of blood smears is useful for estimating the frequency of different Plasmodium stages and host attributes, more sensitive quantitative methods, including qPCR, are needed to accurately estimate and compare infection prevalence among host species.
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Affiliation(s)
- Christa M Seidl
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA; Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA.
| | - Francisco C Ferreira
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA; Center for Vector Biology, Rutgers University, New Brunswick, NJ, USA
| | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kristina L Paxton
- Hawai'i Volcanoes National Park, Resource Management, Hawai'i National Park, HI, USA
| | - Eben H Paxton
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, HI. USA
| | - Carter T Atkinson
- U.S. Geological Survey, Pacific Island Ecosystems Research Center, Hawai'i National Park, HI. USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
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16
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Horne D, Nduba V, Njagi L, Murithi W, Mwongera Z, Logioia G, Peterson G, Segnitz RM, Fennelly K, Hawn T. Tuberculosis Infectiousness is Associated with Distinct Clinical and Inflammatory Profiles. RESEARCH SQUARE 2024:rs.3.rs-3722244. [PMID: 38328225 PMCID: PMC10849670 DOI: 10.21203/rs.3.rs-3722244/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Interrupting transmission events to prevent new acquisition of infection and disease is a critical part of tuberculosis (TB) control efforts. However, knowledge gaps in understanding the biology and determinants of TB transmission, including poor estimates of individual infectiousness and the lack of accurate and convenient biomarkers, undermine efforts to develop interventions. Cough-generated aerosol cultures have been found to predict TB transmission better than any microbiological or clinical markers in cohorts from Uganda and Brazil. We hypothesized that highly infectious individuals with pulmonary TB (defined as positive for cough aerosol cultures) have elevated inflammatory markers and unique transcriptional profiles compared to less infectious individuals (negative for cough aerosol cultures). We performed a prospective, longitudinal study using a cough aerosol sampling system as in other studies. We enrolled 142 participants with treatment-naïve pulmonary TB in Nairobi, Kenya, and assessed the association of clinical, microbiologic, and immunologic characteristics with Mtb aerosolization and transmission in 143 household members. Contacts of the forty-three aerosol culture-positive participants (30%) were more likely to have a positive IGRA (85% vs 53%, P = 0.005) and a higher median IGRA IFNγ level (P < 0.001, median 4.25 IU/ml (0.90-5.91) vs. 0.71 (0.01-3.56)) compared to aerosol culture-negative individuals. We found that higher bacillary burden, younger age, and larger mean upper arm circumference were associated with positive aerosol cultures. In addition, novel host inflammatory profiles, including elevated serum C-reactive protein and sputum cytokines, were associated with aerosol culture status. Notably, we found pre-treatment whole blood transcriptional profiles associated with aerosol culture status, independent of bacillary load. Together, these findings suggest that TB infectiousness is associated with epidemiologic characteristics and inflammatory signatures and that these features may be used to identify highly infectious persons. These results provide new public health tools and insights into TB pathogenesis.
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Affiliation(s)
| | - Videlis Nduba
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | - Lilian Njagi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | - Wilfred Murithi
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | - Zipporah Mwongera
- Centre for Respiratory Diseases Research, Kenya Medical Research Institute
| | | | | | | | - Kevin Fennelly
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH)
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17
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Garchitorena A, Rasoloharimanana LT, Rakotonanahary RJ, Evans MV, Miller AC, Finnegan KE, Cordier LF, Cowley G, Razafinjato B, Randriamanambintsoa M, Andrianambinina S, Popper SJ, Hotahiene R, Bonds MH, Schoenhals M. Morbidity and mortality burden of COVID-19 in rural Madagascar: results from a longitudinal cohort and nested seroprevalence study. Int J Epidemiol 2023; 52:1745-1755. [PMID: 37793001 DOI: 10.1093/ije/dyad135] [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: 03/14/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
INTRODUCTION Three years into the pandemic, there remains significant uncertainty about the true infection and mortality burden of COVID-19 in the World Health Organization Africa region. High quality, population-representative studies in Africa are rare and tend to be conducted in national capitals or large cities, leaving a substantial gap in our understanding of the impact of COVID-19 in rural, low-resource settings. Here, we estimated the spatio-temporal morbidity and mortality burden associated with COVID-19 in a rural health district of Madagascar until the first half of 2021. METHODS We integrated a nested seroprevalence study within a pre-existing longitudinal cohort conducted in a representative sample of 1600 households in Ifanadiana District, Madagascar. Socio-demographic and health information was collected in combination with dried blood spots for about 6500 individuals of all ages, which were analysed to detect IgG and IgM antibodies against four specific proteins of SARS-CoV-2 in a bead-based multiplex immunoassay. We evaluated spatio-temporal patterns in COVID-19 infection history and its associations with several geographic, socio-economic and demographic factors via logistic regressions. RESULTS Eighteen percent of people had been infected by April-June 2021, with seroprevalence increasing with individuals' age. COVID-19 primarily spread along the only paved road and in major towns during the first epidemic wave, subsequently spreading along secondary roads during the second wave to more remote areas. Wealthier individuals and those with occupations such as commerce and formal employment were at higher risk of being infected in the first wave. Adult mortality increased in 2020, particularly for older men for whom it nearly doubled up to nearly 40 deaths per 1000. Less than 10% of mortality in this period would be directly attributed to COVID-19 deaths if known infection fatality ratios are applied to observed seroprevalence in the district. CONCLUSION Our study provides a very granular understanding on COVID-19 transmission and mortality in a rural population of sub-Saharan Africa and suggests that the disease burden in these areas may have been substantially underestimated.
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Affiliation(s)
- Andres Garchitorena
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- NGO Pivot, Ifanadiana, Madagascar
| | | | - Rado Jl Rakotonanahary
- NGO Pivot, Ifanadiana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Michelle V Evans
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Ann C Miller
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Karen E Finnegan
- NGO Pivot, Ifanadiana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Marius Randriamanambintsoa
- Direction de la Démographie et des Statistiques Sociales, Institut National de la Statistique, Antananarivo, Madagascar
| | - Samuel Andrianambinina
- Direction de la Démographie et des Statistiques Sociales, Institut National de la Statistique, Antananarivo, Madagascar
| | - Stephen J Popper
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Raphaël Hotahiene
- Direction de lutte contre les maladies transmissibles, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Matthew H Bonds
- NGO Pivot, Ifanadiana, Madagascar
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
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Bron GM, Wichgers Schreur PJ, de Jong MCM, van Keulen L, Vloet RPM, Koenraadt CJM, Kortekaas J, ten Bosch QA. Quantifying Rift Valley fever virus transmission efficiency in a lamb-mosquito-lamb model. Front Cell Infect Microbiol 2023; 13:1206089. [PMID: 38170150 PMCID: PMC10759236 DOI: 10.3389/fcimb.2023.1206089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024] Open
Abstract
Rift Valley fever virus (RVFV) is a (re)emerging mosquito-borne pathogen impacting human and animal health. How RVFV spreads through a population depends on population-level and individual-level interactions between vector, host and pathogen. Here, we estimated the probability for RVFV to transmit to naive animals by experimentally exposing lambs to a bite of an infectious mosquito, and assessed if and how RVFV infection subsequently developed in the exposed animal. Aedes aegypti mosquitoes, previously infected via feeding on a viremic lamb, were used to expose naive lambs to the virus. Aedes aegypti colony mosquitoes were used as they are easy to maintain and readily feed in captivity. Other mosquito spp. could be examined with similar methodology. Lambs were exposed to either 1-3 (low exposure) or 7-9 (high exposure) infectious mosquitoes. All lambs in the high exposure group became viremic and showed characteristic signs of Rift Valley fever within 2-4 days post exposure. In contrast, 3 out of 12 lambs in the low exposure group developed viremia and disease, with similar peak-levels of viremia as the high exposure group but with some heterogeneity in the onset of viremia. These results suggest that the likelihood for successful infection of a ruminant host is affected by the number of infectious mosquitoes biting, but also highlights that a single bite of an infectious mosquito can result in disease. The per bite mosquito-to-host transmission efficiency was estimated at 28% (95% confidence interval: 15 - 47%). We subsequently combined this transmission efficiency with estimates for life traits of Aedes aegypti or related mosquitoes into a Ross-McDonald mathematical model to illustrate scenarios under which major RVFV outbreaks could occur in naïve populations (i.e., R0 >1). The model revealed that relatively high vector-to-host ratios as well as mosquitoes feeding preferably on competent hosts are required for R0 to exceed 1. Altogether, this study highlights the importance of experiments that mimic natural exposure to RVFV. The experiments facilitate a better understanding of the natural progression of disease and a direct way to obtain epidemiological parameters for mathematical models.
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Affiliation(s)
- Gebbiena M. Bron
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Mart C. M. de Jong
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, Netherlands
| | - Lucien van Keulen
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Rianka P. M. Vloet
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | | | - Jeroen Kortekaas
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Quirine A. ten Bosch
- Quantitative Veterinary Epidemiology, Wageningen University and Research, Wageningen, Netherlands
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19
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Meyer AD, Guerrero SM, Dean NE, Anderson KB, Stoddard ST, Perkins TA. Model-based estimates of chikungunya epidemiological parameters and outbreak risk from varied data types. Epidemics 2023; 45:100721. [PMID: 37890441 DOI: 10.1016/j.epidem.2023.100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Assessing the factors responsible for differences in outbreak severity for the same pathogen is a challenging task, since outbreak data are often incomplete and may vary in type across outbreaks (e.g., daily case counts, serology, cases per household). We propose that outbreaks described with varied data types can be directly compared by using those data to estimate a common set of epidemiological parameters. To demonstrate this for chikungunya virus (CHIKV), we developed a realistic model of CHIKV transmission, along with a Bayesian inference method that accommodates any type of outbreak data that can be simulated. The inference method makes use of the fact that all data types arise from the same transmission process, which is simulated by the model. We applied these tools to data from three real-world outbreaks of CHIKV in Italy, Cambodia, and Bangladesh to estimate nine model parameters. We found that these populations differed in several parameters, including pre-existing immunity and house-to-house differences in mosquito activity. These differences resulted in posterior predictions of local CHIKV transmission risk that varied nearly fourfold: 16% in Italy, 28% in Cambodia, and 62% in Bangladesh. Our inference method and model can be applied to improve understanding of the epidemiology of CHIKV and other pathogens for which outbreaks are described with varied data types.
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Affiliation(s)
- Alexander D Meyer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | | | - Natalie E Dean
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Kathryn B Anderson
- Department of Microbiology and Immunology, The State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA
| | - Steven T Stoddard
- Bavarian Nordic Inc., 6275 Nancy Ridge Drive Suite 110/120, San Diego, CA 92121, USA; Division of Health Promotion and Behavioral Sciences, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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20
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Evans MV, Ramiadantsoa T, Kauffman K, Moody J, Nunn CL, Rabezara JY, Raharimalala P, Randriamoria TM, Soarimalala V, Titcomb G, Garchitorena A, Roche B. Sociodemographic Variables Can Guide Prioritized Testing Strategies for Epidemic Control in Resource-Limited Contexts. J Infect Dis 2023; 228:1189-1197. [PMID: 36961853 PMCID: PMC11007394 DOI: 10.1093/infdis/jiad076] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/08/2023] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Targeted surveillance allows public health authorities to implement testing and isolation strategies when diagnostic resources are limited, and can be implemented via the consideration of social network topologies. However, it remains unclear how to implement such surveillance and control when network data are unavailable. METHODS We evaluated the ability of sociodemographic proxies of degree centrality to guide prioritized testing of infected individuals compared to known degree centrality. Proxies were estimated via readily available sociodemographic variables (age, gender, marital status, educational attainment, household size). We simulated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics via a susceptible-exposed-infected-recovered individual-based model on 2 contact networks from rural Madagascar to test applicability of these findings to low-resource contexts. RESULTS Targeted testing using sociodemographic proxies performed similarly to targeted testing using known degree centralities. At low testing capacity, using proxies reduced infection burden by 22%-33% while using 20% fewer tests, compared to random testing. By comparison, using known degree centrality reduced the infection burden by 31%-44% while using 26%-29% fewer tests. CONCLUSIONS We demonstrate that incorporating social network information into epidemic control strategies is an effective countermeasure to low testing capacity and can be implemented via sociodemographic proxies when social network data are unavailable.
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Affiliation(s)
- Michelle V Evans
- Maladies Infectieuses et Vecteurs : Écologie, Génétique, Évolution et Contrôle, Université Montpellier, CNRS, IRD, Montpellier, France
| | - Tanjona Ramiadantsoa
- Maladies Infectieuses et Vecteurs : Écologie, Génétique, Évolution et Contrôle, Université Montpellier, CNRS, IRD, Montpellier, France
| | - Kayla Kauffman
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
| | - James Moody
- Department of Sociology, Duke University, Durham, North Carolina, USA
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | - Jean Yves Rabezara
- Department of Science and Technology, University of Antsiranana, Antsiranana, Madagascar
| | | | - Toky M Randriamoria
- Association Vahatra, Antananarivo, Madagascar
- Zoologie et Biodiversité Animale, Domaine Sciences et Technologies, Université d’Antananarivo, Antananarivo, Madagascar
| | - Voahangy Soarimalala
- Association Vahatra, Antananarivo, Madagascar
- Institut des Sciences et Techniques de l’Environnement, Université de Fianarantsoa, Fianarantsoa, Madagascar
| | - Georgia Titcomb
- Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, USA
- Marine Science Institute, University of California, Santa Barbara, California, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Andres Garchitorena
- Maladies Infectieuses et Vecteurs : Écologie, Génétique, Évolution et Contrôle, Université Montpellier, CNRS, IRD, Montpellier, France
- Pivot, Ifanadiana, Madagascar
| | - Benjamin Roche
- Maladies Infectieuses et Vecteurs : Écologie, Génétique, Évolution et Contrôle, Université Montpellier, CNRS, IRD, Montpellier, France
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21
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Nyangiri OA, Mulindwa J, Namulondo J, Kitibwa A, Nassuuna J, Elliott A, Kimuda MP, Boobo A, Nerima B, Adriko M, Dunton NJ, Madhan GK, Kristiansen M, Casacuberta-Partal M, Noyes H, Matovu E. Variants of IL6, IL10, FCN2, RNASE3, IL12B and IL17B loci are associated with Schistosoma mansoni worm burden in the Albert Nile region of Uganda. PLoS Negl Trop Dis 2023; 17:e0011796. [PMID: 38033168 PMCID: PMC10715658 DOI: 10.1371/journal.pntd.0011796] [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: 04/01/2023] [Revised: 12/12/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Individuals genetically susceptible to high schistosomiasis worm burden may contribute disproportionately to transmission and could be prioritized for control. Identifying genes involved may guide development of therapy. METHODOLOGY/PRINCIPAL FINDINGS A cohort of 606 children aged 10-15 years were recruited in the Albert Nile region of Uganda and assessed for Schistosoma mansoni worm burden using the Up-Converting Particle Lateral Flow (UCP-LF) test detecting circulating anodic antigen (CAA), point-of-care Circulating Cathodic Antigen (POC-CCA) and Kato-Katz tests. Whole genome genotyping was conducted on 326 children comprising the top and bottom 25% of worm burden. Linear models were fitted to identify variants associated with worm burden in preselected candidate genes. Expression quantitative trait locus (eQTL) analysis was conducted for candidate genes with UCP-LF worm burden included as a covariate. Single Nucleotide Polymorphism loci associated with UCP-LF CAA included IL6 rs2066992 (OR = 0.43, p = 0.0006) and rs7793163 (OR = 2.0, p = 0.0007); IL21 SNP kgp513476 (OR 1.79, p = 0.0025) and IL17B SNP kgp708159 (OR = 0.35, p = 0.0028). A haplotype in the IL10 locus was associated with lower worm burden (OR = 0.53, p = 0.015) and overlapped SNPs rs1800896, rs1800871 and rs1800872. Significant haplotypes (p<0.05, overlapping significant SNP) associated with worm burden were observed in IL6 and the Th17 pathway IL12B and IL17B genes. There were significant eQTL in the IL6, IL5, IL21, IL25 and IFNG regions. CONCLUSIONS Variants associated with S. mansoni worm burden were in IL6, FCN2, RNASE3, IL10, IL12B and IL17B gene loci. However only eQTL associations remained significant after Bonferroni correction. In summary, immune balance, pathogen recognition and Th17 pathways may play a role in modulating Schistosoma worm burden. Individuals carrying risk variants may be targeted first in allocation of control efforts to reduce the burden of schistosomiasis in the community.
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Affiliation(s)
- Oscar Asanya Nyangiri
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- Department of Biochemistry and Sports Sciences, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Joyce Namulondo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anna Kitibwa
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Jacent Nassuuna
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Alison Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Magambo Phillip Kimuda
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Alex Boobo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Barbara Nerima
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Moses Adriko
- Vector Borne & NTD Control Division, Ministry of Health, Uganda
| | - Nathan J. Dunton
- UCL Genomics core facility, University College London, London, United Kingdom
| | | | - Mark Kristiansen
- UCL Genomics core facility, University College London, London, United Kingdom
| | | | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Enock Matovu
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
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22
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Kuenzi AJ, Luis AD. Food availability leads to more connected contact networks among peridomestic zoonotic reservoir hosts. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230809. [PMID: 38026027 PMCID: PMC10646467 DOI: 10.1098/rsos.230809] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
The North American deermouse (Peromyscus maniculatus) is a reservoir host for many zoonotic pathogens. Deermice have been well studied, but few studies have attempted to understand social interactions within the species despite these interactions being key to understanding disease transmission. We performed an experiment to determine if supplemental food or nesting material affected social interactions of deermice and tested if interactions increased with increasing population density. We constructed three simulated buildings that received one of three treatments: food, nesting material, or control. Mice were tagged with passive integrated transponder (PIT) tags, and their movement in and out of buildings was monitored with PIT tag readers. PIT tag readings were used to create contact networks, assuming a contact if two deermice were in the same building at the same time. We found that buildings with food led to contact networks that were approximately 10 times more connected than buildings with nesting material or control buildings. We also saw a significant effect of population density on the average number of contacts per individual. These results suggest that food supplementation which is common in peridomestic settings, can significantly increase contacts between reservoir hosts, potentially leading to increased transmission of zoonotic viruses within the reservoir host and from reservoir hosts to humans.
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Affiliation(s)
- Amy J. Kuenzi
- Department of Biology, Montana Technological University, 1300 Park Street, Butte, MT 59701, USA
| | - Angela D. Luis
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT 59812, USA
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23
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Teicher A. Super-spreaders: a historical review. THE LANCET. INFECTIOUS DISEASES 2023; 23:e409-e417. [PMID: 37352877 DOI: 10.1016/s1473-3099(23)00183-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/07/2023] [Accepted: 03/01/2023] [Indexed: 06/25/2023]
Abstract
The term super-spreader is used for multiple, and sometimes even conflicting, purposes. The reasons for this can be traced back to its complex history. Forerunners of the super-spreader concept-in discussions of so-called dangerous carriers and in analyses of explosive outbreaks during the early 20th century-revolved primarily around gastrointestinal diseases, not respiratory ones. In 1957-58, the H2N2 influenza pandemic and Wells and Riley's studies on tuberculosis drew attention to both the viability of airborne transmission and the existence of significant heterogeneity in infectivity. The term super-spreader was coined in 1972, in relation to computer simulations of influenza epidemics. Initially, super-spreaders were simply an additional feature within stochastic models of epidemics, with little effect on an epidemic's eventual course. The term was later appropriated to explain why outbreaks of airborne diseases continued in vaccinated populations, defying the predictions of contact-transmission-based models. The content and meaning of the term continued to fluctuate, from the mathematical characterisation of sexually active people with gonorrhoea, through HIV carriers with highly infectious semen, to central nodes within a network. This Historical Review reconstructs the historical growth of the concept of super-spreading, and offers insight into its current, highly diversified use.
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Affiliation(s)
- Amir Teicher
- Department of History, Tel Aviv University, Tel Aviv, Israel.
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24
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Lambrechts L, Reiner RC, Briesemeister MV, Barrera P, Long KC, Elson WH, Vizcarra A, Astete H, Bazan I, Siles C, Vilcarromero S, Leguia M, Kawiecki AB, Perkins TA, Lloyd AL, Waller LA, Kitron U, Jenkins SA, Hontz RD, Campbell WR, Carrington LB, Simmons CP, Ampuero JS, Vasquez G, Elder JP, Paz-Soldan VA, Vazquez-Prokopec GM, Rothman AL, Barker CM, Scott TW, Morrison AC. Direct mosquito feedings on dengue-2 virus-infected people reveal dynamics of human infectiousness. PLoS Negl Trop Dis 2023; 17:e0011593. [PMID: 37656759 PMCID: PMC10501553 DOI: 10.1371/journal.pntd.0011593] [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: 03/26/2023] [Revised: 09/14/2023] [Accepted: 08/14/2023] [Indexed: 09/03/2023] Open
Abstract
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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Affiliation(s)
- Louis Lambrechts
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France
| | - Robert C. Reiner
- University of Washington, Seattle, Washington, United States of America
| | - M. Veronica Briesemeister
- Department of Entomology and Nematology, University of California, Davis, California, United States of America
| | - Patricia Barrera
- Department of Entomology and Nematology, University of California, Davis, California, United States of America
- Genomics Laboratory, Pontificia Universidad Católica del Peru, Lima, Peru
| | - Kanya C. Long
- Department of Family Medicine and Public Health, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - William H. Elson
- Department of Entomology and Nematology, University of California, Davis, California, United States of America
| | - Alfonso Vizcarra
- Department of Entomology and Nematology, University of California, Davis, California, United States of America
| | - Helvio Astete
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
- Department of Entomology, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - Isabel Bazan
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - Crystyan Siles
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - Stalin Vilcarromero
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - Mariana Leguia
- Genomics Laboratory, Pontificia Universidad Católica del Peru, Lima, Peru
| | - Anna B. Kawiecki
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - T. Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Alun L. Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Lance A. Waller
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Uriel Kitron
- Department of Environmental Sciences, Emory University, Atlanta, Georgia, United States of America
| | - Sarah A. Jenkins
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - Robert D. Hontz
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - Wesley R. Campbell
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
| | | | - Cameron P. Simmons
- Institute for Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
| | - J. Sonia Ampuero
- Virology and Emerging Infections Department, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - Gisella Vasquez
- Department of Entomology, United States Naval Medical Research Unit No. 6, Lima, Peru
| | - John P. Elder
- School of Public Health, San Diego State University, San Diego, California, United States of America
| | - Valerie A. Paz-Soldan
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | | | - Alan L. Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, Rhode Island, United States of America
| | - Christopher M. Barker
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Thomas W. Scott
- Department of Entomology and Nematology, University of California, Davis, California, United States of America
| | - Amy C. Morrison
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, California, United States of America
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25
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Taylor CL, Egan SL, Gofton AW, Irwin PJ, Oskam CL, Hochuli DF, Banks PB. An invasive human commensal and a native marsupial maintain tick populations at the urban fringe. MEDICAL AND VETERINARY ENTOMOLOGY 2023; 37:460-471. [PMID: 36718907 DOI: 10.1111/mve.12643] [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: 02/05/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Ticks (Acari: Ixodidae) are major disease vectors globally making it increasingly important to understand how altered vertebrate communities in urban areas shape tick population dynamics. In urban landscapes of Australia, little is known about which native and introduced small mammals maintain tick populations preventing host-targeted tick management and leading to human-wildlife conflict. Here, we determined (1) larval, nymphal, and adult tick burdens on host species and potential drivers, (2) the number of ticks supported by the different host populations, and (3) the proportion of medically significant tick species feeding on the different host species in Northern Sydney. We counted 3551 ticks on 241 mammals at 15 sites and found that long-nosed bandicoots (Perameles nasuta) hosted more ticks of all life stages than other small mammals but introduced black rats (Rattus rattus) were more abundant at most sites (33%-100%) and therefore important in supporting larval and nymphal ticks in our study areas. Black rats and bandicoots hosted a greater proportion of medically significant tick species including Ixodes holocyclus than other hosts. Our results show that an introduced human commensal contributes to maintaining urban tick populations and suggests ticks could be managed by controlling rat populations on urban fringes.
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Affiliation(s)
- Casey L Taylor
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, Australia
| | - Siobhon L Egan
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | | | - Peter J Irwin
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Charlotte L Oskam
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Dieter F Hochuli
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, Australia
| | - Peter B Banks
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, New South Wales, Australia
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26
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Lima LL, Atman APF. Complexity in the dengue spreading: A network analysis approach. PLoS One 2023; 18:e0289690. [PMID: 37549129 PMCID: PMC10406222 DOI: 10.1371/journal.pone.0289690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
In an increasingly interconnected society, preventing epidemics has become a major challenge. Numerous infectious diseases spread between individuals by a vector, creating bipartite networks of infection with the characteristics of complex networks. In the case of dengue, a mosquito-borne disease, these infection networks include a vector-the Aedes aegypti mosquito-which has expanded its endemic area due to climate change. In this scenario, innovative approaches are essential to help public agents in the fight against the disease. Using an agent-based model, we investigated the network morphology of a dengue endemic region considering four different serotypes and a small population. The degree, betweenness, and closeness distributions are evaluated for the bipartite networks, considering the interactions up to the second order for each serotype. We observed scale-free features and heavy tails in the degree distribution and betweenness and quantified the decay of the degree distribution with a q-Gaussian fit function. The simulation results indicate that the spread of dengue is primarily driven by human-to-human and human-to-mosquito interaction, reinforcing the importance of controlling the vector to prevent episodes of epidemic outbreaks.
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Affiliation(s)
- L. L. Lima
- Programa de Pos-Graduação em Modelagem Matemática e Computacional, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A. P. F. Atman
- Programa de Pos-Graduação em Modelagem Matemática e Computacional, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Departamento de Física, Centro Federal de Educação Tecnológica de Minas Gerais- CEFET-MG, Belo Horizonte, Minas Gerais, Brazil
- National Institute of Science and Technology for Complex Systems-CEFET-MG, Belo Horizonte, Minas Gerais, Brazil
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27
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Gürtler RE, Enriquez GF, Gaspe MS, Macchiaverna NP, Del Pilar Fernández M, Rodríguez-Planes LI, Provecho YM, Cardinal MV. The Pampa del Indio project: sustainable vector control and long-term declines in the prevalence and abundance of Triatoma infestans infected with Trypanosoma cruzi in the Argentine Chaco. Parasit Vectors 2023; 16:258. [PMID: 37528423 PMCID: PMC10394798 DOI: 10.1186/s13071-023-05861-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND The Gran Chaco region is a major hotspot of Chagas disease. We implemented a 9-year program aimed at suppressing house infestation with Triatoma infestans and stopping vector-borne transmission to creole and indigenous (Qom) residents across Pampa del Indio municipality (Argentine Chaco). The aim of the present study was to assess the intervention effects on parasite-based transmission indices and the spatial distribution of the parasite, and test whether house-level variations in triatomine infection with Trypanosoma cruzi declined postintervention and were influenced by household ethnicity, persistent infestation linked to pyrethroid resistance and other determinants of bug infection. METHODS This longitudinal study assessed house infestation and bug infection with T. cruzi before and after spraying houses with pyrethroids and implemented systematic surveillance-and-response measures across four operational areas over the period 2007-2016. Live triatomines were individually examined for infection by optical microscopy or kinetoplast DNA (kDNA)-PCR and declared to be infected with T. cruzi when assessed positive by either method. RESULTS The prevalence of infection with T. cruzi was 19.4% among 6397 T. infestans examined. Infection ranged widely among the study areas (12.5-26.0%), household ethnicity (15.3-26.9%), bug ecotopes (1.8-27.2%) and developmental stages (5.9-27.6%), and decreased from 24.1% (baseline) to 0.9% (endpoint). Using random-intercept multiple logistic regression, the relative odds of bug infection strongly decreased as the intervention period progressed, and increased with baseline domestic infestation and bug stage and in Qom households. The abundance of infected bugs and the proportion of houses with ≥ 1 infected bug remained depressed postintervention and were more informative of area-wide risk status than the prevalence of bug infection. Global spatial analysis revealed sharp changes in the aggregation of bug infection after the attack phase. Baseline domestic infestation and baseline bug infection strongly predicted the future occurrence of bug infection, as did persistent domestic infestation in the area with multiple pyrethroid-resistant foci. Only 19% of houses had a baseline domestic infestation and 56% had ever had ≥ 1 infected bug. CONCLUSIONS Persistent bug infection postintervention was closely associated with persistent foci generated by pyrethroid resistance. Postintervention parasite-based indices closely agreed with human serosurveys at the study endpoint, suggesting transmission blockage. The program identified households and population subgroups for targeted interventions and opened new opportunities for risk prioritization and sustainable vector control and disease prevention.
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Affiliation(s)
- Ricardo Esteban Gürtler
- Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Gustavo Fabián Enriquez
- Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Sol Gaspe
- Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Natalia Paula Macchiaverna
- Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Lucía Inés Rodríguez-Planes
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina
| | - Yael Mariana Provecho
- Ministerio de Salud de la Nación, Dirección de Control de Enfermedades Transmitidas por Vectores, Buenos Aires, Argentina
| | - Marta Victoria Cardinal
- Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Buenos Aires, Argentina.
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Hassell JM, Muloi DM, VanderWaal KL, Ward MJ, Bettridge J, Gitahi N, Ouko T, Imboma T, Akoko J, Karani M, Muinde P, Nakamura Y, Alumasa L, Furmaga E, Kaitho T, Amanya F, Ogendo A, Fava F, Wee BA, Phan H, Kiiru J, Kang’ethe E, Kariuki S, Robinson T, Begon M, Woolhouse MEJ, Fèvre EM. Epidemiological connectivity between humans and animals across an urban landscape. Proc Natl Acad Sci U S A 2023; 120:e2218860120. [PMID: 37450494 PMCID: PMC10629570 DOI: 10.1073/pnas.2218860120] [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: 11/04/2022] [Accepted: 05/19/2023] [Indexed: 07/18/2023] Open
Abstract
Urbanization is predicted to be a key driver of disease emergence through human exposure to novel, animal-borne pathogens. However, while we suspect that urban landscapes are primed to expose people to novel animal-borne diseases, evidence for the mechanisms by which this occurs is lacking. To address this, we studied how bacterial genes are shared between wild animals, livestock, and humans (n = 1,428) across Nairobi, Kenya-one of the world's most rapidly developing cities. Applying a multilayer network framework, we show that low biodiversity (of both natural habitat and vertebrate wildlife communities), coupled with livestock management practices and more densely populated urban environments, promotes sharing of Escherichia coli-borne bacterial mobile genetic elements between animals and humans. These results provide empirical support for hypotheses linking resource provision, the biological simplification of urban landscapes, and human and livestock demography to urban dynamics of cross-species pathogen transmission at a landscape scale. Urban areas where high densities of people and livestock live in close association with synanthropes (species such as rodents that are more competent reservoirs for zoonotic pathogens) should be prioritized for disease surveillance and control.
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Affiliation(s)
- James M. Hassell
- Global Health Program, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC20008
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, CT06510
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
| | - Dishon M. Muloi
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
- International Livestock Research Institute, 00100Nairobi, Kenya
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Kimberly L. VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN55108
| | - Melissa J. Ward
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
- Nuffield Department of Clinical Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Faculty of Medicine, University of Southampton, SouthamtonSO17 1BJ, United Kingdom
| | - Judy Bettridge
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
- International Livestock Research Institute, 00100Nairobi, Kenya
| | | | - Tom Ouko
- Kenya Medical Research Institute, 00200Nairobi, Kenya
| | | | - James Akoko
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Maurice Karani
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Patrick Muinde
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Yukiko Nakamura
- Faculty of Veterinary Medicine, Hokkaido University, Sapporo060-0818, Japan
| | - Lorren Alumasa
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Erin Furmaga
- Department of Epidemiology, Columbia University, New York, NY10032
| | - Titus Kaitho
- Veterinary Services Department, Kenya Wildlife Service, 00100Nairobi, Kenya
| | - Fredrick Amanya
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Allan Ogendo
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Francesco Fava
- International Livestock Research Institute, 00100Nairobi, Kenya
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133Milan, Italy
| | - Bryan A. Wee
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
| | - Hang Phan
- Nuffield Department of Clinical Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - John Kiiru
- Kenya Medical Research Institute, 00200Nairobi, Kenya
| | | | - Sam Kariuki
- Kenya Medical Research Institute, 00200Nairobi, Kenya
| | - Timothy Robinson
- Food and Agriculture Organization of the United Nations, 00153Rome, Italy
| | - Michael Begon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
| | - Mark E. J. Woolhouse
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Eric M. Fèvre
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
- International Livestock Research Institute, 00100Nairobi, Kenya
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Penn MJ, Laydon DJ, Penn J, Whittaker C, Morgenstern C, Ratmann O, Mishra S, Pakkanen MS, Donnelly CA, Bhatt S. Intrinsic randomness in epidemic modelling beyond statistical uncertainty. COMMUNICATIONS PHYSICS 2023; 6:146. [PMID: 38665405 PMCID: PMC11041706 DOI: 10.1038/s42005-023-01265-2] [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: 02/20/2023] [Accepted: 06/07/2023] [Indexed: 04/28/2024]
Abstract
Uncertainty can be classified as either aleatoric (intrinsic randomness) or epistemic (imperfect knowledge of parameters). The majority of frameworks assessing infectious disease risk consider only epistemic uncertainty. We only ever observe a single epidemic, and therefore cannot empirically determine aleatoric uncertainty. Here, we characterise both epistemic and aleatoric uncertainty using a time-varying general branching process. Our framework explicitly decomposes aleatoric variance into mechanistic components, quantifying the contribution to uncertainty produced by each factor in the epidemic process, and how these contributions vary over time. The aleatoric variance of an outbreak is itself a renewal equation where past variance affects future variance. We find that, superspreading is not necessary for substantial uncertainty, and profound variation in outbreak size can occur even without overdispersion in the offspring distribution (i.e. the distribution of the number of secondary infections an infected person produces). Aleatoric forecasting uncertainty grows dynamically and rapidly, and so forecasting using only epistemic uncertainty is a significant underestimate. Therefore, failure to account for aleatoric uncertainty will ensure that policymakers are misled about the substantially higher true extent of potential risk. We demonstrate our method, and the extent to which potential risk is underestimated, using two historical examples.
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Affiliation(s)
| | | | | | | | | | | | | | - Mikko S. Pakkanen
- Imperial College London, London, UK
- University of Waterloo, Ontario, Canada
| | | | - Samir Bhatt
- Imperial College London, London, UK
- University of Copenhagen, Copenhagen, Denmark
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Blanco-Penedo MJ, Brindle H, Schmidt-Sane M, Bowmer A, Iradukunda C, Mfitundinda H, Rwemisisi J, Mukiibi GN, Fricke C, Carter S, Kaawa-Mafigiri D, Lees S. Risk perception of Ebola virus disease and COVID-19 among transport drivers living in Ugandan border districts. Front Public Health 2023; 11:1123330. [PMID: 37397743 PMCID: PMC10308013 DOI: 10.3389/fpubh.2023.1123330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
Background Cross-border movements between districts bordering Uganda and the Democratic Republic of Congo (DRC) are common due to the interdependence between populations on either side, though this increases the risk of the international spread of infectious diseases. Due to the nature of their work, boda boda drivers (motorcycle taxis), taxis and truck drivers continue to cross the border during epidemics. However, perceived risk of contracting and spreading communicable diseases may be influenced by several factors such as the level of education, packaging and perception of health care messages, limited interaction with local socio-cultural dynamics or personal experiences. This study aims to explore differences in movement patterns and risk perceptions as factors for transmission among transport drivers in Ugandan border districts during the 2018-2020 Ebola Virus Disease (EVD) epidemic and the current COVID-19 pandemic. Methods Between May and June 2021, in-depth interviews and focus group discussions were conducted with transport drivers in three Ugandan districts bordering DRC (Kasese, Kisoro and Hoima). Participants were asked about their knowledge and beliefs about EVD and COVID-19, perceived risk during epidemics, reasons for, and travel patterns during the EVD epidemic and COVID- 19 pandemic. A thematic content analysis was applied. Results Participants' awareness of EVD was higher than that of COVID-19 however, the risk of transmission of Ebola virus was perceived as a remote threat. Measures restricting mobility during the COVID-19 pandemic had a greater impact on transport drivers compared to those implemented during the EVD epidemic, and were perceived as prohibitive rather than protective, largely due to fear of reprisals by security officers. Despite this, drivers were unlikely to be able to comply with the restrictions as they relied on their work as a source of income. Conclusion The vulnerabilities of transport drivers should be considered in the context of epidemics such EVD and COVID-19 in Uganda. Policy makers should address these particularities and assess the impact of public health measures on transport drivers' mobility and involve them in designing of mobility-relatedpolicies.
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Affiliation(s)
- María José Blanco-Penedo
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Hannah Brindle
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Megan Schmidt-Sane
- Institute of Development Studies, University of Sussex, Brighton, United Kingdom
| | - Alex Bowmer
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom
| | - Constance Iradukunda
- Department of Social Work and Social Administration, School of Social Sciences, College of Humanities and Social Sciences, Makerere University, Kampala, Uganda
| | - Herbert Mfitundinda
- Department of Social Work and Social Administration, School of Social Sciences, College of Humanities and Social Sciences, Makerere University, Kampala, Uganda
| | - Jude Rwemisisi
- Department of Social Work and Social Administration, School of Social Sciences, College of Humanities and Social Sciences, Makerere University, Kampala, Uganda
| | | | - Christine Fricke
- Department of Anthropology and African Studies, Johannes Gutenberg University, Mainz, Germany
| | - Simone Carter
- Public Health Emergencies, UNICEF, Kinshasa, Democratic Republic of Congo
| | - David Kaawa-Mafigiri
- Department of Social Work and Social Administration, School of Social Sciences, College of Humanities and Social Sciences, Makerere University, Kampala, Uganda
| | - Shelley Lees
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom
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Puspitarani GA, Fuchs R, Fuchs K, Ladinig A, Desvars-Larrive A. Network analysis of pig movement data as an epidemiological tool: an Austrian case study. Sci Rep 2023; 13:9623. [PMID: 37316653 PMCID: PMC10267221 DOI: 10.1038/s41598-023-36596-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Abstract
Animal movements represent a major risk for the spread of infectious diseases in the domestic swine population. In this study, we adopted methods from social network analysis to explore pig trades in Austria. We used a dataset of daily records of swine movements covering the period 2015-2021. We analyzed the topology of the network and its structural changes over time, including seasonal and long-term variations in the pig production activities. Finally, we studied the temporal dynamics of the network community structure. Our findings show that the Austrian pig production was dominated by small-sized farms while spatial farm density was heterogeneous. The network exhibited a scale-free topology but was very sparse, suggesting a moderate impact of infectious disease outbreaks. However, two regions (Upper Austria and Styria) may present a higher structural vulnerability. The network also showed very high assortativity between holdings from the same federal state. Dynamic community detection revealed a stable behavior of the clusters. Yet trade communities did not correspond to sub-national administrative divisions and may be an alternative zoning approach to managing infectious diseases. Knowledge about the topology, contact patterns, and temporal dynamics of the pig trade network can support optimized risk-based disease control and surveillance strategies.
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Affiliation(s)
- Gavrila A Puspitarani
- Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria.
- Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080, Vienna, Austria.
| | - Reinhard Fuchs
- Department for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES), Zinzendorfgasse 27/1, 8010, Graz, Austria
- Institute of Systems Sciences, Innovation and Sustainability Research, University of Graz, Merangasse 18/1, 8010, Graz, Austria
| | - Klemens Fuchs
- Department for Data, Statistics and Risk Assessment, Austrian Agency for Health and Food Safety (AGES), Zinzendorfgasse 27/1, 8010, Graz, Austria
| | - Andrea Ladinig
- University Clinic for Swine, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Amélie Desvars-Larrive
- Unit of Veterinary Public Health and Epidemiology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
- Complexity Science Hub Vienna, Josefstaedter Strasse 39, 1080, Vienna, Austria
- VetFarm, University of Veterinary Medicine Vienna, Kremesberg 13, 2563, Pottenstein, Austria
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32
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Reitzug F, Ledien J, Chami GF. Associations of water contact frequency, duration, and activities with schistosome infection risk: A systematic review and meta-analysis. PLoS Negl Trop Dis 2023; 17:e0011377. [PMID: 37315020 DOI: 10.1371/journal.pntd.0011377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Schistosomiasis is a water-borne parasitic disease which affects over 230 million people globally. The relationship between contact with open freshwater bodies and the likelihood of schistosome infection remains poorly quantified despite its importance for understanding transmission and parametrising transmission models. METHODS We conducted a systematic review to estimate the average effect of water contact duration, frequency, and activities on schistosome infection likelihood. We searched Embase, MEDLINE (including PubMed), Global Health, Global Index Medicus, Web of Science, and the Cochrane Central Register of Controlled Trials from inception until May 13, 2022. Observational and interventional studies reporting odds ratios (OR), hazard ratios (HR), or sufficient information to reconstruct effect sizes on individual-level associations between water contact and infection with any Schistosoma species were eligible for inclusion. Random-effects meta-analysis with inverse variance weighting was used to calculate pooled ORs and 95% confidence intervals (CIs). RESULTS We screened 1,411 studies and included 101 studies which represented 192,691 participants across Africa, Asia, and South America. Included studies mostly reported on water contact activities (69%; 70/101) and having any water contact (33%; 33/101). Ninety-six percent of studies (97/101) used surveys to measure exposure. A meta-analysis of 33 studies showed that individuals with water contact were 3.14 times more likely to be infected (OR 3.14; 95% CI: 2.08-4.75) when compared to individuals with no water contact. Subgroup analyses showed that the positive association of water contact with infection was significantly weaker in children compared to studies which included adults and children (OR 1.67; 95% CI: 1.04-2.69 vs. OR 4.24; 95% CI: 2.59-6.97). An association of water contact with infection was only found in communities with ≥10% schistosome prevalence. Overall heterogeneity was substantial (I2 = 93%) and remained high across all subgroups, except in direct observation studies (I2 range = 44%-98%). We did not find that occupational water contact such as fishing and agriculture (OR 2.57; 95% CI: 1.89-3.51) conferred a significantly higher risk of schistosome infection compared to recreational water contact (OR 2.13; 95% CI: 1.75-2.60) or domestic water contact (OR 1.91; 95% CI: 1.47-2.48). Higher duration or frequency of water contact did not significantly modify infection likelihood. Study quality across analyses was largely moderate or poor. CONCLUSIONS Any current water contact was robustly associated with schistosome infection status, and this relationship held across adults and children, and schistosomiasis-endemic areas with prevalence greater than 10%. Substantial gaps remain in published studies for understanding interactions of water contact with age and gender, and the influence of these interactions for infection likelihood. As such, more empirical studies are needed to accurately parametrise exposure in transmission models. Our results imply the need for population-wide treatment and prevention strategies in endemic settings as exposure within these communities was not confined to currently prioritised high-risk groups such as fishing populations.
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Affiliation(s)
- Fabian Reitzug
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Julia Ledien
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Goylette F Chami
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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Wegehaupt O, Endo A, Vassall A. Superspreading, overdispersion and their implications in the SARS-CoV-2 (COVID-19) pandemic: a systematic review and meta-analysis of the literature. BMC Public Health 2023; 23:1003. [PMID: 37254143 DOI: 10.1186/s12889-023-15915-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND A recurrent feature of infectious diseases is the observation that different individuals show different levels of secondary transmission. This inter-individual variation in transmission potential is often quantified by the dispersion parameter k. Low values of k indicate a high degree of variability and a greater probability of superspreading events. Understanding k for COVID-19 across contexts can assist policy makers prepare for future pandemics. METHODS A literature search following a systematic approach was carried out in PubMed, Embase, Web of Science, Cochrane Library, medRxiv, bioRxiv and arXiv to identify publications containing epidemiological findings on superspreading in COVID-19. Study characteristics, epidemiological data, including estimates for k and R0, and public health recommendations were extracted from relevant records. RESULTS The literature search yielded 28 peer-reviewed studies. The mean k estimates ranged from 0.04 to 2.97. Among the 28 studies, 93% reported mean k estimates lower than one, which is considered as marked heterogeneity in inter-individual transmission potential. Recommended control measures were specifically aimed at preventing superspreading events. The combination of forward and backward contact tracing, timely confirmation of cases, rapid case isolation, vaccination and preventive measures were suggested as important components to suppress superspreading. CONCLUSIONS Superspreading events were a major feature in the pandemic of SARS-CoV-2. On the one hand, this made outbreaks potentially more explosive but on the other hand also more responsive to public health interventions. Going forward, understanding k is critical for tailoring public health measures to high-risk groups and settings where superspreading events occur.
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Affiliation(s)
- Oliver Wegehaupt
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstr. 115, Freiburg, 79106, Germany.
- Clinic of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Akira Endo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- The Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Anna Vassall
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Global Health, The Academic Medical Center (AMC), The University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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Park Y, Martin MA, Koelle K. Epidemiological inference for emerging viruses using segregating sites. Nat Commun 2023; 14:3105. [PMID: 37248255 DOI: 10.1038/s41467-023-38809-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
Epidemiological models are commonly fit to case and pathogen sequence data to estimate parameters and to infer unobserved disease dynamics. Here, we present an inference approach based on sequence data that is well suited for model fitting early on during the expansion of a viral lineage. Our approach relies on a trajectory of segregating sites to infer epidemiological parameters within a Sequential Monte Carlo framework. Using simulated data, we first show that our approach accurately recovers key epidemiological quantities under a single-introduction scenario. We then apply our approach to SARS-CoV-2 sequence data from France, estimating a basic reproduction number of approximately 2.3-2.7 under an epidemiological model that allows for multiple introductions. Our approach presented here indicates that inference approaches that rely on simple population genetic summary statistics can be informative of epidemiological parameters and can be used for reconstructing infectious disease dynamics during the early expansion of a viral lineage.
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Affiliation(s)
- Yeongseon Park
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, 30322, USA
| | - Michael A Martin
- Graduate Program in Population Biology, Ecology, and Evolution, Emory University, Atlanta, GA, 30322, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
- Emory Center of Excellence for Influenza Research and Response (CEIRR), Atlanta, GA, USA.
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35
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Newbold SC, Ashworth M, Finnoff D, Shogren JF, Thunström L. Physical distancing versus testing with self-isolation for controlling an emerging epidemic. Sci Rep 2023; 13:8185. [PMID: 37210388 DOI: 10.1038/s41598-023-35083-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Two distinct strategies for controlling an emerging epidemic are physical distancing and regular testing with self-isolation. These strategies are especially important before effective vaccines or treatments become widely available. The testing strategy has been promoted frequently but used less often than physical distancing to mitigate COVID-19. We compared the performance of these strategies in an integrated epidemiological and economic model that includes a simple representation of transmission by "superspreading," wherein a relatively small fraction of infected individuals cause a large share of infections. We examined the economic benefits of distancing and testing over a wide range of conditions, including variations in the transmissibility and lethality of the disease meant to encompass the most prominent variants of COVID-19 encountered so far. In a head-to-head comparison using our primary parameter values, both with and without superspreading and a declining marginal value of mortality risk reductions, an optimized testing strategy outperformed an optimized distancing strategy. In a Monte Carlo uncertainty analysis, an optimized policy that combined the two strategies performed better than either one alone in more than 25% of random parameter draws. Insofar as diagnostic tests are sensitive to viral loads, and individuals with high viral loads are more likely to contribute to superspreading events, superspreading enhances the relative performance of testing over distancing in our model. Both strategies performed best at moderate levels of transmissibility, somewhat lower than the transmissibility of the ancestral strain of SARS-CoV-2.
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Affiliation(s)
- Stephen C Newbold
- Department of Economics, University of Wyoming, Laramie, WY, 82071, USA.
| | - Madison Ashworth
- Department of Economics, University of Wyoming, Laramie, WY, 82071, USA
- Fletcher Group, Inc., London, KY, 40741, USA
| | - David Finnoff
- Department of Economics, University of Wyoming, Laramie, WY, 82071, USA
| | - Jason F Shogren
- Department of Economics, University of Wyoming, Laramie, WY, 82071, USA
| | - Linda Thunström
- Department of Economics, University of Wyoming, Laramie, WY, 82071, USA
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Wanelik KM, Begon M, Fenton A, Norman RA, Beldomenico PM. Positive feedback loops exacerbate the influence of superspreaders in disease transmission. iScience 2023; 26:106618. [PMID: 37250299 PMCID: PMC10214397 DOI: 10.1016/j.isci.2023.106618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/13/2023] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
Superspreaders are recognized as being important drivers of disease spread. However, models to date have assumed random occurrence of superspreaders, irrespective of whom they were infected by. Evidence suggests though that those individuals infected by superspreaders may be more likely to become superspreaders themselves. Here, we begin to explore, theoretically, the effects of such a positive feedback loop on (1) the final epidemic size, (2) the herd immunity threshold, (3) the basic reproduction number, R0, and (4) the peak prevalence of superspreaders, using a generic model for a hypothetical acute viral infection and illustrative parameter values. We show that positive feedback loops can have a profound effect on our chosen epidemic outcomes, even when the transmission advantage of superspreaders is moderate, and despite peak prevalence of superspreaders remaining low. We argue that positive superspreader feedback loops in different infectious diseases, including SARS-CoV-2, should be investigated further, both theoretically and empirically.
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Affiliation(s)
- Klara M. Wanelik
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Mike Begon
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andy Fenton
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rachel A. Norman
- Department of Computing Science and Mathematics, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - Pablo M. Beldomenico
- Laboratorio de Ecología de Enfermedades, Instituto de Ciencias Veterinarias del Litoral (Consejo de Investigaciones Científicas y Técnicas - Universidad Nacional del Litoral), Esperanza, Argentina
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Kim Y, Leopardi S, Scaravelli D, Zecchin B, Priori P, Festa F, Drzewnioková P, De Benedictis P, Nouvellet P. Transmission dynamics of lyssavirus in Myotis myotis: mechanistic modelling study based on longitudinal seroprevalence data. Proc Biol Sci 2023; 290:20230183. [PMID: 37072038 PMCID: PMC10113028 DOI: 10.1098/rspb.2023.0183] [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: 04/20/2023] Open
Abstract
We investigated the transmission dynamics of lyssavirus in Myotis myotis and Myotis blythii, using serological, virological, demographic and ecological data collected between 2015 and 2022 from two maternity colonies in northern Italian churches. Despite no lyssavirus detection in 556 bats sampled over 11 events by reverse transcription-polymerase chain reaction (RT-PCR), 36.3% of 837 bats sampled over 27 events showed neutralizing antibodies to European bat lyssavirus 1, with a significant increase in summers. By fitting sets of mechanistic models to seroprevalence data, we investigated factors that influenced lyssavirus transmission within and between years. Five models were selected as a group of final models: in one model, a proportion of exposed bats (median model estimate: 5.8%) became infectious and died while the other exposed bats recovered with immunity without becoming infectious; in the other four models, all exposed bats became infectious and recovered with immunity. The final models supported that the two colonies experienced seasonal outbreaks driven by: (i) immunity loss particularly during hibernation, (ii) density-dependent transmission, and (iii) a high transmission rate after synchronous birthing. These findings highlight the importance of understanding ecological factors, including colony size and synchronous birthing timing, and potential infection heterogeneities to enable more robust assessments of lyssavirus spillover risk.
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Affiliation(s)
- Younjung Kim
- Department of Evolution, Behaviour, and Environment, School of Life Sciences, University of Sussex, BN1 9RH Brighton, UK
| | - Stefania Leopardi
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Dino Scaravelli
- S.T.E.R.N.A. and Museo Ornitologico 'F. Foschi', via Pedrali 12, 47121 Forlì, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Barbara Zecchin
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Pamela Priori
- S.T.E.R.N.A. and Museo Ornitologico 'F. Foschi', via Pedrali 12, 47121 Forlì, Italy
| | - Francesca Festa
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Petra Drzewnioková
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Paola De Benedictis
- FAO and National Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, Legnaro, 35020 Padua, Italy
| | - Pierre Nouvellet
- Department of Evolution, Behaviour, and Environment, School of Life Sciences, University of Sussex, BN1 9RH Brighton, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, SW7 2AZ London, UK
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Vanalli C, Mari L, Casagrandi R, Boag B, Gatto M, Cattadori IM. Modeling the contribution of antibody attack rates to single and dual helminth infections in a natural system. Math Biosci 2023; 360:109010. [PMID: 37088125 DOI: 10.1016/j.mbs.2023.109010] [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: 11/18/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/25/2023]
Abstract
Within-host models of infection can provide important insights into the processes that affect parasite spread and persistence in host populations. However, modeling can be limited by the availability of empirical data, a problem commonly encountered in natural systems. Here, we used six years of immune-infection observations of two gastrointestinal helminths (Trichostrongylus retortaeformis and Graphidium strigosum) from a population of European rabbits (Oryctolagus cuniculus) to develop an age-dependent, mathematical model that explicitly included species-specific and cross-reacting antibody (IgA and IgG) responses to each helminth in hosts with single or dual infections. Different models of single infection were formally compared to test alternative mechanisms of parasite regulation. The two models that best described single infections of each helminth species were then coupled through antibody cross-immunity to examine how the presence of one species could alter the host immune response to, and the within-host dynamics of, the other species. For both single infections, model selection suggested that either IgA or IgG responses could equally explain the observed parasite intensities by host age. However, the antibody attack rate and affinity level changed between the two helminths, it was stronger against T. retortaeformis than against G. strigosum and caused contrasting age-intensity profiles. When the two helminths coinfect the same host, we found variation of the species-specific antibody response to both species together with an asymmetric cross-immune response driven by IgG. Lower attack rate and affinity of antibodies in dual than single infections contributed to the significant increase of both helminth intensities. By combining mathematical modeling with immuno-infection data, our work provides a tractable model framework for disentangling some of the complexities generated by host-parasite and parasite-parasite interactions in natural systems.
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Affiliation(s)
- Chiara Vanalli
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, 16802 PA, USA.
| | - Lorenzo Mari
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Renato Casagrandi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Brian Boag
- The James Hutton Institute, DD2 5DA Invergowrie, UK
| | - Marino Gatto
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milano, Italy
| | - Isabella M Cattadori
- Center for Infectious Disease Dynamics and Department of Biology, The Pennsylvania State University, University Park, 16802 PA, USA
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Coque TM, Cantón R, Pérez-Cobas AE, Fernández-de-Bobadilla MD, Baquero F. Antimicrobial Resistance in the Global Health Network: Known Unknowns and Challenges for Efficient Responses in the 21st Century. Microorganisms 2023; 11:1050. [PMID: 37110473 PMCID: PMC10144039 DOI: 10.3390/microorganisms11041050] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the Global Health challenges of the 21st century. The inclusion of AMR on the global map parallels the scientific, technological, and organizational progress of the healthcare system and the socioeconomic changes of the last 100 years. Available knowledge about AMR has mostly come from large healthcare institutions in high-income countries and is scattered in studies across various fields, focused on patient safety (infectious diseases), transmission pathways and pathogen reservoirs (molecular epidemiology), the extent of the problem at a population level (public health), their management and cost (health economics), cultural issues (community psychology), and events associated with historical periods (history of science). However, there is little dialogue between the aspects that facilitate the development, spread, and evolution of AMR and various stakeholders (patients, clinicians, public health professionals, scientists, economic sectors, and funding agencies). This study consists of four complementary sections. The first reviews the socioeconomic factors that have contributed to building the current Global Healthcare system, the scientific framework in which AMR has traditionally been approached in such a system, and the novel scientific and organizational challenges of approaching AMR in the fourth globalization scenario. The second discusses the need to reframe AMR in the current public health and global health contexts. Given that the implementation of policies and guidelines are greatly influenced by AMR information from surveillance systems, in the third section, we review the unit of analysis ("the what" and "the who") and the indicators (the "operational units of surveillance") used in AMR and discuss the factors that affect the validity, reliability, and comparability of the information to be applied in various healthcare (primary, secondary, and tertiary), demographic, and economic contexts (local, regional, global, and inter-sectorial levels). Finally, we discuss the disparities and similarities between distinct stakeholders' objectives and the gaps and challenges of combatting AMR at various levels. In summary, this is a comprehensive but not exhaustive revision of the known unknowns about how to analyze the heterogeneities of hosts, microbes, and hospital patches, the role of surrounding ecosystems, and the challenges they represent for surveillance, antimicrobial stewardship, and infection control programs, which are the traditional cornerstones for controlling AMR in human health.
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Affiliation(s)
- Teresa M. Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Elena Pérez-Cobas
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miguel D. Fernández-de-Bobadilla
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Southall E, Ogi-Gittins Z, Kaye AR, Hart WS, Lovell-Read FA, Thompson RN. A practical guide to mathematical methods for estimating infectious disease outbreak risks. J Theor Biol 2023; 562:111417. [PMID: 36682408 DOI: 10.1016/j.jtbi.2023.111417] [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: 06/30/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
Mathematical models are increasingly used throughout infectious disease outbreaks to guide control measures. In this review article, we focus on the initial stages of an outbreak, when a pathogen has just been observed in a new location (e.g., a town, region or country). We provide a beginner's guide to two methods for estimating the risk that introduced cases lead to sustained local transmission (i.e., the probability of a major outbreak), as opposed to the outbreak fading out with only a small number of cases. We discuss how these simple methods can be extended for epidemiological models with any level of complexity, facilitating their wider use, and describe how estimates of the probability of a major outbreak can be used to guide pathogen surveillance and control strategies. We also give an overview of previous applications of these approaches. This guide is intended to help quantitative researchers develop their own epidemiological models and use them to estimate the risks associated with pathogens arriving in new host populations. The development of these models is crucial for future outbreak preparedness. This manuscript was submitted as part of a theme issue on "Modelling COVID-19 and Preparedness for Future Pandemics".
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Affiliation(s)
- E Southall
- Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - Z Ogi-Gittins
- Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - A R Kaye
- Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK
| | - W S Hart
- Mathematical Institute, University of Oxford, Oxford, UK
| | | | - R N Thompson
- Mathematics Institute, University of Warwick, Coventry, UK; Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, UK.
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Mbewe RB, Keven JB, Mangani C, Wilson ML, Mzilahowa T, Mathanga DP, Valim C, Laufer MK, Walker ED, Cohee LM. Genotyping of Anopheles mosquito blood meals reveals nonrandom human host selection: implications for human-to-mosquito Plasmodium falciparum transmission. Malar J 2023; 22:115. [PMID: 37029433 PMCID: PMC10080529 DOI: 10.1186/s12936-023-04541-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND Control of malaria parasite transmission can be enhanced by understanding which human demographic groups serve as the infectious reservoirs. Because vector biting can be heterogeneous, some infected individuals may contribute more to human-to-mosquito transmission than others. Infection prevalence peaks in school-age children, but it is not known how often they are fed upon. Genotypic profiling of human blood permits identification of individual humans who were bitten. The present investigation used this method to estimate which human demographic groups were most responsible for transmitting malaria parasites to Anopheles mosquitoes. It was hypothesized that school-age children contribute more than other demographic groups to human-to-mosquito malaria transmission. METHODS In a region of moderate-to-high malaria incidence in southeastern Malawi, randomly selected households were surveyed to collect human demographic information and blood samples. Blood-fed, female Anopheles mosquitoes were sampled indoors from the same houses. Genomic DNA from human blood samples and mosquito blood meals of human origin was genotyped using 24 microsatellite loci. The resultant genotypes were matched to identify which individual humans were sources of blood meals. In addition, Plasmodium falciparum DNA in mosquito abdomens was detected with polymerase chain reaction. The combined results were used to identify which humans were most frequently bitten, and the P. falciparum infection prevalence in mosquitoes that resulted from these blood meals. RESULTS Anopheles females selected human hosts non-randomly and fed on more than one human in 9% of the blood meals. Few humans contributed most of the blood meals to the Anopheles vector population. Children ≤ 5 years old were under-represented in mosquito blood meals while older males (31-75 years old) were over-represented. However, the largest number of malaria-infected blood meals was from school age children (6-15 years old). CONCLUSIONS The results support the hypothesis that humans aged 6-15 years are the most important demographic group contributing to the transmission of P. falciparum to the Anopheles mosquito vectors. This conclusion suggests that malaria control and prevention programmes should enhance efforts targeting school-age children and males.
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Affiliation(s)
- Rex B Mbewe
- Department of Entomology, Michigan State University, East Lansing, MI, USA.
- Department of Physics and Biochemical Sciences, Malawi University of Business and Applied Sciences, Blantyre, Malawi.
| | - John B Keven
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Public Health, College of Health Sciences, University of California-Irvine, Irvine, CA, USA
| | - Charles Mangani
- Malaria Alert Center, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Mark L Wilson
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Themba Mzilahowa
- Malaria Alert Center, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Don P Mathanga
- Malaria Alert Center, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Clarissa Valim
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Miriam K Laufer
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Edward D Walker
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Lauren M Cohee
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
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Halliday FW, Czyżewski S, Laine AL. Intraspecific trait variation and changing life-history strategies explain host community disease risk along a temperature gradient. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220019. [PMID: 36744568 PMCID: PMC9900715 DOI: 10.1098/rstb.2022.0019] [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: 02/07/2023] Open
Abstract
Predicting how climate change will affect disease risk is complicated by the fact that changing environmental conditions can affect disease through direct and indirect effects. Species with fast-paced life-history strategies often amplify disease, and changing climate can modify life-history composition of communities thereby altering disease risk. However, individuals within a species can also respond to changing conditions with intraspecific trait variation. To test the effect of temperature, as well as inter- and intraspecifc trait variation on community disease risk, we measured foliar disease and specific leaf area (SLA; a proxy for life-history strategy) on more than 2500 host (plant) individuals in 199 communities across a 1101 m elevational gradient in southeastern Switzerland. There was no direct effect of increasing temperature on disease. Instead, increasing temperature favoured species with higher SLA, fast-paced life-history strategies. This effect was balanced by intraspecific variation in SLA: on average, host individuals expressed lower SLA with increasing temperature, and this effect was stronger among species adapted to warmer temperatures and lower latitudes. These results demonstrate how impacts of changing temperature on disease may depend on how temperature combines and interacts with host community structure while indicating that evolutionary constraints can determine how these effects are manifested under global change. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
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Affiliation(s)
- Fletcher W. Halliday
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Szymon Czyżewski
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland,Research Centre for Ecological Change, Organismal & Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65, Helsinki FI-00014, Finland
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Association between polymorphisms of IL4, IL13, IL10, STAT6 and IFNG genes, cytokines and immunoglobulin E levels with high burden of Schistosoma mansoni in children from schistosomiasis endemic areas of Cameroon. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 111:105416. [PMID: 36889485 PMCID: PMC10167540 DOI: 10.1016/j.meegid.2023.105416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 03/08/2023]
Abstract
Eliminating schistosomiasis as a public health problem by 2030 requires a better understanding of the disease transmission, especially the asymmetric distribution of worm burden in individuals living and sharing the same environment. It is in this light that this study was designed to identify human genetic determinants associated with high burden of S. mansoni and also with the plasma concentrations of IgE and four cytokines in children from two schistosomiasis endemic areas of Cameroon. In school-aged children of schistosomiasis endemic areas of Makenene and Nom-Kandi of Cameroon, S. mansoni infections and their infection intensities were evaluated in urine and stool samples using respectively the Point-of-care Circulating Cathodic Antigen test (POC-CCA) and the Kato Katz (KK) test. Thereafter, blood samples were collected in children harbouring high burden of schistosome infections as well as in their parents and siblings. DNA extracts and plasma were obtained from blood. Polymorphisms at 14 loci of five genes were assessed using PCR-restriction fragment length polymorphism and amplification-refractory mutation system. The ELISA test enabled to determine the plasma concentrations of IgE, IL-13, IL-10, IL-4 and IFN-γ. The prevalence of S. mansoni infections was significantly higher (P < 0.0001 for POC-CCA; P = 0.001 for KK) in Makenene (48.6% for POC-CCA and 7.9% for KK) compared to Nom-Kandi (31% for POC-CCA and 4.3% for KK). The infection intensities were also higher (P < 0.0001 for POC-CCA; P = 0.001 for KK) in children from Makenene than those from Nom-Kandi. The allele C of SNP rs3024974 of STAT6 was associated with an increased risk of bearing high burden of S. mansoni both in the additive (p = 0.009) and recessive model (p = 0.01) while the allele C of SNP rs1800871 of IL10 was protective (p = 0.0009) against high burden of S. mansoni. The alleles A of SNP rs2069739 of IL13 and G of SNP rs2243283 of IL4 were associated with an increased risk of having low plasma concentrations of IL-13 (P = 0.04) and IL-10 (P = 0.04), respectively. This study showed that host genetic polymorphisms may influence the outcome (high or low worm burden) of S. mansoni infections and also the plasma concentrations of some cytokines.
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Brainard J, Jones NR, Harrison FC, Hammer CC, Lake IR. Super-spreaders of novel coronaviruses that cause SARS, MERS and COVID-19: A systematic review. Ann Epidemiol 2023:S1047-2797(23)00058-3. [PMID: 37001627 DOI: 10.1016/j.annepidem.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 01/12/2023] [Accepted: 03/26/2023] [Indexed: 03/31/2023]
Abstract
PURPOSE Most index cases with novel coronavirus infections transmit disease to just one or two other individuals, but some individuals "super-spread"-they infect many secondary cases. Understanding common factors that super-spreaders may share could inform outbreak models, and be used to guide contact tracing during outbreaks. METHODS We searched in MEDLINE, Scopus, and preprints to identify studies about people documented as transmitting pathogens that cause SARS, MERS, or COVID-19 to at least nine other people. We extracted data to describe them by age, sex, location, occupation, activities, symptom severity, any underlying conditions, disease outcome and undertook quality assessment for outbreaks published by June 2021. RESULTS The most typical super-spreader was a male age 40+. Most SARS or MERS super-spreaders were very symptomatic, the super-spreading occurred in hospital settings and frequently the individual died. In contrast, COVID-19 super-spreaders often had very mild disease and most COVID-19 super-spreading happened in community settings. CONCLUSIONS SARS and MERS super-spreaders were often symptomatic, middle- or older-age adults who had a high mortality rate. In contrast, COVID-19 super-spreaders tended to have mild disease and were any adult age. More outbreak reports should be published with anonymized but useful demographic information to improve understanding of super-spreading, super-spreaders, and the settings in which super-spreading happens.
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Vazquez-Prokopec GM, Morrison AC, Paz-Soldan V, Stoddard ST, Koval W, Waller LA, Alex Perkins T, Lloyd AL, Astete H, Elder J, Scott TW, Kitron U. Inapparent infections shape the transmission heterogeneity of dengue. PNAS NEXUS 2023; 2:pgad024. [PMID: 36909820 PMCID: PMC10003742 DOI: 10.1093/pnasnexus/pgad024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
Transmission heterogeneity, whereby a disproportionate fraction of pathogen transmission events result from a small number of individuals or geographic locations, is an inherent property of many, if not most, infectious disease systems. For vector-borne diseases, transmission heterogeneity is inferred from the distribution of the number of vectors per host, which could lead to significant bias in situations where vector abundance and transmission risk at the household do not correlate, as is the case with dengue virus (DENV). We used data from a contact tracing study to quantify the distribution of DENV acute infections within human activity spaces (AS), the collection of residential locations an individual routinely visits, and quantified measures of virus transmission heterogeneity from two consecutive dengue outbreaks (DENV-4 and DENV-2) that occurred in the city of Iquitos, Peru. Negative-binomial distributions and Pareto fractions showed evidence of strong overdispersion in the number of DENV infections by AS and identified super-spreading units (SSUs): i.e. AS where most infections occurred. Approximately 8% of AS were identified as SSUs, contributing to more than 50% of DENV infections. SSU occurrence was associated more with DENV-2 infection than with DENV-4, a predominance of inapparent infections (74% of all infections), households with high Aedes aegypti mosquito abundance, and high host susceptibility to the circulating DENV serotype. Marked heterogeneity in dengue case distribution, and the role of inapparent infections in defining it, highlight major challenges faced by reactive interventions if those transmission units contributing the most to transmission are not identified, prioritized, and effectively treated.
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Affiliation(s)
| | - Amy C Morrison
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Valerie Paz-Soldan
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Steven T Stoddard
- Division of Health Promotion & Behavioral Sciences, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - William Koval
- Department of Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lance A Waller
- Department of Biostatistics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - T Alex Perkins
- Department of Biology, University of Notre Dame, South Bend, IN 46556, USA
| | - Alun L Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC 27607, USA
| | - Helvio Astete
- Virology Department, Naval Medical Research Unit-6, Iquitos 16003, Peru
| | - John Elder
- Division of Health Promotion & Behavioral Sciences, School of Public Health, San Diego State University, San Diego, CA 92182, USA
| | - Thomas W Scott
- Department of Entomology and Nematology, University of California, Davis, CA 95616, USA
| | - Uriel Kitron
- Department of Environmental Sciences, Emory University, Atlanta, GA 30322, USA
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Guo Z, Zhao S, Lee SS, Hung CT, Wong NS, Chow TY, Yam CHK, Wang MH, Wang J, Chong KC, Yeoh EK. A statistical framework for tracking the time-varying superspreading potential of COVID-19 epidemic. Epidemics 2023; 42:100670. [PMID: 36709540 PMCID: PMC9872564 DOI: 10.1016/j.epidem.2023.100670] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/29/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Timely detection of an evolving event of an infectious disease with superspreading potential is imperative for territory-wide disease control as well as preventing future outbreaks. While the reproduction number (R) is a commonly-adopted metric for disease transmissibility, the transmission heterogeneity quantified by dispersion parameter k, a metric for superspreading potential is seldom tracked. In this study, we developed an estimation framework to track the time-varying risk of superspreading events (SSEs) and demonstrated the method using the three epidemic waves of COVID-19 in Hong Kong. Epidemiological contact tracing data of the confirmed COVID-19 cases from 23 January 2020 to 30 September 2021 were obtained. By applying branching process models, we jointly estimated the time-varying R and k. Individual-based outbreak simulations were conducted to compare the time-varying assessment of the superspreading potential with the typical non-time-varying estimate of k over a period of time. We found that the COVID-19 transmission in Hong Kong exhibited substantial superspreading during the initial phase of the epidemics, with only 1 % (95 % Credible interval [CrI]: 0.6-2 %), 5 % (95 % CrI: 3-7 %) and 10 % (95 % CrI: 8-14 %) of the most infectious cases generated 80 % of all transmission for the first, second and third epidemic waves, respectively. After implementing local public health interventions, R estimates dropped gradually and k estimates increased thereby reducing the risk of SSEs to approaching zero. Outbreak simulations indicated that the non-time-varying estimate of k may overlook the possibility of large outbreaks. Hence, an estimation of the time-varying k as a compliment of R as a monitoring of both disease transmissibility and superspreading potential, particularly when public health interventions were relaxed is crucial for minimizing the risk of future outbreaks.
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Affiliation(s)
- Zihao Guo
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Shi Zhao
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Centre for Health Systems and Policy Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Shui Shan Lee
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chi Tim Hung
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Centre for Health Systems and Policy Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ngai Sze Wong
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Tsz Yu Chow
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Centre for Health Systems and Policy Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Carrie Ho Kwan Yam
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Centre for Health Systems and Policy Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Maggie Haitian Wang
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jingxuan Wang
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ka Chun Chong
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Centre for Health Systems and Policy Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Eng Kiong Yeoh
- Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China; Centre for Health Systems and Policy Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Application of Eugenol in Poultry to Control Salmonella Colonization and Spread. Vet Sci 2023; 10:vetsci10020151. [PMID: 36851455 PMCID: PMC9962070 DOI: 10.3390/vetsci10020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
The poultry sector is an essential component of agriculture that has experienced unprecedented growth during the last few decades. It is especially true for the United States, where the average intake of chicken meat increased from 10 pounds (4.5 kg) per person in 1940 to 65.2 pounds (29.6 kg) per person in 2018, while the country produced 113 billion eggs in 2019 alone. Besides providing nutrition and contributing significantly to the economy, chicken is also a natural reservoir of Salmonella, which is responsible for salmonellosis in humans, one of the significant foodborne illnesses around the globe. The increasing use of chicken manure and antibiotics increases the spread of Salmonella and selects for multi-drug resistant strains. Various plant extracts, primarily essential oils, have been investigated for their antimicrobial activities. The multiple ways through which these plant-derived compounds exert their antimicrobial effects make the development of resistance against them unlikely. Eugenol, an aromatic oil primarily found in clove and cinnamon, has shown antimicrobial activities against various pathogenic bacteria. A few reports have also highlighted the anti-Salmonella effects of eugenol in chicken, especially in reducing the colonization by Salmonella Enteritidis and Salmonella Typhimurium, the primary Salmonella species responsible for human salmonellosis. Besides limiting Salmonella infection in chicken, the supplementation of eugenol also significantly improves intestinal health, improving overall well-being. In this review, we highlight the rising incidences of salmonellosis worldwide and the factors increasing its prevalence. We then propose the usage of eugenol as a natural feed supplement for containing Salmonella in chicken.
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Rabies transmission in the Arctic: An agent-based model reveals the effects of broad-scale movement strategies on contact risk between Arctic foxes. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2022.110207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Corder RM, Arez AP, Ferreira MU. Individual variation in Plasmodium vivax malaria risk: Are repeatedly infected people just unlucky? PLoS Negl Trop Dis 2023; 17:e0011020. [PMID: 36634044 PMCID: PMC9836309 DOI: 10.1371/journal.pntd.0011020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Extensive research has examined why some people have frequent Plasmodium falciparum malaria episodes in sub-Saharan Africa while others remain free of disease most of the time. In contrast, malaria risk heterogeneity remains little studied in regions where P. vivax is the dominant species. Are repeatedly infected people in vivax malaria settings such as the Amazon just unlucky? Here, we briefly review evidence that human genetic polymorphism and acquired immunity after repeated exposure to parasites can modulate the risk of P. vivax infection and disease in predictable ways. One-fifth of the hosts account for 80% or more of the community-wide vivax malaria burden and contribute disproportionally to onward transmission, representing a priority target of more intensive interventions to achieve malaria elimination. Importantly, high-risk individuals eventually develop clinical immunity, even in areas with very low or residual malaria transmission, and may constitute a large but silent parasite reservoir.
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Affiliation(s)
- Rodrigo M. Corder
- Department of Epidemiology and Biostatistics, University of California, Berkeley School of Public Health, Berkeley, California, United States of America
| | - Ana Paula Arez
- Global Health and Tropical Medicine (GHTM), institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal
| | - Marcelo U. Ferreira
- Global Health and Tropical Medicine (GHTM), institute of Hygiene and Tropical Medicine, NOVA University of Lisbon, Lisbon, Portugal
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail: ,
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50
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Wolff GH, Lahondère C, Vinauger C, Rylance E, Riffell JA. Neuromodulation and differential learning across mosquito species. Proc Biol Sci 2023; 290:20222118. [PMID: 36629098 PMCID: PMC9832544 DOI: 10.1098/rspb.2022.2118] [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: 10/27/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Mosquitoes can change their feeding behaviours based on past experiences, such as shifting from biting animals to biting humans or avoiding defensive hosts (Wolff & Riffell 2018 J. Exp. Biol. 221, jeb157131. (doi:10.1242/jeb.157131)). Dopamine is a critical neuromodulator for insects, allowing flexibility in their feeding preferences, but its role in the primary olfactory centre, the antennal lobe (AL), remains unclear (Vinauger et al. 2018 Curr. Biol. 28, 333-344.e8. (doi:10.1016/j.cub.2017.12.015)). It is also unknown whether mosquitoes can learn some odours and not others, or whether different species learn the same odour cues. We assayed aversive olfactory learning in four mosquito species with different host preferences, and found that they differentially learn odours salient to their preferred host. Mosquitoes that prefer humans learned odours found in mammalian skin, but not a flower odour, and a nectar-feeding species only learned a floral odour. Comparing the brains of these four species revealed significantly different innervation patterns in the AL by dopaminergic neurons. Calcium imaging in the Aedes aegypti AL and three-dimensional image analyses of dopaminergic innervation show that glomeruli tuned to learnable odours have significantly higher dopaminergic innervation. Changes in dopamine expression in the insect AL may be an evolutionary mechanism to adapt olfactory learning circuitry without changing brain structure and confer to mosquitoes an ability to adapt to new hosts.
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Affiliation(s)
- Gabriella H. Wolff
- Department of Biology, University of Washington, Seattle, WA 98195-7270, USA
| | - Chloé Lahondère
- Department of Biology, University of Washington, Seattle, WA 98195-7270, USA
| | - Clément Vinauger
- Department of Biology, University of Washington, Seattle, WA 98195-7270, USA
| | - Elizabeth Rylance
- Department of Biology, University of Washington, Seattle, WA 98195-7270, USA
| | - Jeffrey A. Riffell
- Department of Biology, University of Washington, Seattle, WA 98195-7270, USA
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