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Thinking clearly about social aspects of infectious disease transmission. Nature 2021; 595:205-213. [PMID: 34194045 DOI: 10.1038/s41586-021-03694-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Social and cultural forces shape almost every aspect of infectious disease transmission in human populations, as well as our ability to measure, understand, and respond to epidemics. For directly transmitted infections, pathogen transmission relies on human-to-human contact, with kinship, household, and societal structures shaping contact patterns that in turn determine epidemic dynamics. Social, economic, and cultural forces also shape patterns of exposure, health-seeking behaviour, infection outcomes, the likelihood of diagnosis and reporting of cases, and the uptake of interventions. Although these social aspects of epidemiology are hard to quantify and have limited the generalizability of modelling frameworks in a policy context, new sources of data on relevant aspects of human behaviour are increasingly available. Researchers have begun to embrace data from mobile devices and other technologies as useful proxies for behavioural drivers of disease transmission, but there is much work to be done to measure and validate these approaches, particularly for policy-making. Here we discuss how integrating local knowledge in the design of model frameworks and the interpretation of new data streams offers the possibility of policy-relevant models for public health decision-making as well as the development of robust, generalizable theories about human behaviour in relation to infectious diseases.
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Omulo S, Lofgren ET, Lockwood S, Thumbi SM, Bigogo G, Ouma A, Verani JR, Juma B, Njenga MK, Kariuki S, McElwain TF, Palmer GH, Call DR. Carriage of antimicrobial-resistant bacteria in a high-density informal settlement in Kenya is associated with environmental risk-factors. Antimicrob Resist Infect Control 2021; 10:18. [PMID: 33482919 PMCID: PMC7821723 DOI: 10.1186/s13756-021-00886-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The relationship between antibiotic use and antimicrobial resistance varies with cultural, socio-economic, and environmental factors. We examined these relationships in Kibera, an informal settlement in Nairobi-Kenya, characterized by high population density, high burden of respiratory disease and diarrhea. METHODS Two-hundred households were enrolled in a 5-month longitudinal study. One adult (≥ 18 years) and one child (≤ 5 years) participated per household. Biweekly interviews (n = 1516) that included questions on water, sanitation, hygiene, and antibiotic use in the previous two weeks were conducted, and 2341 stool, 2843 hand swabs and 1490 drinking water samples collected. Presumptive E. coli (n = 34,042) were isolated and tested for susceptibility to nine antibiotics. RESULTS Eighty percent of presumptive E. coli were resistant to ≥ 3 antibiotic classes. Stool isolates were resistant to trimethoprim (mean: 81%), sulfamethoxazole (80%), ampicillin (68%), streptomycin (60%) and tetracycline (55%). Ninety-seven households reported using an antibiotic in at least one visit over the study period for a total of 144 episodes and 190 antibiotic doses. Enrolled children had five times the number of episodes reported by enrolled adults (96 vs. 19). Multivariable linear mixed-effects models indicated that children eating soil from the household yard and the presence of informal hand-washing stations were associated with increased numbers of antimicrobial-resistant bacteria (counts increasing by 0·27-0·80 log10 and 0·22-0·51 log10 respectively, depending on the antibiotic tested). Rainy conditions were associated with reduced carriage of antimicrobial-resistant bacteria (1·19 to 3·26 log10 depending on the antibiotic tested). CONCLUSIONS Antibiotic use provided little explanatory power for the prevalence of antimicrobial resistance. Transmission of resistant bacteria in this setting through unsanitary living conditions likely overwhelms incremental changes in antibiotic use. Under such circumstances, sanitation, hygiene, and disease transmission are the limiting factors for reducing the prevalence of resistant bacteria.
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Affiliation(s)
- Sylvia Omulo
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA. .,Washington State University Global Health-Kenya, Nairobi, Kenya. .,Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
| | - Eric T Lofgren
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Svetlana Lockwood
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Samuel M Thumbi
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya.,Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Godfrey Bigogo
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Alice Ouma
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | | | - M Kariuki Njenga
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Samuel Kariuki
- Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Terry F McElwain
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Guy H Palmer
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya.,Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya.,Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
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Macharia PM, Giorgi E, Noor AM, Waqo E, Kiptui R, Okiro EA, Snow RW. Spatio-temporal analysis of Plasmodium falciparum prevalence to understand the past and chart the future of malaria control in Kenya. Malar J 2018; 17:340. [PMID: 30257697 PMCID: PMC6158896 DOI: 10.1186/s12936-018-2489-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 09/21/2018] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Spatial and temporal malaria risk maps are essential tools to monitor the impact of control, evaluate priority areas to reorient intervention approaches and investments in malaria endemic countries. Here, the analysis of 36 years data on Plasmodium falciparum prevalence is used to understand the past and chart a future for malaria control in Kenya by confidently highlighting areas within important policy relevant thresholds to allow either the revision of malaria strategies to those that support pre-elimination or those that require additional control efforts. METHODS Plasmodium falciparum parasite prevalence (PfPR) surveys undertaken in Kenya between 1980 and 2015 were assembled. A spatio-temporal geostatistical model was fitted to predict annual malaria risk for children aged 2-10 years (PfPR2-10) at 1 × 1 km spatial resolution from 1990 to 2015. Changing PfPR2-10 was compared against plausible explanatory variables. The fitted model was used to categorize areas with varying degrees of prediction probability for two important policy thresholds PfPR2-10 < 1% (non-exceedance probability) or ≥ 30% (exceedance probability). RESULTS 5020 surveys at 3701 communities were assembled. Nationally, there was an 88% reduction in the mean modelled PfPR2-10 from 21.2% (ICR: 13.8-32.1%) in 1990 to 2.6% (ICR: 1.8-3.9%) in 2015. The most significant decline began in 2003. Declining prevalence was not equal across the country and did not directly coincide with scaled vector control coverage or changing therapeutics. Over the period 2013-2015, of Kenya's 47 counties, 23 had an average PfPR2-10 of < 1%; four counties remained ≥ 30%. Using a metric of 80% probability, 8.5% of Kenya's 2015 population live in areas with PfPR2-10 ≥ 30%; while 61% live in areas where PfPR2-10 is < 1%. CONCLUSIONS Kenya has made substantial progress in reducing the prevalence of malaria over the last 26 years. Areas today confidently and consistently with < 1% prevalence require a revised approach to control and a possible consideration of strategies that support pre-elimination. Conversely, there remains several intractable areas where current levels and approaches to control might be inadequate. The modelling approaches presented here allow the Ministry of Health opportunities to consider data-driven model certainty in defining their future spatial targeting of resources.
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Affiliation(s)
- Peter M Macharia
- Population Health Unit, Kenya Medical Research Institute-Wellcome Trust Research Programme, Nairobi, Kenya.
| | - Emanuele Giorgi
- Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Abdisalan M Noor
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Ejersa Waqo
- National Malaria Control Programme, Ministry of Health, Nairobi, Kenya
| | - Rebecca Kiptui
- National Malaria Control Programme, Ministry of Health, Nairobi, Kenya
| | - Emelda A Okiro
- Population Health Unit, Kenya Medical Research Institute-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Robert W Snow
- Population Health Unit, Kenya Medical Research Institute-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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Abstract
Infection of the upper airways is very common and is the most common acute illness evaluated in the outpatient setting. The infection is usually caused by viruses including rhinoviruses, influenza viruses, parainfluenza and respiratory syncytial viruses. Influenza is the only viral infection preventable by vaccination and occurs predominately during annual winter epidemics. Bacterial infection such as acute rhinopharyngitis is uncommon and usually presents with either persistent symptoms of an URTI lasting over a week or worsening course after initial improvement or acute onset with high fever and inflammatory changes confined to the pharynx. Fever is common in both bacterial and viral gastroenteritis. High fever is commonly present in many bacterial causes (e.g. Shigella, Salmonella, Shiga toxin-producing E. coli). Fever is often absent or low-grade in other diseases (e.g. enteropathogenic E. coli, cholera). Other febrile conditions cause diarrhoea and need to be differentiated. Fever in CNS infection is the most common presenting symptom in children beyond the neonatal age owing to the presence of inflammatory mediators, particularly IL-1 and TNF in the blood or within the CNS. In MCD, fever was the first symptom in children younger than 5 years and 94% developed fever at some point. Viral exanthems are common causes of febrile illness in children. More than 50 viral agents are known to cause a rash. Historically, exanthems were numbered in the order in which they were differentiated from other exanthems. Thus the first was measles; second, scarlet fever; third, rubella; forth, so-called Filatov-Dukes disease (no longer recognized as an entity); fifth, erythema infectiosum; and sixth, exanthema subitum. As more exanthems were described, numerical assignment became impractical.
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Park SE, Pak GD, Aaby P, Adu-Sarkodie Y, Ali M, Aseffa A, Biggs HM, Bjerregaard-Andersen M, Breiman RF, Crump JA, Cruz Espinoza LM, Eltayeb MA, Gasmelseed N, Hertz JT, Im J, Jaeger A, Parfait Kabore L, von Kalckreuth V, Keddy KH, Konings F, Krumkamp R, MacLennan CA, Meyer CG, Montgomery JM, Ahmet Niang A, Nichols C, Olack B, Panzner U, Park JK, Rabezanahary H, Rakotozandrindrainy R, Sampo E, Sarpong N, Schütt-Gerowitt H, Sooka A, Soura AB, Sow AG, Tall A, Teferi M, Yeshitela B, May J, Wierzba TF, Clemens JD, Baker S, Marks F. The Relationship Between Invasive Nontyphoidal Salmonella Disease, Other Bacterial Bloodstream Infections, and Malaria in Sub-Saharan Africa. Clin Infect Dis 2016; 62 Suppl 1:S23-31. [PMID: 26933016 DOI: 10.1093/cid/civ893] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Country-specific studies in Africa have indicated that Plasmodium falciparum is associated with invasive nontyphoidal Salmonella (iNTS) disease. We conducted a multicenter study in 13 sites in Burkina Faso, Ethiopia, Ghana, Guinea-Bissau, Kenya, Madagascar, Senegal, South Africa, Sudan, and Tanzania to investigate the relationship between the occurrence of iNTS disease, other systemic bacterial infections, and malaria. METHODS Febrile patients received a blood culture and a malaria test. Isolated bacteria underwent antimicrobial susceptibility testing, and the association between iNTS disease and malaria was assessed. RESULTS A positive correlation between frequency proportions of malaria and iNTS was observed (P = .01; r = 0.70). Areas with higher burden of malaria exhibited higher odds of iNTS disease compared to other bacterial infections (odds ratio [OR], 4.89; 95% CI, 1.61-14.90; P = .005) than areas with lower malaria burden. Malaria parasite positivity was associated with iNTS disease (OR, 2.44; P = .031) and gram-positive bacteremias, particularly Staphylococcus aureus, exhibited a high proportion of coinfection with Plasmodium malaria. Salmonella Typhimurium and Salmonella Enteritidis were the predominant NTS serovars (53/73; 73%). Both moderate (OR, 6.05; P = .0001) and severe (OR, 14.62; P < .0001) anemia were associated with iNTS disease. CONCLUSIONS A positive correlation between iNTS disease and malaria endemicity, and the association between Plasmodium parasite positivity and iNTS disease across sub-Saharan Africa, indicates the necessity to consider iNTS as a major cause of febrile illness in malaria-holoendemic areas. Prevention of iNTS disease through iNTS vaccines for areas of high malaria endemicity, targeting high-risk groups for Plasmodium parasitic infection, should be considered.
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Affiliation(s)
- Se Eun Park
- International Vaccine Institute, Seoul, Republic of Korea
| | - Gi Deok Pak
- International Vaccine Institute, Seoul, Republic of Korea
| | - Peter Aaby
- Bandim Health Project, Bissau, Guinea-Bissau Research Center for Vitamins and Vaccines, Copenhagen, Denmark
| | - Yaw Adu-Sarkodie
- Kumasi Centre for Collaborative Research in Tropical Medicine School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mohammad Ali
- International Vaccine Institute, Seoul, Republic of Korea Johns Hopkins University, Baltimore, Maryland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Holly M Biggs
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | | | - Robert F Breiman
- Centers for Disease Control and Prevention, Nairobi, Kenya Emory Global Health Institute, Emory University, Atlanta, Georgia
| | - John A Crump
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina Kilimanjaro Christian Medical Centre, Moshi, Tanzania Duke Global Health Institute, Duke University, Durham, North Carolina Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | | | | | - Julian T Hertz
- Division of Infectious Diseases and International Health, Duke University Medical Center, Durham, North Carolina Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
| | - Anna Jaeger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Karen H Keddy
- National Institute for Communicable Diseases Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Frank Konings
- International Vaccine Institute, Seoul, Republic of Korea
| | - Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, University of Oxford Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Christian G Meyer
- Institute of Tropical Medicine, Eberhard-Karls University Tübingen, Germany
| | | | | | | | | | - Ursula Panzner
- International Vaccine Institute, Seoul, Republic of Korea
| | - Jin Kyung Park
- International Vaccine Institute, Seoul, Republic of Korea
| | | | | | - Emmanuel Sampo
- Schiphra Hospital, Ouagadougou, Burkina Faso Institut Supérieur des Sciences de la Population, University of Ouagadougou, Burkina Faso
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine
| | - Heidi Schütt-Gerowitt
- International Vaccine Institute, Seoul, Republic of Korea Institute of Medical Microbiology, University of Cologne, Germany
| | | | | | - Amy Gassama Sow
- Institute Pasteur Senegal, Dakar Université Cheikh Anta Diop de Dakar, Senegal
| | | | | | | | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - John D Clemens
- International Vaccine Institute, Seoul, Republic of Korea International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka Fielding School of Public Health, University of California, Los Angeles
| | - Stephen Baker
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
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