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Verani JR, Omondi D, Odoyo A, Odiembo H, Ouma A, Ngambi J, Aol G, Audi A, Kiplangat S, Agumba N, Munywoki PK, Onyango C, Hunsperger E, Farrar JL, Kim L, Kobayashi M, Breiman RF, Pimenta FC, da Gloria Carvalho M, Lessa FC, Whitney CG, Bigogo G. Long-term impact of 10-valent pneumococcal conjugate vaccine in Kenya: Nasopharyngeal carriage among children in a rural and an urban site six years after introduction. Vaccine 2024:S0264-410X(24)00782-5. [PMID: 39004525 DOI: 10.1016/j.vaccine.2024.07.021] [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: 10/31/2023] [Revised: 04/12/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND Kenya introduced Synflorix™ (GlaxoSmithKline, PCV10-GSK), a 10-valent pneumococcal conjugate vaccine, in 2011, using three primary doses and, in select areas, catch-up campaigns. Surveys conducted 1-2 years post-introduction showed a stable prevalence of pneumococcal colonization, with declines in vaccine-type carriage. However, little is known about the long-term impact of PCV10-GSK in Kenya. METHODS We conducted a cross-sectional survey of pneumococcal carriage among children aged <5 years in November-December 2017 in Kibera (Nairobi informal settlement, no catch-up) and Asembo (rural western Kenya, 2-dose catch-up for children 1-4 years), using the same methods and settings as prior annual surveys from 2009 to 2013. Participants were randomly selected from an ongoing population-based surveillance platform. Nasopharyngeal swabs were frozen in skim milk-tryptone-glucose-glycerin media within 4 h and underwent culture with broth enrichment for pneumococcus. Isolates were serotyped by polymerase chain reaction and Quellung. RESULTS We enrolled 504 children, including 252 from each site; >90 % of participants had received 3 doses of PCV10-GSK. Pneumococcal colonization was detected in 210 (83.3 %) participants in Kibera and 149 (59.1 %) in Asembo, which was significantly lower than the prevalence observed in 2013 (92.9 % and 85.7 %, respectively). PCV10-GSK serotypes were detected in 35/252 (13.9 %) participants in Kibera and 23/252 (9.1 %) in Asembo, respectively; these prevalences were lower, but not statistically different, from vaccine-type carriage prevalences in 2013 (17.3 % and 13.3 %, respectively). In 2017 in both sites, serotypes 3, 6A, 19A, 19F, and 35B were among the most common serotypes. CONCLUSION Six years post-PCV10-GSK introduction, the prevalence of pneumococcal carriage among children has decreased, and the impact of PCV10-GSK on vaccine-type carriage has plateaued. Kenya recently changed from PCV10-GSK to Pneumosil™ (Serum Institute of India), a 10-valent PCV that includes serotypes 6A and 19A; these data provide historical context for interpreting changes in vaccine-type carriage following the PCV formulation switch.
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Affiliation(s)
- Jennifer R Verani
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States; Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya.
| | - Daniel Omondi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Arthur Odoyo
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Herine Odiembo
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Juliet Ngambi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - George Aol
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Allan Audi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Samwel Kiplangat
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Noel Agumba
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
| | - Patrick K Munywoki
- Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya
| | - Clayton Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya
| | - Elizabeth Hunsperger
- Division of Global Health Protection, Centers for Disease Control and Prevention, PO Box 606-00621, Village Market, Nairobi, Kenya
| | - Jennifer L Farrar
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Lindsay Kim
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Miwako Kobayashi
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322, United States; Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, 29 Princess of Wales Terrace, Johannesburg 2050, South Africa
| | - Fabiana C Pimenta
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Maria da Gloria Carvalho
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Fernanda C Lessa
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States
| | - Cynthia G Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E. Atlanta, GA 30333, United States; Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322, United States
| | - Godfrey Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box: 1578 - 40100, Kisumu, Kenya
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Ng'eno E, Cobos ME, Kiplangat S, Mugoh R, Ouma A, Bigogo G, Omulo S, Peterson AT. Long-term antibiotic exposure landscapes and resistant Escherichia coli colonization in a densely populated setting. PLoS One 2024; 19:e0302521. [PMID: 38980845 PMCID: PMC11232973 DOI: 10.1371/journal.pone.0302521] [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: 02/22/2024] [Accepted: 04/07/2024] [Indexed: 07/11/2024] Open
Abstract
Antibiotic exposure is associated with resistant bacterial colonization, but this relationship can be obscured in community settings owing to horizontal bacterial transmission and broad distributions. Locality-level exposure estimates considering inhabitants' length of stay, exposure history, and exposure conditions of areas nearby could clarify these relationships. We used prescription data filled during 2010-2015 for 23 antibiotic types for members of georeferenced households in a population-based infectious disease surveillance platform. For each antibiotic and locality, we generated exposure estimates, expressed in defined daily doses (DDD) per 1000 inhabitant days of observation (IDO). We also estimated relevant environmental parameters, such as the distance of each locality to water, sanitation, and other amenities. We used data on ampicillin, ceftazidime, and trimethoprim-and-sulfamethoxazole resistant Escherichia coli colonization from stool cultures of asymptomatic individuals in randomly selected households. We tested exposure-colonization associations using permutation analysis of variance and logistic generalized linear mixed-effect models. Overall, exposure was highest for trimethoprim-sulfamethoxazole (1.8 DDD per 1000 IDO), followed by amoxicillin (0.7 DDD per 1000 IDO). Of 1,386 unique household samples from 195 locations tested between September 2015 and January 2016, 90%, 85% and 4% were colonized with E. coli resistant to trimethoprim and sulfamethoxazole, ampicillin, and ceftazidime, respectively. Ceftazidime-resistant E. coli colonization was common in areas with increased trimethoprim-sulfamethoxazole, cloxacillin, and erythromycin exposure. No association with any of the physical environmental variables was observed. We did not detect relationships between distribution patterns of ampicillin or trimethoprim-and-sulfamethoxazole resistant E. coli colonization and the risk factors assessed. Appropriate temporal and spatial scaling of raw antibiotic exposure data to account for evolution and ecological contexts of antibiotic resistance could clarify exposure-colonization relationships in community settings and inform community stewardship program.
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Affiliation(s)
- Eric Ng'eno
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, United States of America
| | - Marlon E Cobos
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, United States of America
| | - Samuel Kiplangat
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Mugoh
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Godfrey Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Sylvia Omulo
- Washington State University Global Health-Kenya, Nairobi, Kenya
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, United States of America
- University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi, Kenya
| | - A Townsend Peterson
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, United States of America
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3
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Agogo GO, Munywoki PK, Audi A, Auko J, Aol G, Oduor C, Kiplangat S, Ouma A, Komo T, Herman-Roloff A, Munyua P, Bigogo G. The effect of COVID-19 pandemic on healthcare seeking in an urban informal settlement in Nairobi and a rural setting in western Kenya. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0002968. [PMID: 38630844 PMCID: PMC11023466 DOI: 10.1371/journal.pgph.0002968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
The COVID-19 pandemic caused widespread changes and disruptions to healthcare seeking behavior. There are limited studies on the effect of the COVID-19 pandemic on healthcare seeking patterns in low-and middle-income countries (LMICs), especially in settings with inequitable access to healthcare in rural and urban informal settlements. We investigated the effect of the COVID-19 pandemic on reported healthcare seeking at health facilities and chemists using morbidity data from participants in an ongoing population-based infectious disease surveillance platform in Asembo in Siaya County, a rural setting in western Kenya and Kibera, an urban informal settlement in Nairobi County. We described healthcare seeking patterns before (from 1st January 2016 to 12th March 2020) and during the pandemic (from 13th March 2020 to 31st August 2022) by gender and age for any reported illness and select clinical syndromes using frequencies and percentages. We used a generalized estimating equation with an exchangeable correlation structure to assess the effect of the pandemic on healthcare seeking adjusting for gender and age. Overall, there was a 19% (adjusted odds ratio, aOR: 0.81; 95% Confidence Interval, CI: 0.79-0.83) decline in odds of seeking healthcare at health facilities for any illness in Asembo during the pandemic, and a 30% (aOR: 0.70; 95% CI: 0.67-0.73) decline in Kibera. Similarly, there was a decline in seeking healthcare by clinical syndromes, e.g., for ARI, aOR: 0.76; 95% CI:0.73-0.79 in Asembo, and aOR: 0.68; 95% CI:0.64-0.72 in Kibera. The pandemic resulted in increased healthcare seeking at chemists (aOR: 1.23; 95% CI: 1.20-1.27 in Asembo, and aOR: 1.40; 95% CI: 1.35-1.46 in Kibera). This study highlights interruptions to healthcare seeking in resource-limited settings due to the COVID-19 pandemic. The pandemic resulted in a substantial decline in seeking care at health facilities, and an increase of the same at chemists.
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Affiliation(s)
- George O. Agogo
- Division of Global Health Protection, U.S. Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Patrick K. Munywoki
- Division of Global Health Protection, U.S. Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Allan Audi
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Joshua Auko
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George Aol
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Clifford Oduor
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Samuel Kiplangat
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Alice Ouma
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Terry Komo
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Amy Herman-Roloff
- Division of Global Health Protection, U.S. Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Peninah Munyua
- Division of Global Health Protection, U.S. Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Godfrey Bigogo
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
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Omore R, Awuor AO, Ogwel B, Okonji C, Sonye C, Oreso C, Akelo V, Amollo M, Ogudi I, Anyango RO, Audi M, Apondi E, Riziki L, Ambila L, Dilruba N, Muok E, Munga S, Ochieng JB, Kotloff KL. The Enterics for Global Health (EFGH) Shigella Surveillance Study in Kenya. Open Forum Infect Dis 2024; 11:S91-S100. [PMID: 38532953 PMCID: PMC10962753 DOI: 10.1093/ofid/ofad654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Background Although Shigella is an important cause of diarrhea in Kenyan children, robust research platforms capable of conducting incidence-based Shigella estimates and eventual Shigella-targeted clinical trials are needed to improve Shigella-related outcomes in children. Here, we describe characteristics of a disease surveillance platform whose goal is to support incidence and consequences of Shigella diarrhea as part of multicounty surveillance aimed at preparing sites and assembling expertise for future Shigella vaccine trials. Methods We mobilized our preexisting expertise in shigellosis, vaccinology, and diarrheal disease epidemiology, which we combined with our experience conducting population-based sampling, clinical trials with high (97%-98%) retention rates, and healthcare utilization surveys. We leveraged our established demographic surveillance system (DSS), our network of healthcare centers serving the DSS, and our laboratory facilities with staff experienced in performing microbiologic and molecular diagnostics to identify enteric infections. We joined these resources with an international network of sites with similar capabilities and infrastructure to form a cohesive scientific network, designated Enterics for Global Health (EFGH), with the aim of expanding and updating our knowledge of the epidemiology and adverse consequences of shigellosis and enriching local research and career development priorities. Conclusions Shigella surveillance data from this platform could help inform Shigella vaccine trials.
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Affiliation(s)
- Richard Omore
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Alex O Awuor
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Billy Ogwel
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Caleb Okonji
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Catherine Sonye
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Caren Oreso
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Victor Akelo
- Department of Clinical Medicine, Liverpool School of Tropical Medicine, Kisumu, Kenya
| | - Manase Amollo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Isaiah Ogudi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Raphael O Anyango
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Marjorie Audi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Evans Apondi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Laura Riziki
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Lilian Ambila
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Nasrin Dilruba
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Erick Muok
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Stephen Munga
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - John B Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Williams RJ, Brintz BJ, Ribeiro Dos Santos G, Huang AT, Buddhari D, Kaewhiran S, Iamsirithaworn S, Rothman AL, Thomas S, Farmer A, Fernandez S, Cummings DAT, Anderson KB, Salje H, Leung DT. Integration of population-level data sources into an individual-level clinical prediction model for dengue virus test positivity. SCIENCE ADVANCES 2024; 10:eadj9786. [PMID: 38363842 PMCID: PMC10871531 DOI: 10.1126/sciadv.adj9786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024]
Abstract
The differentiation of dengue virus (DENV) infection, a major cause of acute febrile illness in tropical regions, from other etiologies, may help prioritize laboratory testing and limit the inappropriate use of antibiotics. While traditional clinical prediction models focus on individual patient-level parameters, we hypothesize that for infectious diseases, population-level data sources may improve predictive ability. To create a clinical prediction model that integrates patient-extrinsic data for identifying DENV among febrile patients presenting to a hospital in Thailand, we fit random forest classifiers combining clinical data with climate and population-level epidemiologic data. In cross-validation, compared to a parsimonious model with the top clinical predictors, a model with the addition of climate data, reconstructed susceptibility estimates, force of infection estimates, and a recent case clustering metric significantly improved model performance.
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Affiliation(s)
- Robert J. Williams
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Ben J. Brintz
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | | | - Angkana T. Huang
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Darunee Buddhari
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Alan L. Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, USA
| | - Stephen Thomas
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Aaron Farmer
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Derek A. T. Cummings
- Department of Biology, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Kathryn B. Anderson
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Daniel T. Leung
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, USA
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Owuor DC, de Laurent ZR, Nyawanda BO, Emukule GO, Kondor R, Barnes JR, Nokes DJ, Agoti CN, Chaves SS. Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons. Sci Rep 2023; 13:22342. [PMID: 38102198 PMCID: PMC10724140 DOI: 10.1038/s41598-023-49157-3] [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: 03/10/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses of HA protein revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1 through acquisition of additional substitutions. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity declined with an increase in age among children aged < 5 years. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines.
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Affiliation(s)
- D Collins Owuor
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Gideon O Emukule
- Influenza Division, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Rebecca Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Sandra S Chaves
- Influenza Division, Centers for Disease Control and Prevention, Nairobi, Kenya
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
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7
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Meme H, Amukoye E, Bowyer C, Chakaya J, Das D, Dobson R, Dragosits U, Fuld J, Gray C, Hahn M, Kiplimo R, Lesosky M, Loh MM, McKendree J, Mortimer K, Ndombi A, Netter L, Obasi A, Orina F, Pearson C, Price H, Quint JK, Semple S, Twigg M, Waelde C, Walnycki A, Warwick M, Wendler J, West SE, Wilson M, Zurba L, Devereux G. Asthma symptoms, spirometry and air pollution exposure in schoolchildren in an informal settlement and an affluent area of Nairobi, Kenya. Thorax 2023; 78:1118-1125. [PMID: 37280096 DOI: 10.1136/thorax-2023-220057] [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: 01/23/2023] [Accepted: 05/03/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND Although 1 billion people live in informal (slum) settlements, the consequences for respiratory health of living in these settlements remain largely unknown. This study investigated whether children living in an informal settlement in Nairobi, Kenya are at increased risk of asthma symptoms. METHODS Children attending schools in Mukuru (an informal settlement in Nairobi) and a more affluent area (Buruburu) were compared. Questionnaires quantified respiratory symptoms and environmental exposures; spirometry was performed; personal exposure to particulate matter (PM2.5) was estimated. RESULTS 2373 children participated, 1277 in Mukuru (median age, IQR 11, 9-13 years, 53% girls), and 1096 in Buruburu (10, 8-12 years, 52% girls). Mukuru schoolchildren were from less affluent homes, had greater exposure to pollution sources and PM2.5. When compared with Buruburu schoolchildren, Mukuru schoolchildren had a greater prevalence of symptoms, 'current wheeze' (9.5% vs 6.4%, p=0.007) and 'trouble breathing' (16.3% vs 12.6%, p=0.01), and these symptoms were more severe and problematic. Diagnosed asthma was more common in Buruburu (2.8% vs 1.2%, p=0.004). Spirometry did not differ between Mukuru and Buruburu. Regardless of community, significant adverse associations were observed with self-reported exposure to 'vapours, dusts, gases, fumes', mosquito coil burning, adult smoker(s) in the home, refuse burning near homes and residential proximity to roads. CONCLUSION Children living in informal settlements are more likely to develop wheezing symptoms consistent with asthma that are more severe but less likely to be diagnosed as asthma. Self-reported but not objectively measured air pollution exposure was associated with increased risk of asthma symptoms.
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Affiliation(s)
- Hellen Meme
- Centre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Evans Amukoye
- Centre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Cressida Bowyer
- Faculty of Creative and Cultural Industries, University of Portsmouth, Portsmouth, UK
| | - Jeremiah Chakaya
- Centre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Darpan Das
- Institute of Occupational Medicine, Edinburgh, UK
| | - Ruaraidh Dobson
- Institute for Social Marketing and Health, University of Stirling, Stirling, UK
| | | | - Jonathan Fuld
- Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Cindy Gray
- School of Social and Political Sciences, University of Glasgow, Glasgow, Glasgow, UK
| | - Matthew Hahn
- Theatre for Development Facilitator, Folkstone, UK
| | - Richard Kiplimo
- Centre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maia Lesosky
- Global Health Trials Unit, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Jean McKendree
- Department of Environment and Geography, University of York, York, UK
| | - Kevin Mortimer
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, College of Health Sciences University of KwaZulu-Natal, Durban, South Africa
| | - Amos Ndombi
- Centre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Louis Netter
- Faculty of Creative and Cultural Industries, University of Portsmouth, Portsmouth, UK
| | - Angela Obasi
- Department of International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK
- Axess Sexual Health, Liverpool University Hospitals NHS Foundation Trust, Liverpool, Liverpool, UK
| | - Fred Orina
- Centre for Respiratory Disease Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Heather Price
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | | | - Sean Semple
- Institute for Social Marketing and Health, University of Stirling, Stirling, UK
| | | | | | - Anna Walnycki
- International Institute for Environment and Development, London, UK
| | - Melaneia Warwick
- School of Design & Creative Arts, Loughborough University, Loughborough, UK
| | | | - Sarah E West
- Department of Environment and Geography, University of York, York, UK
| | - Michael Wilson
- School of Design & Creative Arts, Loughborough University, Loughborough, UK
| | | | - Graham Devereux
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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Munywoki PK, Bigogo G, Nasimiyu C, Ouma A, Aol G, Oduor CO, Rono S, Auko J, Agogo GO, Njoroge R, Oketch D, Odhiambo D, Odeyo VW, Kikwai G, Onyango C, Juma B, Hunsperger E, Lidechi S, Ochieng CA, Lo TQ, Munyua P, Herman-Roloff A. Heterogenous transmission and seroprevalence of SARS-CoV-2 in two demographically diverse populations with low vaccination uptake in Kenya, March and June 2021. Gates Open Res 2023; 7:101. [PMID: 37990692 PMCID: PMC10661969 DOI: 10.12688/gatesopenres.14684.2] [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] [Accepted: 09/29/2023] [Indexed: 11/23/2023] Open
Abstract
Background SARS-CoV-2 has extensively spread in cities and rural communities, and studies are needed to quantify exposure in the population. We report seroprevalence of SARS-CoV-2 in two well-characterized populations in Kenya at two time points. These data inform the design and delivery of public health mitigation measures. Methods Leveraging on existing population based infectious disease surveillance (PBIDS) in two demographically diverse settings, a rural site in western Kenya in Asembo, Siaya County, and an urban informal settlement in Kibera, Nairobi County, we set up a longitudinal cohort of randomly selected households with serial sampling of all consenting household members in March and June/July 2021. Both sites included 1,794 and 1,638 participants in the March and June/July 2021, respectively. Individual seroprevalence of SARS-CoV-2 antibodies was expressed as a percentage of the seropositive among the individuals tested, accounting for household clustering and weighted by the PBIDS age and sex distribution. Results Overall weighted individual seroprevalence increased from 56.2% (95%CI: 52.1, 60.2%) in March 2021 to 63.9% (95%CI: 59.5, 68.0%) in June 2021 in Kibera. For Asembo, the seroprevalence almost doubled from 26.0% (95%CI: 22.4, 30.0%) in March 2021 to 48.7% (95%CI: 44.3, 53.2%) in July 2021. Seroprevalence was highly heterogeneous by age and geography in these populations-higher seroprevalence was observed in the urban informal settlement (compared to the rural setting), and children aged <10 years had the lowest seroprevalence in both sites. Only 1.2% and 1.6% of the study participants reported receipt of at least one dose of the COVID-19 vaccine by the second round of serosurvey-none by the first round. Conclusions In these two populations, SARS-CoV-2 seroprevalence increased in the first 16 months of the COVID-19 pandemic in Kenya. It is important to prioritize additional mitigation measures, such as vaccine distribution, in crowded and low socioeconomic settings.
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Affiliation(s)
- Patrick K. Munywoki
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Godfrey Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Carolyne Nasimiyu
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
- Paul G. Allen School of Global Health, Washington State University, Pullman, Washington, USA
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George Aol
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Clifford O. Oduor
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Samuel Rono
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Joshua Auko
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George O. Agogo
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Ruth Njoroge
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
| | - Dismas Oketch
- Global Health Program, Washington State University – Global Health Kenya (WSU-GH Kenya), Nairobi, Kenya
| | - Dennis Odhiambo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Victor W. Odeyo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Clayton Onyango
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Bonventure Juma
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Elizabeth Hunsperger
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Shirley Lidechi
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | | | - Terrence Q. Lo
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Peninah Munyua
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
| | - Amy Herman-Roloff
- Division for Global Health Protection, Global Health Center, U.S. Centers for Disease Control and Prevention (CDC)-Kenya, Nairobi, Kenya
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Muthumbi EM, Mwanzu A, Mbae C, Bigogo G, Karani A, Mwarumba S, Verani JR, Kariuki S, Scott JAG. The epidemiology of fecal carriage of nontyphoidal Salmonella among healthy children and adults in three sites in Kenya. PLoS Negl Trop Dis 2023; 17:e0011716. [PMID: 37883602 PMCID: PMC10629669 DOI: 10.1371/journal.pntd.0011716] [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: 04/11/2023] [Revised: 11/07/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Despite the importance of non-Typhoidal Salmonella (NTS) disease in Africa, epidemiologic data on carriage and transmission are few. These data are important to understand the transmission of NTS in Africa and to design control strategies. METHOD To estimate the prevalence of stool carriage of NTS in Kenya, we conducted a cross-sectional study in Kilifi, Nairobi, and Siaya, sites with a low, moderate and high incidence of invasive NTS disease, respectively. At each site, we randomly selected 100 participants in each age-group of 0-11 months, 12-59 months, 5-14 years, 15-54 years and ≥55 years. We collected stool, venous blood (for hemoglobin and malaria rapid tests), anthropometric measurements, and administered a questionnaire on Water Access Sanitation and Hygiene (WASH) practices. Stool samples were cultured on selective agar for Salmonella; suspect isolates underwent serotyping and antimicrobial susceptibility testing. RESULT Overall, 53 (3.5%) isolates of NTS were cultured from 1497 samples. Age-adjusted prevalence was 13.1% (95%CI 8.8-17.4) in Kilifi, 0.4% (95%CI 0-1.3) in Nairobi, and 0.9% (95%CI 0-2.0) in Siaya. Prevalence was highest among those aged 15-54 years (6.2%). Of 53 isolates; 5 were S. Enteritidis, 1 was S. Typhimurium. No S. Typhi was isolated. None of the risk factors were associated with carriage of NTS. All isolates were susceptible to all antibiotics tested, including ampicillin, chloramphenicol, ciprofloxacin and co-trimoxazole. CONCLUSION Prevalence of fecal carriage was high in Kilifi, an area of low incidence of invasive NTS disease and was low in areas of higher incidence in Nairobi and Siaya. The age-prevalence, risk factors, geographical and serotype distribution of NTS in carriage differs from invasive disease.
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Affiliation(s)
- Esther M. Muthumbi
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Alfred Mwanzu
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Cecilia Mbae
- Kenya Medical Research Institute–Centre for Microbiology Research, Nairobi, Kenya
| | - Godfrey Bigogo
- Kenya Medical Research Institute–Centre for Global Health Research, Kisumu, Kenya
| | - Angela Karani
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Salim Mwarumba
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
| | - Jennifer R. Verani
- U.S. Centers for Disease Control and Prevention, Division of Global Health Protection, Nairobi, Kenya
| | - Samuel Kariuki
- Kenya Medical Research Institute–Centre for Microbiology Research, Nairobi, Kenya
| | - J. Anthony G. Scott
- Kenya Medical Research Institute–Centre for Geographic Medicine Research, Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Oduor C, Audi A, Kiplangat S, Auko J, Ouma A, Aol G, Nasimiyu C, O. Agogo G, Lo T, Munyua P, Herman-Roloff A, Bigogo G, K. Munywoki P. Estimating excess mortality during the COVID-19 pandemic from a population-based infectious disease surveillance in two diverse populations in Kenya, March 2020-December 2021. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002141. [PMID: 37611028 PMCID: PMC10446178 DOI: 10.1371/journal.pgph.0002141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/16/2023] [Indexed: 08/25/2023]
Abstract
Robust data on the impact of the COVID-19 pandemic on mortality in Africa are relatively scarce. Using data from two well-characterized populations in Kenya we aimed to estimate excess mortality during the COVID-19 pandemic period. The mortality data arise from an ongoing population-based infectious disease surveillance (PBIDS) platform, which has been operational since 2006 in rural western Kenya (Asembo, Siaya County) and an urban informal settlement (Kibera, Nairobi County), Kenya. PBIDS participants were regularly visited at home (2-3 times a year) by field workers who collected demographic data, including deaths. In addition, verbal autopsy (VA) interviews for all identified deaths are conducted. We estimated all-cause and cause-specific mortality rates before and during the height of the COVID-19 pandemic, and we compared associated mortality rates between the periods using incidence rate ratios. Excess deaths during the COVID-19 period were also estimated by modelling expected deaths in the absence of COVID-19 by applying a negative binomial regression model on historical mortality data from January 2016. Overall and monthly excess deaths were determined using the P-score metric. Spearman correlation was used to assess whether there is a relationship between the generated P-score and COVID-19 positivity rate. The all-cause mortality rate was higher during the COVID-19 period compared to the pre-COVID-19 period in Asembo [9.1 (95% CI, 8.2-10.0) vs. 7.8 (95% CI, 7.3-8.3) per 1000 person-years of observation, pyo]. In Kibera, the all-cause mortality rate was slightly lower during the COVID-19 period compared to the pre-COVID-19 period [2.6 (95% CI, 2.2-3.2 per 1000 pyo) vs. 3.1; 95% CI, 2.7-3.4 per 1000 pyo)]. An increase in all-cause mortality was observed (incidence rate ratio, IRR, 1.16; 95% CI, 1.04-1.31) in Asembo, unlike in Kibera (IRR, 0.88; 95% CI, 0.71-1.09). The notable increase in mortality rate in Asembo was observed among persons aged 50 to 64 years (IRR, 2.62; 95% CI, 1.95-3.52), persons aged 65 years and above (5.47; 95% CI, 4.60-6.50) and among females (IRR, 1.25; 95% CI, 1.07-1.46). These age and gender differences were not observed in Kibera. We observed an increase in the mortality rate due to acute respiratory infection, including pneumonia (IRR, 1.45;95% CI, 1.03-2.04), and a reduction in the mortality rate due to pulmonary tuberculosis (IRR, 0.22; 95% CI, 0.05-0.87) among older children and adults in Asembo. There was no statistically significant change in mortality rates due to leading specific causes of death in Kibera. Overall, during the COVID-19 period observed deaths were higher than expected deaths in Asembo (P-score = 6.0%) and lower than expected in Kibera (P-score = -22.3%).Using well-characterized populations in the two diverse geographic locations, we demonstrate a heterogenous impact of the COVID-19 pandemic on all-cause and cause-specific mortality rates in Kenya. We observed more deaths than expected during the COVID-19 period in our rural site in western Kenya contrary to the urban site in Nairobi, the capital city in Kenya.
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Affiliation(s)
- Clifford Oduor
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Allan Audi
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Samwel Kiplangat
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Joshua Auko
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Alice Ouma
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - George Aol
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Carolyne Nasimiyu
- Washington State University (WSU) Global Health Kenya, Nairobi, Kenya
| | - George O. Agogo
- Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Terrence Lo
- Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Peninah Munyua
- Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Amy Herman-Roloff
- Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Godfrey Bigogo
- Center for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu, Kenya
| | - Patrick K. Munywoki
- Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Nairobi, Kenya
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Williams RJ, Brintz BJ, Santos GRD, Huang A, Buddhari D, Kaewhiran S, Iamsirithaworn S, Rothman AL, Thomas S, Farmer A, Fernandez S, Cummings DAT, Anderson KB, Salje H, Leung DT. Integration of population-level data sources into an individual-level clinical prediction model for dengue virus test positivity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.08.23293840. [PMID: 37609267 PMCID: PMC10441499 DOI: 10.1101/2023.08.08.23293840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The differentiation of dengue virus (DENV) infection, a major cause of acute febrile illness in tropical regions, from other etiologies, may help prioritize laboratory testing and limit the inappropriate use of antibiotics. While traditional clinical prediction models focus on individual patient-level parameters, we hypothesize that for infectious diseases, population-level data sources may improve predictive ability. To create a clinical prediction model that integrates patient-extrinsic data for identifying DENV among febrile patients presenting to a hospital in Thailand, we fit random forest classifiers combining clinical data with climate and population-level epidemiologic data. In cross validation, compared to a parsimonious model with the top clinical predictors, a model with the addition of climate data, reconstructed susceptibility estimates, force of infection estimates, and a recent case clustering metric, significantly improved model performance.
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Affiliation(s)
- RJ Williams
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, USA
| | - Ben J. Brintz
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, USA
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, USA
| | | | - Angkana Huang
- Department of Genetics, University of Cambridge, United Kingdom
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Darunee Buddhari
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Alan L. Rothman
- Institute for Immunology and Informatics and Department of Cell and Molecular Biology, University of Rhode Island, Providence, USA
| | - Stephen Thomas
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, USA
| | - Aaron Farmer
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Derek A T Cummings
- Department of Biology, University of Florida, Gainesville, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, USA
| | - Kathryn B Anderson
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, USA
| | - Henrik Salje
- Department of Genetics, University of Cambridge, United Kingdom
| | - Daniel T. Leung
- Division of Infectious Diseases, Department of Internal Medicine, University of Utah, Salt Lake City, USA
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, USA
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12
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Caudell MA, Ayodo C, Ita T, Smith RM, Luvsansharav UO, Styczynski AR, Ramay BM, Kariuki S, Palmer GH, Call DR, Omulo S. Risk Factors for Colonization With Multidrug-Resistant Bacteria in Urban and Rural Communities in Kenya: An Antimicrobial Resistance in Communities and Hospitals (ARCH) Study. Clin Infect Dis 2023; 77:S104-S110. [PMID: 37406050 DOI: 10.1093/cid/ciad223] [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] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Colonization with antimicrobial-resistant bacteria increases the risk of drug-resistant infections. We identified risk factors potentially associated with human colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) in low-income urban and rural communities in Kenya. METHODS Fecal specimens, demographic and socioeconomic data were collected cross-sectionally from clustered random samples of respondents in urban (Kibera, Nairobi County) and rural (Asembo, Siaya County) communities between January 2019 and March 2020. Presumptive ESCrE isolates were confirmed and tested for antibiotic susceptibility using the VITEK2 instrument. We used a path analytic model to identify potential risk factors for colonization with ESCrE. Only 1 participant was included per household to minimize household cluster effects. RESULTS Stool samples from 1148 adults (aged ≥18 years) and 268 children (aged <5 years) were analyzed. The likelihood of colonization increased by 12% with increasing visits to hospitals and clinics. Furthermore, individuals who kept poultry were 57% more likely to be colonized with ESCrE than those who did not. Respondents' sex, age, use of improved toilet facilities, and residence in a rural or urban community were associated with healthcare contact patterns and/or poultry keeping and may indirectly affect ESCrE colonization. Prior antibiotic use was not significantly associated with ESCrE colonization in our analysis. CONCLUSIONS The risk factors associated with ESCrE colonization in communities include healthcare- and community-related factors, indicating that efforts to control antimicrobial resistance in community settings must include community- and hospital-level interventions.
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Affiliation(s)
- Mark A Caudell
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Charchil Ayodo
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Teresa Ita
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Rachel M Smith
- Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ulzii-Orshikh Luvsansharav
- Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashley R Styczynski
- Division of Healthcare Quality Promotion, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brooke M Ramay
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | | | - Guy H Palmer
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Washington State University Global Health-Kenya, Nairobi, Kenya
- University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi, Kenya
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Sylvia Omulo
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Washington State University Global Health-Kenya, Nairobi, Kenya
- University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi, Kenya
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13
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Nooh F, Chernet A, Reither K, Okuma J, Brattig NW, Utzinger J, Probst-Hensch N, Paris DH, Dreyfus A. Prevalence of fever of unidentified aetiology in East African adolescents and adults: a systematic review and meta-analysis. Infect Dis Poverty 2023; 12:55. [PMID: 37231500 DOI: 10.1186/s40249-023-01105-z] [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: 01/17/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Primary health care settings and hospitals of low- and middle-income countries have few accessible diagnostic tools and limited laboratory and human resources capacity to identify multiple pathogens with high accuracy. In addition, there is a paucity of information on fever and its underlying aetiology in the adolescent and adult population in East Africa. The purpose of this study was to estimate the pooled prevalence of fever of unidentified aetiology among adolescent and adult febrile patients seeking health care in East Africa. METHODS We pursued a systematic review using readily available electronic databases (i.e. PubMed, Cumulative Index to Nursing & Allied Health Literature, Scopus, Cochrane Library and Web of Science) without language restriction from inception date of the respective databases to October 31, 2022. We adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Identified studies were screened for relevance. Further analyses based on pre-set eligibility criteria were carried out for final inclusion. Two reviewers independently screened and extracted data. Risk of study bias was assessed. Meta-analysis of the prevalence of fever of unidentified aetiology was performed. RESULTS We identified 14,029 articles of which 25 were eligible for inclusion, reporting data from 8538 participants. The pooled prevalence of febrile cases with unidentified aetiology was 64% [95% confidence interval (CI): 51-77%, I2 = 99.6%] among febrile adolescents and adults in East Africa. For the proportion of patients with identified aetiology, the studies documented bacterial pathogens (human bloodstream infections), bacterial zoonotic pathogens and arboviruses as the main non-malarial causative agents in East Africa. CONCLUSIONS Our study provides evidence that almost two-thirds of adolescent and adult febrile patients attending health care facilities in East Africa might receive inappropriate treatments due to unidentified potential life-threatening fever aetiology. Hence, we call for a comprehensive fever syndromic surveillance to broaden a consequential differential diagnosis of syndromic fever and to considerably improve the course of patients' disease and treatment outcomes.
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Affiliation(s)
- Faisal Nooh
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
- College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia.
- College of Medicine and Health Sciences, University of Hargeisa, Hargeisa, Somaliland.
| | - Afona Chernet
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - James Okuma
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Norbert W Brattig
- Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniel H Paris
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Anou Dreyfus
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Section of Epidemiology, University of Zürich, Zurich, Switzerland
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Beloconi A, Nyawanda BO, Bigogo G, Khagayi S, Obor D, Danquah I, Kariuki S, Munga S, Vounatsou P. Malaria, climate variability, and interventions: modelling transmission dynamics. Sci Rep 2023; 13:7367. [PMID: 37147317 PMCID: PMC10161998 DOI: 10.1038/s41598-023-33868-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
Assessment of the relative impact of climate change on malaria dynamics is a complex problem. Climate is a well-known factor that plays a crucial role in driving malaria outbreaks in epidemic transmission areas. However, its influence in endemic environments with intensive malaria control interventions is not fully understood, mainly due to the scarcity of high-quality, long-term malaria data. The demographic surveillance systems in Africa offer unique platforms for quantifying the relative effects of weather variability on the burden of malaria. Here, using a process-based stochastic transmission model, we show that in the lowlands of malaria endemic western Kenya, variations in climatic factors played a key role in driving malaria incidence during 2008-2019, despite high bed net coverage and use among the population. The model captures some of the main mechanisms of human, parasite, and vector dynamics, and opens the possibility to forecast malaria in endemic regions, taking into account the interaction between future climatic conditions and intervention scenarios.
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Affiliation(s)
- Anton Beloconi
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Bryan O Nyawanda
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Kenya Medical Research Institute - Centre for Global Health Research, Kisumu, Kenya
| | - Godfrey Bigogo
- Kenya Medical Research Institute - Centre for Global Health Research, Kisumu, Kenya
| | - Sammy Khagayi
- Kenya Medical Research Institute - Centre for Global Health Research, Kisumu, Kenya
| | - David Obor
- Kenya Medical Research Institute - Centre for Global Health Research, Kisumu, Kenya
| | - Ina Danquah
- Heidelberg Institute of Global Health (HIGH), Medical Faculty and University Hospital, Heidelberg University, Heidelberg, Germany
| | - Simon Kariuki
- Kenya Medical Research Institute - Centre for Global Health Research, Kisumu, Kenya
| | - Stephen Munga
- Kenya Medical Research Institute - Centre for Global Health Research, Kisumu, Kenya
| | - Penelope Vounatsou
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
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15
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Yu W, Wanza P, Kwoba E, Mwangi T, Okotto-Okotto J, Trajano Gomes da Silva D, Wright JA. Modelling seasonal household variation in harvested rainwater availability: a case study in Siaya County, Kenya. NPJ CLEAN WATER 2023; 6:32. [PMID: 37073161 PMCID: PMC10099009 DOI: 10.1038/s41545-023-00247-9] [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: 09/26/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Rainwater harvesting reliability, the proportion of days annually when rainwater demand is fully met, is challenging to estimate from cross-sectional household surveys that underpin international monitoring. This study investigated the use of a modelling approach that integrates household surveys with gridded precipitation data to evaluate rainwater harvesting reliability, using two local-scale household surveys in rural Siaya County, Kenya as an illustrative case study. We interviewed 234 households, administering a standard questionnaire that also identified the source of household stored drinking water. Logistic mixed effects models estimated stored rainwater availability from household and climatological variables, with random effects accounting for unobserved heterogeneity. Household rainwater availability was significantly associated with seasonality, storage capacity, and access to alternative improved water sources. Most households (95.1%) that consumed rainwater faced insufficient supply of rainwater available for potable needs throughout the year, with intermittencies during the short rains for most households with alternative improved sources. Although not significant, stored rainwater lasts longer for households whose only improved water source was rainwater (301.8 ± 40.2 days) compared to those having multiple improved sources (144.4 ± 63.7 days). Such modelling analysis could enable rainwater harvesting reliability estimation, and thereby national/international monitoring and targeted follow-up fieldwork to support rainwater harvesting.
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Affiliation(s)
- Weiyu Yu
- School of Ecological Technology and Engineering, Shanghai Institute of Technology, Fengxian campus, Shanghai, 201418 China
- School of Geography and Environmental Science, University of Southampton, Building 44, Highfield campus, Southampton, SO17 1BJ UK
| | - Peggy Wanza
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. BOX 1578-1400, Kisian campus, Kisumu-Busia Highway, Kisumu, Kenya
| | - Emmah Kwoba
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. BOX 1578-1400, Kisian campus, Kisumu-Busia Highway, Kisumu, Kenya
| | - Thumbi Mwangi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. BOX 1578-1400, Kisian campus, Kisumu-Busia Highway, Kisumu, Kenya
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA 99164-7090 USA
| | - Joseph Okotto-Okotto
- Victoria Institute for Research on Environment and Development (VIRED) International, P.O. BOX 6423-40103, off Nairobi Road, Rabuor, Kenya
| | - Diogo Trajano Gomes da Silva
- Environmental and Public Health Research and Enterprise Group, School of Applied Sciences, University of Brighton, Cockcroft Building, Lewes Road, Brighton, BN2 4GJ UK
| | - Jim A. Wright
- School of Geography and Environmental Science, University of Southampton, Building 44, Highfield campus, Southampton, SO17 1BJ UK
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Nyiro JU, Nyawanda BO, Bukusi E, Mureithi MW, Murunga N, Nokes DJ, Bigogo G, Otieno NA, Opere VA, Ouma A, Pecenka C, Munywoki PK. Assessment of gestational age at antenatal care visits among Kenyan women to inform delivery of a maternal respiratory syncytial virus (RSV) vaccine in low- and middle-income countries. Wellcome Open Res 2023; 8:154. [PMID: 37502177 PMCID: PMC10369009 DOI: 10.12688/wellcomeopenres.19161.1] [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] [Accepted: 03/15/2023] [Indexed: 07/29/2023] Open
Abstract
Background: Maternal respiratory syncytial virus (RSV) vaccines that are likely to be implementable in low- and middle-income countries (LMICs) are in final stages of clinical trials. Data on the number of women presenting for antenatal care (ANC) per day and proportion attending within the proposed gestational window for vaccine delivery, is a prerequisite to guide development of vaccine vial size and inform vaccine uptake in this setting. Methods: We undertook administrative review and abstraction of ANC attendance records from 2019 registers of 24 selected health facilities, stratified by the level of care, from Kilifi, Siaya and Nairobi counties in Kenya. Additional data were obtained from Mother and Child Health (MCH) booklets of women in each of the Health and Demographic Surveillance System (HDSS) areas of Kilifi, Nairobi and Siaya. Data analysis involved descriptive summaries of the number (mean, median) and proportion of women attending ANC within the gestational window period of 28-32 weeks and 24-36 weeks. Results: A total of 62,153 ANC records were abstracted, 33,872 from Kilifi, 19,438 from Siaya and 8,943 from Nairobi Counties. The median (Interquartile range, IQR) number of women attending ANC per day at a gestational age window of 28-32 and 24-36 weeks, respectively, were: 4 (2-6) and 7 (4-12) in dispensaries, 5 (2-9) and 10 (4-19) in health centres and 6 (4-11) and 16 (10-26) in county referral hospitals. In the HDSS areas of Kilifi, Siaya and Nairobi, pregnant women attending at least one ANC visit, within a window of 28-32 weeks, were: 77% (360/470), 75% (590/791) and 67% (547/821), respectively. Conclusions: About 70% of pregnant women across three distinct geographical regions in Kenya, attend ANC within 28-32 weeks of gestation. A multidose vial size with about five doses per vial, approximates daily ANC attendance and would not incur possible wastage in similar settings.
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Affiliation(s)
- Joyce U. Nyiro
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Bryan O. Nyawanda
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Elizabeth Bukusi
- Kenya Medical Research Institute, Centre for Microbiology Research, Nairobi, Kenya
| | - Marianne W. Mureithi
- Department of Microbiology, University of Nairobi, Nairobi, Nairobi County, Kenya
| | - Nickson Murunga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - D. James Nokes
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- School of Life Sciences, University of Warwick, Coventry, England, UK
| | - Godfrey Bigogo
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Nancy A. Otieno
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Victor A. Opere
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Alice Ouma
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Clint Pecenka
- Center for Vaccine Innovation and Access, PATH, Seattle, Washington, USA
| | - Patrick K. Munywoki
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
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Koltai M, Moyes J, Nyawanda B, Nyiro J, Munywoki PK, Tempia S, Li X, Antillon M, Bilcke J, Flasche S, Beutels P, Nokes DJ, Cohen C, Jit M. Estimating the cost-effectiveness of maternal vaccination and monoclonal antibodies for respiratory syncytial virus in Kenya and South Africa. BMC Med 2023; 21:120. [PMID: 37004062 PMCID: PMC10064962 DOI: 10.1186/s12916-023-02806-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/22/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) causes a substantial burden of acute lower respiratory infection in children under 5 years, particularly in low- and middle-income countries (LMICs). Maternal vaccine (MV) and next-generation monoclonal antibody (mAb) candidates have been shown to reduce RSV disease in infants in phase 3 clinical trials. The cost-effectiveness of these biologics has been estimated using disease burden data from global meta-analyses, but these are sensitive to the detailed age breakdown of paediatric RSV disease, for which there have previously been limited data. METHODS We use original hospital-based incidence data from South Africa (ZAF) and Kenya (KEN) collected between 2010 and 2018 of RSV-associated acute respiratory infection (ARI), influenza-like illness (ILI), and severe acute respiratory infection (SARI) as well as deaths with monthly age-stratification, supplemented with data on healthcare-seeking behaviour and costs to the healthcare system and households. We estimated the incremental cost per DALY averted (incremental cost-effectiveness ratio or ICER) of public health interventions by MV or mAb for a plausible range of prices (5-50 USD for MV, 10-125 USD for mAb), using an adjusted version of a previously published health economic model of RSV immunisation. RESULTS Our data show higher disease incidence for infants younger than 6 months of age in the case of Kenya and South Africa than suggested by earlier projections from community incidence-based meta-analyses of LMIC data. Since MV and mAb provide protection for these youngest age groups, this leads to a substantially larger reduction of disease burden and, therefore, more favourable cost-effectiveness of both interventions in both countries. Using the latest efficacy data and inferred coverage levels based on antenatal care (ANC-3) coverage (KEN: 61.7%, ZAF: 75.2%), our median estimate of the reduction in RSV-associated deaths in children under 5 years in Kenya is 10.5% (95% CI: 7.9, 13.3) for MV and 13.5% (10.7, 16.4) for mAb, while in South Africa, it is 27.4% (21.6, 32.3) and 37.9% (32.3, 43.0), respectively. Starting from a dose price of 5 USD, in Kenya, net cost (for the healthcare system) per (undiscounted) DALY averted for MV is 179 (126, 267) USD, rising to 1512 (1166, 2070) USD at 30 USD per dose; for mAb, it is 684 (543, 895) USD at 20 USD per dose and 1496 (1203, 1934) USD at 40 USD per dose. In South Africa, a MV at 5 USD per dose would be net cost-saving for the healthcare system and net cost per DALY averted is still below the ZAF's GDP per capita at 40 USD dose price (median: 2350, 95% CI: 1720, 3346). For mAb in ZAF, net cost per DALY averted is 247 (46, 510) USD at 20 USD per dose, rising to 2028 (1565, 2638) USD at 50 USD per dose and to 6481 (5364, 7959) USD at 125 USD per dose. CONCLUSIONS Incorporation of new data indicating the disease burden is highly concentrated in the first 6 months of life in two African settings suggests that interventions against RSV disease may be more cost-effective than previously estimated.
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Affiliation(s)
- Mihaly Koltai
- Department for Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Jocelyn Moyes
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bryan Nyawanda
- Kenya Medical Research Institute (KEMRI) - Center for Global Health Research, Kisumu, Kenya
| | - Joyce Nyiro
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medicine Research-Coast, Kilifi, Kenya
| | - Patrick K Munywoki
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Stefano Tempia
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Xiao Li
- Centre for Health Economic Research and Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Marina Antillon
- Centre for Health Economic Research and Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Joke Bilcke
- Centre for Health Economic Research and Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Stefan Flasche
- Department for Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Philippe Beutels
- Centre for Health Economic Research and Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medicine Research-Coast, Kilifi, Kenya
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Cheryl Cohen
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mark Jit
- Department for Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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Nyawanda BO, Murunga N, Otieno NA, Bigogo G, Nyiro JU, Vodicka E, Bulterys M, Nokes DJ, Munywoki PK, Emukule GO. Estimates of the national burden of respiratory syncytial virus in Kenyan children aged under 5 years, 2010-2018. BMC Med 2023; 21:122. [PMID: 37004034 PMCID: PMC10067313 DOI: 10.1186/s12916-023-02787-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/15/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is among the leading childhood causes of viral pneumonia worldwide. Establishing RSV-associated morbidity and mortality is important in informing the development, delivery strategies, and evaluation of interventions. METHODS Using data collected during 2010-2018 from base regions (population-based surveillance studies in western Kenya and the Kilifi Health and Demographic Surveillance Study), we estimated age-specific rates of acute respiratory illness (ARI), severe acute respiratory illness (SARI-defined as hospitalization with cough or difficulty breathing with onset within the past 10 days), and SARI-associated deaths. We extrapolated the rates from the base regions to other regions of Kenya, while adjusting for risk factors of ARI and healthcare seeking behavior, and finally applied the proportions of RSV-positive cases identified from various sentinel and study facilities to the rates to obtain regional age-specific rates of RSV-associated outpatient and non-medically attended ARI and hospitalized SARI and severe ARI that was not hospitalized (non-hospitalized SARI). We applied age-specific RSV case fatality ratios to SARI to obtain estimates of RSV-associated in- and out-of-hospital deaths. RESULTS Among Kenyan children aged < 5 years, the estimated annual incidence of outpatient and non-medically attended RSV-associated ARI was 206 (95% credible interval, CI; 186-229) and 226 (95% CI; 204-252) per 1000 children, respectively. The estimated annual rates of hospitalized and non-hospitalized RSV-associated SARI were 349 (95% CI; 303-404) and 1077 (95% CI; 934-1247) per 100,000 children respectively. The estimated annual number of in- and out-of-hospital deaths associated with RSV infection in Kenya were 539 (95% CI; 420-779) and 1921 (95% CI; 1495-2774), respectively. Children aged < 6 months had the highest burden of RSV-associated severe disease: 2075 (95% CI; 1818-2394) and 44 (95% CI 25-71) cases per 100,000 children for hospitalized SARI and in-hospital deaths, respectively. CONCLUSIONS Our findings suggest a substantial disease burden due to RSV infection, particularly among younger children. Prioritizing development and use of maternal vaccines and affordable long-lasting monoclonal antibodies could help reduce this burden.
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Affiliation(s)
- Bryan O Nyawanda
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya.
| | - Nickson Murunga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nancy A Otieno
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Godfrey Bigogo
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Joyce U Nyiro
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Marc Bulterys
- US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - D James Nokes
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
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Nyawanda BO, Beloconi A, Khagayi S, Bigogo G, Obor D, Otieno NA, Lange S, Franke J, Sauerborn R, Utzinger J, Kariuki S, Munga S, Vounatsou P. The relative effect of climate variability on malaria incidence after scale-up of interventions in western Kenya: A time-series analysis of monthly incidence data from 2008 to 2019. Parasite Epidemiol Control 2023; 21:e00297. [PMID: 37021322 PMCID: PMC10068258 DOI: 10.1016/j.parepi.2023.e00297] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Background Despite considerable progress made over the past 20 years in reducing the global burden of malaria, the disease remains a major public health problem and there is concern that climate change might expand suitable areas for transmission. This study investigated the relative effect of climate variability on malaria incidence after scale-up of interventions in western Kenya. Methods Bayesian negative binomial models were fitted to monthly malaria incidence data, extracted from records of patients with febrile illnesses visiting the Lwak Mission Hospital between 2008 and 2019. Data pertaining to bed net use and socio-economic status (SES) were obtained from household surveys. Climatic proxy variables obtained from remote sensing were included as covariates in the models. Bayesian variable selection was used to determine the elapsing time between climate suitability and malaria incidence. Results Malaria incidence increased by 50% from 2008 to 2010, then declined by 73% until 2015. There was a resurgence of cases after 2016, despite high bed net use. Increase in daytime land surface temperature was associated with a decline in malaria incidence (incidence rate ratio [IRR] = 0.70, 95% Bayesian credible interval [BCI]: 0.59-0.82), while rainfall was associated with increased incidence (IRR = 1.27, 95% BCI: 1.10-1.44). Bed net use was associated with a decline in malaria incidence in children aged 6-59 months (IRR = 0.78, 95% BCI: 0.70-0.87) but not in older age groups, whereas SES was not associated with malaria incidence in this population. Conclusions Variability in climatic factors showed a stronger effect on malaria incidence than bed net use. Bed net use was, however, associated with a reduction in malaria incidence, especially among children aged 6-59 months after adjusting for climate effects. To sustain the downward trend in malaria incidence, this study recommends continued distribution and use of bed nets and consideration of climate-based malaria early warning systems when planning for future control interventions.
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Ita T, Luvsansharav UO, Smith RM, Mugoh R, Ayodo C, Oduor B, Jepleting M, Oguta W, Ouma C, Juma J, Bigogo G, Kariuki S, Ramay BM, Caudell M, Onyango C, Ndegwa L, Verani JR, Bollinger S, Sharma A, Palmer GH, Call DR, Omulo S. Prevalence of colonization with multidrug-resistant bacteria in communities and hospitals in Kenya. Sci Rep 2022; 12:22290. [PMID: 36566323 PMCID: PMC9789952 DOI: 10.1038/s41598-022-26842-3] [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: 05/31/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
We estimated the prevalence of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant Staphylococcus aureus (MRSA) in communities and hospitals in Kenya to identify human colonization with multidrug-resistant bacteria. Nasal and fecal specimen were collected from inpatients and community residents in Nairobi (urban) and Siaya (rural) counties. Swabs were plated on chromogenic agar to presumptively identify ESCrE, CRE and MRSA isolates. Confirmatory identification and antibiotic susceptibility testing were done using the VITEK®2 instrument. A total of 1999 community residents and 1023 inpatients were enrolled between January 2019 and March 2020. ESCrE colonization was higher in urban than rural communities (52 vs. 45%; P = 0.013) and in urban than rural hospitals (70 vs. 63%; P = 0.032). Overall, ESCrE colonization was ~ 18% higher in hospitals than in corresponding communities. CRE colonization was higher in hospital than community settings (rural: 7 vs. 1%; urban: 17 vs. 1%; with non-overlapping 95% confidence intervals), while MRSA was rarely detected (≤ 3% overall). Human colonization with ESCrE and CRE was common, particularly in hospitals and urban settings. MRSA colonization was uncommon. Evaluation of risk factors and genetic mechanisms of resistance can guide prevention and control efforts tailored to different environments.
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Affiliation(s)
- Teresa Ita
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | | | - Rachel M Smith
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Robert Mugoh
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Charchil Ayodo
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Beatrice Oduor
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | | | - Walter Oguta
- Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Caroline Ouma
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jane Juma
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Godfrey Bigogo
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Samuel Kariuki
- Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Brooke M Ramay
- Paul G. Allen School for Global Health, Washington State University, 240 SE Ott Road, Pullman, WA, 99164-7090, USA
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Mark Caudell
- Paul G. Allen School for Global Health, Washington State University, 240 SE Ott Road, Pullman, WA, 99164-7090, USA
| | | | - Linus Ndegwa
- Centers for Disease Control and Prevention, Nairobi, Kenya
| | | | - Susan Bollinger
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Aditya Sharma
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Guy H Palmer
- Washington State University Global Health-Kenya, Nairobi, Kenya
- Paul G. Allen School for Global Health, Washington State University, 240 SE Ott Road, Pullman, WA, 99164-7090, USA
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, 240 SE Ott Road, Pullman, WA, 99164-7090, USA
| | - Sylvia Omulo
- Washington State University Global Health-Kenya, Nairobi, Kenya.
- Paul G. Allen School for Global Health, Washington State University, 240 SE Ott Road, Pullman, WA, 99164-7090, USA.
- University of Nairobi Institute of Tropical and Infectious Diseases, Nairobi, Kenya.
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Herman-Roloff A, Aman R, Samandari T, Kasera K, Emukule GO, Amoth P, Chen TH, Kisivuli J, Weyenga H, Hunsperger E, Onyango C, Juma B, Munyua P, Wako D, Akelo V, Kimanga D, Ndegwa L, Mohamed AA, Okello P, Kariuki S, De Cock KM, Bulterys M. Adapting Longstanding Public Health Collaborations between Government of Kenya and CDC Kenya in Response to the COVID-19 Pandemic, 2020-2021. Emerg Infect Dis 2022; 28:S159-S167. [PMID: 36502403 DOI: 10.3201/eid2813.211550] [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] [Indexed: 12/12/2022] Open
Abstract
Kenya's Ministry of Health (MOH) and the US Centers for Disease Control and Prevention in Kenya (CDC Kenya) have maintained a 40-year partnership during which measures were implemented to prevent, detect, and respond to disease threats. During the COVID-19 pandemic, the MOH and CDC Kenya rapidly responded to mitigate disease impact on Kenya's 52 million residents. We describe activities undertaken jointly by the MOH and CDC Kenya that lessened the effects of COVID-19 during 5 epidemic waves from March through December 2021. Activities included establishing national and county-level emergency operations centers and implementing workforce development and deployment, infection prevention and control training, laboratory diagnostic advancement, enhanced surveillance, and information management. The COVID-19 pandemic provided fresh impetus for the government of Kenya to establish a national public health institute, launched in January 2022, to consolidate its public health activities and counter COVID-19 and future infectious, vaccine-preventable, and emerging zoonotic diseases.
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22
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Shih DC, Silver R, Henao OL, Alemu A, Audi A, Bigogo G, Colston JM, Edu-Quansah EP, Erickson TA, Gashu A, Gbelee GB, Gunter SM, Kosek MN, Logan GG, Mackey JM, Maliga A, Manzanero R, Morazan G, Morey F, Munoz FM, Murray KO, Nelson TV, Olortegui MP, Yori PP, Ronca SE, Schiaffino F, Tayachew A, Tedasse M, Wossen M, Allen DR, Angra P, Balish A, Farron M, Guerra M, Herman-Roloff A, Hicks VJ, Hunsperger E, Kazazian L, Mikoleit M, Munyua P, Munywoki PK, Namwase AS, Onyango CO, Park M, Peruski LF, Sugerman DE, Gutierrez EZ, Cohen AL. Incorporating COVID-19 into Acute Febrile Illness Surveillance Systems, Belize, Kenya, Ethiopia, Peru, and Liberia, 2020-2021. Emerg Infect Dis 2022; 28:S34-S41. [PMID: 36502419 DOI: 10.3201/eid2813.220898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Existing acute febrile illness (AFI) surveillance systems can be leveraged to identify and characterize emerging pathogens, such as SARS-CoV-2, which causes COVID-19. The US Centers for Disease Control and Prevention collaborated with ministries of health and implementing partners in Belize, Ethiopia, Kenya, Liberia, and Peru to adapt AFI surveillance systems to generate COVID-19 response information. Staff at sentinel sites collected epidemiologic data from persons meeting AFI criteria and specimens for SARS-CoV-2 testing. A total of 5,501 patients with AFI were enrolled during March 2020-October 2021; >69% underwent SARS-CoV-2 testing. Percentage positivity for SARS-CoV-2 ranged from 4% (87/2,151, Kenya) to 19% (22/115, Ethiopia). We show SARS-CoV-2 testing was successfully integrated into AFI surveillance in 5 low- to middle-income countries to detect COVID-19 within AFI care-seeking populations. AFI surveillance systems can be used to build capacity to detect and respond to both emerging and endemic infectious disease threats.
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GC-MS Analysis, Antibacterial and Antioxidant Potential of Ethyl Acetate Leaf Extract of Senna singueana (Delile) Grown in Kenya. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5436476. [PMID: 36034966 PMCID: PMC9410794 DOI: 10.1155/2022/5436476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022]
Abstract
Bacterial diseases are a leading cause of mortality and morbidity globally. During bacterial diseases, an elevation of host immune response occurs, which involves the production of free radicals in response to the bacterial infection. The overproduction of free radicals in excess of the antioxidants leads to oxidative stress. Conventional antibiotics are linked to side effects such as hypersensitivity reactions in addition to bacterial pathogens developing resistance against them. Artificial antioxidants are said to be carcinogenic. This study sought to confirm folklore use and validate the antibacterial and antioxidant potential of Senna singueana which has been widely used in the Mbeere community. The in vitro antibacterial potentials of the plant extract were investigated on Bacillus subtilis ATCC 21332, Escherichia coli ATCC 25922, Salmonella typhi ATCC 1408, and Staphylococcus aureus ATCC 25923. Ciprofloxacin (100 µg/ml) drug was used as a standard reference, whereas 5% DMSO was used as a negative reference. The antibacterial tests included disc diffusion and minimum inhibitory and bactericidal concentrations. S. singueana ethyl acetate extract showed broad-spectrum potential against tested bacterial microbes producing mean zones of inhibition (MZI) from 07.67 ± 0.33 to 17.67 ± 0.33 mm. The extract demonstrated a greater effect on Gram-positive than Gram-negative bacterial pathogens. Antibacterial properties of ciprofloxacin were significantly greater in comparison to plant extract in all the dilutions (
), while 5% DMSO was inactive against all the tested bacteria. MBC values were greater than MIC values. Antioxidant properties of the extract were determined through scavenging effects of DPPH and hydroxyl radicals (•OH) as well as ferric reducing antioxidant potential (FRAP) assay. S. singueana demonstrated effects against all radicals formed. Additionally, the extract exhibited ferric reducing abilities. The extract also contained various phytocompounds with known antibacterial and antioxidant properties. This study recommends the therapeutic use of S. singueana as an antibacterial as well as an antioxidant agent.
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Munywoki PK, Nasimiyu C, Alando MD, Otieno N, Ombok C, Njoroge R, Kikwai G, Odhiambo, D, Osita MP, Ouma A, Odour C, Juma B, Ochieng CA, Mutisya I, Ngere I, Dawa J, Osoro E, Njenga MK, Bigogo G, Munyua P, Lo TQ, Hunsperger E, Herman-Roloff A. Seroprevalence and risk factors of SARS-CoV-2 infection in an urban informal settlement in Nairobi, Kenya, December 2020. F1000Res 2022; 10:853. [PMID: 35528961 PMCID: PMC9065925 DOI: 10.12688/f1000research.72914.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/07/2022] [Indexed: 11/20/2022] Open
Abstract
Introduction: Urban informal settlements may be disproportionately affected by the COVID-19 pandemic due to overcrowding and other socioeconomic challenges that make adoption and implementation of public health mitigation measures difficult. We conducted a seroprevalence survey in the Kibera informal settlement, Nairobi, Kenya, to determine the extent of SARS-CoV-2 infection. Methods: Members of randomly selected households from an existing population-based infectious disease surveillance (PBIDS) provided blood specimens between 27
th November and 5
th December 2020. The specimens were tested for antibodies to the SARS-CoV-2 spike protein. Seroprevalence estimates were weighted by age and sex distribution of the PBIDS population and accounted for household clustering. Multivariable logistic regression was used to identify risk factors for individual seropositivity. Results: Consent was obtained from 523 individuals in 175 households, yielding 511 serum specimens that were tested. The overall weighted seroprevalence was 43.3% (95% CI, 37.4 – 49.5%) and did not vary by sex. Of the sampled households, 122(69.7%) had at least one seropositive individual. The individual seroprevalence increased by age from 7.6% (95% CI, 2.4 – 21.3%) among children (<5 years), 32.7% (95% CI, 22.9 – 44.4%) among children 5 – 9 years, 41.8% (95% CI, 33.0 – 51.1%) for those 10-19 years, and 54.9%(46.2 – 63.3%) for adults (≥20 years). Relative to those from medium-sized households (3 and 4 individuals), participants from large (≥5 persons) households had significantly increased odds of being seropositive, aOR, 1.98(95% CI, 1.17 – 1.58), while those from small-sized households (≤2 individuals) had increased odds but not statistically significant, aOR, 2.31 (95% CI, 0.93 – 5.74). Conclusion: In densely populated urban settings, close to half of the individuals had an infection to SARS-CoV-2 after eight months of the COVID-19 pandemic in Kenya. This highlights the importance to prioritize mitigation measures, including COVID-19 vaccine distribution, in the crowded, low socioeconomic settings.
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Affiliation(s)
- Patrick K Munywoki
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Caroline Nasimiyu
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Moshe Dayan Alando
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Nancy Otieno
- Centre for Global Health Research,, Kenya Medical Research Institute, Kisumu, Kenya
| | - Cynthia Ombok
- Global Health Kenya, Washington State University, Nairobi, USA
| | - Ruth Njoroge
- Global Health Kenya, Washington State University, Nairobi, USA
| | - Gilbert Kikwai
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Dennis Odhiambo,
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Mike Powel Osita
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Alice Ouma
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Clifford Odour
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Bonventure Juma
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Caroline A Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Immaculate Mutisya
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Isaac Ngere
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Jeanette Dawa
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Eric Osoro
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - M Kariuki Njenga
- Global Health Kenya, Washington State University, Nairobi, USA
- Paul G. Allen School of Global Health, Washington State University, Pullman, USA
| | - Godfrey Bigogo
- Centre for Global Health Research,, Kenya Medical Research Institute, Kisumu, Kenya
| | - Peninah Munyua
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Terrence Q Lo
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Elizabeth Hunsperger
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
| | - Amy Herman-Roloff
- Center for Global Health, Division of Public Health Protection, U.S. Centers for Disease Control and Prevention, Nairobi, USA
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Mathad V, Mahanshetti N, Naik V. Impact of morbidity among under-five children: A meta-analysis. MGM JOURNAL OF MEDICAL SCIENCES 2022. [DOI: 10.4103/mgmj.mgmj_81_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Bonnewell JP, Rubach MP, Madut DB, Carugati M, Maze MJ, Kilonzo KG, Lyamuya F, Marandu A, Kalengo NH, Lwezaula BF, Mmbaga BT, Maro VP, Crump JA. Performance Assessment of the Universal Vital Assessment Score vs Other Illness Severity Scores for Predicting Risk of In-Hospital Death Among Adult Febrile Inpatients in Northern Tanzania, 2016-2019. JAMA Netw Open 2021; 4:e2136398. [PMID: 34913982 PMCID: PMC8678687 DOI: 10.1001/jamanetworkopen.2021.36398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/26/2021] [Indexed: 12/26/2022] Open
Abstract
Importance Severity scores are used to improve triage of hospitalized patients in high-income settings, but the scores may not translate well to low- and middle-income settings such as sub-Saharan Africa. Objective To assess the performance of the Universal Vital Assessment (UVA) score, derived in 2017, compared with other illness severity scores for predicting in-hospital mortality among adults with febrile illness in northern Tanzania. Design, Setting, and Participants This prognostic study used clinical data collected for the duration of hospitalization among patients with febrile illness admitted to Kilimanjaro Christian Medical Centre or Mawenzi Regional Referral Hospital in Moshi, Tanzania, from September 2016 through May 2019. All adult and pediatric patients with a history of fever within 72 hours or a tympanic temperature of 38.0 °C or higher at screening were eligible for enrollment. Of 3761 eligible participants, 1132 (30.1%) were enrolled in the parent study; of those, 597 adults 18 years or older were included in this analysis. Data were analyzed from December 2019 to September 2021. Exposures Modified Early Warning Score (MEWS), National Early Warning Score (NEWS), quick Sequential Organ Failure Assessment (qSOFA), Systemic Inflammatory Response Syndrome (SIRS) assessment, and UVA. Main Outcomes and Measures The main outcome was in-hospital mortality during the same hospitalization as the participant's enrollment. Crude risk ratios and 95% CIs for in-hospital death were calculated using log-binomial risk regression for proposed score cutoffs for each of the illness severity scores. The area under the receiver operating characteristic curve (AUROC) for estimating the risk of in-hospital death was calculated for each score. Results Among 597 participants, the median age was 43 years (IQR, 31-56 years); 300 participants (50.3%) were female, 198 (33.2%) were HIV-infected, and in-hospital death occurred in 55 (9.2%). By higher risk score strata for each score, compared with lower risk strata, risk ratios for in-hospital death were 3.7 (95% CI, 2.2-6.2) for a MEWS of 5 or higher; 2.7 (95% CI, 0.9-7.8) for a NEWS of 5 or 6; 9.6 (95% CI, 4.2-22.2) for a NEWS of 7 or higher; 4.8 (95% CI, 1.2-20.2) for a qSOFA score of 1; 15.4 (95% CI, 3.8-63.1) for a qSOFA score of 2 or higher; 2.5 (95% CI, 1.2-5.2) for a SIRS score of 2 or higher; 9.1 (95% CI, 2.7-30.3) for a UVA score of 2 to 4; and 30.6 (95% CI, 9.6-97.8) for a UVA score of 5 or higher. The AUROCs, using all ordinal values, were 0.85 (95% CI, 0.80-0.90) for the UVA score, 0.81 (95% CI, 0.75-0.87) for the NEWS, 0.75 (95% CI, 0.69-0.82) for the MEWS, 0.73 (95% CI, 0.67-0.79) for the qSOFA score, and 0.63 (95% CI, 0.56-0.71) for the SIRS score. The AUROC for the UVA score was significantly greater than that for all other scores (P < .05 for all comparisons) except for NEWS (P = .08). Conclusions and Relevance This prognostic study found that the NEWS and the UVA score performed favorably compared with other illness severity scores in predicting in-hospital mortality among a hospitalized cohort of adults with febrile illness in northern Tanzania. Given its reliance on readily available clinical data, the UVA score may have utility in the triage and prognostication of patients admitted to the hospital with febrile illness in low- to middle-income settings such as sub-Saharan Africa.
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Affiliation(s)
- John P. Bonnewell
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Matthew P. Rubach
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Duke Global Health Institute, Duke University, Durham, North Carolina
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Programme in Emerging Infectious Diseases, Duke–National University of Singapore Medical School, Singapore
| | - Deng B. Madut
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Duke Global Health Institute, Duke University, Durham, North Carolina
| | - Manuela Carugati
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Michael J. Maze
- Department of Medicine, University of Otago, Dunedin, New Zealand
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Kajiru G. Kilonzo
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
| | - Furaha Lyamuya
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
| | | | | | | | - Blandina T. Mmbaga
- Duke Global Health Institute, Duke University, Durham, North Carolina
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - Venance P. Maro
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Tumaini University, Moshi, Tanzania
| | - John A. Crump
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
- Duke Global Health Institute, Duke University, Durham, North Carolina
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Department of Medicine, University of Otago, Dunedin, New Zealand
- Centre for International Health, University of Otago, Dunedin, New Zealand
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Ogola JG, Alburkat H, Masika M, Korhonen E, Uusitalo R, Nyaga P, Anzala O, Vapalahti O, Sironen T, Forbes KM. Seroevidence of Zoonotic Viruses in Rodents and Humans in Kibera Informal Settlement, Nairobi, Kenya. Vector Borne Zoonotic Dis 2021; 21:973-978. [DOI: 10.1089/vbz.2021.0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Joseph Ganda Ogola
- Department of Medical Microbiology, KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Hussein Alburkat
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Moses Masika
- Department of Medical Microbiology, KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Essi Korhonen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Ruut Uusitalo
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Philip Nyaga
- Department of Pathology, Microbiology and Parasitology, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Department of Medical Microbiology, KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Kristian M. Forbes
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
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Virhia J. Contextualising health seeking behaviours for febrile illness: Lived experiences of farmers in northern Tanzania. Health Place 2021; 73:102710. [PMID: 34801785 DOI: 10.1016/j.healthplace.2021.102710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/03/2021] [Accepted: 11/06/2021] [Indexed: 01/09/2023]
Abstract
Understanding how people seek treatment for febrile illness can provide important insights into when care is sought and under what circumstances. This is includes examining how people engage with health facilities and the barriers to care they experience. However, a focus on individual actions runs the risk of overemphasising the agency of individuals to make apt health decisions while underestimating the ways which health behaviours are circumscribed by their place-specific social, historic and political contexts. Drawing on the experiences of approximately 100 farmers in a small livestock keeping community in northern Tanzania, this study uses biosocial theory of health to better understand how febrile illness is managed among individuals. The paper draws attention to the ways in which health decisions are mediated by individual, intrinsic and extrinsic health system factors. Some extrinsic factors (such as hospital user fees) are legacies of neoliberal healthcare reform policies which continue to have consequences for how people manage febrile illness in Tanzania. The findings highlight the need for considerations of health behaviours to look beyond the individual and to appreciate the role of the wider health landscape in influencing individual choice and agency when seeking treatment for illness.
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Affiliation(s)
- Jennika Virhia
- Institute of Health & Wellbeing/School of Social & Political Sciences, 27 Bute Gardens, University of Glasgow, G12 8RS, UK.
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29
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Watts C, Atieli H, Alacapa J, Lee MC, Zhou G, Githeko A, Yan G, Wiseman V. Rethinking the economic costs of hospitalization for malaria: accounting for the comorbidities of malaria patients in western Kenya. Malar J 2021; 20:429. [PMID: 34717637 PMCID: PMC8557520 DOI: 10.1186/s12936-021-03958-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria causes significant mortality and morbidity in sub-Saharan Africa, especially among children under five years of age and places a huge economic burden on individuals and health systems. While this burden has been assessed previously, few studies have explored how malaria comorbidities affect inpatient costs. This study in a malaria endemic area in Western Kenya, assessed the total treatment costs per malaria episode including comorbidities in children and adults. METHODS Total economic costs of malaria hospitalizations were calculated from a health system and societal perspective. Patient-level data were collected from patients admitted with a malaria diagnosis to a county-level hospital between June 2016 and May 2017. All treatment documented in medical records were included as health system costs. Patient and household costs included direct medical and non-medical expenses, and indirect costs due to productivity losses. RESULTS Of the 746 patients admitted with a malaria diagnosis, 64% were female and 36% were male. The mean age was 14 years (median 7 years). The mean length of stay was three days. The mean health system cost per patient was Kenyan Shilling (KSh) 4288 (USD 42.0) (95% confidence interval (CI) 95% CI KSh 4046-4531). The total household cost per patient was KSh 1676 (USD 16.4) (95% CI KSh 1488-1864) and consisted of: KSh 161 (USD1.6) medical costs; KSh 728 (USD 7.1) non-medical costs; and KSh 787 (USD 7.7) indirect costs. The total societal cost (health system and household costs) per patient was KSh 5964 (USD 58.4) (95% CI KSh 5534-6394). Almost a quarter of patients (24%) had a reported comorbidity. The most common malaria comorbidities were chest infections, diarrhoea, and anaemia. The inclusion of comorbidities compared to patients with-out comorbidities led to a 46% increase in societal costs (health system costs increased by 43% and patient and household costs increased by 54%). CONCLUSIONS The economic burden of malaria is increased by comorbidities which are associated with longer hospital stays and higher medical costs to patients and the health system. Understanding the full economic burden of malaria is critical if future malaria control interventions are to protect access to care, especially by the poor.
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Affiliation(s)
- Caroline Watts
- The Kirby Institute, University of New South Wales, Sydney, Australia. .,Daffodil Centre, The University of Sydney, Cancer Council NSW, Sydney, Australia.
| | | | - Jason Alacapa
- The School of Public Health and Community Medicine, University of New South Wales, Sydney, Australia
| | - Ming-Chieh Lee
- Program in Public Health, University of California, Irvine, California, USA
| | - Guofa Zhou
- Program in Public Health, University of California, Irvine, California, USA
| | - Andrew Githeko
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, California, USA
| | - Virginia Wiseman
- The Kirby Institute, University of New South Wales, Sydney, Australia.,London School of Hygiene & Tropical Medicine, London, UK
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30
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Owuor DC, de Laurent ZR, Kikwai GK, Mayieka LM, Ochieng M, Müller NF, Otieno NA, Emukule GO, Hunsperger EA, Garten R, Barnes JR, Chaves SS, Nokes DJ, Agoti CN. Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018. Viruses 2021; 13:1956. [PMID: 34696386 PMCID: PMC8539974 DOI: 10.3390/v13101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 12/01/2022] Open
Abstract
The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed 383 A(H1N1)pdm09 viral genomes from hospitalized patients between 2009 and 2018 from seven locations across Kenya. Using these genomes and contemporaneously sampled global sequences, we characterized the spread of the virus in Kenya over several seasons using phylodynamic methods. The transmission dynamics of A(H1N1)pdm09 virus in Kenya were characterized by (i) multiple virus introductions into Kenya over the study period, although only a few of those introductions instigated local seasonal epidemics that then established local transmission clusters, (ii) persistence of transmission clusters over several epidemic seasons across the country, (iii) seasonal fluctuations in effective reproduction number (Re) associated with lower number of infections and seasonal fluctuations in relative genetic diversity after an initial rapid increase during the early pandemic phase, which broadly corresponded to epidemic peaks in the northern and southern hemispheres, (iv) high virus genetic diversity with greater frequency of seasonal fluctuations in 2009-2011 and 2018 and low virus genetic diversity with relatively weaker seasonal fluctuations in 2012-2017, and (v) virus spread across Kenya. Considerable influenza virus diversity circulated within Kenya, including persistent viral lineages that were unique to the country, which may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied low-to-middle-income tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses in humans and to inform vaccination strategies within these regions.
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Affiliation(s)
- D. Collins Owuor
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
| | - Zaydah R. de Laurent
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
| | - Gilbert K. Kikwai
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Lillian M. Mayieka
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Melvin Ochieng
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Nicola F. Müller
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA;
| | - Nancy A. Otieno
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Gideon O. Emukule
- Centers for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, Kenya; (G.O.E.); (S.S.C.)
| | - Elizabeth A. Hunsperger
- Centers for Disease Control and Prevention, Division of Global Health Protection, Nairobi 606-00621, Kenya;
- Centers for Disease Control and Prevention, Division of Global Health Protection, Atlanta, GA 30333, USA
| | - Rebecca Garten
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - John R. Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - Sandra S. Chaves
- Centers for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, Kenya; (G.O.E.); (S.S.C.)
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - D. James Nokes
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), Coventry CV4 7AL, UK
| | - Charles N. Agoti
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
- School of Public Health and Human Sciences, Pwani University, Kilifi 195-80108, Kenya
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31
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Munywoki PK, Nasimiyu C, Alando MD, Otieno N, Ombok C, Njoroge R, Kikwai G, Odhiambo, D, Osita MP, Ouma A, Odour C, Juma B, Ochieng CA, Mutisya I, Ngere I, Dawa J, Osoro E, Njenga MK, Bigogo G, Munyua P, Lo TQ, Hunsperger E, Herman-Roloff A. Seroprevalence and risk factors of SARS-CoV-2 infection in an urban informal settlement in Nairobi, Kenya, December 2020. F1000Res 2021; 10:853. [PMID: 35528961 PMCID: PMC9065925 DOI: 10.12688/f1000research.72914.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Introduction: Urban informal settlements may be disproportionately affected by the COVID-19 pandemic due to overcrowding and other socioeconomic challenges that make adoption and implementation of public health mitigation measures difficult. We conducted a seroprevalence survey in the Kibera informal settlement, Nairobi, Kenya, to determine the extent of SARS-CoV-2 infection. Methods: Members of randomly selected households from an existing population-based infectious disease surveillance (PBIDS) provided blood specimens between 27th November and 5th December 2020. The specimens were tested for antibodies to the SARS-CoV-2 spike protein. Seroprevalence estimates were weighted by age and sex distribution of the PBIDS population and accounted for household clustering. Multivariable logistic regression was used to identify risk factors for individual seropositivity. Results: Consent was obtained from 523 individuals in 175 households, yielding 511 serum specimens that were tested. The overall weighted seroprevalence was 43.3% (95% CI, 37.4 – 49.5%) and did not vary by sex. Of the sampled households, 122(69.7%) had at least one seropositive individual. The individual seroprevalence increased by age from 7.6% (95% CI, 2.4 – 21.3%) among children (<5 years), 32.7% (95% CI, 22.9 – 44.4%) among children 5 – 9 years, 41.8% (95% CI, 33.0 – 51.1%) for those 10-19 years, and 54.9%(46.2 – 63.3%) for adults (≥20 years). Relative to those from medium-sized households (3 and 4 individuals), participants from large (≥5 persons) households had significantly increased odds of being seropositive, aOR, 1.98(95% CI, 1.17 – 1.58), while those from small-sized households (≤2 individuals) had increased odds but not statistically significant, aOR, 2.31 (95% CI, 0.93 – 5.74). Conclusion: In densely populated urban settings, close to half of the individuals had an infection to SARS-CoV-2 after eight months of the COVID-19 pandemic in Kenya. This highlights the importance to prioritize mitigation measures, including COVID-19 vaccine distribution, in the crowded, low socioeconomic settings.
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Wambiya EOA, Otieno PO, Mutua MK, Donfouet HPP, Mohamed SF. Patterns and predictors of private and public health care utilization among residents of an informal settlement in Nairobi, Kenya: a cross-sectional study. BMC Public Health 2021; 21:850. [PMID: 33941131 PMCID: PMC8091493 DOI: 10.1186/s12889-021-10836-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Knowledge of health care utilization is important in low-and middle-income countries where inequalities in the burden of diseases and access to primary health care exist. Limited evidence exists on health seeking and utilization in the informal settlements in Kenya. This study assessed the patterns and predictors of private and public health care utilization in an urban informal settlement in Kenya. METHODS This study used data from the Lown scholars study conducted between June and July 2018. A total of 300 households were randomly selected and data collected from 364 household members who reported having sought care for an illness in the 12 months preceding the study. Data were collected on health-seeking behaviour and explanatory variables (predisposing, enabling, and need factors). Health care utilization patterns were described using proportions. Predictors of private or public health care use were identified using multinomial logistic regression with the reference group being other providers. RESULTS Majority of the participants used private (47%) and public facilities (33%) with 20% using other providers including local pharmacies/drug shops and traditional healers. In the model comparing public facilities vs other facilities, members who were satisfied with the quality of health care (vs not satisfied) were less likely to use public facilities (adjusted relative risk ratio (aRRR) 0.29; CI 0.11-0.76) while members who reported an acute infection (vs no acute infection) were more likely to use public facilities (aRRR 2.31; 95% CI 1.13-4.99) compared to other facilities. In the second model comparing private facilities to other facilities, having health insurance coverage (aRRR 2.95; 95% CI 1.53-5.69), satisfaction with cost of care (aRRR 2.08; CI 1.00-4.36), and having an acute infection (aRRR 2.97; 95% CI 1.50-5.86) were significantly associated with private facility use compared to other facilities. CONCLUSIONS The majority of urban informal settlement dwellers seek care from private health facilities. As Kenya commits to achieving universal health coverage, interventions that improve health care access in informal and low-resource settlements are needed and should be modelled around enabling and need factors, particularly health care financing and quality of health care.
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Affiliation(s)
- Elvis O. A. Wambiya
- African Population and Health Research Center, APHRC Campus, 2nd Floor, Manga Close, Off Kirawa Road, P.O. Box: 10787-00100, Nairobi, Kenya
| | - Peter O. Otieno
- African Population and Health Research Center, APHRC Campus, 2nd Floor, Manga Close, Off Kirawa Road, P.O. Box: 10787-00100, Nairobi, Kenya
| | - Martin Kavao Mutua
- African Population and Health Research Center, APHRC Campus, 2nd Floor, Manga Close, Off Kirawa Road, P.O. Box: 10787-00100, Nairobi, Kenya
| | - Hermann Pythagore Pierre Donfouet
- African Population and Health Research Center, APHRC Campus, 2nd Floor, Manga Close, Off Kirawa Road, P.O. Box: 10787-00100, Nairobi, Kenya
| | - Shukri F. Mohamed
- African Population and Health Research Center, APHRC Campus, 2nd Floor, Manga Close, Off Kirawa Road, P.O. Box: 10787-00100, Nairobi, Kenya
- Department of Global Health and Population, Lown Scholars Program, Harvard T.H. Chan School of Public Health, Boston, MA USA
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Otieno NA, Malik FA, Nganga SW, Wairimu WN, Ouma DO, Bigogo GM, Chaves SS, Verani JR, Widdowson MA, Wilson AD, Bergenfeld I, Gonzalez-Casanova I, Omer SB. Decision-making process for introduction of maternal vaccines in Kenya, 2017-2018. Implement Sci 2021; 16:39. [PMID: 33845842 PMCID: PMC8042952 DOI: 10.1186/s13012-021-01101-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 03/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maternal immunization is a key strategy for reducing morbidity and mortality associated with infectious diseases in mothers and their newborns. Recent developments in the science and safety of maternal vaccinations have made possible development of new maternal vaccines ready for introduction in low- and middle-income countries. Decisions at the policy level remain the entry point for maternal immunization programs. We describe the policy and decision-making process in Kenya for the introduction of new vaccines, with particular emphasis on maternal vaccines, and identify opportunities to improve vaccine policy formulation and implementation process. METHODS We conducted 29 formal interviews with government officials and policy makers, including high-level officials at the Kenya National Immunization Technical Advisory Group, and Ministry of Health officials at national and county levels. All interviews were recorded and transcribed. We analyzed the qualitative data using NVivo 11.0 software. RESULTS All key informants understood the vaccine policy formulation and implementation processes, although national officials appeared more informed compared to county officials. County officials reported feeling left out of policy development. The recent health system decentralization had both positive and negative impacts on the policy process; however, the negative impacts outweighed the positive impacts. Other factors outside vaccine policy environment such as rumours, sociocultural practices, and anti-vaccine campaigns influenced the policy development and implementation process. CONCLUSIONS Public policy development process is complex and multifaceted by its nature. As Kenya prepares for introduction of other maternal vaccines, it is important that the identified policy gaps and challenges are addressed.
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Affiliation(s)
- Nancy A. Otieno
- Division of Global Health Protection, Centre for Global Health Research, Kenya Medical Research Institute, PO Box 1578-40100, Kisumu, Kenya
| | - Fauzia A. Malik
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE, Atlanta, GA 30322 USA
| | - Stacy W. Nganga
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE, Atlanta, GA 30322 USA
| | - Winnie N. Wairimu
- Centre for Global Health Research, Kenya Medical Research Institute, PO Box 1578-40100, Kisumu, Kenya
| | - Dominic O. Ouma
- Centre for Global Health Research, Kenya Medical Research Institute, PO Box 1578-40100, Kisumu, Kenya
| | - Godfrey M. Bigogo
- Division of Global Health Protection, Centre for Global Health Research, Kenya Medical Research Institute, PO Box 1578-40100, Kisumu, Kenya
| | - Sandra S. Chaves
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, PO Box 606-00621, Nairobi, Kenya
| | - Jennifer R. Verani
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, PO Box 606-00621, Nairobi, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, PO Box 606-00621, Nairobi, Kenya
| | - Andrew D. Wilson
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE, Atlanta, GA 30322 USA
| | - Irina Bergenfeld
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE, Atlanta, GA 30322 USA
| | - Ines Gonzalez-Casanova
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE, Atlanta, GA 30322 USA
| | - Saad B. Omer
- Department of Medicine, Division of Pediatrics, Emory University School of Medicine, 1518 Clifton Rd NE, Atlanta, GA 30322 USA
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Field Deployment of a Mobile Biosafety Laboratory Reveals the Co-Circulation of Dengue Viruses Serotype 1 and Serotype 2 in Louga City, Senegal, 2017. J Trop Med 2021; 2021:8817987. [PMID: 33868410 PMCID: PMC8032538 DOI: 10.1155/2021/8817987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 01/19/2023] Open
Abstract
Dengue virus (DENV) is the most prevalent arboviral threat worldwide. This virus belonging to genus Flavivirus, Flaviviridae family, is responsible for a wide spectrum of clinical manifestations, ranging from asymptomatic or mild febrile illness (dengue fever) to life-threatening infections (severe dengue). Many sporadic cases and outbreaks have occurred in Senegal since 1970. Nevertheless, this article describes a field investigation of suspected dengue cases, between 05 September 2017 and 17 December 2017 made possible by the deployment of a Mobile Biosafety Laboratory (MBS-Lab). Overall, 960 human sera were collected and tested in the field for the presence of viral RNA by real-time RT-PCR. Serotyping, sequencing of complete E gene, and phylogenetic analysis were also performed. Out of 960 suspected cases, 131 were confirmed dengue cases. The majority of confirmed cases were from Louga community. Serotyping revealed two serotypes, Dengue 1 (100/104; 96, 15%) and Dengue 2 (04/104; 3, 84%). Phylogenetic analysis of the sequences obtained indicated that the Dengue 1 strain was closely related to strains isolated, respectively, in Singapore (Asia) in 2013 (KX380803.1) outbreak and it cocirculated with a Dengue 2 strain closely related to strains from a Burkina Faso dengue outbreak in 2016 (KY62776.1). Our results showed the co-circulation of two dengue virus serotypes during a single outbreak in a short time period. This co-circulation highlighted the need to improve surveillance in order to prevent future potential severe dengue cases through antibody-dependent enhancement (ADE). Interestingly, it also proved the reliability and usefulness of the MBS-Lab for expedient outbreak response at the point of need, which allows early cases management.
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Otiang E, Chen D, Jiang J, Maina AN, Farris CM, Luce-Fedrow A, Richards AL. Pathogen Carriage by Peri-Domestic Fleas in Western Kenya. Vector Borne Zoonotic Dis 2021; 21:256-263. [PMID: 33481673 DOI: 10.1089/vbz.2020.2709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fleas are carriers for many largely understudied zoonotic, endemic, emerging, and re-emerging infectious disease agents, but little is known about their prevalence and role as a vector in Africa. The aim of this study was to determine the diversity of fleas and the prevalence of infectious agents in them collected from human dwellings in western Kenya. A total of 306 fleas were collected using light traps from 33 human dwellings; 170 (55.56%) were identified as Ctenocephalides spp., 121 (39.54%) as Echidnophaga gallinacea, 13 (4.25%) as Pulex irritans, and 2 (0.65%) as Xenopsylla cheopis. Of the 306 individual fleas tested, 168 (54.9%) tested positive for rickettsial DNA by a genus-specific quantitative real-time PCR (qPCR) assay based on the 17-kDa antigen gene. Species-specific qPCR assays and sequencing revealed presence of Rickettsia asembonensis in 166 (54.2%) and Rickettsia felis in 2 (0.7%) fleas. Borrelia burgdorferi, normally known to be carried by ticks, was detected in four (1.3%) flea DNA preparations. We found no evidence of Yersinia pestis, Bartonella spp., or Orientia spp. Not only were Ctenocephalides spp. the most predominant flea species in the human dwellings, but also almost all of them were harboring R. asembonensis.
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Affiliation(s)
- Elkanah Otiang
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Daniel Chen
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Ju Jiang
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Alice N Maina
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Christina M Farris
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, USA
| | - Alison Luce-Fedrow
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, USA.,Department of Biology, Shippensburg University, Shippensburg, Pennsylvania, USA
| | - Allen L Richards
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, Maryland, USA.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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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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Stauber CE, Person B, Otieno R, Oremo J, Schilling K, Hayat MJ, Ayers T, Quick R. A Cluster Randomized Trial of the Impact of Education through Listening (a Novel Behavior Change Technique) on Household Water Treatment with Chlorine in Vihiga District, Kenya, 2010-2011. Am J Trop Med Hyg 2020; 104:382-390. [PMID: 33146110 DOI: 10.4269/ajtmh.20-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Despite multiple studies demonstrating the effectiveness of household water treatment with chlorine in disinfecting water and preventing diarrhea, social marketing of this intervention in low- and middle-income countries has resulted in only modest uptake. In a cluster randomized trial in Vihiga district, western Kenya, we compared uptake of household water treatment with chlorine among six villages served by community vendors trained in standard social marketing plus education through listening (ETL), an innovative behavior change method, and six villages served by community vendors trained in standard social marketing only. Water treatment uptake, water quality, and childhood diarrhea were measured over 6 months and compared between the two groups of villages. During the 6-month period, we found no association between ETL exposure and reported and confirmed household water treatment with chlorine. In both groups (ETL and comparison), reported use of water treatment was low and did not change during our 6-month follow-up. However, persons confirmed to have chlorinated water had improved bacteriologic water quality. Study findings suggest that ETL implementation was suboptimal, which, along with unexpected changes in the supply and price of chlorine, may have prevented an accurate assessment of the potential impact of ETL on water treatment behavior. Taken together, these observations exemplify the complexities of habits, practices, attitudes, and external factors that can create challenging conditions for implementing behavioral interventions. As a consequence, in this trial, ETL had no measurable impact on water treatment behavior.
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Affiliation(s)
- Christine E Stauber
- 1Department of Population Health Sciences, School of Public Health, Atlanta, Georgia State University, Atlanta, Georgia
| | - Bobbie Person
- 2Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Katharine Schilling
- 2Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Matthew J Hayat
- 1Department of Population Health Sciences, School of Public Health, Atlanta, Georgia State University, Atlanta, Georgia
| | - Tracy Ayers
- 2Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Robert Quick
- 2Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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Milucky J, Pondo T, Gregory CJ, Iuliano D, Chaves SS, McCracken J, Mansour A, Zhang Y, Aleem MA, Wolff B, Whitaker B, Whistler T, Onyango C, Lopez MR, Liu N, Rahman MZ, Shang N, Winchell J, Chittaganpitch M, Fields B, Maldonado H, Xie Z, Lindstrom S, Sturm-Ramirez K, Montgomery J, Wu KH, Van Beneden CA. The epidemiology and estimated etiology of pathogens detected from the upper respiratory tract of adults with severe acute respiratory infections in multiple countries, 2014-2015. PLoS One 2020; 15:e0240309. [PMID: 33075098 PMCID: PMC7571682 DOI: 10.1371/journal.pone.0240309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION Etiology studies of severe acute respiratory infections (SARI) in adults are limited. We studied potential etiologies of SARI among adults in six countries using multi-pathogen diagnostics. METHODS We enrolled both adults with SARI (acute respiratory illness onset with fever and cough requiring hospitalization) and asymptomatic adults (adults hospitalized with non-infectious illnesses, non-household members accompanying SARI patients, adults enrolled from outpatient departments, and community members) in each country. Demographics, clinical data, and nasopharyngeal and oropharyngeal specimens were collected from both SARI patients and asymptomatic adults. Specimens were tested for presence of 29 pathogens utilizing the Taqman® Array Card platform. We applied a non-parametric Bayesian regression extension of a partially latent class model approach to estimate proportions of SARI caused by specific pathogens. RESULTS We enrolled 2,388 SARI patients and 1,135 asymptomatic adults from October 2013 through October 2015. We detected ≥1 pathogen in 76% of SARI patients and 67% of asymptomatic adults. Haemophilus influenzae and Streptococcus pneumoniae were most commonly detected (≥23% of SARI patients and asymptomatic adults). Through modeling, etiology was attributed to a pathogen in most SARI patients (range among countries: 57.3-93.2%); pathogens commonly attributed to SARI etiology included influenza A (14.4-54.4%), influenza B (1.9-19.1%), rhino/enterovirus (1.8-42.6%), and RSV (3.6-14.6%). CONCLUSIONS Use of multi-pathogen diagnostics and modeling enabled attribution of etiology in most adult SARI patients, despite frequent detection of multiple pathogens in the upper respiratory tract. Seasonal flu vaccination and development of RSV vaccine would likely reduce the burden of SARI in these populations.
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Affiliation(s)
- Jennifer Milucky
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Tracy Pondo
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Christopher J. Gregory
- Division of Global Health Protection, Centers for Disease Control and Prevention, Thailand Ministry of Public Health, Thailand
| | - Danielle Iuliano
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Sandra S. Chaves
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, CDC Kenya Office, Kenya
| | - John McCracken
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Adel Mansour
- Division of Global Health Protection, Centers for Disease Control and Prevention, Egypt
| | - Yuzhi Zhang
- Division of Global Health Protection, Centers for Disease Control and Prevention, China
| | | | - Bernard Wolff
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Brett Whitaker
- Division of Viral Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Toni Whistler
- Division of Global Health Protection, Centers for Disease Control and Prevention, Thailand Ministry of Public Health, Thailand
| | - Clayton Onyango
- Kenya Medical Research Institute/Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - Maria Renee Lopez
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Na Liu
- China Centers for Disease Control and Prevention, National Institute for Viral Disease, Beijing, China
| | | | - Nong Shang
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Jonas Winchell
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | | | - Barry Fields
- Division of Global Health Protection, Centers for Disease Control and Prevention, Kenya
| | - Herberth Maldonado
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Zhiping Xie
- China Centers for Disease Control and Prevention, National Institute for Viral Disease, Beijing, China
| | - Stephen Lindstrom
- Division of Viral Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
| | - Katherine Sturm-Ramirez
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, CDC Bangladesh Office, Bangladesh
| | - Joel Montgomery
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kai-Hui Wu
- Influenza Division, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, CDC Bangladesh Office, Bangladesh
| | - Chris A. Van Beneden
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, Georgia, United States of America
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Moirongo RM, Lorenz E, Ntinginya NE, Dekker D, Fernandes J, Held J, Lamshöft M, Schaumburg F, Mangu C, Sudi L, Sie A, Souares A, Heinrich N, Wieser A, Mordmüller B, Owusu-Dabo E, Adegnika AA, Coulibaly B, May J, Eibach D. Regional Variation of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Enterobacterales, Fluoroquinolone-Resistant Salmonella enterica and Methicillin-Resistant Staphylococcus aureus Among Febrile Patients in Sub-Saharan Africa. Front Microbiol 2020; 11:567235. [PMID: 33101240 PMCID: PMC7546812 DOI: 10.3389/fmicb.2020.567235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
Background Antimicrobial resistance (AMR) thwarts the curative power of drugs and is a present-time global problem. We present data on antimicrobial susceptibility and resistance determinants of bacteria the WHO has highlighted as being key antimicrobial resistance concerns in Africa, to strengthen knowledge of AMR patterns in the region. Methods Blood, stool, and urine specimens of febrile patients, aged between ≥ 30 days and ≤ 15 years and hospitalized in Burkina Faso, Gabon, Ghana, and Tanzania were cultured from November 2013 to March 2017 (Patients > 15 years were included in Tanzania). Antimicrobial susceptibility testing was performed for all Enterobacterales and Staphylococcus aureus isolates using disk diffusion method. Extended-spectrum beta-lactamase (ESBL) production was confirmed by double-disk diffusion test and the detection of blaCTX–M, blaTEM and blaSHV. Multilocus sequence typing was conducted for ESBL-producing Escherichia coli and Klebsiella pneumoniae, ciprofloxacin-resistant Salmonella enterica and S. aureus. Ciprofloxacin-resistant Salmonella enterica were screened for plasmid-mediated resistance genes and mutations in gyrA, gyrB, parC, and parE. S. aureus isolates were tested for the presence of mecA and Panton-Valentine Leukocidin (PVL) and further genotyped by spa typing. Results Among 4,052 specimens from 3,012 patients, 219 cultures were positive of which 88.1% (n = 193) were Enterobacterales and 7.3% (n = 16) S. aureus. The prevalence of ESBL-producing Enterobacterales (all CTX-M15 genotype) was 45.2% (14/31; 95% CI: 27.3, 64.0) in Burkina Faso, 25.8% (8/31; 95% CI: 11.9, 44.6) in Gabon, 15.1% (18/119; 95% CI: 9.2, 22.8) in Ghana and 0.0% (0/12; 95% CI: 0.0, 26.5) in Tanzania. ESBL positive non-typhoid Salmonella (n = 3) were detected in Burkina Faso only and methicillin-resistant S. aureus (n = 2) were detected in Ghana only. While sequence type (ST)131 predominated among ESBL E. coli (39.1%;9/23), STs among ESBL K. pneumoniae were highly heterogenous. Ciprofloxacin resistant nt Salmonella were commonest in Burkina Faso (50.0%; 6/12) and all harbored qnrB genes. PVL were found in 81.3% S. aureus. Conclusion Our findings reveal a distinct susceptibility pattern across the various study regions in Africa, with notably high rates of ESBL-producing Enterobacterales and ciprofloxacin-resistant nt Salmonella in Burkina Faso. This highlights the need for local AMR surveillance and reporting of resistances to support appropriate action.
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Affiliation(s)
- Rehema Moraa Moirongo
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Eva Lorenz
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nyanda E Ntinginya
- National Institute for Medical Research-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Denise Dekker
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
| | - José Fernandes
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Jana Held
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Maike Lamshöft
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
| | - Frieder Schaumburg
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Chacha Mangu
- National Institute for Medical Research-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Lwitiho Sudi
- National Institute for Medical Research-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Ali Sie
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | - Aurelia Souares
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Heidelberg Institute of Global Health (HIGH), Heidelberg University Hospital, Heidelberg, Germany
| | - Norbert Heinrich
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Department of Infectious Diseases & Tropical Medicine, Ludwig Maximilians University of Munich, Munich, Germany
| | - Andreas Wieser
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Department of Infectious Diseases & Tropical Medicine, Ludwig Maximilians University of Munich, Munich, Germany.,Faculty of Medicine, Max Von Pettenkofer Institute, Ludwig Maximilians University of Munich, Munich, Germany
| | - Benjamin Mordmüller
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), African Partner Institution, Lambaréné, Gabon
| | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Akim Ayola Adegnika
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), African Partner Institution, Lambaréné, Gabon
| | | | - Jürgen May
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
| | - Daniel Eibach
- Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Heidelberg, Munich, Tübingen, Germany
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40
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Bigogo GM, Audi A, Auko J, Aol GO, Ochieng BJ, Odiembo H, Odoyo A, Widdowson MA, Onyango C, Borgdorff MW, Feikin DR, Carvalho MDG, Whitney CG, Verani JR. Indirect Effects of 10-Valent Pneumococcal Conjugate Vaccine Against Adult Pneumococcal Pneumonia in Rural Western Kenya. Clin Infect Dis 2020; 69:2177-2184. [PMID: 30785189 DOI: 10.1093/cid/ciz139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/11/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Data on pneumococcal conjugate vaccine (PCV) indirect effects in low-income countries with high human immunodeficiency virus (HIV) burden are limited. We examined adult pneumococcal pneumonia incidence before and after PCV introduction in Kenya in 2011. METHODS From 1 January 2008 to 31 December 2016, we conducted surveillance for acute respiratory infection (ARI) among ~12 000 adults (≥18 years) in western Kenya, where HIV prevalence is ~17%. ARI cases (cough or difficulty breathing or chest pain, plus temperature ≥38.0°C or oxygen saturation <90%) presenting to a clinic underwent blood culture and pneumococcal urine antigen testing (UAT). We calculated ARI incidence and adjusted for healthcare seeking. The proportion of ARI cases with pneumococcus detected among those with complete testing (blood culture and UAT) was multiplied by adjusted ARI incidence to estimate pneumococcal pneumonia incidence. RESULTS Pre-PCV (2008-2010) crude and adjusted ARI incidences were 3.14 and 5.30/100 person-years-observation (pyo), respectively. Among ARI cases, 39.0% (340/872) had both blood culture and UAT; 21.2% (72/340) had pneumococcus detected, yielding a baseline pneumococcal pneumonia incidence of 1.12/100 pyo (95% confidence interval [CI]: 1.0-1.3). In each post-PCV year (2012-2016), the incidence was significantly lower than baseline; with incidence rate ratios (IRRs) of 0.53 (95% CI: 0.31-0.61) in 2012 and 0.13 (95% CI: 0.09-0.17) in 2016. Similar declines were observed in HIV-infected (IRR: 0.13; 95% CI: 0.08-0.22) and HIV-uninfected (IRR: 0.10; 95% CI: 0.05-0.20) adults. CONCLUSIONS Adult pneumococcal pneumonia declined in western Kenya following PCV introduction, likely reflecting vaccine indirect effects. Evidence of herd protection is critical for guiding PCV policy decisions in resource-constrained areas.
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Affiliation(s)
- Godfrey M Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu.,Academic Medical Centre, University of Amsterdam, The Netherlands
| | - Allan Audi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Joshua Auko
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - George O Aol
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Benjamin J Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Herine Odiembo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Arthur Odoyo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu
| | - Marc-Alain Widdowson
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Clayton Onyango
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Martien W Borgdorff
- Academic Medical Centre, University of Amsterdam, The Netherlands.,Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Daniel R Feikin
- US Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Jennifer R Verani
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
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41
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Trajano Gomes da Silva D, Ebdon J, Okotto-Okotto J, Ade F, Mito O, Wanza P, Kwoba E, Mwangi T, Yu W, Wright JA. A longitudinal study of the association between domestic contact with livestock and contamination of household point-of-use stored drinking water in rural Siaya County (Kenya). Int J Hyg Environ Health 2020; 230:113602. [PMID: 32911124 PMCID: PMC7607227 DOI: 10.1016/j.ijheh.2020.113602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/08/2022]
Abstract
Background Emerging evidence suggests close domestic proximity of livestock and humans may lead to microbiological contamination of hands, objects, food and water supplies within domestic environments, adversely impacting public health. However, evidence quantifying the relationship between livestock, domestic animals, humans and microbiological contamination of household stored water remains limited. Aim This longitudinal study aimed to examine the relationship between domestic contact with livestock and domestic animals on microbiological contamination of household Point-of-Use (POU) stored drinking water in rural Kenya and assess the influence of choice of faecal indicator on such associations. Methodology A survey was performed in 234 households in Siaya county, Kenya, to observe presence of livestock (cattle, goats, poultry) and domestic animals (cats, dogs) in household compounds, alongside other risk factors for contamination of POU stored drinking water such as sanitation, storage conditions and hygiene practices. Samples from water sources (e.g. piped, spring/wells, boreholes, surface and rainwater) and from POU storage containers were tested for E. coli and intestinal enterococci. Livestock-related risk factors for water contamination were examined through multinomial regression, controlling for confounders. Results Rainwater was the main POU water source and was found to be highly susceptible to contamination. Multivariate analysis showed greater risk of gross (>100 CFU/100 mL) water contamination (with E. coli) for households where goats were observed, and/or where poultry roosted in proximity to stored household water (relative risk RR = 2.71; p = 0.001 and RR = 2.02; p = 0.012 respectively). Presence of a poultry coop was also associated with elevated intestinal enterococci densities (RR = 4.46; p = 0.001). Associations between contamination and livestock risk factors were thus similar for both bacteria groups, but E. coli counts declined more rapidly following collection from surface waters than enterococci counts (p = 0.024). Conclusion The presence of livestock (particularly goats) and poultry within household compounds increases POU water contamination risk, suggesting the need for improved interventions to address cross-contamination within rural domestic settings. Within Siaya county, more effective community education is needed to raise awareness of POU water quality protection, particularly of rainwater. Poultry and goats are risk factors for household stored water contamination. Poultry are risk factors for both enterococci and E. coli contamination. Attenuation of enterococci in household stored water is lower than for E. coli. Residual free chlorine is mostly too low to prevent stored water recontamination.
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Affiliation(s)
- Diogo Trajano Gomes da Silva
- School of Environment and Technology, University of Brighton, Cockcroft Building, Lewes Road, Brighton, BN2 4GJ, UK.
| | - James Ebdon
- School of Environment and Technology, University of Brighton, Cockcroft Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Joseph Okotto-Okotto
- Victoria Institute for Research on Environment and Development (VIRED) International, P.O. Box 6423-40103, Off Nairobi Road, Rabour, Kisumu, Kenya
| | - Frederick Ade
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Oscar Mito
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Peggy Wanza
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Emmah Kwoba
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Thumbi Mwangi
- Centre for Global Health Research, Kenya Medical Research Institute, P.O. Box 1578-40100, Kisumu, Kenya
| | - Weiyu Yu
- School of Geography and Environmental Science, University of Southampton, Building 44, Highfield, Southampton, SO17 1BJ, UK
| | - Jim A Wright
- School of Geography and Environmental Science, University of Southampton, Building 44, Highfield, Southampton, SO17 1BJ, UK
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42
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Moyo SJ, Manyahi J, Blomberg B, Tellevik MG, Masoud NS, Aboud S, Manji K, Roberts AP, Hanevik K, Mørch K, Langeland N. Bacteraemia, Malaria, and Case Fatality Among Children Hospitalized With Fever in Dar es Salaam, Tanzania. Front Microbiol 2020; 11:2118. [PMID: 33013772 PMCID: PMC7511546 DOI: 10.3389/fmicb.2020.02118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/11/2020] [Indexed: 12/31/2022] Open
Abstract
Background Febrile illness is the commonest cause of hospitalization in children <5 years in sub-Saharan Africa, and bacterial bloodstream infections and malaria are major causes of death. Methods From March 2017 to July 2018, we enrolled 2,226 children aged 0–5 years hospitalized due to fever in four major public hospitals of Dar es Salaam, namely, Amana, Temeke, and Mwananyamala Regional Hospitals and Muhimbili National Hospital. We recorded social demographic and clinical data, and we performed blood-culture and HIV-antibody testing. We used qPCR to quantify Plasmodium falciparum parasitaemia and Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) to identify bacterial isolates. Disk diffusion method was used for antimicrobial susceptibility testing. Results Nineteen percent of the children (426/2,226) had pathogens detected from blood. Eleven percent (236/2,226) of the children had bacteraemia/fungaemia and 10% (204/2,063) had P. falciparum malaria. Ten children had concomitant malaria and bacteraemia. Gram-negative bacteria (64%) were more frequent than Gram-positive (32%) and fungi (4%). Over 50% of Gram-negative bacteria were extended-spectrum beta-lactamase (ESBL) producers and multidrug resistant. Methicillin resistant Staphylococcus aureus (MRSA) was found in 11/42 (26.2%). The most severe form of clinical malaria was associated with high parasitaemia (>four million genomes/μL) of P. falciparum in plasma. Overall, in-hospital death was 4% (89/2,146), and it was higher in children with bacteraemia (8%, 18/227) than malaria (2%, 4/194, p = 0.007). Risk factors for death were bacteraemia (p = 0.03), unconsciousness at admission (p < 0.001), and admission at a tertiary hospital (p = 0.003). Conclusion Compared to previous studies in this region, our study showed a reduction in malaria prevalence, a decrease in in-hospital mortality, and an increase in antimicrobial resistance (AMR) including ESBLs and multidrug resistance. An increase of AMR highlights the importance of continued strengthening of diagnostic capability and antimicrobial stewardship programs. We also found malaria and bacteraemia contributed equally in causing febrile illness, but bacteraemia caused higher in-hospital death. The most severe form of clinical malaria was associated with P. falciparum parasitaemia.
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Affiliation(s)
- Sabrina J Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Joel Manyahi
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Marit Gjerde Tellevik
- Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Nahya Salim Masoud
- Department of Paediatrics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Said Aboud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Karim Manji
- Department of Paediatrics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Kristine Mørch
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
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43
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Matheson AI, Mogeni OD, Lacsina JR, Ochieng M, Audi A, Bigogo G, Neatherlin J, Margolis HS, Fields B, Ahenda P, Walson JL, Montgomery JM. No Evidence of Acute Dengue Virus Infections at a Rural Site in Western Kenya, 2011 and 2013. Am J Trop Med Hyg 2020; 103:2054-2058. [PMID: 32876014 DOI: 10.4269/ajtmh.20-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The incidence and spread of dengue virus (DENV) have increased rapidly in recent decades. Dengue is underreported in Africa, but recent outbreaks and seroprevalence data suggest that DENV is widespread there. A lack of ongoing surveillance limits knowledge about its spatial reach and hinders disease control planning. We sought to add data on dengue distribution in Kenya through diagnostic testing of serum specimens from persons with an acute febrile illness (AFI) attending an outpatient clinic in rural western Kenya (Asembo) during rainy seasons. Patients with symptoms not likely to be misclassified as dengue (e.g., diarrhea and anemia), those with a positive diagnostic laboratory results which explained their febrile illness, or those with serum collected more than 5 days after fever onset were excluded. However, febrile patients with a positive malaria smear were included in the study. We used reverse transcription polymerase chain reaction (RT-PCR) to test for DENV and IgM anti-DENV to test for recent infection. Of the 615 serum specimens available for testing, none were dengue positive by either RT-PCR or IgM anti-DENV testing. Dengue did not appear to be a cause of febrile illness in this area of western Kenya, although our relatively small sample size may not have identified DENV infections occurring at low incidence. A more widespread AFI surveillance system that includes dengue diagnostic testing by RT-PCR and antibody-based methods is required to more definitively gauge the size and geographic distribution of DENV infection in western Kenya.
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Affiliation(s)
- Alastair I Matheson
- Department of Global Health, University of Washington, Seattle, Washington.,Department of Epidemiology, University of Washington, Seattle, Washington
| | - Ondari D Mogeni
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Joshua R Lacsina
- Department of Medicine, University of Washington, Seattle, Washington
| | - Melvin Ochieng
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Allan Audi
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya
| | - Godfrey Bigogo
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Kisumu, Kenya
| | - John Neatherlin
- Kenya Medical Research Institute/Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Harold S Margolis
- Dengue Branch, Division of Vectorborne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Barry Fields
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Petronella Ahenda
- School of Public Health, Texas A&M University, College Station, Texas
| | - Judd L Walson
- Department of Medicine, University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington.,Department of Epidemiology, University of Washington, Seattle, Washington
| | - Joel M Montgomery
- Division of Global Health Protection, Centers for Disease Control and Prevention, Atlanta, Georgia
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44
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Farrar JL, Odiembo H, Odoyo A, Bigogo G, Kim L, Lessa FC, Feikin DR, Breiman RF, Whitney CG, Carvalho MG, Pimenta FC. Limited Added Value of Oropharyngeal Swabs for Detecting Pneumococcal Carriage in Adults. Open Forum Infect Dis 2020; 7:ofaa368. [PMID: 32995349 PMCID: PMC7505525 DOI: 10.1093/ofid/ofaa368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/13/2020] [Indexed: 11/14/2022] Open
Abstract
We compared pneumococcal isolation rates and evaluated the benefit of using oropharyngeal (OP) specimens in addition to nasopharyngeal (NP) specimens collected from adults in rural Kenya. Of 846 adults, 52.1% were colonized; pneumococci were detected from both NP and OP specimens in 23.5%, NP only in 22.9%, and OP only in 5.7%. Ten-valent pneumococcal conjugate vaccine strains were detected from both NP and OP in 3.4%, NP only in 4.1%, and OP only in 0.7%. Inclusion of OP swabs increased carriage detection by 5.7%; however, the added cost of collecting and processing OP specimens may justify exclusion from future carriage studies among adults.
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Affiliation(s)
- Jennifer L Farrar
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Herine Odiembo
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Arthur Odoyo
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Godfrey Bigogo
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Lindsay Kim
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fernanda C Lessa
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Daniel R Feikin
- Global Disease Detection Division (GDD) and International Emerging Infections Program (IEIP), Kenya Medical Research Institute (KEMRI)/CDC Public Health and Research Collaboration, Kisumu, Kenya
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, Georgia, USA
| | - Cynthia G Whitney
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria G Carvalho
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fabiana C Pimenta
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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45
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Crump JA, Thomas KM, Benschop J, Knox MA, Wilkinson DA, Midwinter AC, Munyua P, Ochieng JB, Bigogo GM, Verani JR, Widdowson MA, Prinsen G, Cleaveland S, Karimuribo ED, Kazwala RR, Mmbaga BT, Swai ES, French NP, Zadoks RN. Investigating the meat pathway as a source of human nontyphoidal Salmonella bloodstream infections and diarrhea in East Africa. Clin Infect Dis 2020; 73:e1570-e1578. [PMID: 32777036 PMCID: PMC8492120 DOI: 10.1093/cid/ciaa1153] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/04/2020] [Indexed: 11/29/2022] Open
Abstract
Background Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood. Methods We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods. Meat pathway isolates were compared with nontyphoidal serovars of Salmonella enterica (NTS) isolated from persons with bloodstream infections and diarrheal disease from 2007 through 2017 from Kenya by core genome multi-locus sequence typing (cgMLST). Isolates were characterized for antimicrobial resistance, virulence genes, and diversity. Results We isolated NTS from 164 meat pathway samples. Of 172 human NTS isolates, 90 (52.3%) from stool and 82 (47.7%) from blood, 53 (30.8%) were Salmonella Enteritidis sequence type (ST) 11 and 62 (36.0%) were Salmonella Typhimurium ST313. We identified cgMLST clusters within Salmonella Enteritidis ST11, Salmonella Heidelberg ST15, Salmonella Typhimurium ST19, and Salmonella II 42:r:- ST1208 that included both human and meat pathway isolates. Salmonella Typhimurium ST313 was isolated exclusively from human samples. Human and poultry isolates bore more antimicrobial resistance and virulence genes and were less diverse than isolates from other sources. Conclusions Our findings suggest that the meat pathway may be an important source of human infection with some clades of Salmonella Enteritidis ST11 in East Africa, but not of human infection by Salmonella Typhimurium ST313. Research is needed to systematically examine the contributions of other types of meat, animal products, produce, water, and the environment to nontyphoidal Salmonella disease in East Africa.
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Affiliation(s)
- John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand.,Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Kate M Thomas
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Jackie Benschop
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Matthew A Knox
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - David A Wilkinson
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C Midwinter
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Peninah Munyua
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - John B Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Godfrey M Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Jennifer R Verani
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Gerard Prinsen
- School of People, Environment and Planning, Massey University, Palmerston North, New Zealand
| | - Sarah Cleaveland
- Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Esron D Karimuribo
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Rudovick R Kazwala
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Emanuel S Swai
- Department of Veterinary Services, Ministry of Livestock and Fisheries, Dodoma, Tanzania
| | - Nigel P French
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health, and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom.,Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
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46
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Mwanga MJ, Owor BE, Ochieng JB, Ngama MH, Ogwel B, Onyango C, Juma J, Njeru R, Gicheru E, Otieno GP, Khagayi S, Agoti CN, Bigogo GM, Omore R, Addo OY, Mapaseka S, Tate JE, Parashar UD, Hunsperger E, Verani JR, Breiman RF, Nokes DJ. Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018. BMC Infect Dis 2020; 20:504. [PMID: 32660437 PMCID: PMC7359451 DOI: 10.1186/s12879-020-05230-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/03/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Kenya introduced the monovalent G1P [8] Rotarix® vaccine into the infant immunization schedule in July 2014. We examined trends in rotavirus group A (RVA) genotype distribution pre- (January 2010-June 2014) and post- (July 2014-December 2018) RVA vaccine introduction. METHODS Stool samples were collected from children aged < 13 years from four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Hospital, and Siaya County Referral Hospital (children aged < 5 years only). Samples were screened for RVA using enzyme linked immunosorbent assay (ELISA) and VP7 and VP4 genes sequenced to infer genotypes. RESULTS We genotyped 614 samples in pre-vaccine and 261 in post-vaccine introduction periods. During the pre-vaccine introduction period, the most frequent RVA genotypes were G1P [8] (45.8%), G8P [4] (15.8%), G9P [8] (13.2%), G2P [4] (7.0%) and G3P [6] (3.1%). In the post-vaccine introduction period, the most frequent genotypes were G1P [8] (52.1%), G2P [4] (20.7%) and G3P [8] (16.1%). Predominant genotypes varied by year and site in both pre and post-vaccine periods. Temporal genotype patterns showed an increase in prevalence of vaccine heterotypic genotypes, such as the commonly DS-1-like G2P [4] (7.0 to 20.7%, P < .001) and G3P [8] (1.3 to 16.1%, P < .001) genotypes in the post-vaccine introduction period. Additionally, we observed a decline in prevalence of genotypes G8P [4] (15.8 to 0.4%, P < .001) and G9P [8] (13.2 to 5.4%, P < .001) in the post-vaccine introduction period. Phylogenetic analysis of genotype G1P [8], revealed circulation of strains of lineages G1-I, G1-II and P [8]-1, P [8]-III and P [8]-IV. Considerable genetic diversity was observed between the pre and post-vaccine strains, evidenced by distinct clusters. CONCLUSION Genotype prevalence varied from before to after vaccine introduction. Such observations emphasize the need for long-term surveillance to monitor vaccine impact. These changes may represent natural secular variation or possible immuno-epidemiological changes arising from the introduction of the vaccine. Full genome sequencing could provide insights into post-vaccine evolutionary pressures and antigenic diversity.
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Affiliation(s)
- Mike J Mwanga
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya.
| | - Betty E Owor
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya
| | - John B Ochieng
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - Mwanajuma H Ngama
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya
| | - Billy Ogwel
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - Clayton Onyango
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jane Juma
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - Regina Njeru
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya
| | - Elijah Gicheru
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya
| | - Grieven P Otieno
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya
| | - Sammy Khagayi
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - Charles N Agoti
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya
| | - Godfrey M Bigogo
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - Richard Omore
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - O Yaw Addo
- Global Health Institute, Emory University, Atlanta, GA, USA
| | - Seheri Mapaseka
- Department of Virology, South African Medical Research Council/Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Jacqueline E Tate
- Division of Viral Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Umesh D Parashar
- Division of Viral Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elizabeth Hunsperger
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jennifer R Verani
- Division of Global Health Protection, US Centers for Disease Control and Prevention, Nairobi, Kenya
| | | | - D James Nokes
- Wellcome Trust Research Programme, Kenya Medical Research Institute, Kilifi, Kenya.
- School of Life Science, and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, CV47AL, UK.
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47
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Jung S, Moon J, Hwang E. Cluster-Based Analysis of Infectious Disease Occurrences Using Tensor Decomposition: A Case Study of South Korea. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17134872. [PMID: 32640742 PMCID: PMC7370004 DOI: 10.3390/ijerph17134872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/01/2020] [Accepted: 07/04/2020] [Indexed: 11/23/2022]
Abstract
For a long time, various epidemics, such as lower respiratory infections and diarrheal diseases, have caused serious social losses and costs. Various methods for analyzing infectious disease occurrences have been proposed for effective prevention and proactive response to reduce such losses and costs. However, the results of the occurrence analyses were limited because numerous factors affect the outbreak of infectious diseases and there are complex interactions between these factors. To alleviate this limitation, we propose a cluster-based analysis scheme of infectious disease occurrences that can discover commonalities or differences between clusters by grouping elements with similar occurrence patterns. To do this, we collect and preprocess infectious disease occurrence data according to time, region, and disease. Then, we construct a tensor for the data and apply Tucker decomposition to extract latent features in the dimensions of time, region, and disease. Based on these latent features, we conduct k-means clustering and analyze the results for each dimension. To demonstrate the effectiveness of this scheme, we conduct a case study on data from South Korea and report some of the results.
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48
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Ashraf S, Islam M, Unicomb L, Rahman M, Winch PJ, Arnold BF, Benjamin-Chung J, Ram PK, Colford JM, Luby SP. Effect of Improved Water Quality, Sanitation, Hygiene and Nutrition Interventions on Respiratory Illness in Young Children in Rural Bangladesh: A Multi-Arm Cluster-Randomized Controlled Trial. Am J Trop Med Hyg 2020; 102:1124-1130. [PMID: 32100681 PMCID: PMC7204588 DOI: 10.4269/ajtmh.19-0769] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Acute respiratory infections cause mortality in young children. We assessed the effects of water, sanitation, hygiene (WASH) and nutritional interventions on childhood ARI. Geographic clusters of pregnant women from rural Bangladesh were randomly assigned to receive 1) chlorinated drinking water and safe storage (W); 2) upgraded sanitation (S); 3) handwashing promotion (H); 4) combined water, sanitation, and handwashing (WSH); 5) nutrition intervention including lipid-based nutrient supplements; 6) combined WSH plus nutrition (WSHN); or 7) no intervention (control). Masking of participants was not possible. Acute respiratory illness was defined as caregiver-reported persistent cough, panting, wheezing, or difficulty breathing in the past 7 days among index children, those born to enrolled women. We assessed outcomes at 12 and 24 months of intervention using intention to treat. Compared with children in the control group (ARI prevalence, P: 8.9%), caregivers of index children reported significantly lower ARI in the water (P: 6.3%, prevalence ratio (PR): 0.71; 95% CI: 0.53, 0.96), sanitation (P: 6.4%, PR: 0.75, 95% CI: 0.58, 0.96), handwashing (P: 6.4%, PR: 0.68, 95% CI: 0.50, 0.93), and the combined WSH+N arms (P: 5.9%, PR: 0.67, 95% CI: 0.50, 0.90). Those in the nutrition (P: 7.4%, PR: 0.84, 95% CI: 0.63, 1.10) or the WSH arm (P: 8.9%, PR: 0.99, 95% CI: 0.76, 1.28) reported similar ARI prevalence compared with control children. Single targeted water, sanitation, and hygiene interventions reduced reported respiratory illness in young children. There was no apparent respiratory health benefit from combining WASH interventions.
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Affiliation(s)
- Sania Ashraf
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Mahfuza Islam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Leanne Unicomb
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mahbubur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Peter J Winch
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Benjamin F Arnold
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, California
| | - Jade Benjamin-Chung
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, California
| | - Pavani K Ram
- School of Public Health and Health Professions, University at Buffalo, Buffalo, New York
| | - John M Colford
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, California
| | - Stephen P Luby
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California
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49
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Dieng I, Hedible BG, Diagne MM, El Wahed AA, Diagne CT, Fall C, Richard V, Vray M, Weidmann M, Faye O, Sall AA, Faye O. Mobile Laboratory Reveals the Circulation of Dengue Virus Serotype I of Asian Origin in Medina Gounass (Guediawaye), Senegal. Diagnostics (Basel) 2020; 10:diagnostics10060408. [PMID: 32560073 PMCID: PMC7345902 DOI: 10.3390/diagnostics10060408] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/09/2023] Open
Abstract
With the growing success of controlling malaria in Sub-Saharan Africa, the incidence of fever due to malaria is in decline, whereas the proportion of patients with non-malaria febrile illness (NMFI) is increasing. Clinical diagnosis of NMFI is hampered by unspecific symptoms, but early diagnosis is a key factor for both better patient care and disease control. The aim of this study was to determine the arboviral aetiologies of NMFI in low resource settings, using a mobile laboratory based on recombinase polymerase amplification (RPA) assays. The panel of tests for this study was expanded to five arboviruses: dengue virus (DENV), zika virus (ZIKV), yellow fever virus (YFV), chikungunya virus (CHIKV), and rift valley fever virus (RVFV). One hundred and four children aged between one month and 115 months were enrolled and screened. Three of the 104 blood samples of children <10 years presented at an outpatient clinic tested positive for DENV. The results were confirmed by RT-PCR, partial sequencing, and non-structural protein 1 (NS1) antigen capture by ELISA (Biorad, France). Phylogenetic analysis of the derived DENV-1 sequences clustered them with sequences of DENV-1 isolated from Guangzhou, China, in 2014. In conclusion, this mobile setup proved reliable for the rapid identification of the causative agent of NMFI, with results consistent with those obtained in the reference laboratory’s settings.
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Affiliation(s)
- Idrissa Dieng
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Boris Gildas Hedible
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Moussa Moïse Diagne
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Ahmed Abd El Wahed
- Microbiology and Animal Hygiene, University of Goettingen, D-33077 Goettingen, Germany;
| | - Cheikh Tidiane Diagne
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Cheikh Fall
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Vicent Richard
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Muriel Vray
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland FK9 4LA, UK;
| | - Ousmane Faye
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
- Correspondence: (O.F.); (O.F.)
| | - Amadou Alpha Sall
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Oumar Faye
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
- Correspondence: (O.F.); (O.F.)
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50
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Khagayi S, Omore R, Otieno GP, Ogwel B, Ochieng JB, Juma J, Apondi E, Bigogo G, Onyango C, Ngama M, Njeru R, Owor BE, Mwanga MJ, Addo Y, Tabu C, Amwayi A, Mwenda JM, Tate JE, Parashar UD, Breiman RF, Nokes DJ, Verani JR. Effectiveness of Monovalent Rotavirus Vaccine Against Hospitalization With Acute Rotavirus Gastroenteritis in Kenyan Children. Clin Infect Dis 2020; 70:2298-2305. [PMID: 31326980 PMCID: PMC7245145 DOI: 10.1093/cid/ciz664] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/17/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Rotavirus remains a leading cause of pediatric diarrheal illness and death worldwide. Data on rotavirus vaccine effectiveness in sub-Saharan Africa are limited. Kenya introduced monovalent rotavirus vaccine (RV1) in July 2014. We assessed RV1 effectiveness against rotavirus-associated hospitalization in Kenyan children. METHODS Between July 2014 and December 2017, we conducted surveillance for acute gastroenteritis (AGE) in 3 Kenyan hospitals. From children age-eligible for ≥1 RV1 dose, with stool tested for rotavirus and confirmed vaccination history we compared RV1 coverage among rotavirus positive (cases) vs rotavirus negative (controls) using multivariable logistic regression and calculated effectiveness based on adjusted odds ratio. RESULTS Among 677 eligible children, 110 (16%) were rotavirus positive. Vaccination data were available for 91 (83%) cases; 51 (56%) had 2 RV1 doses and 33 (36%) 0 doses. Among 567 controls, 418 (74%) had vaccination data; 308 (74%) had 2 doses and 69 (16%) 0 doses. Overall 2-dose effectiveness was 64% (95% confidence interval [CI], 35%-80%); effectiveness was 67% (95% CI, 30%-84%) for children aged <12 months and 72% (95% CI, 10%-91%) for children aged ≥12 months. Significant effectiveness was seen in children with normal weight for age, length/height for age and weight for length/height; however, no protection was found among underweight, stunted, or wasted children. CONCLUSIONS RV1 in the Kenyan immunization program provides significant protection against rotavirus-associated hospitalization which persisted beyond infancy. Malnutrition appears to diminish vaccine effectiveness. Efforts to improve rotavirus uptake and nutritional status are important to maximize vaccine benefit.
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Affiliation(s)
- Sammy Khagayi
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu
| | - Richard Omore
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu
| | - Grieven P Otieno
- Centre for Geographic Medicine Research–Coast, KEMRI–Wellcome Trust Research Programme, Kilifi, and
| | - Billy Ogwel
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu
| | - John B Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu
| | - Jane Juma
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu
| | - Evans Apondi
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu
| | - Godfrey Bigogo
- Centre for Global Health Research, Kenya Medical Research Institute (KEMRI), Kisumu
| | - Clayton Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention (CDC)–Kenya, Kisumu, Kenya
| | - Mwanajuma Ngama
- Centre for Geographic Medicine Research–Coast, KEMRI–Wellcome Trust Research Programme, Kilifi, and
| | - Regina Njeru
- Centre for Geographic Medicine Research–Coast, KEMRI–Wellcome Trust Research Programme, Kilifi, and
| | - Betty E Owor
- Centre for Geographic Medicine Research–Coast, KEMRI–Wellcome Trust Research Programme, Kilifi, and
| | - Mike J Mwanga
- Centre for Geographic Medicine Research–Coast, KEMRI–Wellcome Trust Research Programme, Kilifi, and
| | - Yaw Addo
- Emory Global Health Institute, Emory University, Atlanta, Georgia
| | - Collins Tabu
- National Vaccines and Immunisations Programme, and
| | - Anyangu Amwayi
- Disease Surveillance and Response Unit, Ministry of Health, Nairobi, Kenya
| | - Jason M Mwenda
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | - Jacqueline E Tate
- Viral Gastroenteritis Branch, Division of Viral Diseases, CDC, Atlanta, Georgia
| | - Umesh D Parashar
- Viral Gastroenteritis Branch, Division of Viral Diseases, CDC, Atlanta, Georgia
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, Georgia
| | - D James Nokes
- Centre for Geographic Medicine Research–Coast, KEMRI–Wellcome Trust Research Programme, Kilifi, and
- School of Life Sciences, and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Jennifer R Verani
- Division of Global Health Protection, CDC–Kenya, Nairobi, Kenya; and
- Division of Global Health Protection, CDC, Atlanta, Georgia
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