Last data update: Nov 04, 2024. (Total: 48056 publications since 2009)
Records 1-30 (of 31 Records) |
Query Trace: Cosmas L[original query] |
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Mortality patterns over a 10-year period in Kibera, an urban informal settlement in Nairobi, Kenya, 2009-2018
Oduor C , Omwenga I , Ouma A , Mutinda R , Kiplangat S , Mogeni OD , Cosmas L , Audi A , Odongo GS , Obor D , Breiman R , Montgomery J , Agogo G , Munywoki P , Bigogo G , Verani JR . Glob Health Action 2023 16 (1) 2238428 BACKGROUND: Reliable mortality data are important for evaluating the impact of health interventions. However, data on mortality patterns among populations living in urban informal settlements are limited. OBJECTIVES: To examine the mortality patterns and trends in an urban informal settlement in Kibera, Nairobi, Kenya. METHODS: Using data from a population-based surveillance platform we estimated overall and cause-specific mortality rates for all age groups using person-year-observation (pyo) denominators and using Poisson regression tested for trends in mortality rates over time. We compared associated mortality rates across groups using incidence rate ratios (IRR). Assignment of probable cause(s) of death was done using the InterVA-4 model. RESULTS: We registered 1134 deaths from 2009 to 2018, yielding a crude mortality rate of 4.4 (95% Confidence Interval [CI]4.2-4.7) per 1,000 pyo. Males had higher overall mortality rates than females (incidence rate ratio [IRR], 1.44; 95% CI, 1.28-1.62). The highest mortality rate was observed among children aged < 12 months (41.5 per 1,000 pyo; 95% CI 36.6-46.9). All-cause mortality rates among children < 12 months were higher than that of children aged 1-4 years (IRR, 8.5; 95% CI, 6.95-10.35). The overall mortality rate significantly declined over the period, from 6.7 per 1,000 pyo (95% CI, 5.7-7.8) in 2009 to 2.7 (95% CI, 2.0-3.4) per 1,000 pyo in 2018. The most common cause of death was acute respiratory infections (ARI)/pneumonia (18.1%). Among children < 5 years, the ARI/pneumonia deaths rate declined significantly over the study period (5.06 per 1,000 pyo in 2009 to 0.61 per 1,000 pyo in 2018; p = 0.004). Similarly, death due to pulmonary tuberculosis among persons 5 years and above significantly declined (0.98 per 1,000 pyo in 2009 to 0.25 per 1,000 pyo in 2018; p = 0.006). CONCLUSIONS: Overall and some cause-specific mortality rates declined over time, representing important public health successes among this population. |
The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries.
Park SE , Pham DT , Pak GD , Panzner U , Maria Cruz Espinoza L , von Kalckreuth V , Im J , Mogeni OD , Schütt-Gerowitt H , Crump JA , Breiman RF , Adu-Sarkodie Y , Owusu-Dabo E , Rakotozandrindrainy R , Bassiahi Soura A , Aseffa A , Gasmelseed N , Sooka A , Keddy KH , May J , Aaby P , Biggs HM , Hertz JT , Montgomery JM , Cosmas L , Olack B , Fields B , Sarpong N , Razafindrabe TJL , Raminosoa TM , Kabore LP , Sampo E , Teferi M , Yeshitela B , El Tayeb MA , Krumkamp R , Dekker DM , Jaeger A , Tall A , Gassama A , Niang A , Bjerregaard-Andersen M , Løfberg SV , Deerin JF , Park JK , Konings F , Carey ME , Van Puyvelde S , Ali M , Clemens J , Dougan G , Baker S , Marks F . BMJ Glob Health 2021 6 (8) BACKGROUND: Invasive non-typhoidal Salmonella (iNTS) is one of the leading causes of bacteraemia in sub-Saharan Africa. We aimed to provide a better understanding of the genetic characteristics and transmission patterns associated with multi-drug resistant (MDR) iNTS serovars across the continent. METHODS: A total of 166 iNTS isolates collected from a multi-centre surveillance in 10 African countries (2010-2014) and a fever study in Ghana (2007-2009) were genome sequenced to investigate the geographical distribution, antimicrobial genetic determinants and population structure of iNTS serotypes-genotypes. Phylogenetic analyses were conducted in the context of the existing genomic frameworks for various iNTS serovars. Population-based incidence of MDR-iNTS disease was estimated in each study site. RESULTS: Salmonella Typhimurium sequence-type (ST) 313 and Salmonella Enteritidis ST11 were predominant, and both exhibited high frequencies of MDR; Salmonella Dublin ST10 was identified in West Africa only. Mutations in the gyrA gene (fluoroquinolone resistance) were identified in S. Enteritidis and S. Typhimurium in Ghana; an ST313 isolate carrying bla (CTX-M-15) was found in Kenya. International transmission of MDR ST313 (lineage II) and MDR ST11 (West African clade) was observed between Ghana and neighbouring West African countries. The incidence of MDR-iNTS disease exceeded 100/100 000 person-years-of-observation in children aged <5 years in several West African countries. CONCLUSIONS: We identified the circulation of multiple MDR iNTS serovar STs in the sampled sub-Saharan African countries. Investment in the development and deployment of iNTS vaccines coupled with intensified antimicrobial resistance surveillance are essential to limit the impact of these pathogens in Africa. |
Impact of 10-valent pneumococcal conjugate vaccine introduction on pneumococcal carriage and antibiotic susceptibility patterns among children aged <5 years and adults with human immunodeficiency virus infection: Kenya, 2009-2013
Kobayashi M , Bigogo G , Kim L , Mogeni OD , Conklin LM , Odoyo A , Odiembo H , Pimenta F , Ouma D , Harris AM , Odero K , Milucky JL , Ouma A , Aol G , Audi A , Onyango C , Cosmas L , Jagero G , Farrar JL , da Gloria Carvalho M , Whitney CG , Breiman RF , Lessa FC . Clin Infect Dis 2020 70 (5) 814-826 BACKGROUND: Kenya introduced 10-valent pneumococcal conjugate vaccine (PCV10) among children <1 year in 2011 with catch-up vaccination among children 1-4 years in some areas. We assessed changes in pneumococcal carriage and antibiotic susceptibility patterns in children <5 years and adults. METHODS: During 2009-2013, we performed annual cross-sectional pneumococcal carriage surveys in 2 sites: Kibera (children <5 years) and Lwak (children <5 years, adults). Only Lwak had catch-up vaccination. Nasopharyngeal and oropharyngeal (adults only) swabs underwent culture for pneumococci; isolates were serotyped. Antibiotic susceptibility testing was performed on isolates from 2009 and 2013; penicillin nonsusceptible pneumococci (PNSP) was defined as penicillin-intermediate or -resistant. Changes in pneumococcal carriage by age (<1 year, 1-4 years, adults), site, and human immunodeficiency virus (HIV) status (adults only) were calculated using modified Poisson regression, with 2009-2010 as baseline. RESULTS: We enrolled 2962 children (2073 in Kibera, 889 in Lwak) and 2590 adults (2028 HIV+, 562 HIV-). In 2013, PCV10-type carriage was 10.3% (Lwak) to 14.6% (Kibera) in children <1 year and 13.8% (Lwak) to 18.7% (Kibera) in children 1-4 years. This represents reductions of 60% and 63% among children <1 year and 52% and 60% among children 1-4 years in Kibera and Lwak, respectively. In adults, PCV10-type carriage decreased from 12.9% to 2.8% (HIV+) and from 11.8% to 0.7% (HIV-). Approximately 80% of isolates were PNSP, both in 2009 and 2013. CONCLUSIONS: PCV10-type carriage declined in children <5 years and adults post-PCV10 introduction. However, PCV10-type and PNSP carriage persisted in children regardless of catch-up vaccination. |
Multicountry distribution and characterization of extended-spectrum beta-lactamase-associated gram-negative bacteria from bloodstream infections in sub-Saharan Africa
Toy T , Pak GD , Duc TP , Campbell JI , El Tayeb MA , Von Kalckreuth V , Im J , Panzner U , Cruz Espinoza LM , Eibach D , Dekker DM , Park SE , Jeon HJ , Konings F , Mogeni OD , Cosmas L , Bjerregaard-Andersen M , Gasmelseed N , Hertz JT , Jaeger A , Krumkamp R , Ley B , Thriemer K , Kabore LP , Niang A , Raminosoa TM , Sampo E , Sarpong N , Soura A , Owusu-Dabo E , Teferi M , Yeshitela B , Poppert S , May J , Kim JH , Chon Y , Park JK , Aseffa A , Breiman RF , Schutt-Gerowitt H , Aaby P , Adu-Sarkodie Y , Crump JA , Rakotozandrindrainy R , Meyer CG , Sow AG , Clemens JD , Wierzba TF , Baker S , Marks F . Clin Infect Dis 2019 69 S449-s458 BACKGROUND: Antimicrobial resistance (AMR) is a major global health concern, yet, there are noticeable gaps in AMR surveillance data in regions such as sub-Saharan Africa. We aimed to measure the prevalence of extended-spectrum beta-lactamase (ESBL) producing Gram-negative bacteria in bloodstream infections from 12 sentinel sites in sub-Saharan Africa. METHODS: Data were generated during the Typhoid Fever Surveillance in Africa Program (TSAP), in which standardized blood cultures were performed on febrile patients attending 12 health facilities in 9 sub-Saharan African countries between 2010 and 2014. Pathogenic bloodstream isolates were identified at the sites and then subsequently confirmed at a central reference laboratory. Antimicrobial susceptibility testing, detection of ESBL production, and conventional multiplex polymerase chain reaction (PCR) testing for genes encoding for beta-lactamase were performed on all pathogens. RESULTS: Five hundred and five pathogenic Gram-negative bloodstream isolates were isolated during the study period and available for further characterization. This included 423 Enterobacteriaceae. Phenotypically, 61 (12.1%) isolates exhibited ESBL activity, and genotypically, 47 (9.3%) yielded a PCR amplicon for at least one of the screened ESBL genes. Among specific Gram-negative isolates, 40 (45.5%) of 88 Klebsiella spp., 7 (5.7%) of 122 Escherichia coli, 6 (16.2%) of 37 Acinetobacter spp., and 2 (1.3%) of 159 of nontyphoidal Salmonella (NTS) showed phenotypic ESBL activity. CONCLUSIONS: Our findings confirm the presence of ESBL production among pathogens causing bloodstream infections in sub-Saharan Africa. With few alternatives for managing ESBL-producing pathogens in the African setting, measures to control the development and proliferation of AMR organisms are urgently needed. |
Health beliefs and patient perspectives of febrile illness in Kilombero, Tanzania
Hercik C , Cosmas L , Mogeni OD , Kohi W , Mfinanga S , Loffredo C , Montgomery JM . Am J Trop Med Hyg 2019 101 (1) 263-270 This qualitative study assessed the knowledge and beliefs surrounding fever syndrome among adult febrile patients seeking health care in Kilombero, Tanzania. From June 11 to July 13, 2014, 10% of all adult (>/= 15 years) febrile patients enrolled in the larger syndromic study, who presented with an axillary temperature >/= 37.5 degrees C and symptom onset </= 5 days prior, were randomly selected to participate in an in-depth physician-patient interview, informed by Health Belief Model constructs. Interviews were audio recorded, translated, and transcribed. Transcripts were coded using NVivo Version 11.1, and the thematic content was analyzed by two separate researchers. Blood and nasopharyngeal/oralpharyngeal specimens were collected and analyzed using both acute febrile illness and respiratory TaqMan Array Cards for multipathogen detection of 56 potential causative agents. A total of 18 participants provided 188 discrete comments. When asked to speculate the causative agent of febrile illness, 33.3% cited malaria and the other 66.6% offered nonbiomedical responses, such as "mosquitoes" and "weather." Major themes emerging related to severity and susceptibility to health hazards included lack of bed net use, misconceptions about bed nets, and mosquito infestation. Certain barriers to treatment were cited, including dependence on traditional healers, high cost of drugs, and poor dispensary services. Overall, we demonstrate low concurrence in speculations of fever etiology according to patients, clinicians, and laboratory testing. Our findings contribute to the important, yet limited, base of knowledge surrounding patient risk perceptions of febrile illness and underscore the potential utility of community-based participatory research to inform disease control programs. |
The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.
Park SE , Pham DT , Boinett C , Wong VK , Pak GD , Panzner U , Espinoza LMC , von Kalckreuth V , Im J , Schutt-Gerowitt H , Crump JA , Breiman RF , Adu-Sarkodie Y , Owusu-Dabo E , Rakotozandrindrainy R , Soura AB , Aseffa A , Gasmelseed N , Keddy KH , May J , Sow AG , Aaby P , Biggs HM , Hertz JT , Montgomery JM , Cosmas L , Fields B , Sarpong N , Razafindrabe TJL , Raminosoa TM , Kabore LP , Sampo E , Teferi M , Yeshitela B , El Tayeb MA , Sooka A , Meyer CG , Krumkamp R , Dekker DM , Jaeger A , Poppert S , Tall A , Niang A , Bjerregaard-Andersen M , Valborg Løfberg S , Seo HJ , Jeon HJ , Deerin JF , Park J , Konings F , Ali M , Clemens JD , Hughes P , Sendagala JN , Vudriko T , Downing R , Ikumapayi UN , Mackenzie GA , Obaro S , Argimon S , Aanensen DM , Page A , Keane JA , Duchene S , Dyson Z , Holt KE , Dougan G , Marks F , Baker S . Nat Commun 2018 9 (1) 5094 There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa. |
Use of the revised World Health Organization cluster survey methodology to classify measles-rubella vaccination campaign coverage in 47 counties in Kenya, 2016
Subaiya S , Tabu C , N'Ganga J , Awes AA , Sergon K , Cosmas L , Styczynski A , Thuo S , Lebo E , Kaiser R , Perry R , Ademba P , Kretsinger K , Onuekwusi I , Gary H , Scobie HM . PLoS One 2018 13 (7) e0199786 INTRODUCTION: To achieve measles elimination, two doses of measles-containing vaccine (MCV) are provided through routine immunization services or vaccination campaigns. In May 2016, Kenya conducted a measles-rubella (MR) vaccination campaign targeting 19 million children aged 9 months-14 years, with a goal of achieving >/=95% coverage. We conducted a post-campaign cluster survey to estimate national coverage and classify coverage in Kenya's 47 counties. METHODS: The stratified multi-stage cluster survey included data from 20,011 children in 8,253 households sampled using the recently revised World Health Organization coverage survey methodology (2015). Point estimates and 95% confidence intervals (95% CI) of national campaign coverage were calculated, accounting for study design. County vaccination coverage was classified as 'pass,' 'fail,' or 'intermediate,' using one-sided hypothesis tests against a 95% threshold. RESULTS: Estimated national MR campaign coverage was 95% (95% CI: 94%-96%). Coverage differed significantly (p < 0.05) by child's school attendance, mother's education, household wealth, and other factors. In classifying coverage, 20 counties passed (>/=95%), two failed (<95%), and 25 were intermediate (unable to classify either way). Reported campaign awareness among caretakers was 92%. After the 2016 MR campaign, an estimated 93% (95% CI: 92%-94%) of children aged 9 months to 14 years had received >/=2 MCV doses; 6% (95% CI: 6%-7%) had 1 MCV dose; and 0.7% (95% CI: 0.6%-0.9%) remained unvaccinated. CONCLUSIONS: Kenya reached the MR campaign target of 95% vaccination coverage, representing a substantial achievement towards increasing population immunity. High campaign awareness reflected the comprehensive social mobilization strategy implemented in Kenya and supports the importance of including strong communications platforms in future vaccination campaigns. In counties with sub-optimal MR campaign coverage, further efforts are needed to increase MCV coverage to achieve the national goal of measles elimination by 2020. |
A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania
Hercik C , Cosmas L , Mogeni OD , Wamola N , Kohi W , Omballa V , Ochieng M , Lidechi S , Bonventure J , Ochieng C , Onyango C , Fields BS , Mfinanga S , Montgomery JM . PLoS One 2017 12 (12) e0189712 INTRODUCTION: In low-resource settings, empiric case management of febrile illness is routine as a result of limited access to laboratory diagnostics. The use of comprehensive fever syndromic surveillance, with enhanced clinical microbiology, advanced diagnostics and more robust epidemiologic investigation, could enable healthcare providers to offer a differential diagnosis of fever syndrome and more appropriate care and treatment. METHODS: We conducted a year-long exploratory study of fever syndrome among patients >/= 1 year if age, presenting to clinical settings with an axillary temperature of >/=37.5 degrees C and symptomatic onset of </=5 days. Blood and naso-pharyngeal/oral-pharyngeal (NP/OP) specimens were collected and analyzed, respectively, using AFI and respiratory TaqMan Array Cards (TAC) for multi-pathogen detection of 57 potential causative agents. Furthermore, we examined numerous epidemiologic correlates of febrile illness, and conducted demographic, clinical, and behavioral domain-specific multivariate regression to statistically establish associations with agent detection. RESULTS: From 15 September 2014-13 September 2015, 1007 febrile patients were enrolled, and 997 contributed an epidemiologic survey, including: 14% (n = 139) 1<5yrs, 19% (n = 186) 5-14yrs, and 67% (n = 672) >/=15yrs. AFI TAC and respiratory TAC were performed on 842 whole blood specimens and 385 NP/OP specimens, respectively. Of the 57 agents surveyed, Plasmodium was the most common agent detected. AFI TAC detected nucleic acid for one or more of seven microbial agents in 49% of AFI blood samples, including: Plasmodium (47%), Leptospira (3%), Bartonella (1%), Salmonella enterica (1%), Coxiella burnetii (1%), Rickettsia (1%), and West Nile virus (1%). Respiratory TAC detected nucleic acid for 24 different microbial agents, including 12 viruses and 12 bacteria. The most common agents detected among our surveyed population were: Haemophilus influenzae (67%), Streptococcus pneumoniae (55%), Moraxella catarrhalis (39%), Staphylococcus aureus (37%), Pseudomonas aeruginosa (36%), Human Rhinovirus (25%), influenza A (24%), Klebsiella pneumoniae (14%), Enterovirus (15%) and group A Streptococcus (12%). Our epidemiologic investigation demonstrated both age and symptomatic presentation to be associated with a number of detected agents, including, but not limited to, influenza A and Plasmodium. Linear regression of fully-adjusted mean cycle threshold (Ct) values for Plasmodium also identified statistically significant lower mean Ct values for older children (20.8), patients presenting with severe fever (21.1) and headache (21.5), as well as patients admitted for in-patient care and treatment (22.4). CONCLUSIONS: This study is the first to employ two syndromic TaqMan Array Cards for the simultaneous survey of 57 different organisms to better characterize the type and prevalence of detected agents among febrile patients. Additionally, we provide an analysis of the association between adjusted mean Ct values for Plasmodium and key clinical and demographic variables, which may further inform clinical decision-making based upon intensity of infection, as observed across endemic settings of sub-Saharan Africa. |
A combined syndromic approach to examine viral, bacterial, and parasitic agents among febrile patients: A pilot study in Kilombero, Tanzania
Hercik C , Cosmas L , Mogeni OD , Wamola N , Kohi W , Houpt E , Liu J , Ochieng C , Onyango C , Fields B , Mfinanga S , Montgomery JM . Am J Trop Med Hyg 2017 98 (2) 625-632 The use of fever syndromic surveillance in sub-Saharan Africa is an effective approach to determine the prevalence of both malarial and nonmalarial infectious agents. We collected both blood and naso/oro-pharyngeal (NP/OP) swabs from consecutive consenting patients >/= 1 year of age, with an axillary temperature >/= 37.5 degrees C, and symptom onset of </= 5 days. Specimens were analyzed using both acute febrile illness (AFI) and respiratory TaqMan array cards (TAC) for multiagent detection of 56 different bloodstream and respiratory agents. In addition, we collected epidemiologic data to further characterize our patient population. We enrolled 205 febrile patients, including 70 children (1 < 15 years of age; 34%) and 135 adults (>/= 15 years of age; 66%). AFI TAC and respiratory TAC were performed on 191 whole blood specimens and 115 NP/OP specimens, respectively. We detected nucleic acid for Plasmodium (57%), Leptospira (2%), and dengue virus (1%) among blood specimens. In addition, we detected 17 different respiratory agents, most notably, Haemophilus influenzae (64%), Streptococcus pneumonia (56%), Moraxella catarrhalis (39%), and respiratory syncytial virus (11%) among NP/OP specimens. Overall median cycle threshold was measured at 26.5. This study provides a proof-of-concept for the use of a multiagent diagnostic approach for exploratory research on febrile illness and underscores the utility of quantitative molecular diagnostics in complex epidemiologic settings of sub-Saharan Africa. |
Incidence of invasive salmonella disease in sub-Saharan Africa: a multicentre population-based surveillance study
Marks F , von Kalckreuth V , Aaby P , Adu-Sarkodie Y , El Tayeb MA , Ali M , Aseffa A , Baker S , Biggs HM , Bjerregaard-Andersen M , Breiman RF , Campbell JI , Cosmas L , Crump JA , Espinoza LM , Deerin JF , Dekker DM , Fields BS , Gasmelseed N , Hertz JT , Van Minh Hoang N , Im J , Jaeger A , Jeon HJ , Kabore LP , Keddy KH , Konings F , Krumkamp R , Ley B , Lofberg SV , May J , Meyer CG , Mintz ED , Montgomery JM , Niang AA , Nichols C , Olack B , Pak GD , Panzner U , Park JK , Park SE , Rabezanahary H , Rakotozandrindrainy R , Raminosoa TM , Razafindrabe TJL , Sampo E , Schütt-Gerowitt H , Sow AG , Sarpong N , Seo HJ , Sooka A , Soura AB , Tall A , Teferi M , Thriemer K , Warren MR , Yeshitela B , Clemens JD , Wierzba TF . Lancet Glob Health 2017 5 (3) e310-e323 BACKGROUND: Available incidence data for invasive salmonella disease in sub-Saharan Africa are scarce. Standardised, multicountry data are required to better understand the nature and burden of disease in Africa. We aimed to measure the adjusted incidence estimates of typhoid fever and invasive non-typhoidal salmonella (iNTS) disease in sub-Saharan Africa, and the antimicrobial susceptibility profiles of the causative agents. METHODS: We established a systematic, standardised surveillance of blood culture-based febrile illness in 13 African sentinel sites with previous reports of typhoid fever: Burkina Faso (two sites), Ethiopia, Ghana, Guinea-Bissau, Kenya, Madagascar (two sites), Senegal, South Africa, Sudan, and Tanzania (two sites). We used census data and health-care records to define study catchment areas and populations. Eligible participants were either inpatients or outpatients who resided within the catchment area and presented with tympanic (≥38.0 degrees C) or axillary temperature (≥37.5 degrees C). Inpatients with a reported history of fever for 72 h or longer were excluded. We also implemented a health-care utilisation survey in a sample of households randomly selected from each study area to investigate health-seeking behaviour in cases of self-reported fever lasting less than 3 days. Typhoid fever and iNTS disease incidences were corrected for health-care-seeking behaviour and recruitment. FINDINGS: Between March 1, 2010, and Jan 31, 2014, 135 Salmonella enterica serotype Typhi (S Typhi) and 94 iNTS isolates were cultured from the blood of 13 431 febrile patients. Salmonella spp accounted for 33% or more of all bacterial pathogens at nine sites. The adjusted incidence rate (AIR) of S Typhi per 100 000 person-years of observation ranged from 0 (95% CI 0-0) in Sudan to 383 (274-535) at one site in Burkina Faso; the AIR of iNTS ranged from 0 in Sudan, Ethiopia, Madagascar (Isotry site), and South Africa to 237 (178-316) at the second site in Burkina Faso. The AIR of iNTS and typhoid fever in individuals younger than 15 years old was typically higher than in those aged 15 years or older. Multidrug-resistant S Typhi was isolated in Ghana, Kenya, and Tanzania (both sites combined), and multidrug-resistant iNTS was isolated in Burkina Faso (both sites combined), Ghana, Kenya, and Guinea-Bissau. INTERPRETATION: Typhoid fever and iNTS disease are major causes of invasive bacterial febrile illness in the sampled locations, most commonly affecting children in both low and high population density settings. The development of iNTS vaccines and the introduction of S Typhi conjugate vaccines should be considered for high-incidence settings, such as those identified in this study. FUNDING: Bill & Melinda Gates Foundation. |
Population-Based Incidence Rates of Diarrheal Disease Associated with Norovirus, Sapovirus, and Astrovirus in Kenya
Shioda K , Cosmas L , Audi A , Gregoricus N , Vinje J , Parashar UD , Montgomery JM , Feikin DR , Breiman RF , Hall AJ . PLoS One 2016 11 (4) e0145943 BACKGROUND: Diarrheal diseases remain a major cause of mortality in Africa and worldwide. While the burden of rotavirus is well described, population-based rates of disease caused by norovirus, sapovirus, and astrovirus are lacking, particularly in developing countries. METHODS: Data on diarrhea cases were collected through a population-based surveillance platform including healthcare encounters and household visits in Kenya. We analyzed data from June 2007 to October 2008 in Lwak, a rural site in western Kenya, and from October 2006 to February 2009 in Kibera, an urban slum. Stool specimens from diarrhea cases of all ages who visited study clinics were tested for norovirus, sapovirus, and astrovirus by RT-PCR. RESULTS: Of 334 stool specimens from Lwak and 524 from Kibera, 85 (25%) and 159 (30%) were positive for norovirus, 13 (4%) and 31 (6%) for sapovirus, and 28 (8%) and 18 (3%) for astrovirus, respectively. Among norovirus-positive specimens, genogroup II predominated in both sites, detected in 74 (87%) in Lwak and 140 (88%) in Kibera. The adjusted community incidence per 100,000 person-years was the highest for norovirus (Lwak: 9,635; Kibera: 4,116), followed by astrovirus (Lwak: 3,051; Kibera: 440) and sapovirus (Lwak: 1,445; Kibera: 879). For all viruses, the adjusted incidence was higher among children aged <5 years (norovirus: 22,225 in Lwak and 17,511 in Kibera; sapovirus: 5,556 in Lwak and 4,378 in Kibera; astrovirus: 11,113 in Lwak and 2,814 in Kibera) compared to cases aged ≥5 years. CONCLUSION: Although limited by a lack of controls, this is the first study to estimate the outpatient and community incidence rates of norovirus, sapovirus, and astrovirus across the age spectrum in Kenya, suggesting a substantial disease burden imposed by these viruses. By applying adjusted rates, we estimate approximately 2.8-3.3 million, 0.45-0.54 million, and 0.77-0.95 million people become ill with norovirus, sapovirus, and astrovirus, respectively, every year in Kenya. |
The Typhoid Fever Surveillance in Africa Program (TSAP): Clinical, diagnostic, and epidemiological methodologies
von Kalckreuth V , Konings F , Aaby P , Adu-Sarkodie Y , Ali M , Aseffa A , Baker S , Breiman RF , Bjerregaard-Andersen M , Clemens JD , Crump JA , Cruz Espinoza LM , Deerin JF , Gasmelseed N , Sow AG , Im J , Keddy KH , Cosmas L , May J , Meyer CG , Mintz ED , Montgomery JM , Olack B , Pak GD , Panzner U , Park SE , Rakotozandrindrainy R , Schutt-Gerowitt H , Soura AB , Warren MR , Wierzba TF , Marks F . Clin Infect Dis 2016 62 Suppl 1 S9-s16 BACKGROUND: New immunization programs are dependent on data from surveillance networks and disease burden estimates to prioritize target areas and risk groups. Data regarding invasive Salmonella disease in sub-Saharan Africa are currently limited, thus hindering the implementation of preventive measures. The Typhoid Fever Surveillance in Africa Program (TSAP) was established by the International Vaccine Institute to obtain comparable incidence data on typhoid fever and invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa through standardized surveillance in multiple countries. METHODS: Standardized procedures were developed and deployed across sites for study site selection, patient enrolment, laboratory procedures, quality control and quality assurance, assessment of healthcare utilization and incidence calculations. RESULTS: Passive surveillance for bloodstream infections among febrile patients was initiated at thirteen sentinel sites in ten countries (Burkina Faso, Ethiopia, Ghana, Guinea-Bissau, Kenya, Madagascar, Senegal, South Africa, Sudan, and Tanzania). Each TSAP site conducted case detection using these standardized methods to isolate and identify aerobic bacteria from the bloodstream of febrile patients. Healthcare utilization surveys were conducted to adjust population denominators in incidence calculations for differing healthcare utilization patterns and improve comparability of incidence rates across sites. CONCLUSIONS: By providing standardized data on the incidence of typhoid fever and iNTS disease in sub-Saharan Africa, TSAP will provide vital input for targeted typhoid fever prevention programs. |
Serologic evidence for hepatitis E virus infection among patients with undifferentiated acute febrile illness in Kibera, Kenya
Furukawa NW , Teshale EH , Cosmas L , Ochieng M , Gikunju S , Fields BS , Montgomery JM . J Clin Virol 2016 77 106-108 BACKGROUND: Hepatitis E (HEV) is an emerging cause of viral hepatitis mainly transmitted through the fecal-oral route. Residents of the Kibera slum of Nairobi, Kenya are at risk for fecal-orally transmitted infections. OBJECTIVE: To quantify the incidence and prevalence of HEV infection among acute febrile illness (AFI) cases using a population-based infectious disease surveillance network. STUDY DESIGN: Cross-sectional serum samples from AFI case-patients between 2009 and 2012 were matched to the age and gender distribution of the Kibera population and tested by IgM and IgG enzyme immunoassays (EIA) and nucleic acid testing (NAT). Serum from healthy residents was also tested by EIA. RESULTS: Of the 482 AFI serum samples tested, 124 (25.7%) and 182 (37.8%) were IgM and IgG reactive, respectively. On multivariate analysis, IgM reactivity was associated with HIV (RR 1.66, 95%CI 1.07, 2.60; p=0.024) while IgG reactivity was associated with increasing age (p<0.001) and HIV (RR 1.93, 95%CI 1.52, 2.46; p<0.001). AFI case-patients were more likely to be IgM (p=0.002) and IgG (p<0.001) reactive compared to healthy residents. The seroincidence by HEV-specific IgM was 84.0 per 1000 person years, however, all 482 samples were negative by NAT. CONCLUSIONS: Serologic evidence for HEV in Kibera suggests a high burden of infection, but NAT did not confirm HEV viremia. Additional testing is needed to determine whether EIAs are susceptible to false positivity in undifferentiated AFI populations before their widespread use. |
Environmental transmission of typhoid fever in an urban slum
Akullian A , Ng'eno E , Matheson AI , Cosmas L , Macharia D , Fields B , Bigogo G , Mugoh M , John-Stewart G , Walson JL , Wakefield J , Montgomery JM . PLoS Negl Trop Dis 2015 9 (12) e0004212 BACKGROUND: Enteric fever due to Salmonella Typhi (typhoid fever) occurs in urban areas with poor sanitation. While direct fecal-oral transmission is thought to be the predominant mode of transmission, recent evidence suggests that indirect environmental transmission may also contribute to disease spread. METHODS: Data from a population-based infectious disease surveillance system (28,000 individuals followed biweekly) were used to map the spatial pattern of typhoid fever in Kibera, an urban informal settlement in Nairobi Kenya, between 2010-2011. Spatial modeling was used to test whether variations in topography and accumulation of surface water explain the geographic patterns of risk. RESULTS: Among children less than ten years of age, risk of typhoid fever was geographically heterogeneous across the study area (p = 0.016) and was positively associated with lower elevation, OR = 1.87, 95% CI (1.36-2.57), p <0.001. In contrast, the risk of typhoid fever did not vary geographically or with elevation among individuals less than 6b ten years of age. CONCLUSIONS: Our results provide evidence of indirect, environmental transmission of typhoid fever among children, a group with high exposure to fecal pathogens in the environment. Spatially targeting sanitation interventions may decrease enteric fever transmission. |
Malaria parasitemia among febrile patients seeking clinical care at an outpatient health facility in an urban informal settlement area in Nairobi, Kenya
Njuguna HN , Montgomery JM , Cosmas L , Wamola N , Oundo JO , Desai M , Buff AM , Breiman RF . Am J Trop Med Hyg 2015 94 (1) 122-127 Nairobi is considered a low-risk area for malaria transmission, but travel can influence transmission of malaria. We investigated the demographic characteristics and travel history of patients with documented fever and malaria in a study clinic in a population-based surveillance system over a 5-year period, January 1, 2007 to December 31, 2011. During the study period, 11,480 (68%) febrile patients had a microscopy test performed for malaria, of which 2,553 (22%) were positive. Malaria was detected year-round with peaks in January, May, and September. Children aged 5-14 years had the highest proportion (28%) of positive results followed by children aged 1-4 years (23%). Almost two-thirds of patients with malaria reported traveling outside Nairobi; 79% of these traveled to three counties in western Kenya. History of recent travel (i.e., in past month) was associated with malaria parasitemia (odds ratio: 10.0, 95% confidence interval: 9.0-11.0). Malaria parasitemia was frequently observed among febrile patients at a health facility in the urban slum of Kibera, Nairobi. The majority of patients had traveled to western Kenya. However, 34% reported no travel history, which raises the possibility of local malaria transmission in this densely populated, urban setting. These findings have important implications for malaria control in large Nairobi settlements. |
Burden of invasive nontyphoidal Salmonella disease in a rural and urban site in Kenya, 2009-2014
Verani JR , Toroitich S , Auko J , Kiplang'at S , Cosmas L , Audi A , Mogeni OD , Aol G , Oketch D , Odiembo H , Katieno J , Wamola N , Onyango CO , Juma BW , Fields BS , Bigogo G , Montgomery JM . Clin Infect Dis 2015 61 Suppl 4 S302-9 BACKGROUND: Invasive infections with nontyphoidal Salmonella (NTS) lead to bacteremia in children and adults and are an important cause of illness in Africa; however, few data on the burden of NTS bacteremia are available. We sought to determine the burden of invasive NTS disease in a rural and urban setting in Kenya. METHODS: We conducted the study in a population-based surveillance platform in a rural setting in western Kenya (Lwak), and an informal urban settlement in Nairobi (Kibera) from 2009 to 2014. We obtained blood culture specimens from participants presenting with acute lower respiratory tract illness or acute febrile illness to a designated outpatient facility in each site, or any hospital admission for a potentially infectious cause (rural site only). Incidence was calculated using a defined catchment population and adjusting for specimen collection and healthcare-seeking practices. RESULTS: A total of 12 683 and 9524 blood cultures were analyzed from Lwak and Kibera, respectively. Of these, 428 (3.4%) and 533 (5.6%) grew a pathogen; among those, 208 (48.6%) and 70 (13.1%) were positive for NTS in Lwak and Kibera, respectively. Overall, the adjusted incidence of invasive NTS disease was higher in Lwak (839.4 per 100 000 person-years of observation [PYO]) than in Kibera (202.5 per 100 000 PYO). The highest adjusted incidences were observed in children <5 years of age (Lwak 3914.3 per 100 000 PYO and Kibera 997.9 per 100 000 PYO). The highest adjusted annual incidence was 1927.3 per 100 000 PYO (in 2010) in Lwak and 220.5 per 100 000 PYO (in 2011) in Kibera; the lowest incidences were 303.3 and 62.5 per 100 000 PYO, respectively (in 2012). In both sites, invasive NTS disease incidence generally declined over the study period. CONCLUSIONS: We observed an extremely high burden of invasive NTS disease in a rural area of Kenya and a lesser, but still substantial, burden in an urban slum. Although the incidences in both sites declined during the study period, invasive NTS infections remain an important cause of morbidity in these settings, particularly among children <5 years old. |
The unrecognized burden of influenza in young Kenyan children, 2008-2012
McMorrow ML , Emukule GO , Njuguna HN , Bigogo G , Montgomery JM , Nyawanda B , Audi A , Breiman RF , Katz MA , Cosmas L , Waiboci LW , Duque J , Widdowson MA , Mott JA . PLoS One 2015 10 (9) e0138272 Influenza-associated disease burden among children in tropical sub-Saharan Africa is not well established, particularly outside of the 2009 pandemic period. We estimated the burden of influenza in children aged 0-4 years through population-based surveillance for influenza-like illness (ILI) and acute lower respiratory tract illness (ALRI). Household members meeting ILI or ALRI case definitions were referred to health facilities for evaluation and collection of nasopharyngeal and oropharyngeal swabs for influenza testing by real-time reverse transcription polymerase chain reaction. Estimates were adjusted for health-seeking behavior and those with ILI and ALRI who were not tested. During 2008-2012, there were 9,652 person-years of surveillance among children aged 0-4 years. The average adjusted rate of influenza-associated hospitalization was 4.3 (95% CI 3.0-6.0) per 1,000 person-years in children aged 0-4 years. Hospitalization rates were highest in the 0-5 month and 6-23 month age groups, at 7.6 (95% CI 3.2-18.2) and 8.4 (95% CI 5.4-13.0) per 1,000 person-years, respectively. The average adjusted rate of influenza-associated medically attended (inpatient or outpatient) ALRI in children aged 0-4 years was 17.4 (95% CI 14.2-19.7) per 1,000 person-years. Few children who had severe laboratory-confirmed influenza were clinically diagnosed with influenza by the treating clinician in the inpatient (0/33, 0%) or outpatient (1/109, 0.9%) settings. Influenza-associated hospitalization rates from 2008-2012 were 5-10 times higher than contemporaneous U.S. estimates. Many children with danger signs were not hospitalized; thus, influenza-associated severe disease rates in Kenyan children are likely higher than hospital-based estimates suggest. |
Severe acute respiratory infection in children in a densely populated urban slum in Kenya, 2007-2011
Breiman RF , Cosmas L , Njenga MK , Williamson J , Mott JA , Katz MA , Erdman DD , Schneider E , Oberste MS , Neatherlin JC , Njuguna H , Ondari DM , Odero K , Okoth GO , Olack B , Wamola N , Montgomery JM , Fields BS , Feikin DR . BMC Infect Dis 2015 15 (95) 95 BACKGROUND: Reducing acute respiratory infection burden in children in Africa remains a major priority and challenge. We analyzed data from population-based infectious disease surveillance for severe acute respiratory illness (SARI) among children <5 years of age in Kibera, a densely populated urban slum in Nairobi, Kenya. METHODS: Surveillance was conducted among a monthly mean of 5,874 (range=5,778-6,411) children <5 years old in two contiguous villages in Kibera. Participants had free access to the study clinic and their health events and utilization were noted during biweekly home visits. Patients meeting criteria for SARI (WHO-defined severe or very severe pneumonia, or oxygen saturation <90%) from March 1, 2007-February 28, 2011 had blood cultures processed for bacteria, and naso- and oro-pharyngeal swabs collected for quantitative real-time reverse transcription polymerase chain reaction testing for influenza viruses, parainfluenza viruses (PIV), respiratory syncytial virus (RSV), adenovirus, and human metapneumovirus (hMPV). Swabs collected during January 1, 2009-February 28, 2010 were also tested for rhinoviruses, enterovirus, parechovirus, Mycoplasma pneumoniae, and Legionella species. Swabs were collected for simultaneous testing from a selected group of control-children visiting the clinic without recent respiratory or diarrheal illnesses. RESULTS: SARI overall incidence was 12.4 cases/100 person-years of observation (PYO) and 30.4 cases/100 PYO in infants. When comparing detection frequency in swabs from 815 SARI cases and 115 healthy controls, only RSV and influenza A virus were significantly more frequently detected in cases, although similar trends neared statistical significance for PIV, adenovirus and hMPV. The incidence for RSV was 2.8 cases/100 PYO and for influenza A was 1.0 cases/100 PYO. When considering all PIV, the rate was 1.1 case/100 PYO and the rate per 100 PYO for SARI-associated disease was 1.5 for adenovirus and 0.9 for hMPV. RSV and influenza A and B viruses were estimated to account for 16.2% and 6.7% of SARI cases, respectively; when taken together, PIV, adenovirus, and hMPV may account for >20% additional cases. CONCLUSIONS: Influenza viruses and RSV (and possibly PIV, hMPV and adenoviruses) are important pathogens to consider when developing technologies and formulating strategies to treat and prevent SARI in children. |
Increased rates of respiratory and diarrheal illnesses in HIV-negative people living with HIV-infected individuals in a densely populated urban slum
Wong JM , Cosmas L , Nyachieo D , Williamson JM , Olack B , Okoth G , Njuguna H , Feikin DR , Burke H , Montgomery JM , Breiman RF . J Infect Dis 2015 212 (5) 745-53 BACKGROUND: Prolonged pathogen shedding and increased duration of illness associated with infections in immunosuppressed individuals put close HIV-negative contacts of HIV-infected people at increased risk of exposure to infectious pathogens. METHODS: We calculated incidence and longitudinal prevalence (number of days per year) of influenza-like illness (ILI), diarrhea, and non-specific febrile illness during 2008 from a population-based surveillance program in the urban slum of Kibera (Kenya) consisting of 1830 HIV-negative household contacts of HIV-infected individuals and 13 677 individuals living in exclusively HIV-negative households. RESULTS: For individuals ≥5 years old, incidence was significantly increased for ILI (IRR, 1.47; P < .05) and diarrhea (IRR, 1.41; P < .05) in HIV-negative household contacts of HIV-infected individuals compared to exclusively HIV-negative households. The risk of illness among HIV-negative people was directly proportional to the number of HIV-infected people living in the home for ILI (IRR, 1.39; P < .05) and diarrhea (IRR, 1.36; P < .01). We found no increased rates of illness in children <5 years old who lived with HIV-infected individuals. CONCLUSIONS: Living with HIV-infected individuals is associated with modestly increased rates of respiratory and diarrheal infections in HIV-negative individuals >5 years old. Targeted interventions are needed, including ensuring that HIV-infected people are receiving appropriate care and treatment. |
Soil-transmitted helminths in pre-school-aged and school-aged children in an urban slum: a cross-sectional study of prevalence, distribution, and associated exposures
Davis SM , Worrell CM , Wiegand RE , Odero KO , Suchdev PS , Ruth LJ , Lopez G , Cosmas L , Neatherlin J , Njenga SM , Montgomery JM , Fox LM . Am J Trop Med Hyg 2014 91 (5) 1002-10 Soil-transmitted helminths (STHs) are controlled by regular mass drug administration. Current practice targets school-age children (SAC) preferentially over pre-school age children (PSAC) and treats large areas as having uniform prevalence. We assessed infection prevalence in SAC and PSAC and spatial infection heterogeneity, using a cross-sectional study in two slum villages in Kibera, Nairobi. Nairobi has low reported STH prevalence. The SAC and PSAC were randomly selected from the International Emerging Infections Program's surveillance platform. Data included residence location and three stools tested by Kato-Katz for STHs. Prevalences among 692 analyzable children were any STH: PSAC 40.5%, SAC 40.7%; Ascaris: PSAC 24.1%, SAC 22.7%; Trichuris: PSAC 24.0%, SAC 28.8%; hookworm < 0.1%. The STH infection prevalence ranged from 22% to 71% between sub-village sectors. The PSAC have similar STH prevalences to SAC and should receive deworming. Small areas can contain heterogeneous prevalences; determinants of STH infection should be characterized and slums should be assessed separately in STH mapping. |
Sustained high incidence of injuries from burns in a densely populated urban slum in Kenya: an emerging public health priority
Wong JM , Nyachieo DO , Benzakri NA , Cosmas L , Ondari D , Yekta S , Montgomery JM , Williamson JM , Breiman RF . Burns 2014 40 (6) 1194-200 INTRODUCTION: Ninety-five percent of burn deaths occur in low- and middle-income countries (LMICs); however, longitudinal household-level studies have not been done in urban slum settings, where overcrowding and unsafe cook stoves may increase likelihood of injury. METHODS: Using a prospective, population-based disease surveillance system in the urban slum of Kibera in Kenya, we examined the incidence of household-level burns of all severities from 2006-2011. RESULTS: Of approximately 28,500 enrolled individuals (6000 households), we identified 3072 burns. The overall incidence was 27.9/1000 person-years-of-observation. Children <5 years old sustained burns at 3.8-fold greater rate compared to (p<0.001) those ≥5 years old. Females ≥5 years old sustained burns at a rate that was 1.35-fold (p<0.001) greater than males within the same age distribution. Hospitalizations were uncommon (0.65% of all burns). CONCLUSIONS: The incidence of burns, 10-fold greater than in most published reports from Africa and Asia, suggests that such injuries may contribute more significantly than previously thought to morbidity in LMICs, and may be increased by urbanization. As migration from rural areas into urban slums rapidly increases in many African countries, characterizing and addressing the rising burden of burns is likely to become a public health priority. |
Mortality trends observed in population-based surveillance of an urban slum settlement, Kibera, Kenya, 2007-2010
Olack B , Feikin DR , Cosmas LO , Odero KO , Okoth GO , Montgomery JM , Breiman RF . PLoS One 2014 9 (1) e85913 BACKGROUND: We used population based infectious disease surveillance to characterize mortality rates in residents of an urban slum in Kenya. METHODS: We analyzed biweekly household visit data collected two weeks before death for 749 cases who died during January 1, 2007 to December 31, 2010. We also selected controls matched by age, gender and having a biweekly household visit within two weeks before death of the corresponding case and compared the symptoms reported. RESULTS: The overall mortality rate was 6.3 per 1,000 person years of observation (PYO) (females: 5.7; males: 6.8). Infant mortality rate was 50.2 per 1000 PYOs, and it was 15.1 per 1,000 PYOs for children <5 years old. Poisson regression indicates a significant decrease over time in overall mortality from (6.0 in 2007 to 4.0 in 2010 per 1000 PYOs; p<0.05) in persons ≥5 years old. This decrease was predominant in females (7.8 to 5.7 per 1000 PYOs; p<0.05). Two weeks before death, significantly higher prevalence for cough (OR = 4.7 [95% CI: 3.7-5.9]), fever (OR = 8.1 [95% CI: 6.1-10.7]), and diarrhea (OR = 9.1 [95% CI: 6.4-13.2]) were reported among participants who died (cases) when compared to participants who did not die (controls). Diarrhea followed by fever were independently associated with deaths (OR = 14.4 [95% CI: 7.1-29.2]), and (OR = 11.4 [95% CI: 6.7-19.4]) respectively. CONCLUSIONS: Despite accessible health care, mortality rates are high among people living in this urban slum; infectious disease syndromes appear to be linked to a substantial proportion of deaths. Rapid urbanization poses an increasing challenge in national efforts to improve health outcomes, including reducing childhood mortality rates. Targeting impoverished people in urban slums with effective interventions such as water and sanitation interventions are needed to achieve national objectives for health. |
Epidemiology of respiratory syncytial virus infection in rural and urban Kenya
Bigogo GM , Breiman RF , Feikin DR , Audi AO , Aura B , Cosmas L , Njenga MK , Fields BS , Omballa V , Njuguna H , Ochieng PM , Mogeni DO , Aol GO , Olack B , Katz MA , Montgomery JM , Burton DC . J Infect Dis 2013 208 Suppl 3 S207-16 BACKGROUND: Information on the epidemiology of respiratory syncytial virus (RSV) infection in Africa is limited for crowded urban areas and for rural areas where the prevalence of malaria is high. METHODS: At referral facilities in rural western Kenya and a Nairobi slum, we collected nasopharyngeal/oropharyngeal (NP/OP) swab specimens from patients with influenza-like illness (ILI) or severe acute respiratory illness (SARI) and from asymptomatic controls. Polymerase chain reaction assays were used for detection of viral pathogens. We calculated age-specific ratios of the odds of RSV detection among patients versus the odds among controls. Incidence was expressed as the number of episodes per 1000 person-years of observation. RESULTS: Between March 2007 and February 2011, RSV was detected in 501 of 4012 NP/OP swab specimens (12.5%) from children and adults in the rural site and in 321 of 2744 NP/OP swab specimens (11.7%) from those in the urban site. Among children aged <5 years, RSV was detected more commonly among rural children with SARI (odds ratio [OR], 2.0; 95% confidence interval [CI], 1.2-3.3), urban children with SARI (OR, 8.5; 95% CI, 3.1-23.6), and urban children with ILI (OR, 3.4; 95% CI, 1.2-9.6), compared with controls. The incidence of RSV disease was highest among infants with SARI aged <1 year (86.9 and 62.8 episodes per 1000 person-years of observation in rural and urban sites, respectively). CONCLUSIONS: An effective RSV vaccine would likely substantially reduce the burden of respiratory illness among children in rural and urban areas in Africa. |
Use of population-based surveillance to determine the incidence of rotavirus gastroenteritis in an urban slum and a rural setting in Kenya
Breiman RF , Cosmas L , Audi A , Mwiti W , Njuguna H , Bigogo GM , Olack B , Ochieng JB , Wamola N , Montgomery JM , Williamson J , Parashar UD , Burton DC , Tate JE , Feikin DR . Pediatr Infect Dis J 2014 33 Suppl 1 S54-61 BACKGROUND: Rotavirus gastroenteritis is a major cause of mortality among children <2 years of age. Disease burden data are important for introducing and sustaining new rotavirus vaccines in immunization programs. METHODS: We analyzed population-based infectious disease surveillance data from 2007 to 2010 from Kenyan sites in rural and urban slum areas. Stool specimens were collected from patients of all ages presenting to study clinics with diarrheal disease and tested for rotavirus by enzyme immunoassay. Incidence rates were adjusted using data on healthcare utilization (from biweekly home visits) and proportion of stools collected at study clinics from patients meeting case definitions. RESULTS: Rotavirus was detected in 285 (9.0%) of 3174 stools tested, including 122 (11.9%) from children <5 years of age and 162 (7.6%) from participants ≥5 years of age. Adjusted incidence rates for infants were 13,419 and 12,135 per 100,000 person-years of observation in rural and urban areas, respectively. Adjusted incidence rates were high in adults across age ranges. The rates suggest that annually, among children <5 years of age, there are >54,500 cases of rotavirus-associated gastroenteritis in rural Nyanza Province and >16,750 cases in Nairobi urban slums. CONCLUSIONS: Community-based surveillance in urban and rural Kenya suggests that rotavirus plays an important role as a cause of acute gastroenteritis in adults, as well as in children. In addition to substantially preventing illness and complications from diarrheal disease in children, rotavirus infant immunization has the potential of indirectly preventing diarrheal disease in older children and adults, assuming children are the predominant sources of transmission. |
Use of population-based surveillance to define the high incidence of shigellosis in an urban slum in Nairobi, Kenya
Njuguna HN , Cosmas L , Williamson J , Nyachieo D , Olack B , Ochieng JB , Wamola N , Oundo JO , Feikin DR , Mintz ED , Breiman RF . PLoS One 2013 8 (3) e58437 BACKGROUND: Worldwide, Shigella causes an estimated 160 million infections and >1 million deaths annually. However, limited incidence data are available from African urban slums. We investigated the epidemiology of shigellosis and drug susceptibility patterns within a densely populated urban settlement in Nairobi, Kenya through population-based surveillance. METHODS: Surveillance participants were interviewed in their homes every 2 weeks by community interviewers. Participants also had free access to a designated study clinic in the surveillance area where stool specimens were collected from patients with diarrhea (≥3 loose stools within 24 hours) or dysentery (≥1 stool with visible blood during previous 24 hours). We adjusted crude incidence rates for participants meeting stool collection criteria at household visits who reported visiting another clinic. RESULTS: RShigella species were isolated from 224 (23%) of 976 stool specimens. The overall adjusted incidence rate was 408/100,000 person years of observation (PYO) with highest rates among adults 34-49 years old (1,575/100,000 PYO). Isolates were: Shigella flexneri (64%), S. dysenteriae (11%), S. sonnei (9%), and S. boydii (5%). Over 90% of all Shigella isolates were resistant to trimethoprim-sulfamethoxazole and sulfisoxazole. Additional resistance included nalidixic acid (3%), ciprofloxacin (1%) and ceftriaxone (1%). CONCLUSION: More than 1 of every 200 persons experience shigellosis each year in this Kenyan urban slum, yielding rates similar to those in some Asian countries. Provision of safe drinking water, improved sanitation, and hygiene in urban slums are needed to reduce disease burden, in addition to development of effective Shigella vaccines. |
Epidemiology, seasonality, and burden of influenza and influenza-like illness in urban and rural Kenya, 2007-2010
Katz MA , Lebo E , Emukule G , Njuguna HN , Aura B , Cosmas L , Audi A , Junghae M , Waiboci LW , Olack B , Bigogo G , Njenga MK , Feikin DR , Breiman RF . J Infect Dis 2012 206 Suppl 1 S53-60 BACKGROUND: The epidemiology and burden of influenza remain poorly defined in sub-Saharan Africa. Since 2005, the Kenya Medical Research Institute and Centers for Disease Control and Prevention-Kenya have conducted population-based infectious disease surveillance in Kibera, an urban informal settlement in Nairobi, and in Lwak, a rural community in western Kenya. METHODS: Nasopharyngeal and oropharyngeal swab specimens were obtained from patients who attended the study clinic and had acute lower respiratory tract (LRT) illness. Specimens were tested for influenza virus by real-time reverse-transcription polymerase chain reaction. We adjusted the incidence of influenza-associated acute LRT illness to account for patients with acute LRT illness who attended the clinic but were not sampled. RESULTS: From March 2007 through February 2010, 4140 cases of acute LRT illness were evaluated in Kibera, and specimens were collected from 1197 (27%); 319 (27%) were positive for influenza virus. In Lwak, there were 6733 cases of acute LRT illness, and specimens were collected from 1641 (24%); 359 (22%) were positive for influenza virus. The crude and adjusted rates of medically attended influenza-associated acute LRT illness were 6.9 and 13.6 cases per 1000 person-years, respectively, in Kibera, and 5.6 and 23.0 cases per 1000 person-years, respectively, in Lwak. In both sites, rates of influenza-associated acute LRT illness were highest among children <2 years old and lowest among adults ≥50 years old. CONCLUSION: In Kenya, the incidence of influenza-associated acute LRT illness was high in both rural and urban settings, particularly among the most vulnerable age groups. |
Secondary household transmission of 2009 pandemic influenza A (H1N1) virus among an urban and rural population in Kenya, 2009-2010
Kim CY , Breiman RF , Cosmas L , Audi A , Aura B , Bigogo G , Njuguna H , Lebo E , Waiboci L , Njenga MK , Feikin DR , Katz MA . PLoS One 2012 7 (6) e38166 BACKGROUND: In Kenya, >1,200 laboratory-confirmed 2009 pandemic influenza A (H1N1) (pH1N1) cases occurred since June 2009. We used population-based infectious disease surveillance (PBIDS) data to assess household transmission of pH1N1 in urban Nairobi (Kibera) and rural Lwak. METHODS: We defined a pH1N1 patient as laboratory-confirmed pH1N1 infection among PBIDS participants during August 1, 2009-February 5, 2010, in Kibera, or August 1, 2009-January 20, 2010, in Lwak, and a case household as a household with a laboratory-confirmed pH1N1 patient. Community interviewers visited PBIDS-participating households to inquire about illnesses among household members. We randomly selected 4 comparison households per case household matched by number of children aged <5. Comparison households had a household visit 10 days before or after the matched patient symptom onset date. We defined influenza-like illnesses (ILI) as self-reported cough or sore throat, and a self-reported fever ≤8 days after the pH1N1 patient's symptom onset in case households and ≤8 days before selected household visit in comparison households. We used the Cochran-Mantel-Haenszel test to compare proportions of ILIs among case and comparison households, and log binomial-model to compare that of Kibera and Lwak. RESULTS: Among household contacts of patients with confirmed pH1N1 in Kibera, 4.6% had ILI compared with 8.2% in Lwak (risk ratio [RR], 0.5; 95% confidence interval [CI], 0.3-0.9). Household contacts of patients were more likely to have ILIs than comparison-household members in both Kibera (RR, 1.8; 95% CI, 1.1-2.8) and Lwak (RR, 2.6; 95% CI, 1.6-4.3). Overall, ILI was not associated with patient age. However, ILI rates among household contacts were higher among children aged <5 years than persons aged ≥5 years in Lwak, but not Kibera. CONCLUSIONS: Substantial pH1N1 household transmission occurred in urban and rural Kenya. Household transmission rates were higher in the rural area. |
Differing burden and epidemiology of non-Typhi Salmonella bacteremia in rural and urban Kenya, 2006-2009
Tabu C , Breiman RF , Ochieng B , Aura B , Cosmas L , Audi A , Olack B , Bigogo G , Ongus JR , Fields P , Mintz E , Burton D , Oundo J , Feikin DR . PLoS One 2012 7 (2) e31237 BACKGROUND: The epidemiology of non-Typhi Salmonella (NTS) bacteremia in Africa will likely evolve as potential co-factors, such as HIV, malaria, and urbanization, also change. METHODS: As part of population-based surveillance among 55,000 persons in malaria-endemic, rural and malaria-nonendemic, urban Kenya from 2006-2009, blood cultures were obtained from patients presenting to referral clinics with fever ≥38.0 degrees C or severe acute respiratory infection. Incidence rates were adjusted based on persons with compatible illnesses, but whose blood was not cultured. RESULTS: NTS accounted for 60/155 (39%) of blood culture isolates in the rural and 7/230 (3%) in the urban sites. The adjusted incidence in the rural site was 568/100,000 person-years, and the urban site was 51/100,000 person-years. In both sites, the incidence was highest in children <5 years old. The NTS-to-typhoid bacteremia ratio in the rural site was 4.6 and in the urban site was 0.05. S. Typhimurium represented >85% of blood NTS isolates in both sites, but only 21% (urban) and 64% (rural) of stool NTS isolates. Overall, 76% of S. Typhimurium blood isolates were multi-drug resistant, most of which had an identical profile in Pulse Field Gel Electrophoresis. In the rural site, the incidence of NTS bacteremia increased during the study period, concomitant with rising malaria prevalence (monthly correlation of malaria positive blood smears and NTS bacteremia cases, Spearman's correlation, p = 0.018 for children, p = 0.16 adults). In the rural site, 80% of adults with NTS bacteremia were HIV-infected. Six of 7 deaths within 90 days of NTS bacteremia had HIV/AIDS as the primary cause of death assigned on verbal autopsy. CONCLUSIONS: NTS caused the majority of bacteremias in rural Kenya, but typhoid predominated in urban Kenya, which most likely reflects differences in malaria endemicity. Control measures for malaria, as well as HIV, will likely decrease the burden of NTS bacteremia in Africa. |
Population-based incidence of typhoid fever in an urban informal settlement and a rural area in Kenya: implications for typhoid vaccine use in Africa
Breiman RF , Cosmas L , Njuguna H , Audi A , Olack B , Ochieng JB , Wamola N , Bigogo GM , Awiti G , Tabu CW , Burke H , Williamson J , Oundo JO , Mintz ED , Feikin DR . PLoS One 2012 7 (1) e29119 BACKGROUND: High rates of typhoid fever in children in urban settings in Asia have led to focus on childhood immunization in Asian cities, but not in Africa, where data, mostly from rural areas, have shown low disease incidence. We set out to compare incidence of typhoid fever in a densely populated urban slum and a rural community in Kenya, hypothesizing higher rates in the urban area, given crowding and suboptimal access to safe water, sanitation and hygiene. METHODS: During 2007-9, we conducted population-based surveillance in Kibera, an urban informal settlement in Nairobi, and in Lwak, a rural area in western Kenya. Participants had free access to study clinics; field workers visited their homes biweekly to collect information about acute illnesses. In clinic, blood cultures were processed from patients with fever or pneumonia. Crude and adjusted incidence rates were calculated. RESULTS: In the urban site, the overall crude incidence of Salmonella enterica serovar Typhi (S. Typhi) bacteremia was 247 cases per 100,000 person-years of observation (pyo) with highest rates in children 5-9 years old (596 per 100,000 pyo) and 2-4 years old (521 per 100,000 pyo). Crude overall incidence in Lwak was 29 cases per 100,000 pyo with low rates in children 2-4 and 5-9 years old (28 and 18 cases per 100,000 pyo, respectively). Adjusted incidence rates were highest in 2-4 year old urban children (2,243 per 100,000 pyo) which were >15-fold higher than rates in the rural site for the same age group. Nearly 75% of S. Typhi isolates were multi-drug resistant. CONCLUSIONS: This systematic urban slum and rural comparison showed dramatically higher typhoid incidence among urban children <10 years old with rates similar to those from Asian urban slums. The findings have potential policy implications for use of typhoid vaccines in increasingly urban Africa. |
Nutritional status of under-five children living in an informal urban settlement in Nairobi, Kenya
Olack B , Burke H , Cosmas L , Bamrah S , Dooling K , Feikin DR , Talley LE , Breiman RF . J Health Popul Nutr 2011 29 (4) 357-63 Malnutrition in sub-Saharan Africa contributes to high rates of childhood morbidity and mortality. However, little information on the nutritional status of children is available from informal settlements. During the period of post-election violence in Kenya during December 2007-March 2008, food shortages were widespread within informal settlements in Nairobi. To investigate whether food insecurity due to post-election violence resulted in high prevalence of acute and chronic malnutrition in children, a nutritional survey was undertaken among children aged 6-59 months within two villages in Kibera, where the Kenya Medical Research Institute/Centers for Disease Control and Prevention conducts population-based surveillance for infectious disease syndromes. During 25 March-4 April 2008, a structured questionnaire was administered to caregivers of 1,310 children identified through surveillance system databases to obtain information on household demographics, food availability, and child-feeding practices. Anthropometric measurements were recorded on all participating children. Indices were reported in z-scores and compared with the World Health Organization (WHO) 2005 reference population to determine the nutritional status of children. Data were analyzed using the Anthro software of WHO and the SAS. Stunting was found in 47.0% of the children; 11.8% were underweight, and 2.6% were wasted. Severe stunting was found in 23.4% of the children; severe underweight in 3.1%, and severe wasting in 0.6%. Children aged 36-47 months had the highest prevalence (58.0%) of stunting while the highest prevalence (4.1%) of wasting was in children aged 6-11 months. Boys were more stunted than girls (p < 0.01), and older children were significantly (p < 0.0001) stunted compared to younger children. In the third year of life, girls were more likely than boys to be wasted (p < 0.01). The high prevalence of chronic malnutrition suggests that stunting is a sustained problem within this urban informal settlement, not specifically resulting from the relatively brief political crisis. The predominance of stunting in older children indicates failure in growth and development during the first two years of life. Food programmes in Kenya have traditionally focused on rural areas and refugee camps. The findings of the study suggest that tackling childhood stunting is a high priority, and there should be fostered efforts to ensure that malnutrition-prevention strategies include the urban poor. |
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