Last data update: May 16, 2025. (Total: 49299 publications since 2009)
Records 1-30 (of 83 Records) |
Query Trace: Juma J[original query] |
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Complete genome of an mpox clade 1b virus from Kenya
Langat SK , Gathii K , Limbaso K , Roba A , Ndia M , Mutai B , Pilarowski G , Ochieng M , Juma B , Onyango C , Nyunja A , Okunga E , Ofula V , Oluniyi P , Chepkorir E , Lutomiah J , Herman-Roloff A , Lucchi N , Limo H , Langat D , Khamadi S , Kiiru J , Amoth P , Waitumbi J , Songok E . Microbiol Resour Announc 2025 e0005025 ![]() ![]() We report the genome of a case of mpox detected in Kenya involving a truck driver with travel history to Uganda. Whole genome sequencing and phylogenetic analysis of the mpox virus (MPXV) showed that the genome clustered with clade Ib, which was recently identified in the Democratic Republic of Congo. |
Investigating the role of cytomegalovirus as a cause of stillbirths and child deaths in low and middle-income countries through postmortem minimally invasive tissue sampling
Velaphi S , Madewell ZJ , Tippett-Barr B , Blau DM , Rogena EA , Lala SG , Mahtab S , Swart PJ , Akelo V , Onyango D , Otieno K , Rogena EA , Were JA , Bassat Q , Carrilho C , Mandomando I , Torres-Fernandez D , Varo R , Luke R , Moses F , Nwajiobi-Princewill P , Ogbuanu IU , Ojulong J , El Arifeen S , Gurley ES , Assefa N , Gedefa L , Madrid L , Scott JAG , Wale H , Juma J , Keita AM , Kotloff KL , Sow SO , Tapia MD , Mutevedzi P , Whitney CG , Madhi SA . Clin Infect Dis 2025 BACKGROUND: There is paucity of information on the role of cytomegalovirus (CMV) infection as a cause of stillbirths or childhood deaths in low-and middle-income countries (LMICs). We investigated attribution of CMV-disease in the causal pathway to stillbirths and deaths in children <5 years of age in seven LMICs participating in the Child Health and Mortality Prevention Surveillance (CHAMPS) network. METHODS: We analyzed stillbirths and decedents enrolled between December 2016 and July 2023. Deaths were investigated using post-mortem minimally invasive tissue sampling with histopathology and molecular diagnostic investigations of tissues and body fluids, along with review of clinical records. Multi-disciplinary expert panels reviewed findings and reported on the causal pathway to death. RESULTS: CMV was detected in 19.5%(1140/5841) of all evaluated deaths, including 5.0% (111/2204), 6.2% (139/2229), 41.2% (107/260), 68.1%(323/474) and 68.2%(460/674) of stillbirths, neonates (deaths 0-<28 days postnatal), young infants (28-<90 days), older infants (90-<365 days) and children (12-<60 months), respectively. CMV-disease was attributed in the causal pathway to death in 0.9%(20/2204) of stillbirths, 0.8%(17/2229) of neonates, 13.1% (34/260) of young infants, 9.7%(46/474) of older infants and 3.3%(22/674) of children. Decedents with CMV-disease compared with those without CMV-disease in the causal pathway, were more likely to have severe microcephaly (38.2% vs. 21.1%; aOR 2.2, 95%CI: 1.3-3.6) and HIV-infected (36.9% vs. 6.2%; aOR: 10.9, 95%CI: 6.5-18.5). CONCLUSIONS: CMV-disease is an important contributor to deaths during infancy and childhood and is often associated with severe microcephaly and HIV-infection. Improving management of CMV in HIV-infected children and a vaccine to prevent CMV are needed interventions. |
Elevating larval source management as a key strategy for controlling malaria and other vector-borne diseases in Africa
Okumu F , Moore SJ , Selvaraj P , Yafin AH , Juma EO , Shirima GG , Majambere S , Hardy A , Knols BGJ , Msugupakulya BJ , Finda M , Kahamba N , Thomsen E , Ahmed A , Zohdy S , Chaki P , DeChant P , Fornace K , Govella N , Gowelo S , Hakizimana E , Hamainza B , Ijumba JN , Jany W , Kafy HT , Kaindoa EW , Kariuki L , Kiware S , Kweka EJ , Lobo NF , Marrenjo D , Matoke-Muhia D , Mbogo C , McCann RS , Monroe A , Ndenga BA , Ngowo HS , Ochomo E , Opiyo M , Reithinger R , Sikaala CH , Tatarsky A , Takudzwa D , Trujillano F , Sherrard-Smith E . Parasit Vectors 2025 18 (1) 45 ![]() ![]() Larval source management (LSM) has a long history of advocacy and successes but is rarely adopted where funds are limited. The World Health Organization (WHO) guidelines on malaria prevention recommend the use of LSM as a supplementary intervention to the core vector control methods (insecticide-treated nets and indoor residual spraying), arguing that its feasibility in many settings can be limited by larval habitats being numerous, transient, and difficult to find or treat. Another key argument is that there is insufficient high-quality evidence for its effectiveness to support wide-scale implementation. However, the stagnation of progress towards malaria elimination demands that we consider additional options to the current emphasis on insecticidal commodities targeting adult mosquitoes inside homes. This letter is the result of a global, crossdisciplinary collaboration comprising: (a) detailed online expert discussions, (b) a narrative review of countries that have eliminated local malaria transmission, and (c) a mathematical modeling exercise using two different approaches. Together, these efforts culminated in seven key recommendations for elevating larval source management as a strategy for controlling malaria and other mosquito-borne diseases in Africa (Box 1). LSM encompasses the use of larvicide (a commodity) as well as various environmental sanitation measures. Together, these efforts lead to the long-term reduction of mosquito populations, which benefits the entire community by controlling both disease vector and nuisance mosquitoes. In this paper, we argue that the heavy reliance on large-scale cluster-randomized controlled trials (CRTs) to generate evidence on epidemiological endpoints restricts the recommendation of approaches to only those interventions that can be measured by functional units and deliver relatively uniform impact and, therefore, are more likely to receive financial support for conducting these trials. The explicit impacts of LSM may be better captured by using alternative evaluation approaches, especially high-quality operational data and a recognition of locally distinct outcomes and tailored strategies. LSM contributions are also evidenced by the widespread use of LSM strategies in nearly all countries that have successfully achieved malaria elimination. Two modelling approaches demonstrate that a multifaceted strategy, which incorporates LSM as a central intervention alongside other vector control methods, can effectively mitigate key biological threats such as insecticide resistance and outdoor biting, leading to substantial reductions in malaria cases in representative African settings. This argument is extended to show that the available evidence is sufficient to establish the link between LSM approaches and reduced disease transmission of mosquito-borne illnesses. What is needed now is a significant boost in the financial resources and public health administration structures necessary to train, employ and deploy local-level workforces tasked with suppressing mosquito populations in scientifically driven and ecologically sensitive ways. In conclusion, having WHO guidelines that recognize LSM as a key intervention to be delivered in multiple contextualized forms would open the door to increased flexibility for funding and aid countries in implementing the strategies that they deem appropriate. Financially supporting the scale-up of LSM with high-quality operations monitoring for vector control in combination with other core tools can facilitate better health. The global health community should reconsider how evidence and funding are used to support LSM initiatives. |
Epidemiology and response to the COVID-19 pandemic in the Dadaab Refugee Camp Complex, Kenya, March 2020-December 2022
Ope M , Musyoka R , Kosar A , Osman M , Hassan A , Mohammed H , Munyua P , Juma B , Hunsperger E , Mohammed S , Burton J , Eidex RB . Travel Med Infect Dis 2024 63 102785 INTRODUCTION: Refugee settings may increase the risk of SARS-CoV-2 infection and death, yet data on the response to the pandemic in these populations is scarce. METHODS: We describe interventions to mitigate SARS-CoV-2 transmission in Dadaab Refugee Camp Complex, Kenya and performed descriptive analyses using March 2020 to December 2022 data from Kenya's national SARS-CoV-2 repository and line list of positive cases maintained by United Nations High Commissioner for Refugees (UNHCR). We calculated case fatality rates (CFR) and attack rates per 100,000 (AR) using the 2019 national census and population statistics from UNHCR and compared them to national figures. RESULTS: SARS-CoV-2 infection was first reported in April and May 2020, among host community members and refugees respectively. Of 964 laboratory-confirmed cases, 700 (72.6 %) were refugees. The AR was 82.7 (95 % CI 72.6-92.8) for host community members, 228.3 (95 % CI 211.3-245.4) for refugees and 721.1 (95 % CI 718.7-723.5) nationally. The CFR was 1.5 % (95 % CI 0.15-3.18) for host community members, 1.76 % (95 % CI 1.71-1.80) nationally and 7.4 % (95 % CI 5.4-9.4) for refugees. Mitigation measures implemented by the Government of Kenya, UNHCR and partners during the pandemic included multisectoral coordination, movement restrictions, mass gathering bans, and health promotion. Social distancing, symptom screening and mandatory mask usage were enforced during mass gatherings. Testing capacity was bolstered, quarantine and isolation facilities established, and vaccination initiated. CONCLUSIONS: Despite a low AR and UNHCR's swift and comprehensive response, refugees' CFR was high, underscoring their vulnerability and need for targeted interventions during epidemic responses. |
Infodemics and vaccine confidence: Protocol for social listening and insight generation to inform action
Kolis J , Brookmeyer K , Chuvileva Y , Voegeli C , Juma S , Ishizumi A , Renfro K , Wilhelm E , Tice H , Fogarty H , Kocer I , Helms J , Verma A . JMIR Public Health Surveill 2024 10 e51909 BACKGROUND: In the fall of 2020, the COVID-19 infodemic began to affect public confidence in and demand for COVID-19 vaccines in the United States. While polls indicated what consumers felt regarding COVID-19 vaccines, they did not provide an understanding of why they felt that way or the social and informational influences that factored into vaccine confidence and uptake. It was essential for us to better understand how information ecosystems were affecting the confidence in and demand for COVID-19 vaccines in the United States. OBJECTIVE: The US Centers for Disease Control and Prevention (CDC) established an Insights Unit within the COVID-19 Response's Vaccine Task Force in January 2021 to assist the agency in acting more swiftly to address the questions, concerns, perceptions, and misinformation that appeared to be affecting uptake of COVID-19 vaccines. We established a novel methodology to rapidly detect and report on trends in vaccine confidence and demand to guide communication efforts and improve programmatic quality in near real time. METHODS: We identified and assessed data sources for inclusion through an informal landscape analysis using a snowball method. Selected data sources provided an expansive look at the information ecosystem of the United States regarding COVID-19 vaccines. The CDC's Vaccinate with Confidence framework and the World Health Organization's behavioral and social drivers for vaccine decision-making framework were selected as guiding principles for interpreting generated insights and their impact. We used qualitative thematic analysis methods and a consensus-building approach to identify prevailing and emerging themes, assess their potential threat to vaccine confidence, and propose actions to increase confidence and demand. RESULTS: As of August 2022, we have produced and distributed 34 reports to >950 recipients within the CDC and externally. State and local health departments, nonprofit organizations, professional associations, and congressional committees have referenced and used the reports for learning about COVID-19 vaccine confidence and demand, developing communication strategies, and demonstrating how the CDC monitored and responded to misinformation. A survey of the reports' end users found that nearly 75% (40/53) of respondents found them "very" or "extremely" relevant and 52% (32/61) used the reports to inform communication strategies. In addition, our methodology underwent continuous process improvement to increase the rigor of the research process, the validity of the findings, and the usability of the reports. CONCLUSIONS: This methodology can serve as a diagnostic technique for rapidly identifying opportunities for public health interventions and prevention. As the methodology itself is adaptable, it could be leveraged and scaled for use in a variety of public health settings. Furthermore, it could be considered beyond acute public health crises to support adherence to guidance and recommendations and could be considered within routine monitoring and surveillance systems. |
Investigation and successful control of a Candida auris outbreak at a tertiary health care facility in Kenya
Ombajo LA , Kanyua A , Ngugi R , Malcolm C , Berkow E , Gade L , Bancroft E , Osoro J , Njoroge R , Juma P , Ngirita M , Bore RC , Litvintseva A , Lyman M , Toda M . IJID Regions 2024 13 ![]() ![]() Objectives: This study aimed to conduct an epidemiological and genomic investigation of a hospital outbreak of Candida auris, and implement measures for its control. Methods: We collected demographic and clinical data from medical records of patients with C. auris from January 2017 to June 2019 after identifying increased cases in April 2019. Point-prevalence surveys for C. auris colonisation were conducted in the critical care units (CCU). Antifungal susceptibility testing and genomic sequencing of isolates were performed. A bundle of infection prevention and control measures was instituted. Results: Thirty-two patients with C. auris were identified. All patients had a history of CCU admission. A total of 283 screening swabs were obtained and 57 isolates of C. auris identified. Antifungal susceptibility testing was performed on 48 isolates. All but two isolates were resistant to fluconazole; one isolate was also resistant to amphotericin B. Forty-one of 46 isolate genomes were clonally related and formed a distinct genetic cluster in Clade III. C. auris colonisation reduced from 42% in June 2019 to 1% in August 2019, and no new hospital-acquired colonisation was identified in the subsequent 9 months. Conclusions: We identified a new genetic subcluster of Clade III C. auris. We also show that strict implementation of infection prevention measures can lead to substantial reductions in C. auris transmission. © 2024 The Authors |
Climate change, malaria and neglected tropical diseases: a scoping review
Klepac P , Hsieh JL , Ducker CL , Assoum M , Booth M , Byrne I , Dodson S , Martin DL , Turner CMR , van Daalen KR , Abela B , Akamboe J , Alves F , Brooker SJ , Ciceri-Reynolds K , Cole J , Desjardins A , Drakeley C , Ediriweera DS , Ferguson NM , Gabrielli AF , Gahir J , Jain S , John MR , Juma E , Kanayson P , Deribe K , King JD , Kipingu AM , Kiware S , Kolaczinski J , Kulei WJ , Laizer TL , Lal V , Lowe R , Maige JS , Mayer S , McIver L , Mosser JF , Nicholls RS , Nunes-Alves C , Panjwani J , Parameswaran N , Polson K , Radoykova HS , Ramani A , Reimer LJ , Reynolds ZM , Ribeiro I , Robb A , Sanikullah KH , Smith DRM , Shirima GG , Shott JP , Tidman R , Tribe L , Turner J , Vaz Nery S , Velayudhan R , Warusavithana S , Wheeler HS , Yajima A , Abdilleh AR , Hounkpatin B , Wangmo D , Whitty CJM , Campbell-Lendrum D , Hollingsworth TD , Solomon AW , Fall IS . Trans R Soc Trop Med Hyg 2024 To explore the effects of climate change on malaria and 20 neglected tropical diseases (NTDs), and potential effect amelioration through mitigation and adaptation, we searched for papers published from January 2010 to October 2023. We descriptively synthesised extracted data. We analysed numbers of papers meeting our inclusion criteria by country and national disease burden, healthcare access and quality index (HAQI), as well as by climate vulnerability score. From 42 693 retrieved records, 1543 full-text papers were assessed. Of 511 papers meeting the inclusion criteria, 185 studied malaria, 181 dengue and chikungunya and 53 leishmaniasis; other NTDs were relatively understudied. Mitigation was considered in 174 papers (34%) and adaption strategies in 24 (5%). Amplitude and direction of effects of climate change on malaria and NTDs are likely to vary by disease and location, be non-linear and evolve over time. Available analyses do not allow confident prediction of the overall global impact of climate change on these diseases. For dengue and chikungunya and the group of non-vector-borne NTDs, the literature privileged consideration of current low-burden countries with a high HAQI. No leishmaniasis papers considered outcomes in East Africa. Comprehensive, collaborative and standardised modelling efforts are needed to better understand how climate change will directly and indirectly affect malaria and NTDs. |
Epidemiology of SARS-CoV-2 in Kakuma Refugee Camp Complex, Kenya, 2020-2021(1)
Ope M , Musyoka R , Kiogora J , Wambugu J , Hunsperger E , Emukule GO , Munyua P , Juma B , Simiyu E , Gagnidze L , Burton J , Eidex RB . Emerg Infect Dis 2024 30 (5) 900-907 Understanding SARS-CoV-2 infection in populations at increased risk for poor health is critical to reducing disease. We describe the epidemiology of SARS-CoV-2 infection in Kakuma Refugee Camp Complex, Kenya. We performed descriptive analyses of SARS-CoV-2 infection in the camp and surrounding community during March 16, 2020‒December 31, 2021. We identified cases in accordance with national guidelines.We estimated fatality ratios and attack rates over time using locally weighted scatterplot smoothing for refugees, host community members, and national population. Of the 18,864 SARS-CoV-2 tests performed, 1,024 were positive, collected from 664 refugees and 360 host community members. Attack rates were 325.0/100,000 population (CFR 2.9%) for refugees,150.2/100,000 population (CFR 1.11%) for community, and 628.8/100,000 population (CFR 1.83%) nationwide. During 2020-2021, refugees experienced a lower attack rate but higher CFR than the national population, underscoring the need to prioritize SARS-CoV-2 mitigation measures, including vaccination. |
Use of sentinel surveillance platforms for monitoring SARS-CoV-2 activity: Evidence from analysis of Kenya Influenza Sentinel Surveillance Data
Owusu D , Ndegwa LK , Ayugi J , Kinuthia P , Kalani R , Okeyo M , Otieno NA , Kikwai G , Juma B , Munyua P , Kuria F , Okunga E , Moen AC , Emukule GO . JMIR Public Health Surveill 2024 10 e50799 BACKGROUND: Little is known about the cocirculation of influenza and SARS-CoV-2 viruses during the COVID-19 pandemic and the use of respiratory disease sentinel surveillance platforms for monitoring SARS-CoV-2 activity in sub-Saharan Africa. OBJECTIVE: We aimed to describe influenza and SARS-CoV-2 cocirculation in Kenya and how the SARS-CoV-2 data from influenza sentinel surveillance correlated with that of universal national surveillance. METHODS: From April 2020 to March 2022, we enrolled 7349 patients with severe acute respiratory illness or influenza-like illness at 8 sentinel influenza surveillance sites in Kenya and collected demographic, clinical, underlying medical condition, vaccination, and exposure information, as well as respiratory specimens, from them. Respiratory specimens were tested for influenza and SARS-CoV-2 by real-time reverse transcription polymerase chain reaction. The universal national-level SARS-CoV-2 data were also obtained from the Kenya Ministry of Health. The universal national-level SARS-CoV-2 data were collected from all health facilities nationally, border entry points, and contact tracing in Kenya. Epidemic curves and Pearson r were used to describe the correlation between SARS-CoV-2 positivity in data from the 8 influenza sentinel sites in Kenya and that of the universal national SARS-CoV-2 surveillance data. A logistic regression model was used to assess the association between influenza and SARS-CoV-2 coinfection with severe clinical illness. We defined severe clinical illness as any of oxygen saturation <90%, in-hospital death, admission to intensive care unit or high dependence unit, mechanical ventilation, or a report of any danger sign (ie, inability to drink or eat, severe vomiting, grunting, stridor, or unconsciousness in children younger than 5 years) among patients with severe acute respiratory illness. RESULTS: Of the 7349 patients from the influenza sentinel surveillance sites, 76.3% (n=5606) were younger than 5 years. We detected any influenza (A or B) in 8.7% (629/7224), SARS-CoV-2 in 10.7% (768/7199), and coinfection in 0.9% (63/7165) of samples tested. Although the number of samples tested for SARS-CoV-2 from the sentinel surveillance was only 0.2% (60 per week vs 36,000 per week) of the number tested in the universal national surveillance, SARS-CoV-2 positivity in the sentinel surveillance data significantly correlated with that of the universal national surveillance (Pearson r=0.58; P<.001). The adjusted odds ratios (aOR) of clinical severe illness among participants with coinfection were similar to those of patients with influenza only (aOR 0.91, 95% CI 0.47-1.79) and SARS-CoV-2 only (aOR 0.92, 95% CI 0.47-1.82). CONCLUSIONS: Influenza substantially cocirculated with SARS-CoV-2 in Kenya. We found a significant correlation of SARS-CoV-2 positivity in the data from 8 influenza sentinel surveillance sites with that of the universal national SARS-CoV-2 surveillance data. Our findings indicate that the influenza sentinel surveillance system can be used as a sustainable platform for monitoring respiratory pathogens of pandemic potential or public health importance. |
Social network strategy (SNS) for HIV testing: a new approach for identifying individuals with undiagnosed HIV infection in Tanzania
Rwabiyago OE , Katale A , Bingham T , Grund JM , Machangu O , Medley A , Nkomela ZM , Kayange A , King'ori GN , Juma JM , Ismail A , Kategile U , Akom E , Mlole NT , Schaad N , Maokola W , Nyagonde N , Magesa D , Kazitanga JC , Maruyama H , Temu F , Kimambo S , Sando D , Mbatia R , Chalamila ST , Ogwang BE , Njelekela MA , Kazaura K , Wong VJ , Gongo R , Njau PF , Mbunda A , Nondi J , Bateganya M , Greene J , Breda M , Mgomella G , Rwebembera A , Swaminathan M . AIDS Care 2024 1-10 Social network strategy (SNS) testing uses network connections to refer individuals at high risk to HIV testing services (HTS). In Tanzania, SNS testing is offered in communities and health facilities. In communities, SNS testing targets key and vulnerable populations (KVP), while in health facilities it complements index testing by reaching unelicited index contacts. Routine data were used to assess performance and trends over time in PEPFAR-supported sites between October 2021 and March 2023. Key indicators included SNS social contacts tested, and new HIV-positives individuals identified. Descriptive and statistical analysis were conducted. Univariable and multivariable analysis were applied, and variables with P-values <0.2 at univariable analysis were considered for multivariable analysis. Overall, 121,739 SNS contacts were tested, and 7731 (6.4%) previously undiagnosed individuals living with HIV were identified. Tested contacts and identified HIV-positives were mostly aged ≥15 years (>99.7%) and females (80.6% of tests, 79.4% of HIV-positives). Most SNS contacts were tested (78,363; 64.7%) and diagnosed (6376; 82.5%) in communities. SNS tests and HIV-positives grew 11.5 and 6.1-fold respectively, from October-December 2021 to January-March 2023, with majority of clients reached in communities vs. facilities (78,763 vs. 42,976). These results indicate that SNS testing is a promising HIV case-finding approach in Tanzania. |
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.
Pop M , Walker AW , Paulson J , Lindsay B , Antonio M , Hossain MA , Oundo J , Tamboura B , Mai V , Astrovskaya I , Corrada Bravo H , Rance R , Stares M , Levine MM , Panchalingam S , Kotloff K , Ikumapayi UN , Ebruke C , Adeyemi M , Ahmed D , Ahmed F , Alam MT , Amin R , Siddiqui S , Ochieng JB , Ouma E , Juma J , Mailu E , Omore R , Morris JG , Breiman RF , Saha D , Parkhill J , Nataro JP , Stine OC . Genome Biol 2014 15 (6) R76 ![]() BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease. RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age. CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques. |
Burden of child mortality from malaria in high endemic areas: results from the CHAMPS Network using minimally invasive tissue sampling
Ogbuanu IU , Otieno K , Varo R , Sow SO , Ojulong J , Duduyemi B , Kowuor D , Cain CJ , Rogena EA , Onyango D , Akelo V , Tippett Barr BA , terKuile F , Kotloff KL , Tapia MD , Keita AM , Juma J , Assefa N , Assegid N , Acham Y , Madrid L , Scott JAG , Arifeen SE , Gurley ES , Mahtab S , Dangor Z , Wadula J , Dutoit J , Madhi SA , Mandomando I , Torres-Fernandez D , Kincardett M , Mabunda R , Mutevedzi P , Madewell ZJ , Blau DM , Whitney CG , Samuels AM , Bassat Q . J Infect 2024 BACKGROUND: Malaria is a leading cause of childhood mortality worldwide. However, accurate estimates of malaria prevalence and causality among patients who die at the country level are lacking due to the limited specificity of diagnostic tools used to attribute etiologies. Accurate estimates are crucial for prioritizing interventions and resources aimed at reducing malaria-related mortality. METHODS: Seven Child Health and Mortality Prevention Surveillance (CHAMPS) Network sites collected comprehensive data on stillbirths and children <5 years, using minimally invasive tissue sampling (MITS). A DeCoDe (Determination of Cause of Death) panel employed standardized protocols for assigning underlying, intermediate, and immediate causes of death, integrating sociodemographic, clinical, laboratory (including extensive microbiology, histopathology, and malaria testing), and verbal autopsy data. Analyses were conducted to ascertain the strength of evidence for cause of death (CoD), describe factors associated with malaria-related deaths, estimate malaria-specific mortality, and assess the proportion of preventable deaths. FINDINGS: Between December 3, 2016, and December 31, 2022, 2673 deaths underwent MITS and had a CoD attributed from four CHAMPS sites with at least 1 malaria-attributed death. No malaria-attributable deaths were documented among 891 stillbirths or 924 neonatal deaths, therefore this analysis concentrates on the remaining 858 deaths among children aged 1-59 months. Malaria was in the causal chain for 42.9% (126/294) of deaths from Sierra Leone, 31.4% (96/306) in Kenya, 18.2% (36/198) in Mozambique, 6.7% (4/60) in Mali, and 0.3% (1/292) in South Africa. Compared to non-malaria related deaths, malaria-related deaths skewed towards older infants and children (p<0.001), with 71.0% among ages 12-59 months. Malaria was the sole infecting pathogen in 184 (70.2%) of malaria-attributed deaths, whereas bacterial and viral co-infections were identified in the causal pathway in 24·0% and 12.2% of cases, respectively. Malnutrition was found at a similar level in the causal pathway of both malaria (26.7%) and non-malaria (30.7%, p=0.256) deaths. Less than two-thirds (164/262; 62.6%) of malaria deaths had received antimalarials prior to death. Nearly all (98·9%) malaria-related deaths were deemed preventable. INTERPRETATION: Malaria remains a significant cause of childhood mortality in the CHAMPS malaria-endemic sites. The high bacterial co-infection prevalence among malaria deaths underscores the potential benefits of antibiotics for severe malaria patients. Compared to non-malaria deaths, many of malaria-attributed deaths are preventable through accessible malaria control measures. FUNDING: This work was supported by the Bill & Melinda Gates Foundation [OPP1126780]. |
Detection of Anopheles stephensi mosquitoes by molecular surveillance, Kenya
Ochomo EO , Milanoi S , Abong'o B , Onyango B , Muchoki M , Omoke D , Olanga E , Njoroge L , Juma EO , Otieno JD , Matoke-Muhia D , Kamau L , Rafferty C , Gimnig JE , Shieshia M , Wacira D , Mwangangi J , Maia M , Chege C , Omar A , Rono MK , Abel L , O'Meara WP , Obala A , Mbogo C , Kariuki L . Emerg Infect Dis 2023 29 (12) 2498-2508 ![]() The Anopheles stephensi mosquito is an invasive malaria vector recently reported in Djibouti, Ethiopia, Sudan, Somalia, Nigeria, and Ghana. The World Health Organization has called on countries in Africa to increase surveillance efforts to detect and report this vector and institute appropriate and effective control mechanisms. In Kenya, the Division of National Malaria Program conducted entomological surveillance in counties at risk for An. stephensi mosquito invasion. In addition, the Kenya Medical Research Institute conducted molecular surveillance of all sampled Anopheles mosquitoes from other studies to identify An. stephensi mosquitoes. We report the detection and confirmation of An. stephensi mosquitoes in Marsabit and Turkana Counties by using endpoint PCR and morphological and sequence identification. We demonstrate the urgent need for intensified entomological surveillance in all areas at risk for An. stephensi mosquito invasion, to clarify its occurrence and distribution and develop tailored approaches to prevent further spread. |
Heterogenous transmission and seroprevalence of SARS-CoV-2 in two demographically diverse populations with low vaccination uptake in Kenya, March and June 2021
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 . Gates Open Res 2023 7 101 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. |
Food insecurity and the risk of HIV acquisition: Findings from population-based surveys in six sub-Saharan African countries (2016-2017) (preprint)
Low A , Gummerson E , Schwitters A , Bonifacio R , Teferi M , Mutenda N , Ayton S , Juma J , Ahpoe C , Ginindza C , Patel H , Biraro S , Sachathep K , Hakim AJ , Barradas D , Hassani AS , Kirungi W , Jackson K , Goeke L , Philips N , Mulenga L , Ward J , Hong S , Rutherford G , Findley S . medRxiv 2021 2021.09.27.21263917 Introduction Food insecurity has a bidirectional relationship with HIV infection, with hunger driving compensatory risk behaviors, while infection can increase poverty. We used a laboratory recency assay to estimate the timing of HIV infection vis-à-vis the timing of severe food insecurity (SFI).Methods Data from population-based surveys in Zambia, Eswatini, Lesotho, Uganda, and Tanzania and Namibia were used. We defined SFI as having no food ≥three times in the past month. Recent HIV infection was identified using the HIV-1 LAg avidity assay, with a viral load (>1000 copies/ml) and no detectable antiretrovirals indicating an infection in the past 6 months. Logistic regression was conducted to assess correlates of SFI. Poisson regression was conducted on pooled data, adjusted by country to determine the association of SFI with recent HIV infection and risk behaviors, with effect heterogeneity evaluated for each country. All analyses were done using weighted data.Results Of 112,955 participants aged 15-59, 10.3% lived in households reporting SFI. SFI was most common in urban, woman-headed households. Among women and not men, SFI was associated with a two-fold increase in risk of recent HIV infection (adjusted relative risk [aRR] 2.08, 95% CI 1.09-3.97), with lower risk in high prevalence countries (Eswatini and Lesotho). SFI was associated with transactional sex (aRR 1.28, 95% CI 1.17-1.41), a history of forced sex (aRR 1.36, 95% CI 1.11-1.66), and condom-less sex with a partner of unknown or positive HIV status (aRR 1.08, 95% CI 1.02-1.14) in all women, and intergenerational sex (partner ≥10 years older) in women aged 15-24 (aRR 1.23, 95% CI 1.03-1.46), although this was heterogeneous. Recent receipt of food support was protective (aRR 0.36, 95% CI 0.14-0.88).Conclusion SFI increased risk for HIV acquisition in women by two-fold. Worsening food scarcity due to climactic extremes could imperil HIV epidemic control.What is already knownThe link between food insecurity and the adoption of high-risk sexual behaviors as a coping mechanism has been shown in several settings.HIV infection can also drive food insecurity due to debilitating illness reducing productivity, the costs of treatment diverting money from supplies, and potentially reduced labor migration.Food insecurity has been associated with chronic HIV infection, but it has not been linked with HIV acquisition.What are the new findingsThis study of 112,955 adults across six countries in sub-Saharan Africa provides unique information on the association between acute food insecurity and recent HIV infection in women, as well as the potential behavioral and biological mediators, including community viremia as a measure of infectiousness.The data enabled a comprehensive analysis of factors associated with risk of infection, and how these factors differed by country and gender. Women living in food insecure households had a two-fold higher risk of recent HIV acquisition, and reported higher rates of transactional sex, early sexual debut, forced sex, intergenerational sex and sex without a condom with someone of unknown or positive HIV status. This pattern was not seen in men.This study is also the first to demonstrate a protective association for food support, which was associated with a lower risk of recent HIV infection in women.What do the new findings implyIn light of worsening food insecurity due to climate change and the recent COVID-19 pandemic, our results support further exploration of gender-specific pathways of response to acute food insecurity, particularly how women’s changes in sexual behavior heighten their risk of HIV acquisition.These and other data support the inclusion of food insecurity in HIV risk assessments for women, as well as the exploration of provision of food support to those households at highest risk based on geographic and individual factors.Competing Interest StatementThe authors have declared no competing interest.Clinical Protocols https://phia.icap.columbia.edu/ Funding StatementThis project has been supported by the Presid nt Emergency Plan for AIDS Relief (PEPFAR) through the Centers for Disease Control and Prevention (CDC) under the terms of cooperative agreement #U2GGH001226.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The PHIA protocol and data collection tools were approved by national ethics committees for each country, and the institutional review boards at Columbia University Irving Medical Center, the US Centers for Disease Control and Prevention (CDC) and the University of California, San Francisco in the case of Namibia. Due to the inclusion of six countries and the multiple ethical boards involved, we are providing the protocol numbers for the Columbia University Irving Medical Center, which approved all protocols (AAAQ0753, AAAQ7860, AAAQ8408, AAAQ8537, AAAR2051, AAAQ889). All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data used in this manuscript are publicly available at https://phia-data.icap.columbia.edu/. https://phia-data.icap.columbia.edu/ |
Enteropathogen antibody dynamics and force of infection among children in low-resource settings (preprint)
Arnold BF , Martin DL , Juma J , Mkocha H , Ochieng JB , Cooley GM , Omore R , Goodhew EB , Morris JF , Costantini V , Vinje J , Lammie PJ , Priest JW . bioRxiv 2019 522920 Little is known about enteropathogen seroepidemiology among children in low-resource settings. We measured serological IgG responses to eight enteropathogens (Giardia intestinalis, Cryptosporidium parvum, Entamoeba histolytica, Salmonella enterica, enterotoxigenic Escherichia coli, Vibrio cholerae, Campylobacter jejuni, norovirus) in cohorts from Haiti, Kenya, and Tanzania. We studied antibody dynamics and force of infection across pathogens and cohorts. Enteropathogens shared common seroepidemiologic features that enabled between-pathogen comparisons of transmission. Overall, exposure was intense: for most pathogens the window of primary infection was <3 years old; for highest transmission pathogens primary infection occurred within the first year. Longitudinal profiles revealed significant IgG boosting and waning above seropositivity cutoffs, underscoring the value of longitudinal designs to estimate force of infection. Seroprevalence and force of infection were rank-preserving across pathogens, illustrating the measures provide similar information about transmission heterogeneity. Our findings suggest multiplex antibody assays are a promising approach to measure population-level enteropathogen transmission in serologic surveillance. |
Preventing HIV among adolescent boys and young men through PEPFAR-supported voluntary medical male circumcision in 15 Sub-Saharan African Countries, 2018-2021
Peck ME , Ong K , Lucas T , Thomas AG , Wandira R , Ntwaaga B , Mkhontfo M , Zegeye T , Yohannes F , Mulatu D , Gultie T , Juma AW , Odoyo-June E , Maida A , Msungama W , Canda M , Mutandi G , Zemburuka BLT , Kankindi I , Vranken P , Maphothi N , Loykissoonlal D , Bunga S , Grund JM , Kazaura KJ , Kabuye G , Chituwo O , Muyunda B , Kamboyi R , Lingenda G , Mandisarisa J , Peterson A , Malaba R , Xaba S , Moyo T , Toledo C . AIDS Educ Prev 2023 35 67-81 Voluntary medical male circumcision (VMMC) is an HIV prevention intervention that has predominantly targeted adolescent and young men, aged 10-24 years. In 2020, the age eligibility for VMMC shifted from 10 to 15 years of age. This report describes the VMMC client age distribution from 2018 to 2021, at the site, national, and regional levels, among 15 countries in southern and eastern Africa. Overall, in 2018 and 2019, the highest proportion of VMMCs were performed among 10-14-year-olds (45.6% and 41.2%, respectively). In 2020 and 2021, the 15-19-year age group accounted for the highest proportion (37.2% and 50.4%, respectively) of VMMCs performed across all age groups. Similarly, in 2021 at the site level, 68.1% of VMMC sites conducted the majority of circumcisions among men aged 15-24 years. This analysis highlights that adolescent boys and young men are the primary recipients of VMMC receiving an important lifetime reduction in HIV risk. |
Dynamic incidence of typhoid fever over a 10-year period (2010-2019) in Kibera, an urban informal settlement in Nairobi, Kenya
Ng'eno E , Lind M , Audi A , Ouma A , Oduor C , Munywoki PK , Agogo GO , Odongo G , Kiplangat S , Wamola N , Osita MP , Mugoh R , Ochieng C , Omballa V , Mogeni OD , Mikoleit M , Fields BS , Montgomery JM , Gauld J , Breiman RF , Juma B , Hunsperger E , Widdowson MA , Bigogo G , Mintz ED , Verani JR . Am J Trop Med Hyg 2023 109 (1) 22-31 Typhoid fever burden can vary over time. Long-term data can inform prevention strategies; however, such data are lacking in many African settings. We reexamined typhoid fever incidence and antimicrobial resistance (AMR) over a 10-year period in Kibera, a densely populated urban informal settlement where a high burden has been previously described. We used data from the Population Based Infectious Diseases Surveillance platform to estimate crude and adjusted incidence rates and prevalence of AMR in nearly 26,000 individuals of all ages. Demographic and healthcare-seeking information was collected through household visits. Blood cultures were processed for patients with acute fever or lower respiratory infection. Between 2010 and 2019, 16,437 participants were eligible for blood culture and 11,848 (72.1%) had a culture performed. Among 11,417 noncontaminated cultures (96.4%), 237 grew Salmonella enterica serovar Typhi (2.1%). Overall crude and adjusted incidences were 95 and 188 cases per 100,000 person-years of observation (pyo), respectively. Annual crude incidence varied from 144 to 233 between 2010 and 2012 and from 9 to 55 between 2013 and 2018 and reached 130 per 100,000 pyo in 2019. Children 5-9 years old had the highest overall incidence (crude, 208; adjusted, 359 per 100,000 pyo). Among isolates tested, 156 of 217 were multidrug resistant (resistant to chloramphenicol, ampicillin, and trimethoprim/sulfamethoxazole [71.9%]) and 6 of 223 were resistant to ciprofloxacin (2.7%). Typhoid fever incidence resurged in 2019 after a prolonged period of low rates, with the highest incidence among children. Typhoid fever control measures, including vaccines, could reduce morbidity in this setting. |
Seroprevalence and risk factors of SARS-CoV-2 infection in an urban informal settlement in Nairobi, Kenya, December 2020 (preprint)
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 . F1000Res 2021 10 853 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. |
Prevalence of Salmonella in stool during the Vaccine Impact on Diarrhea in Africa (VIDA) Study, 2015-2018
Kasumba IN , Powell H , Omore R , Hossain MJ , Sow SO , Ochieng JB , Badji H , Verani JR , Widdowson MA , Sen S , Nasrin S , Permala-Booth J , Jones JA , Roose A , Nasrin D , Sugerman CE , Juma J , Awuor A , Jones JCM , Doh S , Okoi C , Zaman SMA , Antonio M , Hunsperger E , Onyango C , Platts-Mills J , Liu J , Houpt E , Neuzil KM , Kotloff KL , Tennant SM . Clin Infect Dis 2023 76 S87-s96 BACKGROUND: Non-typhoidal Salmonella (NTS) is a common cause of gastroenteritis in young children, with limited data on NTS serovars and antimicrobial resistance in Africa. METHODS: We determined the prevalence of Salmonella spp. and frequency of antimicrobial resistance among serovars identified in stools of 0-59 month-old children with moderate-to-severe diarrhea (MSD) and controls enrolled in the Vaccine Impact on Diarrhea in Africa (VIDA) Study in The Gambia, Mali, and Kenya in 2015-2018, and compared with data from the Global Enteric Multicenter Study (GEMS; 2007-2010) and the GEMS-1A study (2011). Salmonella spp. was detected by quantitative real-time PCR (qPCR) and culture-based methods. Identification of serovars was determined by microbiological methods. RESULTS: By qPCR, the prevalence of Salmonella spp. among MSD cases was 4.0%, 1.6%, and 1.9% and among controls was 4.6%, 2.4%, and 1.6% in The Gambia, Mali, and Kenya, respectively, during VIDA. We observed year-to-year variation in serovar distribution and variation between sites. In Kenya, Salmonella enterica serovar Typhimurium decreased (78.1% to 23.1%; P < .001) among cases and controls from 2007 to 2018, whereas serogroup O:8 increased (8.7% to 38.5%; P = .04). In The Gambia, serogroup O:7 decreased from 2007 to 2018 (36.3% to 0%; P = .001) but S. enterica serovar Enteritidis increased during VIDA (2015 to 2018; 5.9% to 50%; P = .002). Only 4 Salmonella spp. were isolated in Mali during all 3 studies. Multidrug resistance was 33.9% in Kenya and 0.8% in The Gambia across all 3 studies. Ceftriaxone resistance was only observed in Kenya (2.3%); NTS isolates were susceptible to ciprofloxacin at all sites. CONCLUSIONS: Understanding variability in serovar distribution will be important for the future deployment of vaccines against salmonellosis in Africa. |
Histo-Blood Group Antigen Null Phenotypes Associated With a Decreased Risk of Clinical Rotavirus Vaccine Failure Among Children <2 Years of Age Participating in the Vaccine Impact on Diarrhea in Africa (VIDA) Study in Kenya, Mali, and the Gambia
Schwartz LM , Oshinsky J , Reymann M , Esona MD , Bowen MD , Jahangir Hossain M , Zaman SMA , Jones JCM , Antonio M , Badji H , Sarwar G , Sow SO , Sanogo D , Keita AM , Tamboura B , Traoré A , Onwuchekwa U , Omore R , Verani JR , Awuor AO , Ochieng JB , Juma J , Ogwel B , Parashar UD , Tate JE , Kasumba IN , Tennant SM , Neuzil KM , Rowhani-Rahbar A , Elizabeth Halloran M , Atmar RL , Pasetti MF , Kotloff KL . Clin Infect Dis 2023 76 S153-s161 ![]() ![]() BACKGROUND: Previously studied risk factors for rotavirus vaccine failure have not fully explained reduced rotavirus vaccine effectiveness in low-income settings. We assessed the relationship between histo-blood group antigen (HBGA) phenotypes and clinical rotavirus vaccine failure among children <2 years of age participating in the Vaccine Impact on Diarrhea in Africa Study in 3 sub-Saharan African countries. METHODS: Saliva was collected and tested for HBGA phenotype in children who received rotavirus vaccine. The association between secretor and Lewis phenotypes and rotavirus vaccine failure was examined overall and by infecting rotavirus genotype using conditional logistic regression in 218 rotavirus-positive cases with moderate-to-severe diarrhea and 297 matched healthy controls. RESULTS: Both nonsecretor and Lewis-negative phenotypes (null phenotypes) were associated with decreased rotavirus vaccine failure across all sites (matched odds ratio, 0.30 [95% confidence interval: 0.16-0.56] or 0.39 [0.25-0.62], respectively]. A similar decrease in risk against rotavirus vaccine failure among null HBGA phenotypes was observed for cases with P[8] and P[4] infection and their matched controls. While we found no statistically significant association between null HBGA phenotypes and vaccine failure among P[6] infections, the matched odds ratio point estimate for Lewis-negative individuals was >4. CONCLUSIONS: Our study demonstrated a significant relationship between null HBGA phenotypes and decreased rotavirus vaccine failure in a population with P[8] as the most common infecting genotype. Further studies are needed in populations with a large burden of P[6] rotavirus diarrhea to understand the role of host genetics in reduced rotavirus vaccine effectiveness. |
Antibiotic-prescribing practices for management of childhood diarrhea in 3 Sub-Saharan African countries: Findings from the vaccine impact on diarrhea in Africa (vida) study, 2015-2018
Awuor AO , Ogwel B , Powell H , Verani JR , Sow SO , Hossain MJ , Ochieng JB , Juma J , Jamka LP , Roose A , Doh S , Deichsel EL , Onwuchekwa U , Keita AM , Antonio M , Jones JCM , Zaman SMA , Badji H , Kasumba IN , Nasrin D , Platts-Mills JA , Houpt ER , Berendes DM , Sugerman CE , Widdowson MA , Tennant SM , Mintz ED , Omore R , Kotloff KL . Clin Infect Dis 2023 76 S32-s40 BACKGROUND: Despite antibiotic prescription being recommended for dysentery and suspected cholera only, diarrhea still triggers unwarranted antibiotic prescription. We evaluated antibiotic-prescribing practices and their predictors among children aged 2-59 months in the Vaccine Impact on Diarrhea in Africa (VIDA) Study performed in The Gambia, Mali, and Kenya. METHODS: VIDA was a prospective case-control study (May 2015-July 2018) among children presenting for care with moderate-to-severe diarrhea (MSD). We defined inappropriate antibiotic use as prescription or use of antibiotics when not indicated by World Health Organization (WHO) guidelines. We used logistic regression to assess factors associated with antibiotic prescription for MSD cases who had no indication for an antibiotic, at each site. RESULTS: VIDA enrolled 4840 cases. Among 1757 (36.3%) who had no apparent indication for antibiotic treatment, 1358 (77.3%) were prescribed antibiotics. In The Gambia, children who presented with a cough (adjusted odds ratio [aOR]: 2.05; 95% confidence interval [95% CI]: 1.21-3.48) were more likely to be prescribed an antibiotic. In Mali, those who presented with dry mouth (aOR: 3.16; 95% CI: 1.02-9.73) were more likely to be prescribed antibiotics. In Kenya, those who presented with a cough (aOR: 2.18; 95% CI: 1.01-4.70), decreased skin turgor (aOR: 2.06; 95% CI: 1.02-4.16), and were very thirsty (aOR: 4.15; 95% CI: 1.78-9.68) were more likely to be prescribed antibiotics. CONCLUSIONS: Antibiotic prescription was associated with signs and symptoms inconsistent with WHO guidelines, suggesting the need for antibiotic stewardship and clinician awareness of diarrhea case-management recommendations in these settings. |
Exploring survey-based water, sanitation, and animal associations with enteric pathogen carriage: Comparing results in a cohort of cases with moderate-to-severe diarrhea to those in controls in the Vaccine Impact on Diarrhea in Africa (VIDA) Study, 2015-2018
Berendes DM , Omore R , Prentice-Mott G , Fagerli K , Kim S , Nasrin D , Powell H , Jahangir Hossain M , Sow SO , Doh S , Jones JCM , Ochieng JB , Juma J , Awuor AO , Ogwel B , Verani JR , Widdowson MA , Kasumba IN , Tennant SM , Roose A , Zaman SMA , Liu J , Sugerman CE , Platts-Mills JA , Houpt ER , Kotloff KL , Mintz ED . Clin Infect Dis 2023 76 S140-s152 BACKGROUND: The magnitude of pediatric enteric pathogen exposures in low-income settings necessitates substantive water and sanitation interventions, including animal feces management. We assessed associations between pediatric enteric pathogen detection and survey-based water, sanitation, and animal characteristics within the Vaccine Impact on Diarrhea in Africa case-control study. METHODS: In The Gambia, Kenya, and Mali, we assessed enteric pathogens in stool of children aged <5 years with moderate-to-severe diarrhea and their matched controls (diarrhea-free in prior 7 days) via the TaqMan Array Card and surveyed caregivers about household drinking water and sanitation conditions and animals living in the compound. Risk ratios (RRs) and 95% confidence intervals (CIs) were calculated using modified Poisson regression models, stratified for cases and controls and adjusted for age, sex, site, and demographics. RESULTS: Bacterial (cases, 93%; controls, 72%), viral (63%, 56%), and protozoal (50%, 38%) pathogens were commonly detected (cycle threshold <35) in the 4840 cases and 6213 controls. In cases, unimproved sanitation (RR, 1.56; 95% CI, 1.12-2.17), as well as cows (RR, 1.61; 95% CI, 1.16-2.24) and sheep (RR, 1.48; 95% CI, 1.11-1.96) living in the compound, were associated with Shiga toxin-producing Escherichia coli. In controls, fowl (RR, 1.30; 95% CI, 1.15-1.47) were associated with Campylobacter spp. In controls, surface water sources were associated with Cryptosporidium spp., Shigella spp., heat-stable toxin-producing enterotoxigenic E. coli, and Giardia spp. CONCLUSIONS: Findings underscore the importance of enteric pathogen exposure risks from animals alongside more broadly recognized water and sanitation risk factors in children. |
Etiology, presentation, and risk factors for diarrheal syndromes in 3 Sub-Saharan African countries after the introduction of rotavirus vaccines from the Vaccine Impact on Diarrhea in Africa (VIDA) Study
Buchwald AG , Verani JR , Keita AM , Jahangir Hossain M , Roose A , Sow SO , Omore R , Doh S , Jones JCM , Nasrin D , Zaman SMA , Okoi C , Antonio M , Ochieng JB , Juma J , Onwuchekwa U , Powell H , Platts-Mills JA , Tennant SM , Kotloff KL . Clin Infect Dis 2023 76 S12-s22 BACKGROUND: Diarrheal disease is heterogeneous, including watery diarrhea (WD) and dysentery, some cases of which become persistent diarrhea (PD). Changes in risk over time necessitate updated knowledge of these syndromes in sub-Saharan Africa. METHODS: The Vaccine Impact on Diarrhea in Africa (VIDA) study was an age-stratified, case-control study of moderate-to-severe diarrhea among children <5 years old in The Gambia, Mali, and Kenya (2015-2018). We analyzed cases with follow-up of about 60 days after enrollment to detect PD (lasting ≥14 days), examined the features of WD and dysentery, and examined determinants for progression to and sequelae from PD. Data were compared with those from the Global Enteric Multicenter Study (GEMS) to detect temporal changes. Etiology was assessed from stool samples using pathogen attributable fractions (AFs), and predictors were assessed using χ2 tests or multivariate regression, where appropriate. RESULTS: Among 4606 children with moderate-to-severe diarrhea, 3895 (84.6%) had WD and 711 (15.4%) had dysentery. PD was more frequent among infants (11.3%) than in children 12-23 months (9.9%) or 24-59 months (7.3%), P = .001 and higher in Kenya (15.5%) than in The Gambia (9.3%) or Mali (4.3%), P < .001; the frequencies were similar among children with WD (9.7%) and those with dysentery (9.4%). Compared to children not treated with antibiotics, those who received antibiotics had a lower frequency of PD overall (7.4% vs 10.1%, P = .01), and particularly among those with WD (6.3% vs 10.0%; P = .01) but not among children with dysentery (8.5% vs 11.0%; P = .27). For those with watery PD, Cryptosporidium and norovirus had the highest AFs among infants (0.16 and 0.12, respectively), while Shigella had the highest AF (0.25) in older children. The odds of PD decreased significantly over time in Mali and Kenya while increasing significantly in The Gambia. CONCLUSIONS: The burden of PD endures in sub-Saharan Africa, with nearly 10% of episodes of WD and dysentery becoming persistent. |
Shigella in Africa: New insights from the Vaccine Impact on Diarrhea in Africa (VIDA) Study
Kasumba IN , Badji H , Powell H , Hossain MJ , Omore R , Sow SO , Verani JR , Platts-Mills JA , Widdowson MA , Zaman SMA , Jones J , Sen S , Permala-Booth J , Nasrin S , Roose A , Nasrin D , Ochieng JB , Juma J , Doh S , Jones JCM , Antonio M , Awuor AO , Sugerman CE , Watson N , Focht C , Liu J , Houpt E , Kotloff KL , Tennant SM . Clin Infect Dis 2023 76 S66-s76 BACKGROUND: We evaluated the burden of Shigella spp from children aged 0-59 months with medically attended moderate-to-severe diarrhea and matched controls at sites in Mali, The Gambia, and Kenya participating in the Vaccine Impact on Diarrhea in Africa (VIDA) study from 2015 to 2018. METHODS: Shigella spp were identified using coprocultures and serotyping in addition to quantitative polymerase chain reaction (qPCR). Episode-specific attributable fractions (AFe) for Shigella were calculated using Shigella DNA quantity; cases with AFe ≥0.5 were considered to have shigellosis. RESULTS: The prevalence of Shigella was determined to be 359 of 4840 (7.4%) cases and 83 of 6213 (1.3%) controls by culture, and 1641 of 4836 (33.9%) cases and 1084 of 4846 (22.4%) controls by qPCR (cycle threshold <35); shigellosis was higher in The Gambia (30.8%) than in Mali (9.3%) and Kenya (18.7%). Bloody diarrhea attributed to Shigella was more common in 24- to 59-month-old children (50.1%) than 0- to 11-month-old infants (39.5%). The Shigella flexneri serogroup predominated among cases (67.6% of isolates), followed by Shigella sonnei (18.2%), Shigella boydii (11.8%), and Shigella dysenteriae (2.3%). The most frequent S. flexneri serotypes were 2a (40.6%), 1b (18.8%), 6 (17.5%), 3a (9.0%), and 4a (5.1%). Drug-specific resistance among 353 (98.3%) Shigella cases with AMR data was as follows: trimethoprim-sulfamethoxazole (94.9%), ampicillin (48.4%), nalidixic acid (1.7%), ceftriaxone (0.3%), azithromycin (0.3%), and ciprofloxacin (0.0%). CONCLUSIONS: A high prevalence of shigellosis continues in sub-Saharan Africa. Strains are highly resistant to commonly used antibiotics while remaining susceptible to ciprofloxacin, ceftriaxone, and azithromycin. |
Prevalence, clinical severity, and seasonality of adenovirus 40/41, astrovirus, sapovirus, and rotavirus among young children with moderate-to-severe diarrhea: Results from the Vaccine Impact on Diarrhea in Africa (VIDA) Study
Keita AM , Doh S , Sow SO , Powell H , Omore R , Jahangir Hossain M , Ogwel B , Ochieng JB , Jones JCM , Zaman SMA , Awuor AO , Juma J , Nasrin D , Liu J , Traoré A , Onwuchekwa U , Badji H , Sarwar G , Antonio M , Houpt ER , Tennant SM , Kasumba IN , Jamka LP , Roose A , Platts-Mills JA , Verani JR , Tate JE , Parashar UD , Neuzil KM , Kotloff KL . Clin Infect Dis 2023 76 S123-s131 ![]() BACKGROUND: While rotavirus causes severe diarrheal disease in children aged <5 years, data on other viral causes in sub-Saharan Africa are limited. METHODS: In the Vaccine Impact on Diarrhea in Africa study (2015-2018), we analyzed stool from children aged 0-59 months with moderate-to-severe diarrhea (MSD) and without diarrhea (controls) in Kenya, Mali, and The Gambia using quantitative polymerase chain reaction. We derived the attributable fraction (AFe) based on the association between MSD and the pathogen, accounting for other pathogens, site, and age. A pathogen was attributable if the AFe was ≥0.5.The severity of attributable MSD was defined by a modified Vesikari score (mVS). Monthly cases were plotted against temperature and rainfall to assess seasonality. RESULTS: Among 4840 MSD cases, proportions attributed to rotavirus, adenovirus 40/41, astrovirus, and sapovirus were 12.6%, 2.7%, 2.9%, and 1.9%, respectively. Attributable rotavirus, adenovirus 40/41, and astrovirus MSD cases occurred at all sites, with mVS of 11, 10, and 7, respectively. MSD cases attributable to sapovirus occurred in Kenya, with mVS of 9. Astrovirus and adenovirus 40/41 peaked during the rainy season in The Gambia, while rotavirus peaked during the dry season in Mali and The Gambia. CONCLUSIONS: In sub-Saharan Africa, rotavirus was the most common cause of MSD; adenovirus 40/41, astrovirus, and sapovirus contributed to a lesser extent among children aged <5 years. Rotavirus- and adenovirus 40/41-attributable MSD were most severe. Seasonality varied by pathogen and location. Efforts to increase the coverage of rotavirus vaccines and to improve prevention and treatment for childhood diarrhea should continue. |
Giardia detection and codetection with other enteric pathogens in young children in the Vaccine Impact on Diarrhea in Africa (VIDA) Case-Control Study: 2015-2018
Marcenac P , Traoré A , Kim S , Prentice-Mott G , Berendes DM , Powell H , Kasumba IN , Nasrin D , Jones JCM , Zaman SMA , Ochieng JB , Juma J , Sanogo D , Widdowson MA , Verani JR , Liu J , Houpt ER , Jahangir Hossain M , Sow SO , Omore R , Tennant SM , Mintz ED , Kotloff KL . Clin Infect Dis 2023 76 S106-s113 BACKGROUND: Giardia has been associated with reduced risk of diarrhea in children in low-resource settings, but the mechanism underlying this association is unknown. To assess whether Giardia may shape colonization or infection with other enteric pathogens and impact associations with diarrhea, we examined Giardia and enteric pathogen codetection among children <5 years old in Kenya, The Gambia, and Mali as part of the Vaccine Impact on Diarrhea in Africa study. METHODS: We tested for Giardia and other enteric pathogens using enzyme-linked immunosorbent assays and real-time polymerase chain reaction (PCR) on stool, respectively. We evaluated associations between Giardia and enteric pathogen detection using multivariable logistic regression models separately for children with moderate-to-severe diarrhea (MSD, cases) and free of diarrhea (controls). RESULTS: Among 11 039 enrolled children, Giardia detection was more common among controls (35%) than cases (28%, P < .001). Campylobacter coli/jejuni detection was associated with Giardia in controls in The Gambia (adjusted odds ratio [aOR] [95% confidence interval {CI}]: 1.51 [1.22‒1.86]) and cases across all sites (1.16 [1.00‒1.33]). Among controls, the odds of astrovirus (1.43 [1.05‒1.93]) and Cryptosporidium spp. (1.24 [1.06‒1.46]) detection were higher among children with Giardia. Among cases, the odds of rotavirus detection were lower in children with Giardia in Mali (.45 [.30‒.66]) and Kenya (.31 [.17‒.56]). CONCLUSIONS: Giardia was prevalent in children <5 years old and was associated with detection of other enteric pathogens, with differing associations in cases versus controls and by site. Giardia may affect colonization or infection by certain enteric pathogens associated with MSD, suggesting an indirect mechanism of clinical impact. |
Epidemiology of enteroaggregative, enteropathogenic, and shiga toxin-producing escherichia coli among children aged <5 years in 3 countries in Africa, 2015-2018: Vaccine Impact on Diarrhea in Africa (VIDA) Study
Ochieng JB , Powell H , Sugerman CE , Omore R , Ogwel B , Juma J , Awuor AO , Sow SO , Sanogo D , Onwuchekwa U , Keita AM , Traoré A , Badji H , Hossain MJ , Jones JCM , Kasumba IN , Nasrin D , Roose A , Liang Y , Jamka LP , Antonio M , Platts-Mills JA , Liu J , Houpt ER , Mintz ED , Hunsperger E , Onyango CO , Strockbine N , Widdowson MA , Verani JR , Tennant SM , Kotloff KL . Clin Infect Dis 2023 76 S77-s86 ![]() BACKGROUND: To address knowledge gaps regarding diarrheagenic Escherichia coli (DEC) in Africa, we assessed the clinical and epidemiological features of enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), and Shiga toxin-producing E. coli (STEC) positive children with moderate-to-severe diarrhea (MSD) in Mali, The Gambia, and Kenya. METHODS: Between May 2015 and July 2018, children aged 0-59 months with medically attended MSD and matched controls without diarrhea were enrolled. Stools were tested conventionally using culture and multiplex polymerase chain reaction (PCR), and by quantitative PCR (qPCR). We assessed DEC detection by site, age, clinical characteristics, and enteric coinfection. RESULTS: Among 4840 children with MSD and 6213 matched controls enrolled, 4836 cases and 1 control per case were tested using qPCR. Of the DEC detected with TAC, 61.1% were EAEC, 25.3% atypical EPEC (aEPEC), 22.4% typical EPEC (tEPEC), and 7.2% STEC. Detection was higher in controls than in MSD cases for EAEC (63.9% vs 58.3%, P < .01), aEPEC (27.3% vs 23.3%, P < .01), and STEC (9.3% vs 5.1%, P < .01). EAEC and tEPEC were more frequent in children aged <23 months, aEPEC was similar across age strata, and STEC increased with age. No association between nutritional status at follow-up and DEC pathotypes was found. DEC coinfection with Shigella/enteroinvasive E. coli was more common among cases (P < .01). CONCLUSIONS: No significant association was detected between EAEC, tEPEC, aEPEC, or STEC and MSD using either conventional assay or TAC. Genomic analysis may provide a better definition of the virulence factors associated with diarrheal disease. |
Norovirus disease among children <5 years in 3 Sub-Saharan African countries: Findings from the Vaccine Impact on Diarrhea in Africa (VIDA) Study, 2015-2018
Omore R , Powell H , Sow SO , Jahangir Hossain M , Ogwel B , Doh S , Ochieng JB , Jones JCM , Zaman SMA , Awuor AO , Juma J , Kasumba IN , Roose A , Jamka LP , Nasrin D , Liu J , Keita AM , Traoré A , Onwuchekwa U , Badji H , Sarwar G , Antonio M , Sugerman CE , Mintz ED , Houpt ER , Verani JR , Widdowson MA , Tennant SM , Platts-Mills JA , Tate JE , Parashar UD , Kotloff KL . Clin Infect Dis 2023 76 S114-s122 ![]() BACKGROUND: To address a paucity of data from sub-Saharan Africa, we examined the prevalence, severity, and seasonality of norovirus genogroup II (NVII) among children <5 years old in The Gambia, Kenya, and Mali following rotavirus vaccine introduction. METHODS: Population-based surveillance was conducted to capture medically-attended moderate-to-severe diarrhea (MSD) cases, defined as a child 0-59 months old passing ≥3 loose stools in a 24-hour period with ≥1 of the following: sunken eyes, poor skin turgor, dysentery, intravenous rehydration, or hospitalization within 7 days of diarrhea onset. Diarrhea-free matched controls randomly selected from a censused population were enrolled at home. Stools from cases and controls were tested for enteropathogens, including norovirus and rotavirus, by TaqMan quantitative polymerase chain reaction (PCR) and conventional reverse transcription PCR. We used multiple logistic regression to derive adjusted attributable fractions (AFe) for each pathogen causing MSD, which takes into consideration the prevalence in both cases and controls, for each site and age. A pathogen was considered etiologic if AFe was ≥0.5. In further analyses focusing on the predominant NVII strains, we compared rotavirus and NVII severity using a 20-point modified Vesikari score and examined seasonal fluctuations. RESULTS: From May 2015 to July 2018, we enrolled 4840 MSD cases and 6213 controls. NVI was attributed to only 1 MSD episode. NVII was attributed to 185 (3.8%) of all MSD episodes and was the sole attributable pathogen in 139 (2.9%); peaking (36.0%) at age 6-8 months with majority (61.2%) aged 6-11 months. MSD cases whose episodes were attributed to NVII alone compared with rotavirus alone were younger (median age, 8 vs 12 months, P < .0001) and had less severe illness (median Vesikari severity score, 9 vs 11, P = .0003) but equally likely to be dehydrated. NVII occurred year-round at all study sites. CONCLUSIONS: Infants aged 6-11 months bear the greatest burden of norovirus disease, with NVII predominating. An early infant vaccine schedule and rigorous adherence to guidelines recommended for management of dehydrating diarrhea may offer substantial benefit in these African settings. |
Voluntary medical male circumcisions for HIV prevention - 13 countries in eastern and southern Africa, 2017-2021
Peck ME , Ong KS , Lucas T , Harvey P , Lekone P , Letebele M , Thomas VT , Maziya V , Mkhontfo M , Gultie T , Mulatu D , Shimelis M , Zegeye T , Juma AW , Odoyo-June E , Musingila PK , Njenga J , Auld A , Kapito M , Maida A , Msungama W , Canda M , Come J , Malimane I , Aupokolo M , Zemburuka B , Kankindi I , Malamba S , Remera E , Tubane E , Machava R , Maphothi N , Vranken P , Amuri M , Kazaura KJ , Simbeye D , Alamo S , Kabuye G , Chituwo O , Kamboyi R , Masiye J , Mandisarisa J , Xaba S , Toledo C . MMWR Morb Mortal Wkly Rep 2023 72 (10) 256-260 In 2007, voluntary medical male circumcision (VMMC) was endorsed by the World Health Organization (WHO) and the Joint United Nations Programme on HIV/AIDS after it was found to be associated with approximately a 60% reduction in the risk for female-to-male transmission of HIV (1). As a result of this endorsement, the U.S. President's Emergency Plan for AIDS Relief (PEPFAR), through partnerships with U.S. government agencies, including CDC, the U.S. Department of Defense, and the U.S. Agency for International Development, started supporting VMMCs performed in prioritized countries in southern and eastern Africa. During 2010-2016, CDC supported 5,880,372 VMMCs in 12 countries (2,3). During 2017-2021, CDC supported 8,497,297 VMMCs performed in 13 countries. In 2020, the number of VMMCs performed declined 31.8% compared with the number in 2019, primarily because of COVID-19-related disruptions to VMMC service delivery. PEPFAR 2017-2021 Monitoring, Evaluation, and Reporting data were used to provide an update and describe CDC's contribution to the scale-up of the VMMC program, which is important to meeting the 2025 Joint United Nations Programme on HIV/AIDS (UNAIDS) target of 90% of males aged 15-59 years having access to VMMC services in prioritized countries to help end the AIDS epidemic by 2030 (4). |
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