Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
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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). |
Effects of COVID-19 pandemic on voluntary medical male circumcision services for HIV prevention, Sub-Saharan Africa, 2020
Peck ME , Ong KS , Lucas T , Prainito A , Thomas AG , Brun A , Kiggundu V , Yansaneh A , Busang L , Kgongwana K , Kelaphile D , Seipone K , Letebele MH , Makadzange PF , Marwiro A , Sesinyi M , Lapidos T , Lukhele N , Maziya V , Mkhontfo M , Gultie T , Mulatu D , Shimelis M , Zegeye T , Teka T , Bulterys M , Njenga JN , Odoyo-June E , Juma AW , Soo L , Talam N , Brown M , Chakare T , Nonyana N , Khoabane MA , Auld AF , Maida A , Msungama W , Kapito M , Nyirenda R , Matchere F , Odek J , Canda M , Malimane I , Come J , Gaspar N , Langa A , Aupokolo MA , Vejorerako KC , Kahindi L , Mali D , Zegeye A , Mangoya D , Zemburuka BL , Bamwesigye J , Kankindi I , Kayirangwa E , Malamba SS , Roels T , Kayonde L , Zimulinda E , Ndengo E , Nsanzimana S , Remera E , Rwibasira GN , Sangwayire B , Semakula M , Rugira E , Rugwizangoga E , Tubane E , Yoboka E , Lawrence J , Loykissoonlal D , Maphothi N , Achut V , Bunga S , Moi M , Amuri M , Kazaura K , Simbeye D , Fida N , Kayange AA , Seleman M , Akao J , Alamo ST , Kabuye G , Kyobutungi S , Makumbi FE , Mudiope P , Nantez B , Chituwo O , Godfrey L , Muyunda B , Kamboyi R , Masiye J , Lifuka E , Mandisarisa J , Mhangara M , Xaba S , Toledo C . Emerg Infect Dis 2022 28 (13) S262-s269 Beginning in March 2020, to reduce COVID-19 transmission, the US President's Emergency Plan for AIDS Relief supporting voluntary medical male circumcision (VMMC) services was delayed in 15 sub-Saharan African countries. We reviewed performance indicators to compare the number of VMMCs performed in 2020 with those performed in previous years. In all countries, the annual number of VMMCs performed decreased 32.5% (from 3,898,960 in 2019 to 2,631,951 in 2020). That reduction is largely attributed to national and local COVID-19 mitigation measures instituted by ministries of health. Overall, 66.7% of the VMMC global annual target was met in 2020, compared with 102.0% in 2019. Countries were not uniformly affected; South Africa achieved only 30.7% of its annual target in 2020, but Rwanda achieved 123.0%. Continued disruption to the VMMC program may lead to reduced circumcision coverage and potentially increased HIV-susceptible populations. Strategies for modifying VMMC services provide lessons for adapting healthcare systems during a global pandemic. |
Diagnostic accuracy of the Panbio COVID-19 antigen rapid test device for SARS-CoV-2 detection in Kenya, 2021: A field evaluation
Irungu JK , Munyua P , Ochieng C , Juma B , Amoth P , Kuria F , Kiiru J , Makayotto L , Abade A , Bulterys M , Hunsperger E , Emukule GO , Onyango C , Samandari T , Barr BAT , Akelo V , Weyenga H , Munywoki PK , Bigogo G , Otieno NA , Kisivuli JA , Ochieng E , Nyaga R , Hull N , Herman-Roloff A , Aman R . PLoS One 2023 18 (1) e0277657 BACKGROUND: Accurate and timely diagnosis is essential in limiting the spread of SARS-CoV-2 infection. The reference standard, rRT-PCR, requires specialized laboratories, costly reagents, and a long turnaround time. Antigen RDTs provide a feasible alternative to rRT-PCR since they are quick, relatively inexpensive, and do not require a laboratory. The WHO requires that Ag RDTs have a sensitivity ≥80% and specificity ≥97%. METHODS: This evaluation was conducted at 11 health facilities in Kenya between March and July 2021. We enrolled persons of any age with respiratory symptoms and asymptomatic contacts of confirmed COVID-19 cases. We collected demographic and clinical information and two nasopharyngeal specimens from each participant for Ag RDT testing and rRT-PCR. We calculated the diagnostic performance of the Panbio™ Ag RDT against the US Centers for Disease Control and Prevention's (CDC) rRT-PCR test. RESULTS: We evaluated the Ag RDT in 2,245 individuals where 551 (24.5%, 95% CI: 22.8-26.3%) tested positive by rRT-PCR. Overall sensitivity of the Ag RDT was 46.6% (95% CI: 42.4-50.9%), specificity 98.5% (95% CI: 97.8-99.0%), PPV 90.8% (95% CI: 86.8-93.9%) and NPV 85.0% (95% CI: 83.4-86.6%). Among symptomatic individuals, sensitivity was 60.6% (95% CI: 54.3-66.7%) and specificity was 98.1% (95% CI: 96.7-99.0%). Among asymptomatic individuals, sensitivity was 34.7% (95% CI 29.3-40.4%) and specificity was 98.7% (95% CI: 97.8-99.3%). In persons with onset of symptoms <5 days (594/876, 67.8%), sensitivity was 67.1% (95% CI: 59.2-74.3%), and 53.3% (95% CI: 40.0-66.3%) among those with onset of symptoms >7 days (157/876, 17.9%). The highest sensitivity was 87.0% (95% CI: 80.9-91.8%) in symptomatic individuals with cycle threshold (Ct) values ≤30. CONCLUSION: The overall sensitivity and NPV of the Panbio™ Ag RDT were much lower than expected. The specificity of the Ag RDT was high and satisfactory; therefore, a positive result may not require confirmation by rRT-PCR. The kit may be useful as a rapid screening tool only for symptomatic patients in high-risk settings with limited access to rRT-PCR. A negative result should be interpreted based on clinical and epidemiological information and may require retesting by rRT-PCR. |
Prevalence of colonization with multidrug-resistant bacteria in communities and hospitals in Kenya.
Ita T , Luvsansharav UO , Smith RM , Mugoh R , Ayodo C , Oduor B , Jepleting M , Oguta W , Ouma C , Juma J , Bigogo G , Kariuki S , Ramay BM , Caudell M , Onyango C , Ndegwa L , Verani JR , Bollinger S , Sharma A , Palmer GH , Call DR , Omulo S . Sci Rep 2022 12 (1) 22290 We estimated the prevalence of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), carbapenem-resistant Enterobacterales (CRE), and methicillin-resistant Staphylococcus aureus (MRSA) in communities and hospitals in Kenya to identify human colonization with multidrug-resistant bacteria. Nasal and fecal specimen were collected from inpatients and community residents in Nairobi (urban) and Siaya (rural) counties. Swabs were plated on chromogenic agar to presumptively identify ESCrE, CRE and MRSA isolates. Confirmatory identification and antibiotic susceptibility testing were done using the VITEK®2 instrument. A total of 1999 community residents and 1023 inpatients were enrolled between January 2019 and March 2020. ESCrE colonization was higher in urban than rural communities (52 vs. 45%; P = 0.013) and in urban than rural hospitals (70 vs. 63%; P = 0.032). Overall, ESCrE colonization was ~ 18% higher in hospitals than in corresponding communities. CRE colonization was higher in hospital than community settings (rural: 7 vs. 1%; urban: 17 vs. 1%; with non-overlapping 95% confidence intervals), while MRSA was rarely detected (≤ 3% overall). Human colonization with ESCrE and CRE was common, particularly in hospitals and urban settings. MRSA colonization was uncommon. Evaluation of risk factors and genetic mechanisms of resistance can guide prevention and control efforts tailored to different environments. |
Adapting Longstanding Public Health Collaborations between Government of Kenya and CDC Kenya in Response to the COVID-19 Pandemic, 2020-2021.
Herman-Roloff A , Aman R , Samandari T , Kasera K , Emukule GO , Amoth P , Chen TH , Kisivuli J , Weyenga H , Hunsperger E , Onyango C , Juma B , Munyua P , Wako D , Akelo V , Kimanga D , Ndegwa L , Mohamed AA , Okello P , Kariuki S , DeCock KM , Bulterys M . Emerg Infect Dis 2022 28 (13) S159-s167 Kenya's Ministry of Health (MOH) and the US Centers for Disease Control and Prevention in Kenya (CDC Kenya) have maintained a 40-year partnership during which measures were implemented to prevent, detect, and respond to disease threats. During the COVID-19 pandemic, the MOH and CDC Kenya rapidly responded to mitigate disease impact on Kenya's 52 million residents. We describe activities undertaken jointly by the MOH and CDC Kenya that lessened the effects of COVID-19 during 5 epidemic waves from March through December 2021. Activities included establishing national and county-level emergency operations centers and implementing workforce development and deployment, infection prevention and control training, laboratory diagnostic advancement, enhanced surveillance, and information management. The COVID-19 pandemic provided fresh impetus for the government of Kenya to establish a national public health institute, launched in January 2022, to consolidate its public health activities and counter COVID-19 and future infectious, vaccine-preventable, and emerging zoonotic diseases. |
Progress towards the UNAIDS 90-90-90 targets among persons aged 50 and older living with HIV in 13 African countries
Farley SM , Wang C , Bray RM , Low AJ , Delgado S , Hoos D , Kakishozi AN , Harris TG , Nyirenda R , Wadonda N , Li M , Amuri M , Juma J , Kancheya N , Pietersen I , Mutenda N , Natanael S , Aoko A , Ngugi EW , Asiimwe F , Lecher S , Ward J , Chikwanda P , Mugurungi O , Moyo B , Nkurunziza P , Aibo D , Kabala A , Biraro S , Ndagije F , Musuka G , Ndongmo C , Shang J , Dokubo EK , Dimite LE , McCullough-Sanden R , Bissek AC , Getaneh Y , Eshetu F , Nkumbula T , Tenthani L , Kayigamba FR , Kirungi W , Musinguzi J , Balachandra S , Kayirangwa E , Ayite A , West CA , Bodika S , Sleeman K , Patel HK , Brown K , Voetsch AC , El-Sadr WM , Justman JJ . J Int AIDS Soc 2022 25 Suppl 4 e26005 INTRODUCTION: Achieving optimal HIV outcomes, as measured by global 90-90-90 targets, that is awareness of HIV-positive status, receipt of antiretroviral (ARV) therapy among aware and viral load (VL) suppression among those on ARVs, respectively, is critical. However, few data from sub-Saharan Africa (SSA) are available on older people (50+) living with HIV (OPLWH). We examined 90-90-90 progress by age, 15-49 (as a comparison) and 50+ years, with further analyses among 50+ (55-59, 60-64, 65+ vs. 50-54), in 13 countries (Cameroon, Cote d'Ivoire, Eswatini, Ethiopia, Kenya, Lesotho, Malawi, Namibia, Rwanda, Tanzania, Uganda, Zambia and Zimbabwe). METHODS: Using data from nationally representative Population-based HIV Impact Assessments, conducted between 2015and 2019, participants from randomly selected households provided demographic and clinical information and whole blood specimens for HIV serology, VL and ARV testing. Survey weighted outcomes were estimated for 90-90-90 targets. Country-specific Poisson regression models examined 90-90-90 variation among OPLWH age strata. RESULTS: Analyses included 24,826 HIV-positive individuals (15-49 years: 20,170; 50+ years: 4656). The first, second and third 90 outcomes were achieved in 1, 10 and 5 countries, respectively, by those aged 15-49, while OPLWH achieved outcomes in 3, 13 and 12 countries, respectively. Among those aged 15-49, women were more likely to achieve 90-90-90 targets than men; however, among OPLWH, men were more likely to achieve first and third 90 targets than women, with second 90 achievement being equivalent. Country-specific 90-90-90 regression models among OPLWH demonstrated minimal variation by age stratum across 13 countries. Among OLPWH, no first 90 target differences were noted by age strata; three countries varied in the second 90 by older age strata but not in a consistent direction; one country showed higher achievement of the third 90 in an older age stratum. CONCLUSIONS: While OPLWH in these 13 countries were slightly more likely than younger people to be aware of their HIV-positive status (first 90), this target was not achieved in most countries. However, OPLWH achieved treatment (second 90) and VL suppression (third 90) targets in more countries than PLWH <50. Findings support expanded HIV testing, prevention and treatment services to meet ongoing OPLWH health needs in SSA. |
Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya.
Ochieng C , Chen JC , Osita MP , Katz LS , Griswold T , Omballa V , Ng'eno E , Ouma A , Wamola N , Opiyo C , Achieng L , Munywoki PK , Hendriksen RS , Freeman M , Mikoleit M , Juma B , Bigogo G , Mintz E , Verani JR , Hunsperger E , Carleton HA . PLoS Negl Trop Dis 2022 16 (8) e0010704 A high burden of Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) bacteremia has been reported from urban informal settlements in sub-Saharan Africa, yet little is known about the introduction of these strains to the region. Understanding regional differences in the predominant strains of S. Typhi can provide insight into the genomic epidemiology. We genetically characterized 310 S. Typhi isolates from typhoid fever surveillance conducted over a 12-year period (2007-2019) in Kibera, an urban informal settlement in Nairobi, Kenya, to assess the circulating strains, their antimicrobial resistance attributes, and how they relate to global S. Typhi isolates. Whole genome multi-locus sequence typing (wgMLST) identified 4 clades, with up to 303 pairwise allelic differences. The identified genotypes correlated with wgMLST clades. The predominant clade contained 290 (93.5%) isolates with a median of 14 allele differences (range 0-52) and consisted entirely of genotypes 4.3.1.1 and 4.3.1.2. Resistance determinants were identified exclusively in the predominant clade. Determinants associated with resistance to aminoglycosides were observed in 245 isolates (79.0%), sulphonamide in 243 isolates (78.4%), trimethoprim in 247 isolates (79.7%), tetracycline in 224 isolates (72.3%), chloramphenicol in 247 isolates (79.6%), β-lactams in 239 isolates (77.1%) and quinolones in 62 isolates (20.0%). Multidrug resistance (MDR) determinants (defined as determinants conferring resistance to ampicillin, chloramphenicol and cotrimoxazole) were found in 235 (75.8%) isolates. The prevalence of MDR associated genes was similar throughout the study period (2007-2012: 203, 76.3% vs 2013-2019: 32, 72.7%; Fisher's Exact Test: P = 0.5478, while the proportion of isolates harboring quinolone resistance determinants increased (2007-2012: 42, 15.8% and 2013-2019: 20, 45.5%; Fisher's Exact Test: P<0.0001) following a decline in S. Typhi in Kibera. Some isolates (49, 15.8%) harbored both MDR and quinolone resistance determinants. There were no determinants associated with resistance to cephalosporins or azithromycin detected among the isolates sequenced in this study. Plasmid markers were only identified in the main clade including IncHI1A and IncHI1B(R27) in 226 (72.9%) isolates, and IncQ1 in 238 (76.8%) isolates. Molecular clock analysis of global typhoid isolates and isolates from Kibera suggests that genotype 4.3.1 has been introduced multiple times in Kibera. Several genomes from Kibera formed a clade with genomes from Kenya, Malawi, South Africa, and Tanzania. The most recent common ancestor (MRCA) for these isolates was from around 1997. Another isolate from Kibera grouped with several isolates from Uganda, sharing a common ancestor from around 2009. In summary, S. Typhi in Kibera belong to four wgMLST clades one of which is frequently associated with MDR genes and this poses a challenge in treatment and control. |
Food insecurity and the risk of HIV acquisition: findings from population-based surveys in six sub-Saharan African countries (2016-2017)
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 . BMJ Open 2022 12 (7) e058704 OBJECTIVE: To assess the potential bidirectional relationship between food insecurity and HIV infection in sub-Saharan Africa. DESIGN: Nationally representative HIV impact assessment household-based surveys. SETTING: Zambia, Eswatini, Lesotho, Uganda and Tanzania and Namibia. PARTICIPANTS: 112 955 survey participants aged 15-59 years with HIV and recency test results. MEASURES: Recent HIV infection (within 6 months) classified using the HIV-1 limited antigen avidity assay, in participants with an unsuppressed viral load (>1000 copies/mL) and no detectable antiretrovirals; severe food insecurity (SFI) defined as having no food in the house ≥three times in the past month. RESULTS: Overall, 10.3% of participants lived in households reporting SFI. SFI was most common in urban, woman-headed households, and in people with chronic HIV infection. Among women, SFI was associated with a twofold increase in risk of recent HIV infection (adjusted relative risk (aRR) 2.08, 95% CI 1.09 to 3.97). SFI was also associated with transactional sex (aRR 1.28, 95% CI 1.17 to 1.41), a history of forced sex (aRR 1.36, 95% CI 1.11 to 1.66) and condom-less sex with a partner of unknown or positive HIV status (aRR 1.08, 95% CI 1.02 to 1.14) in all women, and intergenerational sex (partner ≥10 years older) in women aged 15-24 years (aRR 1.23, 95% CI 1.03 to 1.46). Recent receipt of food support was protective against HIV acquisition (aRR 0.36, 95% CI 0.14 to 0.88). CONCLUSION: SFI increased risk for HIV acquisition in women by twofold. Heightened food insecurity during climactic extremes could imperil HIV epidemic control, and food support to women with SFI during these events could reduce HIV transmission. |
Genome Sequence of Escherichia coli Isolated from an Adult in Kibera, an Urban Informal Settlement in Nairobi, Kenya.
Kikwai GK , Juma B , Nindo F , Ochieng C , Wamola N , Mbogo K , Call DR , Hunsperger E . Microbiol Resour Announc 2022 11 (4) e0124121 An Escherichia coli strain (sequence type 636) was isolated from an adult residing in an urban informal settlement in Nairobi, Kenya, and was sequenced using the Illumina MiSeq platform. The draft genome was 5,075,726 bp, with a Col(BS512) plasmid plus aph(6)-Id, bla(TEM-1B), and dfrA7 genes, which encode kanamycin, ampicillin, and trimethoprim resistance proteins, respectively. |
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