Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-17 (of 17 Records) |
Query Trace: Onyango CO[original query] |
---|
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. |
Incorporating COVID-19 into acute febrile illness surveillance systems, Belize, Kenya, Ethiopia, Peru, and Liberia, 2020-2021
Shih DC , Silver R , Henao OL , Alemu A , Audi A , Bigogo G , Colston JM , Edu-Quansah EP , Erickson TA , Gashu A , Gbelee GB Jr , Gunter SM , Kosek MN , Logan GG , Mackey JM , Maliga A , Manzanero R , Morazan G , Morey F , Munoz FM , Murray KO , Nelson TV , Olortegui MP , Yori PP , Ronca SE , Schiaffino F , Tayachew A , Tedasse M , Wossen M , Allen DR , Angra P , Balish A , Farron M , Guerra M , Herman-Roloff A , Hicks VJ , Hunsperger E , Kazazian L , Mikoleit M , Munyua P , Munywoki PK , Namwase AS , Onyango CO , Park M , Peruski LF , Sugerman DE , Gutierrez EZ , Cohen AL . Emerg Infect Dis 2022 28 (13) S34-s41 Existing acute febrile illness (AFI) surveillance systems can be leveraged to identify and characterize emerging pathogens, such as SARS-CoV-2, which causes COVID-19. The US Centers for Disease Control and Prevention collaborated with ministries of health and implementing partners in Belize, Ethiopia, Kenya, Liberia, and Peru to adapt AFI surveillance systems to generate COVID-19 response information. Staff at sentinel sites collected epidemiologic data from persons meeting AFI criteria and specimens for SARS-CoV-2 testing. A total of 5,501 patients with AFI were enrolled during March 2020-October 2021; >69% underwent SARS-CoV-2 testing. Percentage positivity for SARS-CoV-2 ranged from 4% (87/2,151, Kenya) to 19% (22/115, Ethiopia). We show SARS-CoV-2 testing was successfully integrated into AFI surveillance in 5 low- to middle-income countries to detect COVID-19 within AFI care-seeking populations. AFI surveillance systems can be used to build capacity to detect and respond to both emerging and endemic infectious disease threats. |
Postmortem Study of Cause of Death Among Children Hospitalized With Respiratory Illness in Kenya
Njuguna HN , Zaki SR , Roberts DJ , Rogena EA , Walong E , Fligner CL , Keating MK , Gachii AK , Maleche-Obimbo E , Irimu G , Mathaiya J , Orata N , Lopokoiyit R , Michuki J , Emukule GO , Onyango CO , Gikunju S , Owuor C , Muturi PK , Bunei M , Gloria Carvalho M , Fields B , Mott JA , Widdowson MA , Chaves SS . Pediatr Infect Dis J 2021 40 (8) 715-722 BACKGROUND: In resource-limited settings, acute respiratory infections continue to be the leading cause of death in young children. We conducted postmortem investigations in children <5 years hospitalized with a clinical diagnosis of respiratory disease at Kenya's largest referral hospital. METHODS: We collected respiratory and other tissues postmortem to examine pathologic processes using histology, molecular and immunohistochemistry assays. Nasopharyngeal, trachea, bronchi and lung specimens were tested using 21-target respiratory pathogen real-time reverse transcription polymerase chain reaction assays deployed on Taqman Array Cards. Expert panels reviewed all findings to determine causes of death and associated pathogens. RESULTS: From 2014 to 2015, we investigated 64 pediatric deaths (median age 7 months). Pneumonia was determined as cause of death in 70% (42/52) of cases where death was associated with an infectious disease process. The main etiologies of pneumonia deaths were respiratory syncytial virus (RSV) (n = 7, 19%), Pneumocystis jirovecii (n = 7, 19%), influenza A (n = 5, 14%) and Streptococcus pneumoniae (n = 5, 14%)-10% of cases had multi-pathogen involvement. Among the other 10 deaths associated with a nonpneumonia infectious process, 4 did not have an etiology assigned, the others were associated with miliary tuberculosis (2), cerebral thrombosis due to HIV (1), Enterobacteriaceae (1), rotavirus (1), and 1 case of respiratory infection with severe hypokalemia associated with RSV. CONCLUSIONS: In spite of well-established vaccination programs in Kenya, some deaths were still vaccine preventable. Accelerated development of RSV monoclonal antibodies and vaccines, introduction of seasonal influenza vaccination, and maintenance or improved uptake of existing vaccines can contribute to further reductions in childhood mortality. |
High incidence of human brucellosis in a rural pastoralist community in Kenya, 2015
Munyua P , Osoro E , Hunsperger E , Ngere I , Muturi M , Mwatondo A , Marwanga D , Ngere P , Tiller R , Onyango CO , Njenga K , Widdowson MA . PLoS Negl Trop Dis 2021 15 (2) e0009049 BACKGROUND: Brucellosis occurs globally with highly variable incidence in humans from very low in North America and Western Europe to high in the Middle East and Asia. There are few data in Sub-Saharan Africa. This study estimated the incidence of human brucellosis in a pastoralist community in Kenya. METHODS: Between February 2015 and January 2016, we enrolled persons living in randomly selected households in Kajiado County. Free health care was offered at three facilities in the study area. Those who met the study clinical case definition completed a standardized questionnaire on demographics, clinical history and presentation. A blood sample was collected and tested by Rose Bengal test (RBT), then later tested at the Kenya Medical Research Institute laboratory for Brucella IgG and IgM by ELISA. Those who tested positive by both RBT and ELISA (IgG or IgM antibodies) were classified as confirmed while those that only tested positive for IgG or IgM antibodies were classified as probable. Further, sera were tested by polymerase chain reaction using a TaqMan Array Card (TAC) for a panel of pathogens causing AFI including Brucella spp. Annual incidence of brucellosis was calculated as the number of confirmed cases in one year/total number in the study population. RESULTS: We enrolled a cohort of 4746 persons in 804 households. Over half (52.3%) were males and the median age was 18 years (Interquartile range (IQR) 9 months- 32 years). A total of 236 patients were enrolled at three health facilities; 64% were females and the median age was 40.5 years (IQR 28-53 years). Thirty-nine (16.5%) were positive for Brucella antibodies by IgG ELISA, 5/236 (2.1%) by IgM ELISA and 4/236 (1.7%) by RBT. Ten percent 22/217 were positive by TAC. We confirmed four (1.7%) brucellosis cases giving an annual incidence of 84/100,000 persons/year (95% CI 82, 87). The incidence did not significantly vary by gender, age and location of residence. CONCLUSION: We report a high incidence of brucellosis in humans among members of this pastoralist community. Brucellosis was the most common cause febrile illness in this community. |
The impact of maternal HIV infection on the burden of respiratory syncytial virus among pregnant women and their infants, western Kenya
Nyawanda BO , Otieno NA , Otieno MO , Emukule GO , Bigogo G , Onyango CO , Lidechi S , Nyaundi J , Langley GE , Widdowson MA , Chaves SS . J Infect Dis 2020 225 (12) 2097-2105 BACKGROUND: Respiratory syncytial virus (RSV) is an important cause of respiratory illness worldwide, however, burden data on mother-infant pairs remain sparse in sub-Saharan Africa where HIV is prevalent. We evaluated the impact of maternal HIV infection on the burden of RSV among mothers and their infants in western Kenya. METHODS: We enrolled pregnant women (≤20 weeks gestation) and followed them and their newborns weekly for up to 3-6 months post-partum, to document cases of acute respiratory illness (ARI). Nasal/ oropharyngeal swabs were collected and tested for RSV using polymerase chain reaction. Analyses were stratified by maternal HIV-status, and incidence computed per 1,000 person-months. RESULTS: Compared to RSV-negative ARI cases, RSV-positive cases were associated with cough, apnoea and hospitalization among infants. RSV incidence per 1,000 person-months among mothers was 4.0 (95% confidence interval (CI), 3.2-4.4), and was twice that among the HIV-infected (8.4; 95% CI, 5.7-12.0) compared to the HIV-uninfected mothers (3.1; 95% CI 2.3-4.0). Among infants, incidence per 1,000 person-months was 15.4 (95% CI, 12.5-18.8); incidence did not differ by HIV exposure or prematurity. CONCLUSION: HIV-infection may increase the risk of RSV illness among pregnant women. Future maternal RSV vaccines may have added benefit in high HIV prevalence areas. |
Menstrual cups and cash transfer to reduce sexual and reproductive harm and school dropout in adolescent schoolgirls: study protocol of a cluster-randomised controlled trial in western Kenya
Zulaika G , Kwaro D , Nyothach E , Wang D , Zielinski-Gutierrez E , Mason L , Eleveld A , Chen T , Kerubo E , van Eijk A , Pace C , Obor D , Juma J , Oyaro B , Niessen L , Bigogo G , Ngere I , Henry C , Majiwa M , Onyango CO , Ter Kuile FO , Phillips-Howard PA . BMC Public Health 2019 19 (1) 1317 BACKGROUND: Adolescent girls in sub-Saharan Africa are disproportionally vulnerable to sexual and reproductive health (SRH) harms. In western Kenya, where unprotected transactional sex is common, young females face higher rates of school dropout, often due to pregnancy, and sexually transmitted infections (STIs), including HIV. Staying in school has shown to protect girls against early marriage, teen pregnancy, and HIV infection. This study evaluates the impact of menstrual cups and cash transfer interventions on a composite of deleterious outcomes (HIV, HSV-2, and school dropout) when given to secondary schoolgirls in western Kenya, with the aim to inform evidence-based policy to improve girls' health, school equity, and life-chances. METHODS: Single site, 4-arm, cluster randomised controlled superiority trial. Secondary schools are the unit of randomisation, with schoolgirls as the unit of measurement. Schools will be randomised into one of four intervention arms using a 1:1:1:1 ratio and block randomisation: (1) menstrual cup arm; (2) cash transfer arm, (3) cups and cash combined intervention arm, or (4) control arm. National and county agreement, and school level consent will be obtained prior to recruitment of schools, with parent consent and girls' assent obtained for participant enrolment. Participants will be trained on safe use of interventions, with all arms receiving puberty and hygiene education. Annually, the state of latrines, water availability, water treatment, handwashing units and soap in schools will be measured. The primary endpoint is a composite of incident HIV, HSV-2, and all-cause school dropout, after 3 years follow-up. School dropout will be monitored each term via school registers and confirmed through home visits. HIV and HSV-2 incident infections and risk factors will be measured at baseline, mid-line and end-line. Intention to treat analysis will be conducted among all enrolled participants. Focus group discussions will provide contextual information on uptake of interventions. Monitoring for safety will occur throughout. DISCUSSION: If proved safe and effective, the interventions offer a potential contribution toward girls' schooling, health, and equity in low- and middle-income countries. TRIAL REGISTRATION: ClinicalTrials.gov NCT03051789 , 15th February 2017. |
Comparison of respiratory pathogen yields from Nasopharyngeal/Oropharyngeal swabs and sputum specimens collected from hospitalized adults in rural Western Kenya
Nyawanda BO , Njuguna HN , Onyango CO , Makokha C , Lidechi S , Fields B , Winchell JM , Katieno JS , Nyaundi J , Ade F , Emukule GO , Mott JA , Otieno N , Widdowson MA , Chaves SS . Sci Rep 2019 9 (1) 11237 Molecular diagnostic methods are becoming increasingly available for assessment of acute lower respiratory illnesses (ALRI). However, nasopharyngeal/oropharyngeal (NP/OP) swabs may not accurately reflect etiologic agents from the lower respiratory tract where sputum specimens are considered as a more representative sample. The pathogen yields from NP/OP against sputum specimens have not been extensively explored, especially in tropical countries. We compared pathogen yields from NP/OP swabs and sputum specimens from patients ≥18 years hospitalized with ALRI in rural Western Kenya. Specimens were tested for 30 pathogens using TaqMan Array Cards (TAC) and results compared using McNemar’s test. The agreement for pathogen detection between NP/OP and sputum specimens ranged between 85–100%. More viruses were detected from NP/OP specimens whereas Klebsiella pneumoniae and Mycobacterium tuberculosis were more common in sputum specimens. There was no clear advantage in using sputum over NP/OP specimens to detect pathogens of ALRI in adults using TAC in the context of this tropical setting. |
Successes and challenges of the One Health approach in Kenya over the last decade
Munyua PM , Njenga MK , Osoro EM , Onyango CO , Bitek AO , Mwatondo A , Muturi MK , Musee N , Bigogo G , Otiang E , Ade F , Lowther SA , Breiman RF , Neatherlin J , Montgomery J , Widdowson MA . BMC Public Health 2019 19 465 More than 75% of emerging infectious diseases are zoonotic in origin and a transdisciplinary, multi-sectoral One Health approach is a key strategy for their effective prevention and control. In 2004, US Centers for Disease Control and Prevention office in Kenya (CDC Kenya) established the Global Disease Detection Division of which one core component was to support, with other partners, the One Health approach to public health science. After catalytic events such as the global expansion of highly pathogenic H5N1 and the 2006 East African multi-country outbreaks of Rift Valley Fever, CDC Kenya supported key Kenya government institutions including the Ministry of Health and the Ministry of Agriculture, Livestock, and Fisheries to establish a framework for multi-sectoral collaboration at national and county level and a coordination office referred to as the Zoonotic Disease Unit (ZDU). The ZDU has provided Kenya with an institutional framework to highlight the public health importance of endemic and epidemic zoonoses including RVF, rabies, brucellosis, Middle East Respiratory Syndrome Coronavirus, anthrax and other emerging issues such as anti-microbial resistance through capacity building programs, surveillance, workforce development, research, coordinated investigation and outbreak response. This has led to improved outbreak response, and generated data (including discovery of new pathogens) that has informed disease control programs to reduce burden of and enhance preparedness for endemic and epidemic zoonotic diseases, thereby enhancing global health security. Since 2014, the Global Health Security Agenda implemented through CDC Kenya and other partners in the country has provided additional impetus to maintain this effort and Kenya's achievement now serves as a model for other countries in the region. Significant gaps remain in implementation of the One Health approach at subnational administrative levels; there are sustainability concerns, competing priorities and funding deficiencies. |
Comparison of minimally invasive tissue sampling with conventional autopsy to detect pulmonary pathology among respiratory deaths in a resource-limited setting
Roberts DJ , Njuguna HN , Fields B , Fligner CL , Zaki SR , Keating MK , Rogena E , Walong E , Gachii AK , Maleche-Obimbo E , Irimu G , Mathaiya J , Orata N , Lopokoiyit R , Michuki J , Emukule GO , Onyango CO , Gikunju S , Owuor C , Muturi PK , Bunei M , Widdowson MA , Mott JA , Chaves SS . Am J Clin Pathol 2019 152 (1) 36-49 OBJECTIVES: We compared minimally invasive tissue sampling (MITS) with conventional autopsy (CA) in detection of respiratory pathology/pathogens among Kenyan children younger than 5 years who were hospitalized with respiratory disease and died during hospitalization. METHODS: Pulmonary MITS guided by anatomic landmarks was followed by CA. Lung tissues were triaged for histology and molecular testing using TaqMan Array Cards (TACs). MITS and CA results were compared for adequacy and concordance. RESULTS: Adequate pulmonary tissue was obtained by MITS from 54 (84%) of 64 respiratory deaths. Comparing MITS to CA, full histologic diagnostic concordance was present in 23 (36%) cases and partial concordance in 19 (30%), an overall 66% concordance rate. Pathogen detection using TACs had full concordance in 27 (42%) and partial concordance in 24 (38%) cases investigated, an overall 80% concordance rate. CONCLUSIONS: MITS is a viable alternative to CA in respiratory deaths in resource-limited settings, especially if combined with ancillary tests to optimize diagnostic accuracy. |
Determining the cause of death among children hospitalized with respiratory illness in Kenya: Protocol for Pediatric Respiratory Etiology Surveillance Study (PRESS)
Njuguna HN , Zaki SR , Roberts DJ , Fligner CL , Keating MK , Rogena E , Walong E , Gachii AK , Maleche-Obimbo E , Irimu G , Mathaiya J , Orata N , Lopokoiyit R , Maina J , Emukule GO , Onyango CO , Gikunju S , Owuor C , Kinuthia P , Bunei M , Fields B , Widdowson MA , Mott JA , Chaves SS . JMIR Res Protoc 2019 8 (1) e10854 BACKGROUND: In sub-Saharan Africa, where the burden of respiratory disease-related deaths is the highest, information on the cause of death remains inadequate because of poor access to health care and limited availability of diagnostic tools. Postmortem examination can aid in the ascertainment of causes of death. This manuscript describes the study protocol for the Pediatric Respiratory Etiology Surveillance Study (PRESS). OBJECTIVE: This study protocol aims to identify causes and etiologies associated with respiratory disease-related deaths among children (age 1-59 months) with respiratory illness admitted to the Kenyatta National Hospital (KNH), the largest public hospital in Kenya, through postmortem examination coupled with innovative approaches to laboratory investigation. METHODS: We prospectively followed children hospitalized with respiratory illness until the end of clinical care or death. In case of death, parents or guardians were offered grief counseling, and postmortem examination was offered. Lung tissue specimens were collected using minimally invasive tissue sampling and conventional autopsy where other tissues were collected. Tissues were tested using histopathology, immunohistochemistry, and multipathogen molecular-based assays to identify pathogens. For each case, clinical and laboratory data were reviewed by a team of pathologists, clinicians, laboratorians, and epidemiologists to assign a cause of and etiology associated with death. RESULTS: We have enrolled pediatric cases of respiratory illness hospitalized at the KNH at the time of this submission; of those, 14.8% (140/945) died while in the hospital. Both analysis and interpretation of laboratory results and writing up of findings are expected in 2019-2020. CONCLUSIONS: Postmortem studies can help identify major pathogens contributing to respiratory-associated deaths in children. This information is needed to develop evidence-based prevention and treatment policies that target important causes of pediatric respiratory mortality and assist with the prioritization of local resources. Furthermore, PRESS can provide insights into the interpretation of results using multipathogen testing platforms in resource-limited settings. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/10854. |
An intensive, active surveillance reveals continuous invasion and high diversity of rhinovirus in households
Kamau E , Onyango CO , Otieno GP , Kiyuka PK , Agoti CN , Medley GF , Cane PA , Nokes DJ , Munywoki PK . J Infect Dis 2018 219 (7) 1049-1057 We report on infection patterns in 5 households (78 participants) delineating the natural history of human rhinovirus (HRV). Nasopharyngeal collections were obtained every 3-4 days irrespective of symptoms, over a 6-month period, with molecular screening for HRV and typing by sequencing VP4/VP2 junction. Overall, 311/3468 (8.9%) collections were HRV positive: 256 were classified into 3 species: 104 (40.6%) HRV-A; 14 (5.5%) HRV-B, and 138 (53.9%) HRV-C. Twenty-six known HRV types (13 HRV-A, 3 HRV-B, and 10 HRV-C) were identified (A75, C1, and C35 being most frequent). We observed continuous invasion and temporal clustering of HRV types in households (range 5-13 over 6 months). Intrahousehold transmission was independent of clinical status but influenced by age. Most (89.0%) of HRV infection episodes were limited to <14 days. Individual repeat infections were frequent (range 1-7 over 6 months), decreasing with age, and almost invariably heterotypic, indicative of lasting type-specific immunity and low cross-type protection. |
The contribution of respiratory pathogens to fatal and non-fatal respiratory hospitalizations: a pilot study of Taqman Array Cards (TAC) in Kenya
Njuguna HN , Chaves SS , Emukule GO , Nyawanda B , Omballa V , Juma B , Onyango CO , Mott JA , Fields B . BMC Infect Dis 2017 17 (1) 591 BACKGROUND: Respiratory diseases cause substantial morbidity and mortality worldwide, with sub-Saharan Africa bearing the greatest burden. Identifying etiologies of respiratory disease is important to inform cost effective treatment, prevention and control strategies. Testing for all of the different pathogens that are potentially associated with respiratory illnesses is challenging. We piloted the use of a multi-pathogen respiratory Taqman Array Cards (TAC) to identify pathogens in respiratory samples collected from non-fatal and fatal cases and their matched asymptomatic controls. METHODS: This is a case control study comparing viral and bacterial pathogens detected among non-fatal and fatal cases to those detected among age and time matched asymptomatic controls. We used McNemar's test to compare proportions of pathogens detected among cases (non-fatal and fatal) to their matched asymptomatic controls. We used Mann-Whitney test to compare the distribution of median Cycle threshold (Ct) values among non-fatal and fatal cases to their corresponding asymptomatic controls. RESULTS: There were 72 fatal and 72 non-fatal cases matched to 72 controls. We identified at least one pathogen in 109/144 (76%) cases and 59/72 (82%) controls. For most pathogens, the median Ct values were lower among cases (fatal and non-fatal) compared to asymptomatic controls. CONCLUSIONS: Similar rates of pathogen detection among cases and controls make interpretation of results challenging. Ct-values might be helpful in interpreting clinical relevance of detected pathogens using multi-pathogen diagnostic tools. |
Evaluation of TaqMan Array Card (TAC) for the Detection of Central Nervous System Infections in Kenya.
Onyango CO , Loparev V , Lidechi S , Bhullar V , Schmid DS , Radford K , Lo MK , Rota P , Johnson BW , Munoz J , Oneko M , Burton D , Black CM , Neatherlin J , Montgomery JM , Fields B . J Clin Microbiol 2017 55 (7) 2035-2044 Infections of the central nervous system (CNS) are often acute with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan Array Card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid (CSF). The 21-pathogen TAC assays include two parasites (Balamuthia mandrillaris and Acanthamoeba), six bacterial pathogens (Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Mycoplasma pneumoniae, Mycobacterium tuberculosis, and Bartonella) and 13 viruses (parechovirus, dengue, nipah, varicella zoster, mumps, measles, lyssa, herpes simplex virus 1 and 2, Epstein Barr virus, enterovirus, cytomegalovirus and chikungunya). The card also includes human RNAse P as a nucleic acid extraction control and an internal manufacturer control (glyceraldehyde 3-phosphate dehydrogenase (GAPDH)). This CNS-TAC can test up to eight samples for all 21 agents within 2.5 hours following nucleic acid extraction. The assay was validated for linearity, limit of detection, sensitivity and specificity by either using live viruses (dengue, mumps and measles) or nucleic acid material (nipah and chikungunya). Of the 120 samples tested by individual real-time PCR (IRTP), 35 were positive for eight different targets while CNS-TAC detected 37 positive samples across nine different targets. The TAC assays showed 85.6% sensitivity and 96.7% specificity across the assays. This assay may be useful for outbreak investigation and surveillance of suspected neurological disease. |
Plasmodium Parasitemia Associated With Increased Survival in Ebola Virus-Infected Patients.
Rosenke K , Adjemian J , Munster VJ , Marzi A , Falzarano D , Onyango CO , Ochieng M , Juma B , Fischer RJ , Prescott JB , Safronetz D , Omballa V , Owuor C , Hoenen T , Groseth A , Martellaro C , van Doremalen N , Zemtsova G , Self J , Bushmaker T , McNally K , Rowe T , Emery SL , Feldmann F , Williamson BN , Best SM , Nyenswah TG , Grolla A , Strong JE , Kobinger G , Bolay FK , Zoon KC , Stassijns J , Giuliani R , de Smet M , Nichol ST , Fields B , Sprecher A , Massaquoi M , Feldmann H , de Wit E . Clin Infect Dis 2016 63 (8) 1026-33 BACKGROUND: The ongoing Ebola outbreak in West Africa has resulted in 28 646 suspected, probable, and confirmed Ebola virus infections. Nevertheless, malaria remains a large public health burden in the region affected by the outbreak. A joint Centers for Disease Control and Prevention/National Institutes of Health diagnostic laboratory was established in Monrovia, Liberia, in August 2014, to provide laboratory diagnostics for Ebola virus. METHODS: All blood samples from suspected Ebola virus-infected patients admitted to the Medecins Sans Frontieres ELWA3 Ebola treatment unit in Monrovia were tested by quantitative real-time polymerase chain reaction for the presence of Ebola virus and Plasmodium species RNA. Clinical outcome in laboratory-confirmed Ebola virus-infected patients was analyzed as a function of age, sex, Ebola viremia, and Plasmodium species parasitemia. RESULTS: The case fatality rate of 1182 patients with laboratory-confirmed Ebola virus infections was 52%. The probability of surviving decreased with increasing age and decreased with increasing Ebola viral load. Ebola virus-infected patients were 20% more likely to survive when Plasmodium species parasitemia was detected, even after controlling for Ebola viral load and age; those with the highest levels of parasitemia had a survival rate of 83%. This effect was independent of treatment with antimalarials, as this was provided to all patients. Moreover, treatment with antimalarials did not affect survival in the Ebola virus mouse model. CONCLUSIONS: Plasmodium species parasitemia is associated with an increase in the probability of surviving Ebola virus infection. More research is needed to understand the molecular mechanism underlying this remarkable phenomenon and translate it into treatment options for Ebola virus infection. |
Ebola laboratory response at the Eternal Love Winning Africa Campus, Monrovia, Liberia, 2014-2015
de Wit E , Rosenke K , Fischer RJ , Marzi A , Prescott J , Bushmaker T , van Doremalen N , Emery SL , Falzarano D , Feldmann F , Groseth A , Hoenen T , Juma B , McNally KL , Ochieng M , Omballa V , Onyango CO , Owuor C , Rowe T , Safronetz D , Self J , Williamson BN , Zemtsova G , Grolla A , Kobinger G , Rayfield M , Stroher U , Strong JE , Best SM , Ebihara H , Zoon KC , Nichol ST , Nyenswah TG , Bolay FK , Massaquoi M , Feldmann H , Fields B . J Infect Dis 2016 214 S169-S176 West Africa experienced the first epidemic of Ebola virus infection, with by far the greatest number of cases in Guinea, Sierra Leone, and Liberia. The unprecedented epidemic triggered an unparalleled response, including the deployment of multiple Ebola treatment units and mobile/field diagnostic laboratories. The National Institute of Allergy and Infectious Diseases and the Centers for Disease Control and Prevention deployed a joint laboratory to Monrovia, Liberia, in August 2014 to support the newly founded Ebola treatment unit at the Eternal Love Winning Africa (ELWA) campus. The laboratory operated initially out of a tent structure but quickly moved into a fixed-wall building owing to severe weather conditions, the need for increased security, and the high sample volume. Until May 2015, when the laboratory closed, the site handled close to 6000 clinical specimens for Ebola virus diagnosis and supported the medical staff in case patient management. Laboratory operation and safety, as well as Ebola virus diagnostic assays, are described and discussed; in addition, lessons learned for future deployments are reviewed. |
Development of a TaqMan Array Card for Acute Febrile Illness Outbreak Investigation and Surveillance of Emerging Pathogens including Ebola Virus.
Liu J , Ochieng C , Wiersma S , Stroher U , Towner JS , Whitmer S , Nichol ST , Moore CC , Kersh GJ , Kato C , Sexton C , Petersen J , Massung R , Hercik C , Crump JA , Kibiki G , Maro A , Mujaga B , Gratz J , Jacob ST , Banura P , Scheld WM , Juma B , Onyango CO , Montgomery JM , Houpt E , Fields B . J Clin Microbiol 2015 54 (1) 49-58 Acute febrile illness (AFI) is associated with substantial morbidity and mortality worldwide yet an etiologic agent is often not identified. Convalescent serology is impractical, blood culture is slow, and many pathogens are fastidious or impossible to cultivate. We developed a real-time PCR based TaqMan Array Card (TAC) that can test six to eight samples within 2.5 hours from sample to results and simultaneously detect 26 AFI associated organisms, including 15 viruses (Chikungunya, Crimean-Congo hemorrhagic fever virus, Dengue, Ebola virus, Bundibugyo virus, Sudan virus, Hantaviruses (HTN and SEO), Hepatitis E, Marburg, Nipah virus, O'nyong-nyong virus, Rift Valley fever virus, West Nile virus, Yellow fever virus), eight bacteria (Bartonella spp., Brucella spp., Coxiella burnetii, Leptospira spp., Rickettsia spp., Salmonella enterica and Salmonella enterica serovar Typhi, Yersinia pestis), and three protozoa (Leishmania spp., Plasmodium spp., Trypanosoma brucei). Two extrinsic controls (Phocine Herpesvirus 1 and bacteriophage MS2) were included to assure extraction and amplification efficiency. Analytical validation was performed on spiked specimens for linearity, intra-assay precision, inter-assay precision, limit of detection, and specificity. The performance of the card on clinical specimens was evaluated with 1,050 blood samples by comparison to the individual real-time PCR assays, and TAC exhibited overall 88% (278/315, 95% confidence interval 84% to 92%) sensitivity and 99% (5261/5326, 98% to 99%) specificity. This TaqMan Array Card can be used in field settings as a rapid screen for outbreak investigation or pathogen surveillance, including Ebola virus. |
Burden of invasive nontyphoidal Salmonella disease in a rural and urban site in Kenya, 2009-2014
Verani JR , Toroitich S , Auko J , Kiplang'at S , Cosmas L , Audi A , Mogeni OD , Aol G , Oketch D , Odiembo H , Katieno J , Wamola N , Onyango CO , Juma BW , Fields BS , Bigogo G , Montgomery JM . Clin Infect Dis 2015 61 Suppl 4 S302-9 BACKGROUND: Invasive infections with nontyphoidal Salmonella (NTS) lead to bacteremia in children and adults and are an important cause of illness in Africa; however, few data on the burden of NTS bacteremia are available. We sought to determine the burden of invasive NTS disease in a rural and urban setting in Kenya. METHODS: We conducted the study in a population-based surveillance platform in a rural setting in western Kenya (Lwak), and an informal urban settlement in Nairobi (Kibera) from 2009 to 2014. We obtained blood culture specimens from participants presenting with acute lower respiratory tract illness or acute febrile illness to a designated outpatient facility in each site, or any hospital admission for a potentially infectious cause (rural site only). Incidence was calculated using a defined catchment population and adjusting for specimen collection and healthcare-seeking practices. RESULTS: A total of 12 683 and 9524 blood cultures were analyzed from Lwak and Kibera, respectively. Of these, 428 (3.4%) and 533 (5.6%) grew a pathogen; among those, 208 (48.6%) and 70 (13.1%) were positive for NTS in Lwak and Kibera, respectively. Overall, the adjusted incidence of invasive NTS disease was higher in Lwak (839.4 per 100 000 person-years of observation [PYO]) than in Kibera (202.5 per 100 000 PYO). The highest adjusted incidences were observed in children <5 years of age (Lwak 3914.3 per 100 000 PYO and Kibera 997.9 per 100 000 PYO). The highest adjusted annual incidence was 1927.3 per 100 000 PYO (in 2010) in Lwak and 220.5 per 100 000 PYO (in 2011) in Kibera; the lowest incidences were 303.3 and 62.5 per 100 000 PYO, respectively (in 2012). In both sites, invasive NTS disease incidence generally declined over the study period. CONCLUSIONS: We observed an extremely high burden of invasive NTS disease in a rural area of Kenya and a lesser, but still substantial, burden in an urban slum. Although the incidences in both sites declined during the study period, invasive NTS infections remain an important cause of morbidity in these settings, particularly among children <5 years old. |
- Page last reviewed:Feb 1, 2024
- Page last updated:May 06, 2024
- Content source:
- Powered by CDC PHGKB Infrastructure