Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-14 (of 14 Records) |
Query Trace: Okumu E[original query] |
---|
Feasibility and utility of a combined nasogastric-tube-and-string-test device for bacteriologic confirmation of pulmonary tuberculosis in young children
Khambati N , Song R , Smith JP , Bijker EM , McCarthy K , Click ES , McHembere W , Okumu A , Musau S , Okeyo E , Perez-Velez CM , Cain K . Diagn Microbiol Infect Dis 2024 109 (3) 116302 For microbiological confirmation of pediatric pulmonary tuberculosis (PTB), gastric aspirates (GA) are often operationally unfeasible without hospitalization, and the encapsulated orogastric string test is not easily swallowed in young children. The Combined-NasoGastric-Tube-and-String-Test (CNGTST) enables dual collection of GA and string specimens. In a prospective cohort study in Kenya, we examined its feasibility in children under five with presumptive PTB and compared the bacteriological yield of string to GA. Paired GA and string samples were successfully collected in 95.6 % (281/294) of children. Mycobacterium tuberculosis was isolated from 7.0 % (38/541) of GA and 4.3 % (23/541) of string samples, diagnosing 8.2 % (23/281) of children using GA and 5.3 % (15/281) using string. The CNGTST was feasible in nearly all children. Yield from string was two-thirds that of GA despite a half-hour median dwelling time. In settings where the feasibility of hospitalisation for GA is uncertain, the string component can be used to confirm PTB. |
Correction: Methods and indicators for measuring patterns of human exposure to malaria vectors
Monroe A , Moore S , Okumu F , Kiware S , Lobo NF , Koenker H , Sherrard-Smith E , Gimnig J , Killeen GF . Malar J 2023 22 (1) 270 Following publication of the article [1], the authors flagged that there were some minor errors in the formulas of Additional file 1. These errors have since been corrected in the file. As a result of this correction, Fig. 2, which uses the illustrative data in Additional file 1, has also been corrected: in panel c of the figure, the value '60%' has been updated to '58%'. The authors would like to highlight that this corresponding update to the figure does not affect how their article should be interpreted; however, to ensure accurate calculations, it is important to ensure you use the corrected file if inputting your own data. The authors thank you for reading this erratum and apologize for any inconvenience caused. |
Machine learning to predict bacteriologic confirmation of Mycobacterium tuberculosis in infants and very young children
Smith JP , Milligan K , McCarthy KD , McHembere W , Okeyo E , Musau SK , Okumu A , Song R , Click ES , Cain KP . PLOS Digit Health 2023 2 (5) e0000249 Diagnosis of tuberculosis (TB) among young children (<5 years) is challenging due to the paucibacillary nature of clinical disease and clinical similarities to other childhood diseases. We used machine learning to develop accurate prediction models of microbial confirmation with simply defined and easily obtainable clinical, demographic, and radiologic factors. We evaluated eleven supervised machine learning models (using stepwise regression, regularized regression, decision tree, and support vector machine approaches) to predict microbial confirmation in young children (<5 years) using samples from invasive (reference-standard) or noninvasive procedure. Models were trained and tested using data from a large prospective cohort of young children with symptoms suggestive of TB in Kenya. Model performance was evaluated using areas under the receiver operating curve (AUROC) and precision-recall curve (AUPRC), accuracy metrics. (i.e., sensitivity, specificity), F-beta scores, Cohen's Kappa, and Matthew's Correlation Coefficient. Among 262 included children, 29 (11%) were microbially confirmed using any sampling technique. Models were accurate at predicting microbial confirmation in samples obtained from invasive procedures (AUROC range: 0.84-0.90) and from noninvasive procedures (AUROC range: 0.83-0.89). History of household contact with a confirmed case of TB, immunological evidence of TB infection, and a chest x-ray consistent with TB disease were consistently influential across models. Our results suggest machine learning can accurately predict microbial confirmation of M. tuberculosis in young children using simply defined features and increase the bacteriologic yield in diagnostic cohorts. These findings may facilitate clinical decision making and guide clinical research into novel biomarkers of TB disease in young children. |
Performance of Xpert MTB/RIF and mycobacterial culture on multiple specimen types for diagnosis of tuberculosis disease in young children and clinical characterization according to standardized research case definitions
Click ES , Song R , Smith JP , McHembere W , Fajans M , Hariri P , Okeyo E , McCarthy KD , Gethi D , Odeny L , Musau S , Okumu A , Orwa J , Perez-Velez CM , Wright CA , Andres MM , Marais BJ , Schaaf HS , Graham SM , Cruz AT , Cain KP . Pediatr Infect Dis J 2022 41 (8) 671-677 BACKGROUND: Tuberculosis (TB) is a leading cause of illness and death in children globally. Improved bacteriologic and clinical diagnostic approaches in children are urgently needed. METHODS: In a prospective cohort study, a consecutive series of young (<5 years) children presenting with symptoms suggestive of TB and parenchymal abnormality on chest radiograph in inpatient and outpatient settings in Kisumu County, Kenya from October 2013 to August 2015 were evaluated at baseline and over 6 months. Up to 14 specimens per child were tested for the Mycobacterium tuberculosis complex by fluorescence microscopy, Xpert MTB/RIF and mycobacterial culture. Using detailed clinical characterization, cases were retrospectively classified according to standardized research case definitions and the sensitivity and specificity of microbiological tests on different specimen types were determined. RESULTS: Among 300 young children enrolled, 266 had sufficient information to be classified according to the research clinical case definition. Of these, 36% (96/266) had TB disease; 32% (31/96) with bacteriologically confirmed intrathoracic TB. Compared to culture, the sensitivity of a single Xpert test ranged from 60 to 67% and specificity from 97.5 to 100% for different specimen types. CONCLUSIONS: Despite extensive specimen collection and laboratory testing, TB could not be bacteriologically confirmed in almost two-thirds of children with intrathoracic TB classified by research clinical case definitions. Improved diagnostic tests are needed to identify children with TB and to exclude other potential causes of illness. |
Need for caution when interpreting Xpert MTB/RIF results for rifampin resistance among children.
Murithi W , Click ES , McCarthy KD , Okeyo E , Sitati R , Anyango I , Okumu A , McHembere W , Song R , Cain K . Int J Tuberc Lung Dis 2021 25 (11) 911-916 BACKGROUND: Recommended by the World Health Organization as an initial diagnostic test for TB in children, Xpert(®) MTB/RIF is widely implemented in many countries, including Kenya.METHODS: Three hundred HIV-positive and negative children (<5 years) were enrolled in Kisumu County, Kenya, from October 2013 to August 2015. Multiple specimen types were collected from each child and tested using Xpert, liquid culture, and phenotypic drug susceptibility testing (DST). Samples positive for rifampin (RIF) resistance on Xpert were tested using line-probe assay and sequencing.RESULTS: Of 32 children with bacteriologically confirmed TB, 27 had positive Xpert results. Of these, 3/27 (11%, 95% CI 4-28) had RIF resistance detected on Xpert, but not by phenotypic DST, line-probe assay, or sequencing. For these three children, five Xpert tests showed RIF resistance; all five tests had semi-quantitative "very low" results and delay or absence of probe D signal, whereas no Xpert results with higher semi-quantitative results showed RIF resistance. All three children responded well to standard TB treatment.CONCLUSIONS: False RIF resistance may be detected in pediatric specimens. Further study is needed to determine if false RIF resistance is associated with low bacterial load. |
Sensitive and feasible specimen collection and testing strategies for diagnosing tuberculosis in young children
Song R , Click ES , McCarthy KD , Heilig CM , McHembere W , Smith JP , Fajans M , Musau SK , Okeyo E , Okumu A , Orwa J , Gethi D , Odeny L , Lee SH , Perez-Velez CM , Wright CA , Cain KP . JAMA Pediatr 2021 175 (5) e206069 IMPORTANCE: Criterion-standard specimens for tuberculosis diagnosis in young children, gastric aspirate (GA) and induced sputum, are invasive and rarely collected in resource-limited settings. A far less invasive approach to tuberculosis diagnostic testing in children younger than 5 years as sensitive as current reference standards is important to identify. OBJECTIVE: To characterize the sensitivity of preferably minimally invasive specimen and assay combinations relative to maximum observed yield from all specimens and assays combined. DESIGN, SETTING, AND PARTICIPANTS: In this prospective cross-sectional diagnostic study, the reference standard was a panel of up to 2 samples of each of 6 specimen types tested for Mycobacterium tuberculosis complex by Xpert MTB/RIF assay and mycobacteria growth indicator tube culture. Multiple different combinations of specimens and tests were evaluated as index tests. A consecutive series of children was recruited from inpatient and outpatient settings in Kisumu County, Kenya, between October 2013 and August 2015. Participants were children younger than 5 years who had symptoms of tuberculosis (unexplained cough, fever, malnutrition) and parenchymal abnormality on chest radiography or who had cervical lymphadenopathy. Children with 1 or more evaluable specimen for 4 or more primary study specimen types were included in the analysis. Data were analyzed from February 2015 to October 2020. MAIN OUTCOMES AND MEASURES: Cumulative and incremental diagnostic yield of combinations of specimen types and tests relative to the maximum observed yield. RESULTS: Of the 300 enrolled children, the median (interquartile range) age was 2.0 (1.0-3.6) years, and 151 (50.3%) were female. A total of 294 met criteria for analysis. Of 31 participants with confirmed tuberculosis (maximum observed yield), 24 (sensitivity, 77%; interdecile range, 68%-87%) had positive results on up to 2 GA samples and 20 (sensitivity, 64%; interdecile range, 53%-76%) had positive test results on up to 2 induced sputum samples. The yields of 2 nasopharyngeal aspirate (NPA) samples (23 of 31 [sensitivity, 74%; interdecile range, 64%-84%]), of 1 NPA sample and 1 stool sample (22 of 31 [sensitivity, 71%; interdecile range, 60%-81%]), or of 1 NPA sample and 1 urine sample (21.5 of 31 [sensitivity, 69%; interdecile range, 58%-80%]) were similar to reference-standard specimens. Combining up to 2 each of GA and NPA samples had an average yield of 90% (28 of 31). CONCLUSIONS AND RELEVANCE: NPA, in duplicate or in combination with stool or urine specimens, was readily obtainable and had diagnostic yield comparable with reference-standard specimens. This combination could improve tuberculosis diagnosis among children in resource-limited settings. Combining GA and NPA had greater yield than that of the current reference standards and may be useful in certain clinical and research settings. |
Methods and indicators for measuring patterns of human exposure to malaria vectors
Monroe A , Moore S , Okumu F , Kiware S , Lobo NF , Koenker H , Sherrard-Smith E , Gimnig J , Killeen GF . Malar J 2020 19 (1) 207 BACKGROUND: Effective targeting and evaluation of interventions that protect against adult malaria vectors requires an understanding of how gaps in personal protection arise. An improved understanding of human and mosquito behaviour, and how they overlap in time and space, is critical to estimating the impact of insecticide-treated nets (ITNs) and determining when and where supplemental personal protection tools are needed. Methods for weighting estimates of human exposure to biting Anopheles mosquitoes according to where people spend their time were first developed over half a century ago. However, crude indoor and outdoor biting rates are still commonly interpreted as indicative of human-vector contact patterns without any adjustment for human behaviour or the personal protection effects of ITNs. MAIN TEXT: A small number of human behavioural variables capturing the distribution of human populations indoors and outdoors, whether they are awake or asleep, and if and when they use an ITN over the course of the night, can enable a more accurate representation of human biting exposure patterns. However, to date no clear guidance is available on what data should be collected, what indicators should be reported, or how they should be calculated. This article presents an integrated perspective on relevant indicators of human-vector interactions, the critical entomological and human behavioural data elements required to quantify human-vector interactions, and recommendations for collecting and analysing such data. CONCLUSIONS: If collected and used consistently, this information can contribute to an improved understanding of how malaria transmission persists in the context of current intervention tools, how exposure patterns may change as new vector control tools are introduced, and the potential impact and limitations of these tools. This article is intended to consolidate understanding around work on this topic to date and provide a consistent framework for building upon it. Additional work is needed to address remaining questions, including further development and validation of methods for entomological and human behavioural data collection and analysis. |
Cognitive testing of an instrument to evaluate acceptability and use of pre-exposure prophylaxis products among women
Zissette S , Atujuna M , Tolley EE , Okumu E , Auerbach JD , Hodder SL , Aral SO , Adimora AA . Appl Cogn Psychol 2019 34 (1) 78-84 Given the range of pre-exposure prophylaxis (PrEP) products currently being tested to prevent HIV in women, a standardized Acceptability and Use of PrEP Products Among Women Tool may facilitate comparisons of product acceptability and use across different geographies, trials, and users. We conducted three rounds of cognitive interviewing over 2 months in 2016, with 28 South African women who had experience participating in a range of PrEP product trials. The final instrument contained 41 items, including five new items that improved construct validity and 22 items modified for clarity. Changes were made due to unclear wording, difficulty answering, participant embarrassment, low response variability, and administrative formatting. Cognitive interviewing provided a means to address issues that would have inhibited this tool's ability to accurately collect data otherwise. This rapid, low-cost study provided valuable insight into participants' understanding of questions and demonstrated the utility of cognitive interviewing in international clinical trials. |
Tuberculosis case finding using population-based disease surveillance platforms in urban and rural Kenya
Bigogo G , Cain K , Nyole D , Masyongo G , Auko JA , Wamola N , Okumu A , Agaya J , Montgomery J , Borgdorff M , Burton D . BMC Infect Dis 2018 18 (1) 262 BACKGROUND: Tuberculosis (TB) case finding is an important component of TB control because it can reduce transmission of Mycobacterium tuberculosis (MTB) through prompt detection and treatment of infectious patients. METHODS: Using population-based infectious disease surveillance (PBIDS) platforms with links to health facilities in Kenya we implemented intensified TB case finding in the community and at the health facilities, as an adjunct to routine passive case finding conducted by the national TB program. From 2011 to 2014, PBIDS participants >/=15 years were screened either at home or health facilities for possible TB symptoms which included cough, fever, night sweats or weight loss in the preceding 2 weeks. At home, participants with possible TB symptoms had expectorated sputum collected. At the clinic, HIV-infected participants with possible TB symptoms were invited to produce sputum. Those without HIV but with symptoms lasting 7 days including the visit day had chest radiographs performed, and had sputum collected if the radiographs were abnormal. Sputum samples were tested for the presence of MTB using the Xpert MTB/RIF assay. TB detection rates were calculated per 100,000 persons screened. RESULTS: Of 11,191 participants aged >/=15 years screened at home at both sites, 2695 (23.9%) reported possible TB symptoms, of whom 2258 (83.8%) produced sputum specimens. MTB was detected in 32 (1.4%) of the specimens resulting in a detection rate of 286/100,000 persons screened. At the health facilities, a total of 11,762 person were screened, 7500 (63.8%) had possible TB symptoms of whom 1282 (17.1%) produced sputum samples. MTB was detected in 69 (5.4%) of the samples, resulting in an overall detection rate of 587/100,000 persons screened. The TB detection rate was higher in persons with HIV compared to those without at both home (HIV-infected - 769/100,000, HIV-uninfected 141/100,000, rate ratio (RR) - 5.45, 95% CI 3.25-22.37), and health facilities (HIV-infected 3399/100,000, HIV-uninfected 294/100,000, RR 11.56, 95% CI 6.18-18.44). CONCLUSION: Facility-based intensified TB case finding detected more TB cases per the number of specimens tested and the number of persons screened, including those with HIV, than home-based TB screening and should be further evaluated to determine its potential programmatic impact. |
No evidence of Mycobacterium tuberculosis in breast milk of 18 women with confirmed TB disease in Kisumu, Kenya
Click ES , Ouma GS , DeGruy K , Murithi W , Okonji JA , McCarthy KD , Musau S , Okumu A , Alexander H , Posey J , Cain KP . Int J Tuberc Lung Dis 2018 22 (4) 464-465 Mycobacterium tuberculosis complex (MTC) is | comprised of highly related mycobacteria. M. tuberculosis causes tuberculosis (TB) disease primarily in | humans, and M. bovis in cows. However, M. bovis | can cause disease in humans, primarily via ingestion | of infected cow’s milk, and is associated with cervical | lymphadenitis. In humans, TB usually manifests as | pulmonary disease but may affect non-pulmonary | sites. In young children, cervical lymphadenitis is a | common manifestation |
Comparison of Mycobacterium tuberculosis complex Yield and Contamination Rates using Lowenstein-Jensen with and without Antibiotics in Western Kenya
Okumu A , McCarthy K , Orwa J , Williamson J , Musau S , Alexander H , Cavanaugh S , Modi S , Cain K . J Med Sci Clin Res 2017 5 (8) BACKGROUND: While molecular methods have been recently endorsed for diagnosis of tuberculosis (TB), mycobacterial culture remains the gold standard. Lowenstein-Jensen (LJ) is often used for the cultivation of Mycobacterium tuberculosis complex (MTBC); however contamination often renders a subset of cultures useless. We compared the MTBC yield and contamination rate of processed sputum inoculated on LJ with antibiotics (LJ PACT) to LJ without antibiotics (LJ). METHODOLOGY: Sputum samples were obtained from people living with HIV enrolled in a TB screening study in western Kenya, processed using NALC/NaOH-Na citrate, then inoculated on LJ PACT and LJ media. Cultures were evaluated weekly with growth identified as acid-fast bacilli by Ziehl-Neelsen bright-field microscopy. MTBC and nontuberculous mycobacteria (NTM) were identified by immunochromatographic and line probe assays. RESULTS: A total of 700 sputum samples were cultured on both LJ PACT and LJ between March and June 2012. Of those cultured on LJ PACT, 29 (4.1%) grew MTBC, 613 (87.6%) were negative, 12 (1.7%) grew NTM, and 46 (6.6%) were contaminated; on LJ, 28 (4%) grew MTBC, 553 (79%) were negative, 9 (1.3%) grew NTM, and 110 (15.7%) were contaminated. The difference in contamination on LJ PACT and LJ was statistically significant (p<0.0001), while the difference in MTBC growth was not (p=0.566). |
Assessing the effect of decentralisation of laboratory diagnosis for drug-resistant tuberculosis in Kenya
Sharma A , Musau S , Heilig CM , Okumu AO , Opiyo EO , Basiye FL , Miruka FO , Kioko JK , Sitienei JK , Cain KP . Int J Tuberc Lung Dis 2015 19 (11) 1348-53 SETTING: Drug susceptibility testing (DST) is recommended in Kenya to identify multidrug-resistant tuberculosis (MDR-TB) in persons registered for tuberculosis (TB) retreatment. DST is performed at a central laboratory with a two-step growth-based process and a regional laboratory with a simultaneous molecular- and growth-based process. OBJECTIVE: To compare proportions of retreatment cases who underwent DST and turnaround times for hospitals referring to the central vs. regional laboratory. DESIGN: Cases were persons registered for TB retreatment from 1 January 2012 to 31 December 2013. Records of 11 hospitals and 7 hospitals referring patients to the regional and central laboratories, respectively, were reviewed. RESULTS: Respectively 238/432 (55%) and 88/355 (25%) cases from hospitals referring to the regional and central laboratories underwent DST. The mean time from case registration to receipt of DST results and initiation of MDR-TB treatment was quicker in hospitals referring to the regional laboratory. The time required for the transportation of specimens, specimen testing and receipt of DST results at hospitals was shorter for the regional laboratory (P < 0.05). CONCLUSION: Testing was faster and more complete at hospitals referring to the regional laboratory. A comprehensive review of MDR-TB detection in Kenya is required to increase the proportion of cases receiving DST. |
Experience in implementing a quality management system in a tuberculosis laboratory, Kisumu, Kenya
Musau S , McCarthy K , Okumu A , Shinnick T , Wandiga S , Williamson J , Cain K . Int J Tuberc Lung Dis 2015 19 (6) 693-5 We implemented a quality management system (QMS) and documented our improvements in a tuberculosis (TB) laboratory in Kisumu, Kenya. After implementation of the QMS, a sustained reduction in culture contamination rates for solid (from 15.4% to 5.3%) and liquid media (from 15.2% to 9.3%) was observed, and waste from product expiry was reduced significantly. External quality assurance (EQA) results were satisfactory before and after QMS implementation, and a client survey after implementation revealed 98% satisfaction. The laboratory attained ISO 15189 accreditation in October 2013. The implementation of QMS facilitated the attainment of target quality indicators, reduced waste due to expiry and led to high client satisfaction. |
Consistently high estimates for the proportion of human exposure to malaria vector populations occurring indoors in rural Africa
Huho B , Briet O , Seyoum A , Sikaala C , Bayoh N , Gimnig J , Okumu F , Diallo D , Abdulla S , Smith T , Killeen G . Int J Epidemiol 2013 42 (1) 235-47 BACKGROUND: Insecticide-treated nets (ITNs) and indoor residual spraying (IRS) are highly effective tools for controlling malaria transmission in Africa because the most important vectors, from the Anopheles gambiae complex and the A. funestus group, usually prefer biting humans indoors at night. METHODS: Matched surveys of mosquito and human behaviour from six rural sites in Burkina Faso, Tanzania, Zambia, and Kenya, with ITN use ranging from 0.2% to 82.5%, were used to calculate the proportion of human exposure to An. gambiae sensu lato and An. funestus s.l. that occurs indoors (pi(i)), as an indicator of the upper limit of personal protection that indoor vector control measures can provide...... |
- Page last reviewed:Feb 1, 2024
- Page last updated:May 06, 2024
- Content source:
- Powered by CDC PHGKB Infrastructure