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Article ; Online: Feasibility and utility of a combined nasogastric-tube-and-string-test device for bacteriologic confirmation of pulmonary tuberculosis in young children.

Khambati, Nisreen / Song, Rinn / Smith, Jonathan P / Bijker, Else Margreet / McCarthy, Kimberly / Click, Eleanor S / Mchembere, Walter / Okumu, Albert / Musau, Susan / Okeyo, Elisha / Perez-Velez, Carlos M / Cain, Kevin

Diagnostic microbiology and infectious disease

2024 Volume 109, Issue 3, Page(s) 116302

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2024-04-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	604920-5
ISSN	1879-0070 ; 0732-8893
ISSN (online)	1879-0070
ISSN	0732-8893
DOI	10.1016/j.diagmicrobio.2024.116302
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Article: Implementing an intensified mentorship approach towards accelerated medical laboratory accreditation in 10 counties in Kenya.

Musau, Susan K / Mwachari, Christina / Kirui, Elvis / Muthoni, Junghae / Lascko, Taylor / Blanco, Natalia / Abimiku, Alash'le / Koech, Emily

African journal of laboratory medicine

2022 Volume 11, Issue 1, Page(s) 1814

Abstract: Background: Despite Kenya's roll-out of the Strengthening Laboratory Management Towards Accreditation programme in 2010, most laboratories had not made significant or tangible improvements towards accreditation by 2016. In April 2016, the University of ... ...

Abstract	Background: Despite Kenya's roll-out of the Strengthening Laboratory Management Towards Accreditation programme in 2010, most laboratories had not made significant or tangible improvements towards accreditation by 2016. In April 2016, the University of Maryland, Baltimore enrolled 27 facilities in the standard Strengthening Laboratory Management Towards Accreditation programme. Objective: This study aimed to describe and evaluate the implementation of an intensified mentorship strategy on laboratory accreditation. Methods: In October 2017, the University of Maryland, Baltimore implemented intensive mentorship in 27 hospital laboratories in Nairobi, Kiambu, Meru, Embu, Muranga, Nyeri, Laikipia, Nyandarua, Tharaka-Nithi, and Kirinyaga counties in Kenya. Laboratories were paired with competent mentors whose skills were matched to facility gaps. Baseline and follow-up assessments were done between April 2016 and March 2019 using the World Health Organization's Stepwise Laboratory Quality Improvement Process Towards Accreditation Checklist and overall scores of the 12 Quality System Essentials and star ratings (from zero to five, based on scores) used to evaluate the effectiveness of the intensified mentorship. Results: In September 2017, 14 laboratories scored zero stars, three scored one star, eight scored two stars, one scored three stars, and one laboratory was accredited. By March 2019, eight laboratories were accredited, five scored four stars, 10 scored three stars, three scored two stars, and only one scored one star. The average score change with the intensified approach was 81.5 versus 53.9 for the standard approach. Conclusion: The intensified mentorship strategy resulted in fast-tracked progress towards laboratory accreditation and can be adopted in similar resource-limited settings.
Language	English
Publishing date	2022-07-01
Publishing country	South Africa
Document type	Journal Article
ZDB-ID	2708535-1
ISSN	2225-2010 ; 2225-2002
ISSN (online)	2225-2010
ISSN	2225-2002
DOI	10.4102/ajlm.v11i1.1814
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Article ; Online: Machine learning to predict bacteriologic confirmation of Mycobacterium tuberculosis in infants and very young children.

Smith, Jonathan P / Milligan, Kyle / McCarthy, Kimberly D / Mchembere, Walter / Okeyo, Elisha / Musau, Susan K / Okumu, Albert / Song, Rinn / Click, Eleanor S / Cain, Kevin P

PLOS digital health

2023 Volume 2, Issue 5, Page(s) e0000249

Abstract: 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 ... ...

Abstract	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.
Language	English
Publishing date	2023-05-17
Publishing country	United States
Document type	Journal Article
ISSN	2767-3170
ISSN (online)	2767-3170
DOI	10.1371/journal.pdig.0000249
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Article ; Online: Sensitive and Feasible Specimen Collection and Testing Strategies for Diagnosing Tuberculosis in Young Children.

Song, Rinn / Click, Eleanor S / McCarthy, Kimberly D / Heilig, Charles M / Mchembere, Walter / Smith, Jonathan P / Fajans, Mark / Musau, Susan K / Okeyo, Elisha / Okumu, Albert / Orwa, James / Gethi, Dickson / Odeny, Lazarus / Lee, Scott H / Perez-Velez, Carlos M / Wright, Colleen A / Cain, Kevin P

JAMA pediatrics

2021 Volume 175, Issue 5, Page(s) e206069

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Child, Preschool ; Cross-Sectional Studies ; Feces/microbiology ; Female ; Humans ; Infant ; Kenya ; Male ; Nasopharynx/microbiology ; Prospective Studies ; Reference Standards ; Sensitivity and Specificity ; Specimen Handling/methods ; Tuberculosis, Pulmonary/diagnosis ; Urine/microbiology
Language	English
Publishing date	2021-05-03
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2701223-2
ISSN	2168-6211 ; 2168-6203
ISSN (online)	2168-6211
ISSN	2168-6203
DOI	10.1001/jamapediatrics.2020.6069
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Article ; Online: 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.

The Pediatric infectious disease journal

2022 Volume 41, Issue 8, Page(s) 671–677

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Child ; Child, Preschool ; Humans ; Mycobacterium tuberculosis/genetics ; Prospective Studies ; Retrospective Studies ; Sensitivity and Specificity ; Sputum/microbiology ; Tuberculosis/diagnosis
Language	English
Publishing date	2022-07-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000003582
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Book ; Online: Multidimensional poverty in Kenya

Kabubo-Mariara, Jane / Wambugu, Anthony / Musau, Susan

Analysis of maternal and child wellbeing

2011

Keywords	Public Economics
Language	English
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: No evidence of

Click, Eleanor S / Ouma, Gregory S / DeGruy, Kyle / Murithi, Wilfred / Okonji, Julie A / McCarthy, Kimberly D / Musau, Susan / Okumu, Albert / Alexander, Heather / Posey, James / Cain, Kevin P

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

2018 Volume 22, Issue 4, Page(s) 464–465

MeSH term(s)	Adult ; Female ; HIV Infections/complications ; Humans ; Milk, Human/microbiology ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/isolation & purification ; Postpartum Period ; Sputum/microbiology ; Tuberculosis/complications ; Tuberculosis/microbiology ; Young Adult
Language	English
Publishing date	2018-03-21
Publishing country	France
Document type	Letter ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1385624-8
ISSN	1815-7920 ; 1027-3719
ISSN (online)	1815-7920
ISSN	1027-3719
DOI	10.5588/ijtld.17.0375
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Article ; Online: Comparative Yield of Different Diagnostic Tests for Tuberculosis among People Living with HIV in Western Kenya.

Cavanaugh, Joseph S / Modi, Surbhi / Musau, Susan / McCarthy, Kimberly / Alexander, Heather / Burmen, Barbara / Heilig, Charles M / Shiraishi, Ray W / Cain, Kevin

PloS one

2016 Volume 11, Issue 3, Page(s) e0152364

Abstract: Background: Diagnosis followed by effective treatment of tuberculosis (TB) reduces transmission and saves lives in persons living with HIV (PLHIV). Sputum smear microscopy is widely used for diagnosis, despite limited sensitivity in PLHIV. Evidence is ... ...

Abstract	Background: Diagnosis followed by effective treatment of tuberculosis (TB) reduces transmission and saves lives in persons living with HIV (PLHIV). Sputum smear microscopy is widely used for diagnosis, despite limited sensitivity in PLHIV. Evidence is needed to determine the optimal diagnostic approach for these patients. Methods: From May 2011 through June 2012, we recruited PLHIV from 15 HIV treatment centers in western Kenya. We collected up to three sputum specimens for Ziehl-Neelsen (ZN) and fluorescence microscopy (FM), GeneXpert MTB/RIF (Xpert), and culture, regardless of symptoms. We calculated the incremental yield of each test, stratifying results by CD4 cell count and specimen type; data were analyzed to account for complex sampling. Results: From 778 enrolled patients, we identified 88 (11.3%) laboratory-confirmed TB cases. Of the 74 cases who submitted 2 specimens for microscopy and Xpert testing, ZN microscopy identified 25 (33.6%); Xpert identified those plus an additional 18 (incremental yield = 24.4%). Xpert testing of spot specimens identified 48 (57.0%) of 84 cases; whereas Xpert testing of morning specimens identified 50 (66.0%) of 76 cases. Two Xpert tests detected 22/24 (92.0%) TB cases with CD4 counts <100 cells/μL and 30/45 (67.0%) of cases with CD4 counts ≥100 cells/μl. Conclusions: In PLHIV, Xpert substantially increased diagnostic yield compared to smear microscopy and had the highest yield when used to test morning specimens and specimens from PLHIV with CD4 count <100 cells/μL. TB programs unable to replace smear microscopy with Xpert for all symptomatic PLHIV should consider targeted replacement and using morning specimens.
MeSH term(s)	Adult ; CD4 Lymphocyte Count ; Demography ; Diagnostic Tests, Routine ; Female ; HIV Infections/complications ; HIV Infections/immunology ; Humans ; Kenya ; Male ; Sensitivity and Specificity ; Sputum/microbiology ; Tuberculosis/complications ; Tuberculosis/diagnosis ; Young Adult
Language	English
Publishing date	2016
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0152364
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