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Article ; Online: Beyond the Numbers: Interpreting WHO's

Sabiiti, Wilber

The East African health research journal

2017 Volume 1, Issue 1, Page(s) 2–7

Abstract: By 2000, 5 East African Community (EAC) member states-Uganda, Kenya, Tanzania, Rwanda, and Burundi-had adopted the World Health Organization's (WHO's) policy of directly observed treatment short-course (DOTS) for tuberculosis (TB). This policy is meant ... ...

Abstract	By 2000, 5 East African Community (EAC) member states-Uganda, Kenya, Tanzania, Rwanda, and Burundi-had adopted the World Health Organization's (WHO's) policy of directly observed treatment short-course (DOTS) for tuberculosis (TB). This policy is meant to speed up the control of TB through effective diagnosis and treatment. However, the rate of reduction of TB burden has been slow, and as of 2016, 3 EAC member states-Uganda, Kenya, and Tanzania-are still categorised as high TB burden countries. We analysed WHO's
Language	English
Publishing date	2017-03-01
Publishing country	Burundi
Document type	Journal Article
ISSN	2520-5285
ISSN (online)	2520-5285
DOI	10.24248/EAHRJ-D-16-00364
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Article ; Online: Klebsiella pneumoniae carbapenamases in Escherichia coli isolated from humans and livestock in rural south-western Uganda.

Tuhamize, Barbra / Asiimwe, Benon B / Kasaza, Kennedy / Sabiiti, Wilber / Holden, Mathew / Bazira, Joel

PloS one

2023 Volume 18, Issue 7, Page(s) e0288243

Abstract: Background: The accumulation of resistance genes in Escherichia coli (E. coli) strains imposes limitations in the therapeutic options available for the treatment of infections caused by E.coli. Production of Klebsiella pneumoniae carbapenemase (KPC) by ... ...

Abstract	Background: The accumulation of resistance genes in Escherichia coli (E. coli) strains imposes limitations in the therapeutic options available for the treatment of infections caused by E.coli. Production of Klebsiella pneumoniae carbapenemase (KPC) by E. coli renders it resistant to broad-spectrum β-lactam antibiotics. Globally there is existing evidence of spread of carbapenem-resistant E. coli in both humans and livestock driven by acquisition of the several other carbapenemase genes. Overall, there is little information regarding the extent of KPC gene distribution in E. coli. We set out to determine the prevalence, and evaluate the phenotypic and genotypic patterns of KPC in E. coli isolated from humans and their livestock in rural south western Uganda. Methods: A laboratory-based, descriptive cross-sectional study was conducted involving 96 human and 96 livestock isolates collected from agro-pastoralist communities in Mbarara district in south western Uganda. Phenotypic and molecular methods (PCR) were used for presence and identification of KPC genes in the E. coli isolates. A chi-square test of independence was used to evaluate the differences in resistant patterns between carbapenems and isolates. Results: The overall prevalence of carbapenem resistance by disk diffusion susceptibility testing (DST) for both humans and livestock isolates were 41.7% (80/192). DST-based resistance was identical in both human and livestock isolates (41.7%). The prevalence of carbapenem resistance based on Modified Hodge Test (MHT) was 5% (2/40) and 10% (4/40) for humans and livestock isolates respectively. Both human and livestock isolates, 48.7% (95/192) had the KPC gene, higher than phenotypic expression; 41.7% (80/192). blaKPC gene prevalence was overall similar in human isolates (51%; 49/96) vs livestock isolates (47.9%; 46/96). Approximately, 19% (15/80) of the isolates were phenotypically resistant to carbapenems and over 70% (79/112) of the phenotypically sensitive strains harbored the blaKPC gene. Conclusion: Our results suggest that both human and livestock isolates of E. coli in our setting carry the blaKPC gene with a high percentage of strains not actively expressing the blaKPC gene. The finding of fewer isolates carrying the KPC gene than those phenotypically resistant to carbapenems suggests that other mechanisms are playing a role in this phenomenon, calling for further researcher into this phenomenon.
MeSH term(s)	Humans ; Animals ; Escherichia coli/metabolism ; Klebsiella pneumoniae ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Livestock/metabolism ; Cross-Sectional Studies ; Uganda/epidemiology ; Carbapenems/pharmacology ; Carbapenems/therapeutic use ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; beta-Lactamases/metabolism ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents ; Carbapenems ; Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2023-07-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0288243
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Article ; Online: Corrigendum to "A practical approach to render tuberculosis samples safe for application of tuberculosis molecular bacterial load assay in clinical settings without a biosafety level 3 laboratory" [Tuberculosis 138 (2023) 102275 1-5].

Mtafya, Bariki / Qwaray, Paschal / John, Joseph / Sichone, Emanuel / Shoo, Alice / Gillespie, Stephen H / Ntinginya, Nyanda Elias / Sabiiti, Wilber

Tuberculosis (Edinburgh, Scotland)

2023 Volume 142, Page(s) 102321

Language	English
Publishing date	2023-02-16
Publishing country	Scotland
Document type	Published Erratum
ZDB-ID	2046804-0
ISSN	1873-281X ; 1472-9792
ISSN (online)	1873-281X
ISSN	1472-9792
DOI	10.1016/j.tube.2023.102321
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Article ; Online: Detection and Quantification of Viable Mycobacterium tuberculosis Bacilli in Saline-Processed Stool Samples by Tuberculosis Molecular Bacterial Load Assay: a Potential Alternative for Processing Stool.

Musisi, Emmanuel / Ssesolo, Abdul / Sloan, Derek J / Gillespie, Stephen H / Sabiiti, Wilber

Microbiology spectrum

2022 Volume 10, Issue 3, Page(s) e0027422

MeSH term(s)	Bacterial Load ; Humans ; Mycobacterium tuberculosis/genetics ; Sputum ; Tuberculosis/diagnosis ; Tuberculosis/microbiology
Language	English
Publishing date	2022-05-12
Publishing country	United States
Document type	Letter ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.00274-22
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Article ; Online: Localization and phenotyping of tuberculosis bacteria using a combination of deep learning and SVMs.

Zachariou, Marios / Arandjelović, Ognjen / Dombay, Evelin / Sabiiti, Wilber / Mtafya, Bariki / Ntinginya, Nyanda Elias / Sloan, Derek J

Computers in biology and medicine

2023 Volume 167, Page(s) 107573

Abstract: Successful treatment of pulmonary tuberculosis (TB) depends on early diagnosis and careful monitoring of treatment response. Identification of acid-fast bacilli by fluorescence microscopy of sputum smears is a common tool for both tasks. Microscopy-based ...

Abstract	Successful treatment of pulmonary tuberculosis (TB) depends on early diagnosis and careful monitoring of treatment response. Identification of acid-fast bacilli by fluorescence microscopy of sputum smears is a common tool for both tasks. Microscopy-based analysis of the intracellular lipid content and dimensions of individual Mycobacterium tuberculosis (Mtb) cells also describe phenotypic changes which may improve our biological understanding of antibiotic therapy for TB. However, fluorescence microscopy is a challenging, time-consuming and subjective procedure. In this work, we automate examination of fields of view (FOVs) from microscopy images to determine the lipid content and dimensions (length and width) of Mtb cells. We introduce an adapted variation of the UNet model to efficiently localising bacteria within FOVs stained by two fluorescence dyes; auramine O to identify Mtb and LipidTox Red to identify intracellular lipids. Thereafter, we propose a feature extractor in conjunction with feature descriptors to extract a representation into a support vector multi-regressor and estimate the length and width of each bacterium. Using a real-world data corpus from Tanzania, the proposed method i) outperformed previous methods for bacterial detection with a 8% improvement (Dice coefficient) and ii) estimated the cell length and width with a root mean square error of less than 0.01%. Our network can be used to examine phenotypic characteristics of Mtb cells visualised by fluorescence microscopy, improving consistency and time efficiency of this procedure compared to manual methods.
MeSH term(s)	Humans ; Deep Learning ; Tuberculosis ; Mycobacterium tuberculosis ; Microscopy, Fluorescence ; Lipids ; Sensitivity and Specificity
Chemical Substances	Lipids
Language	English
Publishing date	2023-10-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2023.107573
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Article ; Online: A practical approach to render tuberculosis samples safe for application of tuberculosis molecular bacterial load assay in clinical settings without a biosafety level 3 laboratory.

Mtafya, Bariki / Qwaray, Paschal / John, Joseph / Sichone, Emanuel / Shoo, Alice / Gillespie, Stephen H / Ntinginya, Nyanda Elias / Sabiiti, Wilber

Tuberculosis (Edinburgh, Scotland)

2022 Volume 138, Page(s) 102275

Abstract: Background: Mycobacterium tuberculosis is a category B infectious pathogen requiring level-3-containment laboratories for handling. We assessed the efficacy of heat and Guanidine thiocyanate (GTC) to inactivate M. tuberculosis prior to performance of ... ...

Abstract	Background: Mycobacterium tuberculosis is a category B infectious pathogen requiring level-3-containment laboratories for handling. We assessed the efficacy of heat and Guanidine thiocyanate (GTC) to inactivate M. tuberculosis prior to performance of tuberculosis Molecular Bacterial Load Assay (TB-MBLA). Method: We performed in vitro experiments using M.tb, H37Rv reference strain and replicated in sputum specimens. A 0.5 MacFarland standard of M. tuberculosis was serially diluted to 1x10 Results: No M. tuberculosis growth was observed in MGIT for GTC or heat treated H37Rv cultures. All untreated H37Rv dilutions were MGIT positive except the most diluted specimens. Heat and GTC treatment of H37Rv reduced TB-MBLA load by 2.1log Conclusion: Heat or GTC renders M. tuberculosis non-viable and eliminates the need for BSL3 laboratory for performing TB-MBLA in routine healthcare settings.
MeSH term(s)	Humans ; Mycobacterium tuberculosis ; Bacterial Load ; Laboratories ; Containment of Biohazards ; Sensitivity and Specificity ; Tuberculosis/diagnosis ; Tuberculosis/microbiology ; Sputum/microbiology
Language	English
Publishing date	2022-11-15
Publishing country	Scotland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2046804-0
ISSN	1873-281X ; 1472-9792
ISSN (online)	1873-281X
ISSN	1472-9792
DOI	10.1016/j.tube.2022.102275
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Article: Systematic assessment of clinical and bacteriological markers for tuberculosis reveals discordance and inaccuracy of symptom-based diagnosis for treatment response monitoring.

Mtafya, Bariki / Sabi, Issa / John, Joseph / Sichone, Emanuel / Olomi, Wilyhelmina / Gillespie, Stephen H / Ntinginya, Nyanda E / Sabiiti, Wilber

Frontiers in medicine

2022 Volume 9, Page(s) 992451

Abstract: Background: Clinical symptoms are the benchmark of tuberculosis (TB) diagnosis and monitoring of treatment response but are not clear how they relate to TB bacteriology, particularly the novel tuberculosis-molecular bacterial load assay (TB-MBLA).: ... ...

Abstract	Background: Clinical symptoms are the benchmark of tuberculosis (TB) diagnosis and monitoring of treatment response but are not clear how they relate to TB bacteriology, particularly the novel tuberculosis-molecular bacterial load assay (TB-MBLA). Methods: Presumptive cases were bacteriologically confirmed for TB and assessed for symptoms and bacteriological resolution using smear microscopy (SM), culture, and TB-MBLA over 6-month treatment course. Kaplan-Meier and Kappa statistics were used to test the relationship between symptoms and bacteriological positivity. Results: A cohort of 46 bacteriologically confirmed TB cases were analyzed for treatment response over a 6-month treatment course. Pre-treatment symptoms and bacteriological positivity concurred in over 70% of the cases. This agreement was lost in over 50% of cases whose chest pain, night sweat, and loss of appetite had resolved by week 2 of treatment. Cough resolved at a 3.2% rate weekly and was 0.3% slower than the combined bacteriological (average of MGIT and TB-MBLA positivity) resolution rate, 3.5% per week. A decrease in TB-MBLA positivity reflected a fall in bacillary load, 5.7 ± 1.3- at baseline to 0.30 ± 1.0- log Conclusion: The probability of clinical symptoms reflecting bacteriological positivity weakens as the patient progresses on anti-TB therapy, making the symptom-based diagnosis a less reliable marker of treatment response.
Language	English
Publishing date	2022-10-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2022.992451
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Article ; Online: A systematic review of strategies adopted to scale up COVID-19 testing in low-, middle- and high-income countries.

Muttamba, Winters / O'Hare, Bernadette Ann-Marie / Saxena, Vibhor / Bbuye, Mudarshiru / Tyagi, Parul / Ramsay, Andrew / Kirenga, Bruce / Sabiiti, Wilber

BMJ open

2022 Volume 12, Issue 11, Page(s) e060838

Abstract: Objective: We undertook a systematic review of strategies adopted to scale up COVID-19 testing in countries across income levels to identify successful approaches and facilitate learning.: Methods: Scholarly articles in English from PubMed, Google ... ...

Abstract	Objective: We undertook a systematic review of strategies adopted to scale up COVID-19 testing in countries across income levels to identify successful approaches and facilitate learning. Methods: Scholarly articles in English from PubMed, Google scholar and Google search engine describing strategies used to increase COVID-19 testing in countries were reviewed. Deductive analysis to allocate relevant text from the reviewed publications/reports to the a priori themes was done. Main results: The review covered 32 countries, including 11 high-income, 2 upper-middle-income, 13 lower-middle-income and 6 low-income countries. Most low- and middle-income countries (LMICs) increased the number of laboratories available for testing and deployed sample collection and shipment to the available laboratories. The high-income countries (HICs) that is, South Korea, Germany, Singapore and USA developed molecular diagnostics with accompanying regulatory and legislative framework adjustments to ensure the rapid development and use of the tests. HICs like South Korea leveraged existing manufacturing systems to develop tests, while the LMICs leveraged existing national disease control programmes (HIV, tuberculosis, malaria) to increase testing. Continent-wide, African Centres for Disease Control and Prevention-led collaborations increased testing across most African countries through building capacity by providing testing kits and training. Conclusion: Strategies taken appear to reflect the existing systems or economies of scale that a particular country could leverage. LMICs, for example, drew on the infectious disease control programmes already in place to harness expertise and laboratory capacity for COVID-19 testing. There however might have been strategies adopted by other countries but were never published and thus did not appear anywhere in the searched databases.
MeSH term(s)	Humans ; Developed Countries ; Developing Countries ; COVID-19 Testing ; COVID-19/diagnosis ; Income
Language	English
Publishing date	2022-11-17
Publishing country	England
Document type	Systematic Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2599832-8
ISSN	2044-6055 ; 2044-6055
ISSN (online)	2044-6055
ISSN	2044-6055
DOI	10.1136/bmjopen-2022-060838
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Article ; Online: Treatment seeking and antibiotic use for urinary tract infection symptoms in the time of COVID-19 in Tanzania and Uganda.

Olamijuwon, Emmanuel / Keenan, Katherine / Mushi, Martha F / Kansiime, Catherine / Konje, Eveline T / Kesby, Mike / Neema, Stella / Asiimwe, Benon / Mshana, Stephen E / Fredricks, Kathryn J / Sunday, Benjamin / Bazira, Joel / Sandeman, Alison / Sloan, Derek J / Mwanga, Joseph R / Sabiiti, Wilber / Holden, Matthew Tg

Journal of global health

2024 Volume 14, Page(s) 5007

Abstract: Background: There is still little empirical evidence on how the outbreak of coronavirus disease 2019 (COVID-19) and associated regulations may have disrupted care-seeking for non-COVID-19 conditions or affected antibiotic behaviours in low- and middle- ... ...

Abstract	Background: There is still little empirical evidence on how the outbreak of coronavirus disease 2019 (COVID-19) and associated regulations may have disrupted care-seeking for non-COVID-19 conditions or affected antibiotic behaviours in low- and middle-income countries (LMICs). We aimed to investigate the differences in treatment-seeking behaviours and antibiotic use for urinary tract infection (UTI)-like symptoms before and during the pandemic at recruitment sites in two East African countries with different COVID-19 control policies: Mbarara, Uganda and Mwanza, Tanzania. Methods: In this repeated cross-sectional study, we used data from outpatients (pregnant adolescents aged >14 and adults aged >18) with UTI-like symptoms who visited health facilities in Mwanza, Tanzania and Mbarara, Uganda. We assessed the prevalence of self-reported behaviours (delays in care-seeking, providers visited, antibiotics taken) at three different time points, labelled as 'pre-COVID-19 phase' (February 2019 to February 2020), 'COVID-19 phase 1' (March 2020 to April 2020), and 'COVID-19 phase 2' (July 2021 to February 2022). Results: In both study sites, delays in care-seeking were less common during the pandemic than they were in the pre-COVID phase. Patients in Mwanza, Tanzania had shorter care-seeking pathways during the pandemic compared to before it, but this difference was not observed in Mbarara, Uganda. Health centres were the dominant sources of antibiotics in both settings. Over time, reported antibiotic use for UTI-like symptoms became more common in both settings. During the COVID-19 phases, there was a significant increase in self-reported use of antibiotics like metronidazole (<30% in the pre-COVID-19 phase to 40% in COVID phase 2) and doxycycline (30% in the pre-COVID-19 phase to 55% in COVID phase 2) that were not recommended for treating UTI-like symptoms in the National Treatment Guidelines in Mbarara, Uganda. Conclusions: There was no clear evidence that patients with UTI-like symptoms attending health care facilities had longer or more complex treatment pathways despite strict government-led interventions related to COVID-19. However, antibiotic use increased over time, including some antibiotics not recommended for treating UTI, which has implications for future antimicrobial resistance.
MeSH term(s)	Adult ; Pregnancy ; Female ; Adolescent ; Humans ; Anti-Bacterial Agents/therapeutic use ; Cross-Sectional Studies ; Uganda/epidemiology ; Tanzania/epidemiology ; COVID-19 ; Urinary Tract Infections/drug therapy ; Urinary Tract Infections/epidemiology ; Urinary Tract Infections/diagnosis
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-01-19
Publishing country	Scotland
Document type	Journal Article
ZDB-ID	2741629-X
ISSN	2047-2986 ; 2047-2986
ISSN (online)	2047-2986
ISSN	2047-2986
DOI	10.7189/jogh.14.05007
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Article ; Online: Global inequity of COVID-19 diagnostics: challenges and opportunities.

Narayanasamy, Shanti / Okware, Brenda / Muttamba, Winters / Patel, Kirtika / Duedu, Kwabena Obeng / Ravi, Nirmal / Ellermeier, Nathan / Shey, Muki / Woods, Christopher W / Sabiiti, Wilber

Journal of epidemiology and community health

2022

Language	English
Publishing date	2022-10-06
Publishing country	England
Document type	Journal Article
ZDB-ID	391868-3
ISSN	1470-2738 ; 0142-467X ; 0141-7681 ; 0143-005X
ISSN (online)	1470-2738
ISSN	0142-467X ; 0141-7681 ; 0143-005X
DOI	10.1136/jech-2022-219333
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