Conference Material > Poster
Mun L, Gomez D, Sitali N, Rajabzoda A, Azamova S, et al.
MSF Scientific Days International 2022. 2022 May 9; DOI:10.57740/x1vy-hx80
Journal Article > ResearchAbstract Only
Trop Med Int Health. 2021 January 6; Volume 26 (Issue 4); 421-427.; DOI:10.1111/tmi.13543
Gil H, Margaryan H, Azamat I, Ziba B, Bayram H, et al.
Trop Med Int Health. 2021 January 6; Volume 26 (Issue 4); 421-427.; DOI:10.1111/tmi.13543
OBJECTIVES
In this retrospective study, we evaluated the diagnostic accuracy of molecular tests (MT) for the detection of DR‐TB, compared to the gold standard liquid‐based Drug Susceptibility Testing (DST) in Karakalpakstan.
METHODS
A total of 6,670 specimens received in the Republican TB No 1 Hospital Laboratory of Karakalpakstan between January and July 2017 from new and retreatment patients were analyzed. Samples were tested using Xpert MTB/RIF and line probe assays (LPA) for the detection of mutations associated with resistance. The sensitivity and specificity of MTs were calculated relative to results based on DST.
RESULTS
The accuracy of MT for detection of rifampicin resistance was high, with sensitivity and specificity over 98%. However, we observed reduced sensitivity of LPA for detection of resistance; 86% for isoniazid (95%CI 82‐90%), 86% for fluoroquinolones (95%CI 68‐96%), 70% for capreomycin (95%CI 46‐88%) and 23% for kanamycin (95%CI 13‐35%).
CONCLUSIONS
We show that MTs are a useful tool for rapid and safe diagnosis of DR‐TB, however, clinicians should be aware of their limitations. Although detection of rifampicin resistance was highly accurate, our data suggests that resistance mutations circulating in the Republic of Karakalpakstan for other drugs were not detected by the methods used here. This merits further investigation.
In this retrospective study, we evaluated the diagnostic accuracy of molecular tests (MT) for the detection of DR‐TB, compared to the gold standard liquid‐based Drug Susceptibility Testing (DST) in Karakalpakstan.
METHODS
A total of 6,670 specimens received in the Republican TB No 1 Hospital Laboratory of Karakalpakstan between January and July 2017 from new and retreatment patients were analyzed. Samples were tested using Xpert MTB/RIF and line probe assays (LPA) for the detection of mutations associated with resistance. The sensitivity and specificity of MTs were calculated relative to results based on DST.
RESULTS
The accuracy of MT for detection of rifampicin resistance was high, with sensitivity and specificity over 98%. However, we observed reduced sensitivity of LPA for detection of resistance; 86% for isoniazid (95%CI 82‐90%), 86% for fluoroquinolones (95%CI 68‐96%), 70% for capreomycin (95%CI 46‐88%) and 23% for kanamycin (95%CI 13‐35%).
CONCLUSIONS
We show that MTs are a useful tool for rapid and safe diagnosis of DR‐TB, however, clinicians should be aware of their limitations. Although detection of rifampicin resistance was highly accurate, our data suggests that resistance mutations circulating in the Republic of Karakalpakstan for other drugs were not detected by the methods used here. This merits further investigation.
Journal Article > Case Report/SeriesFull Text
Oxf Med Case Reports. 2023 July 18; Volume 2023 (Issue 7); omad071.; DOI:10.1093/omcr/omad071
Olubiyo R, Chukwumeze F, Lawal AM, Oloruntuyi G, Musoka H, et al.
Oxf Med Case Reports. 2023 July 18; Volume 2023 (Issue 7); omad071.; DOI:10.1093/omcr/omad071
Yeast-related bloodstream infections (BSIs) in pediatric patients are associated with severe acute malnutrition (SAM), hematological/oncological malignancies and admission to an intensive care unit. These infections are rarely described from low- and middle-income countries. We describe a case series of pediatric patients diagnosed with severe sepsis and yeast isolated from their blood culture in a conflict-affected area of Nigeria from October 2018 to November 2021. We identified 20 patients with yeast BSIs, among whom 17 were also diagnosed with SAM. We recommend the inclusion of antifungal treatment for empiric treatment guidelines for children with SAM and severe sepsis in similar settings.
Journal Article > ResearchFull Text
Water Practice and Technology. 2024 March 29; DOI:10.2166/wpt.2024.074
Caballero A, Garcia M, Pérez-Sabino F, Lickes S, Guzmán-Quilo C, et al.
Water Practice and Technology. 2024 March 29; DOI:10.2166/wpt.2024.074
There is a need for access to clean potable water worldwide. However, almost every source of surface water in Guatemala is contaminated. This study assesses the potential exposure to water contaminants in proximity to Medecins Sans Frontieres's (MSF) chronic kidney disease clinic population in La Gomera, Guatemala during wet and dry seasons. Five municipal wells and four artisanal wells (servicing approximately 18.9% of La Gomera) were selected for their proximity to MSF La Gomera clinic to determine the presence of coliforms, physicochemical parameters, heavy metals, and pesticide residues. Water samples were collected over 3 consecutive days during La Gomera's wet season and again during the dry season. Wet season 2022: Total coliforms and Escherichia coli exceeded the acceptable limits for several artisanal wells but were not detected in municipal wells. Mercury and arsenic were detected in all wells during at least one sampling period. Dry season 2023: Total coliforms exceeded the acceptable limits for all wells and E. coli was detected in all four artisanal wells. Lead and arsenic were detected in all wells. Our results suggest that water from artisanal wells does not meet COGUANOR or WHO microbiological criteria for human consumption.
Journal Article > ResearchFull Text
PLOS One. 2020 August 21; Volume 15 (Issue 8); e0237787.; DOI:10.1371/journal.pone.0237787
Mesic A, Khan WH, Lenglet AD, Lynen L, Ishaq S, et al.
PLOS One. 2020 August 21; Volume 15 (Issue 8); e0237787.; DOI:10.1371/journal.pone.0237787
INTRODUCTION
Afghanistan is affected by one of the world's longest protracted armed conflicts, frequent natural disasters, disease outbreaks and large population movements and it suffers from a high burden of tuberculosis (TB), including rifampicin-resistant TB (RR-TB). The study shows Médecins Sans Frontières' experiences with care for patients with RR-TB in Kandahar Province. We describe the uptake of RR-TB treatment, how World Health Organisation criteria for the choice between the short and an individualized regimen were implemented, and treatment outcomes.
METHODS
This is a retrospective cohort analysis of routinely collected data from RR-TB patients enrolled in care from 2016 until 2019. Descriptive analysis was performed to present characteristics of patients and treatment outcomes. Multivariable Cox analysis was performed to identify risk factors for having an unfavourable treatment outcome.
RESULTS
Out of 146 enrolled RR-TB patients, 112 (76.7%) started treatment: 41 (36.6%) and 71 (63.4%) with the short and individualized treatment regimen, respectively. Of 82 with results for fluoroquinolone susceptibility, 39 (47.6%) had fluoroquinolone-resistant TB. Seven patients with initially fluoroquinolone-resistant TB and three pregnant women started the short regimen and 18 patients eligible for the short regimen started the injectable-free individualized regimen. Overall, six-month smear and culture conversion were 98.7% and 97.1%, respectively; treatment success was 70.1%. Known initial fluoroquinolone resistance (aHR 3.77, 95%CI:1.53-9.27) but not choice of regimen predicted having an unfavourable outcome.
CONCLUSION
Even though criteria for the choice of treatment regimen were not applied strictly, we have achieved acceptable outcomes in this cohort. To expand RR-TB care, treatment regimens should fit provision at primary health care level and take patient preferences into account.
Afghanistan is affected by one of the world's longest protracted armed conflicts, frequent natural disasters, disease outbreaks and large population movements and it suffers from a high burden of tuberculosis (TB), including rifampicin-resistant TB (RR-TB). The study shows Médecins Sans Frontières' experiences with care for patients with RR-TB in Kandahar Province. We describe the uptake of RR-TB treatment, how World Health Organisation criteria for the choice between the short and an individualized regimen were implemented, and treatment outcomes.
METHODS
This is a retrospective cohort analysis of routinely collected data from RR-TB patients enrolled in care from 2016 until 2019. Descriptive analysis was performed to present characteristics of patients and treatment outcomes. Multivariable Cox analysis was performed to identify risk factors for having an unfavourable treatment outcome.
RESULTS
Out of 146 enrolled RR-TB patients, 112 (76.7%) started treatment: 41 (36.6%) and 71 (63.4%) with the short and individualized treatment regimen, respectively. Of 82 with results for fluoroquinolone susceptibility, 39 (47.6%) had fluoroquinolone-resistant TB. Seven patients with initially fluoroquinolone-resistant TB and three pregnant women started the short regimen and 18 patients eligible for the short regimen started the injectable-free individualized regimen. Overall, six-month smear and culture conversion were 98.7% and 97.1%, respectively; treatment success was 70.1%. Known initial fluoroquinolone resistance (aHR 3.77, 95%CI:1.53-9.27) but not choice of regimen predicted having an unfavourable outcome.
CONCLUSION
Even though criteria for the choice of treatment regimen were not applied strictly, we have achieved acceptable outcomes in this cohort. To expand RR-TB care, treatment regimens should fit provision at primary health care level and take patient preferences into account.
Journal Article > ResearchFull Text
Sci Rep. 2021 October 21; Volume 11 (Issue 1); 20814.; DOI:10.1038/s41598-021-00149-1
Chukwumeze F, Lenglet AD, Olubiyo R, Lawal AM, Oluyide B, et al.
Sci Rep. 2021 October 21; Volume 11 (Issue 1); 20814.; DOI:10.1038/s41598-021-00149-1
Pediatric community-acquired bloodstream infections (CA-BSIs) in sub Saharan African humanitarian contexts are rarely documented. Effective treatment of these infections is additionally complicated by increasing rates of antimicrobial resistance. We describe the findings from epidemiological and microbiological surveillance implemented in pediatric patients with suspected CA-BSIs presenting for care at a secondary hospital in the conflict affected area of Zamfara state, Nigeria. Any child (> 2 months of age) presenting to Anka General Hospital from November 2018 to August 2020 with clinical severe sepsis at admission had clinical and epidemiological information and a blood culture collected at admission. Bacterial isolates were tested for antibiotic susceptibility. We calculated frequencies of epidemiological, microbiological and clinical parameters. We explored risk factors for death amongst severe sepsis cases using univariable and multivariable Poisson regression, adjusting for time between admission and hospital exit. We included 234 severe sepsis patients with 195 blood culture results. There were 39 positive blood cultures. Of the bacterial isolates, 14 were Gram positive and 18 were Gram negative; 5 were resistant to empiric antibiotics: methicillin-resistant Staphylococcus aureus (MRSA; n = 2) and Extended Spectrum Beta-Lactamase positive enterobacterales (n = 3). We identified no significant association between sex, age-group, ward, CA-BSI, appropriate intravenous antibiotic, malaria positivity at admission, suspected focus of sepsis, clinical severity and death in the multivariable regression. There is an urgent need for access to good clinical microbiological services, including point of care methods, and awareness and practice around rational antibiotic in healthcare staff in humanitarian settings to reduce morbidity and mortality from sepsis in children.
Conference Material > Poster
Philip RR, Chukwumeze F, Lawal AM, Oloruntuyi G, Musoka H, et al.
MSF Paediatric Days 2022. 2022 November 30; DOI:10.57740/s90v-q391
Journal Article > ResearchFull Text
Microbiol Spectr. 2023 January 9; Volume 11 (Issue 1); DOI:10.1128/spectrum.03698-22
Rekart ML, Mun L, Aung A, Gomez D, Mulanda WK, et al.
Microbiol Spectr. 2023 January 9; Volume 11 (Issue 1); DOI:10.1128/spectrum.03698-22
We report the findings of a prospective laboratory diagnostic accuracy study to evaluate the sensitivity, specificity, and predictive values of the Xpert MTB/RIF Ultra assay for Mycobacterium tuberculosis detection in fresh stool specimens from children under 15?years of age with confirmed tuberculosis (TB) disease from Dushanbe, Tajikistan. Six hundred eighty-eight (688) participants were enrolled from April 2019 to October 2021. We identified 16 participants (2.3%) with confirmed TB disease, defined as =1 TB sign/symptom plus microbiologic confirmation. With the Xpert MTB/RIF Ultra assay for stool, we found a sensitivity of 68.8% (95% CI, 46.0 to 91.5) and a specificity of 98.7% (95% CI, 97.8 to 99.5) in confirmed TB disease. Our results are comparable to other published studies; however, our cohort was larger and our confirmed TB disease rate lower than most. We also demonstrated that this assay was feasible to implement in a centralized hospital laboratory in a low-middle-income Central Asian country. However, we encountered obstacles such as lack of staffing, material ruptures, outdated government protocols, and decreased case presentation due to COVID-19. We found eight patients whose only positive test was an Xpert Ultra stool assay. None needed treatment during the study; however, three were treated later, suggesting such cases require close observation. Our report is the first from Central Asia and one of a few from a low-middle-income country. We believe our study demonstrates the generalizability of the Xpert MTB/RIF Ultra assay on fresh stool specimens from children and provides further evidence supporting WHO’s approval of this diagnostic strategy.
IMPORTANCE
The importance of this report is that it provides further support for WHO’s recent recommendation that fresh stool is an acceptable sample for GeneXpert TB testing in children, especially small children who often cannot produce an adequate sputum sample. Diagnosing TB in this age group is difficult, and many cases are missed, leading to unacceptable rates of TB illness and death. In our large cohort of children from Dushanbe, Tajikistan, the GeneXpert stool test was positive in 69% of proven cases of TB, and there were very few false-positive tests. We also showed that this diagnostic strategy was feasible to implement in a low-middle-income country with an inefficient health care delivery system. We hope that many more programs will adopt this form of diagnosing TB in children.
IMPORTANCE
The importance of this report is that it provides further support for WHO’s recent recommendation that fresh stool is an acceptable sample for GeneXpert TB testing in children, especially small children who often cannot produce an adequate sputum sample. Diagnosing TB in this age group is difficult, and many cases are missed, leading to unacceptable rates of TB illness and death. In our large cohort of children from Dushanbe, Tajikistan, the GeneXpert stool test was positive in 69% of proven cases of TB, and there were very few false-positive tests. We also showed that this diagnostic strategy was feasible to implement in a low-middle-income country with an inefficient health care delivery system. We hope that many more programs will adopt this form of diagnosing TB in children.