Journal Article > ResearchFull Text
PLOS Med. 2016 March 1; Volume 13 (Issue 3); DOI:10.1371/journal.pmed.1001967
Sissoko D, Laouenan C, Folkesson E, M’Lebing A, Beavogui A, et al.
PLOS Med. 2016 March 1; Volume 13 (Issue 3); DOI:10.1371/journal.pmed.1001967
Ebola virus disease (EVD) is a highly lethal condition for which no specific treatment has proven efficacy. In September 2014, while the Ebola outbreak was at its peak, the World Health Organization released a short list of drugs suitable for EVD research. Favipiravir, an antiviral developed for the treatment of severe influenza, was one of these. In late 2014, the conditions for starting a randomized Ebola trial were not fulfilled for two reasons. One was the perception that, given the high number of patients presenting simultaneously and the very high mortality rate of the disease, it was ethically unacceptable to allocate patients from within the same family or village to receive or not receive an experimental drug, using a randomization process impossible to understand by very sick patients. The other was that, in the context of rumors and distrust of Ebola treatment centers, using a randomized design at the outset might lead even more patients to refuse to seek care. Therefore, we chose to conduct a multicenter non-randomized trial, in which all patients would receive favipiravir along with standardized care. The objectives of the trial were to test the feasibility and acceptability of an emergency trial in the context of a large Ebola outbreak, and to collect data on the safety and effectiveness of favipiravir in reducing mortality and viral load in patients with EVD. The trial was not aimed at directly informing future guidelines on Ebola treatment but at quickly gathering standardized preliminary data to optimize the design of future studies.
Journal Article > ReviewFull Text
Lancet Infect Dis. 2018 August 1; Volume 18 (Issue 8); E248-E258.; DOI:10.1016/S1473-3099(18)30093-8
Ombelet S, Ronat JB, Walsh T, Yansouni CP, Cox J, et al.
Lancet Infect Dis. 2018 August 1; Volume 18 (Issue 8); E248-E258.; DOI:10.1016/S1473-3099(18)30093-8
Low-resource settings are disproportionately burdened by infectious diseases and antimicrobial resistance. Good quality clinical bacteriology through a well functioning reference laboratory network is necessary for effective resistance control, but low-resource settings face infrastructural, technical, and behavioural challenges in the implementation of clinical bacteriology. In this Personal View, we explore what constitutes successful implementation of clinical bacteriology in low-resource settings and describe a framework for implementation that is suitable for general referral hospitals in low-income and middle-income countries with a moderate infrastructure. Most microbiological techniques and equipment are not developed for the specific needs of such settings. Pending the arrival of a new generation diagnostics for these settings, we suggest focus on improving, adapting, and implementing conventional, culture-based techniques. Priorities in low-resource settings include harmonised, quality assured, and tropicalised equipment, consumables, and techniques, and rationalised bacterial identification and testing for antimicrobial resistance. Diagnostics should be integrated into clinical care and patient management; clinically relevant specimens must be appropriately selected and prioritised. Open-access training materials and information management tools should be developed. Also important is the need for onsite validation and field adoption of diagnostics in low-resource settings, with considerable shortening of the time between development and implementation of diagnostics. We argue that the implementation of clinical bacteriology in low-resource settings improves patient management, provides valuable surveillance for local antibiotic treatment guidelines and national policies, and supports containment of antimicrobial resistance and the prevention and control of hospital-acquired infections.
Protocol > Research Study
PLOS One. 2022 April 25; Volume 17 (Issue 4); e0267491.; DOI:10.1371/journal.pone.0267491
Ombelet S, Natale A, Ronat JB, Vandenberg O, Jacobs J, et al.
PLOS One. 2022 April 25; Volume 17 (Issue 4); e0267491.; DOI:10.1371/journal.pone.0267491
Use of equipment-free, “manual” blood cultures is still widespread in low-resource settings, as requirements for implementation of automated systems are often not met. Quality of manual blood culture bottles currently on the market, however, is usually unknown. An acceptable quality in terms of yield and speed of growth can be ensured by evaluating the bottles using simulated blood cultures. In these experiments, bottles from different systems are inoculated in parallel with blood and a known quantity of bacteria. Based on literature review and personal experiences, we propose a short and practical protocol for an efficient evaluation of manual blood culture bottles, aimed at research or reference laboratories in low-resource settings. Recommendations include: (1) practical equivalence of horse blood and human blood; (2) a diverse selection of 10 to 20 micro-organisms to be tested (both slow- and fast-growing reference organisms); (3) evaluation of both adult and pediatric bottle formulations and blood volumes; (4) a minimum sample size of 120 bottles per bottle type; (5) a formal assessment of usability. Different testing scenarios for increasing levels of reliability are provided, along with practical tools such as worksheets and surveys that can be used by laboratories wishing to evaluate manual blood culture bottles.
Journal Article > ResearchFull Text
Biphasic versus monophasic manual blood culture bottles for low-resource settings: an in-vitro study
Lancet Microbe. 2021 December 13; Volume S2666-5247 (Issue 21); 00241-X.; DOI:10.1016/S2666-5247(21)00241-X
Ombelet S, Natale A, Ronat JB, Kesteman T, Vandenberg O, et al.
Lancet Microbe. 2021 December 13; Volume S2666-5247 (Issue 21); 00241-X.; DOI:10.1016/S2666-5247(21)00241-X
BACKGROUND
Manual blood culture bottles (BCBs) are frequently used in low-resource settings. There are few BCB performance evaluations, especially evaluations comparing them with automated systems. We evaluated two manual BCBs (Bi-State BCB and BacT/ALERT BCB) and compared their yield and time to growth detection with those of automated BacT/ALERT system.
METHODS
BCBs were spiked in triplicate with 177 clinical isolates representing pathogens common in low-resource settings (19 bacterial and one yeast species) in adult and paediatric volumes, resulting in 1056 spiked BCBs per BCB system. Growth in manual BCBs was evaluated daily by visually inspecting the broth, agar slant, and, for BacT/ALERT BCB, colour change of the growth indicator. The primary outcomes were BCB yield (proportion of spiked BCB showing growth) and time to detection (proportion of positive BCB with growth detected on day 1 of incubation). 95% CI for yield and growth on day 1 were calculated using bootstrap method for clustered data using. Secondary outcomes were time to colony for all BCBs (defined as number of days between incubation and colony growth sufficient to use for further testing) and difference between time to detection in broth and on agar slant for the Bi-State BCBs.
FINDINGS
Overall yield was 95·9% (95% CI 93·9–98·0) for Bi-State BCB and 95·5% (93·3–97·8) for manual BacT/ALERT, versus 96·1% (94·0–98·1) for the automated BacT/ALERT system (p=0·61). Day 1 growth was present in 920 (90·8%) of 1013 positive Bi-State BCB and 757 (75·0%) of 1009 positive manual BacT/ALERT BCB, versus 1008 (99·3%) of 1015 automated bottles. On day 2, detection rates were 100% for BI-State BCB, 97·7% for manual BacT/ALERT BCB, and 100% for automated bottles. For Bi-State BCB, growth mostly occurred simultaneously in broth and slant (81·7%). Sufficient colony growth on the slant to perform further tests was present in only 44·1% of biphasic bottles on day 2 and 59·0% on day 3.
INTERPRETATION
The yield of manual BCB was comparable with the automated system, suggesting that manual blood culture systems are an acceptable alternative to automated systems in low-resource settings. Bi-State BCB outperformed manual BacT/ALERT bottles, but the agar slant did not allow earlier detection nor earlier colony growth. Time to detection for manual blood culture systems still lags that of automated systems, and research into innovative and affordable methods of growth detection in manual BCBs is encouraged.
Manual blood culture bottles (BCBs) are frequently used in low-resource settings. There are few BCB performance evaluations, especially evaluations comparing them with automated systems. We evaluated two manual BCBs (Bi-State BCB and BacT/ALERT BCB) and compared their yield and time to growth detection with those of automated BacT/ALERT system.
METHODS
BCBs were spiked in triplicate with 177 clinical isolates representing pathogens common in low-resource settings (19 bacterial and one yeast species) in adult and paediatric volumes, resulting in 1056 spiked BCBs per BCB system. Growth in manual BCBs was evaluated daily by visually inspecting the broth, agar slant, and, for BacT/ALERT BCB, colour change of the growth indicator. The primary outcomes were BCB yield (proportion of spiked BCB showing growth) and time to detection (proportion of positive BCB with growth detected on day 1 of incubation). 95% CI for yield and growth on day 1 were calculated using bootstrap method for clustered data using. Secondary outcomes were time to colony for all BCBs (defined as number of days between incubation and colony growth sufficient to use for further testing) and difference between time to detection in broth and on agar slant for the Bi-State BCBs.
FINDINGS
Overall yield was 95·9% (95% CI 93·9–98·0) for Bi-State BCB and 95·5% (93·3–97·8) for manual BacT/ALERT, versus 96·1% (94·0–98·1) for the automated BacT/ALERT system (p=0·61). Day 1 growth was present in 920 (90·8%) of 1013 positive Bi-State BCB and 757 (75·0%) of 1009 positive manual BacT/ALERT BCB, versus 1008 (99·3%) of 1015 automated bottles. On day 2, detection rates were 100% for BI-State BCB, 97·7% for manual BacT/ALERT BCB, and 100% for automated bottles. For Bi-State BCB, growth mostly occurred simultaneously in broth and slant (81·7%). Sufficient colony growth on the slant to perform further tests was present in only 44·1% of biphasic bottles on day 2 and 59·0% on day 3.
INTERPRETATION
The yield of manual BCB was comparable with the automated system, suggesting that manual blood culture systems are an acceptable alternative to automated systems in low-resource settings. Bi-State BCB outperformed manual BacT/ALERT bottles, but the agar slant did not allow earlier detection nor earlier colony growth. Time to detection for manual blood culture systems still lags that of automated systems, and research into innovative and affordable methods of growth detection in manual BCBs is encouraged.
Conference Material > Abstract
Ronat JB, Natale A, Rochard A, Boillot B, Hubert J, et al.
MSF Scientific Days UK 2019: Innovation. 2019 May 8
INTRODUCTION
Within MSF projects, many patients we treat have invasive bacterial infections, often in settings with increasing levels of antimicrobial resistance. However these projects frequently lack laboratory capacity to diagnose such pathogens, which complicates appropriate patient care. Since next-generation diagnostics adapted to low-resource settings (LRS) are unlikely to become available within the next five to ten years, MSF is currently working to rapidly develop a stand- alone, transportable laboratory, the “Mini-Lab”, which uses existing diagnostics and antibiotic susceptibility testing (AST) of bloodstream infections, and adapts these to LRS. We describe the testing process for a prototype of the Mini-Lab, early results and lessons learned.
METHODS
Development of the Mini-Lab involved a user-centered, iterative process with a mixed group of experts (ergonomists, designers, pedagogy specialists, and microbiologists) to develop technical requirements, calls for tenders, product selection, component development, and materials testing. In Jan 2019, we assembled all components (including tests, equipment, benches) into a full working prototype, installed at Laboratoire Hospitalo-Universitaire, Brussels. Individual test components are undergoing validation in European reference laboratories for diagnostic accuracy. We are assessing ergonomics, appropriateness and user-friendliness of the setup, diagnostic testing, and user guidance tools. Methods used include simulation of routine laboratory work, with non-microbiology students carrying out sample processing and test procedures, with simulated samples of known bacteria, and with evaluator observation and user questionnaires to collect feedback. 135 evaluator observations and 14 questionnaires were done.
ETHICS
This innovation project did not involve human participants or their data; the MSF Ethics Framework for Innovation was used to help identify and mitigate potential harms.
RESULTS
The assembled prototype consists of six foldable, sturdy transport boxes (~120kg each), transformable into standalone laboratory benches (80x120cm, adjustable working height, embedded power connections and light sources). It also includes all necessary laboratory materials, including 29 reagents and tests, with an average shelf-life of 18 months, and only eight requiring a cold chain. Pictograms posted on the modules guide users through the diagnostic workflow. An assessment of the prototype's user friendliness, carried out from 28 Jan 2019 to 14 Feb 2019) has already provided valuable information on optimizing Mini-Lab assembly and workflow management. This included feedback on the placement of materials, adaptation of light sources for users’ visual comfort, addition of new consumables, and workflow refinement.
CONCLUSION
The development of the Mini-Lab has now reached the testing phase of a prototype including all components. Test users have responded positively with regard to ergonomics of the bench and modules, tests, and pictogram-based guidance, while module weight has emerged as a constraint. By identifying needed improvements early, these results will provide critical information for our iterative design process. All feasible, useful improvements will be made before the first Mini-Lab field evaluation, which is planned at an MSF-supported burn centre in Haiti, beginning in May 2019.
CONFLICTS OF INTEREST
None declared.
Within MSF projects, many patients we treat have invasive bacterial infections, often in settings with increasing levels of antimicrobial resistance. However these projects frequently lack laboratory capacity to diagnose such pathogens, which complicates appropriate patient care. Since next-generation diagnostics adapted to low-resource settings (LRS) are unlikely to become available within the next five to ten years, MSF is currently working to rapidly develop a stand- alone, transportable laboratory, the “Mini-Lab”, which uses existing diagnostics and antibiotic susceptibility testing (AST) of bloodstream infections, and adapts these to LRS. We describe the testing process for a prototype of the Mini-Lab, early results and lessons learned.
METHODS
Development of the Mini-Lab involved a user-centered, iterative process with a mixed group of experts (ergonomists, designers, pedagogy specialists, and microbiologists) to develop technical requirements, calls for tenders, product selection, component development, and materials testing. In Jan 2019, we assembled all components (including tests, equipment, benches) into a full working prototype, installed at Laboratoire Hospitalo-Universitaire, Brussels. Individual test components are undergoing validation in European reference laboratories for diagnostic accuracy. We are assessing ergonomics, appropriateness and user-friendliness of the setup, diagnostic testing, and user guidance tools. Methods used include simulation of routine laboratory work, with non-microbiology students carrying out sample processing and test procedures, with simulated samples of known bacteria, and with evaluator observation and user questionnaires to collect feedback. 135 evaluator observations and 14 questionnaires were done.
ETHICS
This innovation project did not involve human participants or their data; the MSF Ethics Framework for Innovation was used to help identify and mitigate potential harms.
RESULTS
The assembled prototype consists of six foldable, sturdy transport boxes (~120kg each), transformable into standalone laboratory benches (80x120cm, adjustable working height, embedded power connections and light sources). It also includes all necessary laboratory materials, including 29 reagents and tests, with an average shelf-life of 18 months, and only eight requiring a cold chain. Pictograms posted on the modules guide users through the diagnostic workflow. An assessment of the prototype's user friendliness, carried out from 28 Jan 2019 to 14 Feb 2019) has already provided valuable information on optimizing Mini-Lab assembly and workflow management. This included feedback on the placement of materials, adaptation of light sources for users’ visual comfort, addition of new consumables, and workflow refinement.
CONCLUSION
The development of the Mini-Lab has now reached the testing phase of a prototype including all components. Test users have responded positively with regard to ergonomics of the bench and modules, tests, and pictogram-based guidance, while module weight has emerged as a constraint. By identifying needed improvements early, these results will provide critical information for our iterative design process. All feasible, useful improvements will be made before the first Mini-Lab field evaluation, which is planned at an MSF-supported burn centre in Haiti, beginning in May 2019.
CONFLICTS OF INTEREST
None declared.
Journal Article > CommentaryFull Text
Lancet Microbe. 2020 June 1; Volume 1 (Issue 2); e56-e58.; DOI:10.1016/S2666-5247(20)30012-4
Natale A, Ronat JB, Mazoyer A, Rochard A, Boillot B, et al.
Lancet Microbe. 2020 June 1; Volume 1 (Issue 2); e56-e58.; DOI:10.1016/S2666-5247(20)30012-4
Journal Article > ReviewFull Text
Front Med (Lausanne). 2019 June 18; Volume 6; 131.; DOI:10.3389/fmed.2019.00131
Ombelet S, Barbe B, Affolabi D, Ronat JB, Lompo P, et al.
Front Med (Lausanne). 2019 June 18; Volume 6; 131.; DOI:10.3389/fmed.2019.00131
Bloodstream infections (BSI) have a substantial impact on morbidity and mortality worldwide. Despite scarcity of data from many low- and middle-income countries (LMICs), there is increasing awareness of the importance of BSI in these countries. For example, it is estimated that the global mortality of non-typhoidal Salmonella bloodstream infection in children under 5 already exceeds that of malaria. Reliable and accurate diagnosis of these infections is therefore of utmost importance. Blood cultures are the reference method for diagnosis of BSI. LMICs face many challenges when implementing blood cultures, due to financial, logistical, and infrastructure-related constraints. This review aims to provide an overview of the state-of-the-art of sampling and processing of blood cultures, with emphasis on its use in LMICs. Laboratory processing of blood cultures is relatively straightforward and can be done without the need for expensive and complicated equipment. Automates for incubation and growth monitoring have become the standard in high-income countries (HICs), but they are still too expensive and not sufficiently robust for imminent implementation in most LMICs. Therefore, this review focuses on "manual" methods of blood culture, not involving automated equipment. In manual blood cultures, a bottle consisting of a broth medium supporting bacterial growth is incubated in a normal incubator and inspected daily for signs of growth. The collection of blood for blood culture is a crucial step in the process, as the sensitivity of blood cultures depends on the volume sampled; furthermore, contamination of the blood culture (accidental inoculation of environmental and skin bacteria) can be avoided by appropriate antisepsis. In this review, we give recommendations regarding appropriate blood culture sampling and processing in LMICs. We present feasible methods to detect and speed up growth and discuss some challenges in implementing blood cultures in LMICs, such as the biosafety aspects, supply chain and waste management.
Journal Article > ResearchFull Text
Diagnostics (Basel). 2023 January 31; Volume 13 (Issue 3); 523.; DOI:10.3390/diagnostics13030523
Natale A, Oueslati S, Rochard A, Lopez-Baez D, Ombelet S, et al.
Diagnostics (Basel). 2023 January 31; Volume 13 (Issue 3); 523.; DOI:10.3390/diagnostics13030523
Culture media is fundamental in clinical bacteriology for the detection and isolation of bacterial pathogens. However, in-house media preparation could be challenging in low-resource settings. InTray® cassettes (Biomed Diagnostics) could be a valid alternative as they are compact, ready-to-use media preparations. In this study, we evaluate the use of two InTray media as a subculture alternative for the diagnosis of bloodstream infections: the InTray® Müller-Hinton (MH) chocolate and the InTray® Colorex™ Screen. The InTray MH chocolate was evaluated in 2 steps: firstly, using simulated positive blood cultures (reference evaluation study), and secondly, using positive blood cultures from a routine clinical laboratory (clinical evaluation study). The Colorex Screen was tested using simulated poly-microbial blood cultures. The sensitivity and specificity of the InTray MH chocolate were respectively 99.2% and 90% in the reference evaluation study and 97.1% and 88.2% in the clinical evaluation study. The time to detection (TTD) was ≤20 h in most positive blood cultures (99.8% and 97% in the two studies, respectively). The InTray® MH Chocolate agar showed good performance when used directly from clinical blood cultures for single bacterial infections. However, mixed flora is more challenging to interpret on this media than on Colorex™ Screen, even for an experienced microbiologist.
Journal Article > CommentaryFull Text
Lancet Infect Dis. 2018 March 5; Volume 18 (Issue 8); e248-e258.; DOI:10.1016/S1473-3099(18)30093-8
Ombelet S, Ronat JB, Walsh T, Yansouni CP, Cox J, et al.
Lancet Infect Dis. 2018 March 5; Volume 18 (Issue 8); e248-e258.; DOI:10.1016/S1473-3099(18)30093-8
Low-resource settings are disproportionately burdened by infectious diseases and antimicrobial resistance. Good quality clinical bacteriology through a well functioning reference laboratory network is necessary for effective resistance control, but low-resource settings face infrastructural, technical, and behavioural challenges in the implementation of clinical bacteriology. In this Personal View, we explore what constitutes successful implementation of clinical bacteriology in low-resource settings and describe a framework for implementation that is suitable for general referral hospitals in low-income and middle-income countries with a moderate infrastructure. Most microbiological techniques and equipment are not developed for the specific needs of such settings. Pending the arrival of a new generation diagnostics for these settings, we suggest focus on improving, adapting, and implementing conventional, culture-based techniques. Priorities in low-resource settings include harmonised, quality assured, and tropicalised equipment, consumables, and techniques, and rationalised bacterial identification and testing for antimicrobial resistance. Diagnostics should be integrated into clinical care and patient management; clinically relevant specimens must be appropriately selected and prioritised. Open-access training materials and information management tools should be developed. Also important is the need for onsite validation and field adoption of diagnostics in low-resource settings, with considerable shortening of the time between development and implementation of diagnostics. We argue that the implementation of clinical bacteriology in low-resource settings improves patient management, provides valuable surveillance for local antibiotic treatment guidelines and national policies, and supports containment of antimicrobial resistance and the prevention and control of hospital-acquired infections.
Conference Material > Slide Presentation
Ronat JB, Natale A, Rochard A, Boillot B, Hubert J, et al.
MSF Scientific Days UK 2019: Innovation. 2019 May 8; DOI:10.7490/f1000research.1116735.1