Journal Article > ResearchFull Text
Diagnostics (Basel). 31 January 2023; Volume 13 (Issue 3); 523.; DOI:10.3390/diagnostics13030523
Natale A, Oueslati S, Rochard A, Lopez-Baez D, Ombelet S, et al.
Diagnostics (Basel). 31 January 2023; 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 > ResearchFull Text
Diagnostics (Basel). 30 August 2022; Volume 12 (Issue 9); 2106.; DOI:10.3390/diagnostics12092106
Ronat JB, Oueslati S, Natale A, Kesteman T, Elamin W, et al.
Diagnostics (Basel). 30 August 2022; Volume 12 (Issue 9); 2106.; DOI:10.3390/diagnostics12092106
Easy and robust antimicrobial susceptibility testing (AST) methods are essential in clinical bacteriology laboratories (CBL) in low-resource settings (LRS). We evaluated the Beckman Coulter MicroScan lyophilized broth microdilution panel designed to support Médecins Sans Frontières (MSF) CBL activity in difficult settings, in particular with the Mini-Lab. We evaluated the custom-designed MSF MicroScan Gram-pos microplate (MICPOS1) for Staphylococcus and Enterococcus species, MSF MicroScan Gram-neg microplate (MICNEG1) for Gram-negative bacilli, and MSF MicroScan Fastidious microplate (MICFAST1) for Streptococci and Haemophilus species using 387 isolates from routine CBLs from LRS against the reference methods. Results showed that, for all selected antibiotics on the three panels, the proportion of the category agreement was above 90% and the proportion of major and very major errors was below 3%, as per ISO standards. The use of the Prompt inoculation system was found to increase the MIC and the major error rate for some antibiotics when testing Staphylococci. The readability of the manufacturer’s user manual was considered challenging for low-skilled staff. The inoculations and readings of the panels were estimated as easy to use. In conclusion, the three MSF MicroScan MIC panels performed well against clinical isolates from LRS and provided a convenient, robust, and standardized AST method for use in CBL in LRS.
Journal Article > ReviewFull Text
Lancet Infect Dis. 1 August 2018; 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. 1 August 2018; 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.
Journal Article > ReviewFull Text
Clin Microbiol Infect. 1 October 2021; Volume 27 (Issue 10); 1414-1421.; DOI:10.1016/j.cmi.2021.04.015
Ronat JB, Natale A, Kesteman T, Andremont A, Elamin W, et al.
Clin Microbiol Infect. 1 October 2021; Volume 27 (Issue 10); 1414-1421.; DOI:10.1016/j.cmi.2021.04.015
BACKGROUND
In low- and middle-income countries (LMICs), data related to antimicrobial resistance (AMR) are often inconsistently collected. Humanitarian, private and non-governmental medical organizations (NGOs), working with or in parallel to public medical systems, are sometimes present in these contexts. Yet, what is the role of NGOs in the fight against AMR, and how can they contribute to AMR data collection in contexts where reporting is scarce? How can context-adapted, high-quality clinical bacteriology be implemented in remote, challenging and underserved areas of the world?
OBJECTIVES
The aim was to provide an overview of AMR data collection challenges in LMICs and describe one initiative, the Mini-Lab project developed by Médecins Sans Frontières (MSF), that attempts to partially address them.
SOURCES
We conducted a literature review using PubMed and Google scholar databases to identify peer-reviewed research and grey literature from publicly available reports and websites.
CONTENT
We address the necessity of and difficulties related to obtaining AMR data in LMICs, as well as the role that actors outside of public medical systems can play in the collection of this information. We then describe how the Mini-Lab can provide simplified bacteriological diagnosis and AMR surveillance in challenging settings.
IMPLICATIONS
NGOs are responsible for a large amount of healthcare provision in some very low-resourced contexts. As a result, they also have a role in AMR control, including bacteriological diagnosis and the collection of AMR-related data. Actors outside the public medical system can actively contribute to implementing and adapting clinical bacteriology in LMICs and can help improve AMR surveillance and data collection.
In low- and middle-income countries (LMICs), data related to antimicrobial resistance (AMR) are often inconsistently collected. Humanitarian, private and non-governmental medical organizations (NGOs), working with or in parallel to public medical systems, are sometimes present in these contexts. Yet, what is the role of NGOs in the fight against AMR, and how can they contribute to AMR data collection in contexts where reporting is scarce? How can context-adapted, high-quality clinical bacteriology be implemented in remote, challenging and underserved areas of the world?
OBJECTIVES
The aim was to provide an overview of AMR data collection challenges in LMICs and describe one initiative, the Mini-Lab project developed by Médecins Sans Frontières (MSF), that attempts to partially address them.
SOURCES
We conducted a literature review using PubMed and Google scholar databases to identify peer-reviewed research and grey literature from publicly available reports and websites.
CONTENT
We address the necessity of and difficulties related to obtaining AMR data in LMICs, as well as the role that actors outside of public medical systems can play in the collection of this information. We then describe how the Mini-Lab can provide simplified bacteriological diagnosis and AMR surveillance in challenging settings.
IMPLICATIONS
NGOs are responsible for a large amount of healthcare provision in some very low-resourced contexts. As a result, they also have a role in AMR control, including bacteriological diagnosis and the collection of AMR-related data. Actors outside the public medical system can actively contribute to implementing and adapting clinical bacteriology in LMICs and can help improve AMR surveillance and data collection.
Protocol > Research Protocol
PLOS One. 25 April 2022; 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. 25 April 2022; 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. 13 December 2021; 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. 13 December 2021; 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 International 2019: Innovation. 8 May 2019
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 > ResearchFull Text
Nat Microbiol. 21 March 2016; Volume 1 (Issue 4); DOI:10.1038/nmicrobiol.2016.27
Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, et al.
Nat Microbiol. 21 March 2016; Volume 1 (Issue 4); DOI:10.1038/nmicrobiol.2016.27
Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.
Journal Article > CommentaryFull Text
Lancet Microbe. 1 June 2020; 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. 1 June 2020; Volume 1 (Issue 2); e56-e58.; DOI:10.1016/S2666-5247(20)30012-4
Journal Article > CommentaryFull Text
Lancet Infect Dis. 5 March 2018; 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. 5 March 2018; 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.