Journal Article > ResearchFull Text
PLOS One. 2014 August 11; Volume 9 (Issue 8); DOI:10.1371/journal.pone.0101017
Ronat JB, Kakol J, Khoury M, Yun O, Brown V, et al.
PLOS One. 2014 August 11; Volume 9 (Issue 8); DOI:10.1371/journal.pone.0101017
In low- and middle-income countries, bloodstream infections are an important cause of mortality in patients with burns. Increasingly implicated in burn-associated infections are highly drug-resistant pathogens with limited treatment options. We describe the epidemiology of bloodstream infections in patients with burns in a humanitarian surgery project in Iraq.
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.
Journal Article > ReviewFull Text
Clin Microbiol Infect. 2021 October 1; 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. 2021 October 1; 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.
Journal Article > ReviewFull Text
Clin Microbiol Infect. 2021 May 18; Volume 27 (Issue 10); 1400-1408.; DOI: 10.1016/j.cmi.2021.05.016
Orekan J, Barbe B, Oeng S, Ronat JB, Letchford J, et al.
Clin Microbiol Infect. 2021 May 18; Volume 27 (Issue 10); 1400-1408.; DOI: 10.1016/j.cmi.2021.05.016
BACKGROUND
Culture media are fundamental in clinical microbiology. In laboratories in low- and middle-income countries (LMICs), they are mostly prepared in-house, which is challenging.
OBJECTIVES
This narrative review describes challenges related to culture media in LMICs, compiles best practices for in-house media preparation, gives recommendations to improve access to quality-assured culture media products in LMICs and formulates outstanding questions for further research.
SOURCES
Scientific literature was searched using PubMed and predefined MeSH terms. In addition, grey literature was screened, including manufacturer's websites and manuals as well as microbiology textbooks.
CONTENT
Bacteriology laboratories in LMICs often face challenges at multiple levels: lack of clean water and uninterrupted power supply, high environmental temperatures and humidity, dust, inexperienced and poorly trained staff, and a variable supply of consumables (often of poor quality). To deal with this at a base level, one should be very careful in selecting culture media. It is recommended to look for products supported by the national reference laboratory that are being distributed by an in-country supplier. Correct storage is key, as is appropriate preparation and waste management. Centralized media acquisition has been advocated for LMICs, a role that can be taken up by the national reference laboratories, next to guidance and support of the local laboratories. In addition, there is an important role in tropicalization and customization of culture media formulations for private in vitro diagnostic manufacturers, who are often still unfamiliar with the LMIC market and the plethora of bacteriology products.
IMPLICATION
The present narrative review will assist clinical microbiology laboratories in LMICs to establish best practices for handling culture media by defining quality, regulatory and research paths.
Culture media are fundamental in clinical microbiology. In laboratories in low- and middle-income countries (LMICs), they are mostly prepared in-house, which is challenging.
OBJECTIVES
This narrative review describes challenges related to culture media in LMICs, compiles best practices for in-house media preparation, gives recommendations to improve access to quality-assured culture media products in LMICs and formulates outstanding questions for further research.
SOURCES
Scientific literature was searched using PubMed and predefined MeSH terms. In addition, grey literature was screened, including manufacturer's websites and manuals as well as microbiology textbooks.
CONTENT
Bacteriology laboratories in LMICs often face challenges at multiple levels: lack of clean water and uninterrupted power supply, high environmental temperatures and humidity, dust, inexperienced and poorly trained staff, and a variable supply of consumables (often of poor quality). To deal with this at a base level, one should be very careful in selecting culture media. It is recommended to look for products supported by the national reference laboratory that are being distributed by an in-country supplier. Correct storage is key, as is appropriate preparation and waste management. Centralized media acquisition has been advocated for LMICs, a role that can be taken up by the national reference laboratories, next to guidance and support of the local laboratories. In addition, there is an important role in tropicalization and customization of culture media formulations for private in vitro diagnostic manufacturers, who are often still unfamiliar with the LMIC market and the plethora of bacteriology products.
IMPLICATION
The present narrative review will assist clinical microbiology laboratories in LMICs to establish best practices for handling culture media by defining quality, regulatory and research paths.
Journal Article > ReviewFull Text
Int J Antimicrob Agents. 2017 July 10; Volume 50 (Issue 5); 629-639.; DOI:10.1016/j.ijantimicag.2017.07.002
Bernabe KJ, Langendorf C, Ford NP, Ronat JB
Int J Antimicrob Agents. 2017 July 10; Volume 50 (Issue 5); 629-639.; DOI:10.1016/j.ijantimicag.2017.07.002
Growing data suggest that antimicrobial-resistant bacterial infections are common in low- and middle-income countries. This review summarises the microbiology of key bacterial syndromes encountered in West Africa and estimates the prevalence of antimicrobial resistance (AMR) that could compromise first-line empirical treatment. We systematically searched for studies reporting on the epidemiology of bacterial infection and prevalence of AMR in West Africa within key clinical syndromes. Within each syndrome, the pooled proportion and 95% confidence interval were calculated for each pathogen-antibiotic pair using random-effects models. Among 281 full-text articles reviewed, 120 met the eligibility criteria. The majority of studies originated from Nigeria (70; 58.3%), Ghana (15; 12.5%) and Senegal (15; 12.5%). Overall, 43 studies (35.8%) focused on urinary tract infections (UTI), 38 (31.7%) on bloodstream infections (BSI), 27 (22.5%) on meningitis, 7 (5.8%) on diarrhoea and 5 (4.2%) on pneumonia. Children comprised the majority of subjects. Studies of UTI reported moderate to high rates of AMR to commonly used antibiotics including evidence of the emergence of cephalosporin resistance. We found moderate rates of AMR among common bloodstream pathogens to typical first-line antibiotics including ampicillin, cotrimoxazole, gentamicin and amoxicillin/clavulanate. Among S. pneumoniae strains isolated in patients with meningitis, levels of penicillin resistance were low to moderate with no significant resistance noted to ceftriaxone or cefotaxime. AMR was common in this region, particularly in hospitalized patients with BSI and both outpatient and hospitalized patients with UTI. This raises concern given the limited diagnostic capability and second-line treatment options in the public sector in West Africa.
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.
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.
Conference Material > Video (panel)
Truppa C, Ronat JB, Karah N, Shomar RA
MSF Scientific Days Asia 2021. 2021 August 25
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.
Journal Article > ResearchFull Text
Diagnostics (Basel). 2022 August 30; Volume 12 (Issue 9); 2106.; DOI:10.3390/diagnostics12092106
Ronat JB, Oueslati S, Natale A, Kesteman T, Elamin W, et al.
Diagnostics (Basel). 2022 August 30; 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.