Journal Article > ResearchFull Text
East Afr Med J. 2017 March 31; Volume 6 (Issue 2); 383.; DOI:10.4102/ajlm.v6i2.383
Orikiriza P, Nyehangane D, Atwine D, Kisakye JJ, Kassaza K, et al.
East Afr Med J. 2017 March 31; Volume 6 (Issue 2); 383.; DOI:10.4102/ajlm.v6i2.383
BACKGROUND
To confirm presence of Mycobacterium tuberculosis complex, some tuberculosis culture laboratories still rely on para-nitrobenzoic acid (PNB), a traditional technique that requires sub-culturing of clinical isolates and two to three weeks to give results. Rapid identification tests have improved turnaround times for mycobacterial culture results. Considering the challenges of the PNB method, we assessed the performance of the SD Bioline TB Ag MPT64 assay by using PNB as gold standard to detect M. tuberculosis complex from acid-fast bacilli (AFB) positive cultures.
OBJECTIVES
The aim of this study was to determine the sensitivity, specificity and turnaround time of the SD MPT64 assay for identification of M. tuberculosis complex, in a setting with high prevalence of tuberculosis and HIV.
METHODS
A convenience sample of 690 patients, with tuberculosis symptoms, was enrolled at Epicentre Mbarara Research Centre between April 2010 and June 2011. The samples were decontaminated using NALC-NaOH and re-suspended sediments inoculated in Mycobacterium Growth Indicator Tubes (MGIT) media, then incubated at 37 °C for a maximum of eight weeks. A random sample of 50 known negative cultures and 50 non-tuberculous mycobacteria isolates were tested for specificity, while sensitivity was based on AFB positivity. The time required from positive culture to reporting of results was also assessed with PNB used as the gold standard.
RESULTS
Of the 138 cultures that were AFB-positive, the sensitivity of the SD MPT64 assay was 100.0% [95% CI: 97.3 - 100] and specificity was 100.0% (95% CI, 96.4 - 100). The median time from a specimen receipt to confirmation of strain was 10 days [IQR: 8-12] with SD MPT64 and 24 days [IQR: 22-26] with PNB.
CONCLUSION
The SD MPT64 assay is comparable to PNB for identification of M. tuberculosis complex and reduces the time to detection.
To confirm presence of Mycobacterium tuberculosis complex, some tuberculosis culture laboratories still rely on para-nitrobenzoic acid (PNB), a traditional technique that requires sub-culturing of clinical isolates and two to three weeks to give results. Rapid identification tests have improved turnaround times for mycobacterial culture results. Considering the challenges of the PNB method, we assessed the performance of the SD Bioline TB Ag MPT64 assay by using PNB as gold standard to detect M. tuberculosis complex from acid-fast bacilli (AFB) positive cultures.
OBJECTIVES
The aim of this study was to determine the sensitivity, specificity and turnaround time of the SD MPT64 assay for identification of M. tuberculosis complex, in a setting with high prevalence of tuberculosis and HIV.
METHODS
A convenience sample of 690 patients, with tuberculosis symptoms, was enrolled at Epicentre Mbarara Research Centre between April 2010 and June 2011. The samples were decontaminated using NALC-NaOH and re-suspended sediments inoculated in Mycobacterium Growth Indicator Tubes (MGIT) media, then incubated at 37 °C for a maximum of eight weeks. A random sample of 50 known negative cultures and 50 non-tuberculous mycobacteria isolates were tested for specificity, while sensitivity was based on AFB positivity. The time required from positive culture to reporting of results was also assessed with PNB used as the gold standard.
RESULTS
Of the 138 cultures that were AFB-positive, the sensitivity of the SD MPT64 assay was 100.0% [95% CI: 97.3 - 100] and specificity was 100.0% (95% CI, 96.4 - 100). The median time from a specimen receipt to confirmation of strain was 10 days [IQR: 8-12] with SD MPT64 and 24 days [IQR: 22-26] with PNB.
CONCLUSION
The SD MPT64 assay is comparable to PNB for identification of M. tuberculosis complex and reduces the time to detection.
Journal Article > ResearchFull Text
J Infect Dis. 2016 May 25; Volume 215 (Issue 1); 64–69.; DOI:10.1093/infdis/jiw206
Muehlenbachs A, de la Rosa Vazquez O, Bausch DG, Schafer IJ, Paddock C, et al.
J Infect Dis. 2016 May 25; Volume 215 (Issue 1); 64–69.; DOI:10.1093/infdis/jiw206
Here we describe clinicopathologic features of EVD in pregnancy. One woman infected with Sudan virus in Gulu, Uganda in 2000 had a stillbirth and survived, and another woman with Bundibugyo virus had a livebirth with maternal and infant death in Isiro, the Democratic Republic of the Congo in 2012. Ebolavirus antigen was seen in the syncytiotrophoblast and placental maternal mononuclear cells by immunohistochemistry, and no antigen was seen in fetal placental stromal cells or fetal organs. In the Gulu case, ebolavirus antigen localized to malaria pigment-laden macrophages. These data suggest trophoblast infection may be a mechanism of transplacental ebolavirus transmission.
Conference Material > Video (talk)
Langendorf C
Epicentre Scientific Day Paris 2022. 2022 June 21
Journal Article > ReviewFull Text
Clin Chem Lab Med. 2012 March 16; Volume 50 (Issue 7); 1221-1227.; DOI:10.1515/cclm-2011-0618
Kosack CS
Clin Chem Lab Med. 2012 March 16; Volume 50 (Issue 7); 1221-1227.; DOI:10.1515/cclm-2011-0618
In medical humanitarian assistance, the diagnosis of diseases plays a crucial role. Laboratory investigations are one of the main diagnostic tools utilized in Médecins Sans Frontières' (MSF) programs. Currently MSF supports and/or operates more than 130 laboratories in approximately 45 countries. The variety of analysis offered depends largely on the context of the program and the availability of context adapted tools and ranges from sophisticated laboratories specializing in tuberculosis culture to small laboratories within a primary health care program or operating as mobile clinics. The largest laboratories in MSF are found in programs with the main objective to diagnose, treat and monitor patients with tuberculosis and/or human immunodeficiency virus. Other MSF programs are either disease-specific (e.g., malaria, Chagas, kala azar or visceral leishmaniasis, sleeping sickness, malnutrition, sexually transmitted infections) or are integrated in primary or secondary health care structures.
Conference Material > Abstract
Langendorf C
Epicentre Scientific Day Paris 2022. 2022 June 1
BACKGROUND
The Mini-Lab is a simplified and modular bacteriology laboratory being developed by MSF to improve access to microbiology diagnostics and antibiotic resistance surveillance in resource-limited settings. After a first pilot study in Haiti in 2020, this second evaluation aimed to assess the performance and ease-of use of the Mini-Lab integrated in the clinical routine of an MSF-supported hospital which has had no prior access to microbiology.
METHODS
The study was conducted after the implementation of the Mini-Lab in an MSFsupported hospital in Carnot, CAR, along with an antibiotic stewardship program. We included hospitalized patients with successful blood culture sampling on admission or during hospitalization, and who consented to study participation. The bacteria identified from blood culture in the Mini-Lab were shipped to a reference laboratory in Bicêtre hospital, France for identification (ID) and antibiotic susceptibility testing (AST) using reference methods. Laboratory technicians evaluated the usability of the Mini-Lab through repeated ease-of use questionnaires and competency assessment.
RESULTS
Between September 2021 and February 2022, we included 835 patients who had a total of 960 blood cultures. Positivity rate with pathogens was 12.5%. Over 121 pathogens identified in the Mini-Lab, 74 have been tested with reference methods so far and 68 (92.0%) gave ID results concordant with the Mini-Lab with 97.4% agreement to genus. No particular organism-antibiotic combination caused systematic errors on AST. Upon completion of the initial training, the laboratory technicians reported most of the aspects of the Mini-Lab easy to use, except for preparation and reading of ID and AST methods, which were reported to be simple after 3 months of experience. Assessment of the laboratory technicians' competencies after the initial training yielded very high scores (>90%) and 100% after 3 months.
CONCLUSION
The comparison of the Mini-Lab results with the reference methods for ID and AST showed overall very good results. We did not highlight any major malfunction preventing its deployment in other resource-limited countries.
KEY MESSAGE
The performances of the simplified and modular bacteriology laboratory, the Mini-Lab, are overall very good. We did not highlight any major malfunctions preventing its deployment in other fields.
This abstract is not to be quoted for publication
The Mini-Lab is a simplified and modular bacteriology laboratory being developed by MSF to improve access to microbiology diagnostics and antibiotic resistance surveillance in resource-limited settings. After a first pilot study in Haiti in 2020, this second evaluation aimed to assess the performance and ease-of use of the Mini-Lab integrated in the clinical routine of an MSF-supported hospital which has had no prior access to microbiology.
METHODS
The study was conducted after the implementation of the Mini-Lab in an MSFsupported hospital in Carnot, CAR, along with an antibiotic stewardship program. We included hospitalized patients with successful blood culture sampling on admission or during hospitalization, and who consented to study participation. The bacteria identified from blood culture in the Mini-Lab were shipped to a reference laboratory in Bicêtre hospital, France for identification (ID) and antibiotic susceptibility testing (AST) using reference methods. Laboratory technicians evaluated the usability of the Mini-Lab through repeated ease-of use questionnaires and competency assessment.
RESULTS
Between September 2021 and February 2022, we included 835 patients who had a total of 960 blood cultures. Positivity rate with pathogens was 12.5%. Over 121 pathogens identified in the Mini-Lab, 74 have been tested with reference methods so far and 68 (92.0%) gave ID results concordant with the Mini-Lab with 97.4% agreement to genus. No particular organism-antibiotic combination caused systematic errors on AST. Upon completion of the initial training, the laboratory technicians reported most of the aspects of the Mini-Lab easy to use, except for preparation and reading of ID and AST methods, which were reported to be simple after 3 months of experience. Assessment of the laboratory technicians' competencies after the initial training yielded very high scores (>90%) and 100% after 3 months.
CONCLUSION
The comparison of the Mini-Lab results with the reference methods for ID and AST showed overall very good results. We did not highlight any major malfunction preventing its deployment in other resource-limited countries.
KEY MESSAGE
The performances of the simplified and modular bacteriology laboratory, the Mini-Lab, are overall very good. We did not highlight any major malfunctions preventing its deployment in other fields.
This abstract is not to be quoted for publication
Conference Material > Video (talk)
Malaeb R, Nagwan Y
Epicentre Scientific Day Paris 2022. 2022 June 21
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 > ResearchFull Text
Pan Afr Med J. 2017 December 31; Volume 30; 44.; DOI:10.11604/pamj.2018.30.44.14663
Yambasu EE, Reid AJ, Owiti P, Manzi M, Sia Murray MJ, et al.
Pan Afr Med J. 2017 December 31; Volume 30; 44.; DOI:10.11604/pamj.2018.30.44.14663
INTRODUCTION
Transmissible blood-borne infections are a serious threat to blood transfusion safety in West African countries; and yet blood remains a key therapeutic product in the clinical management of patients. Sierra Leone screens blood donors for blood-borne infections but has not implemented prevention of mother-to-child transmission for hepatitis B. This study aimed to describe the overall prevalence of hepatitis B and C, HIV and syphilis among blood donors in Sierra Leone in 2016 and to compare the differences between volunteer versus family replacement donors, as well as urban versus rural donors.
METHODS
Retrospective, cross-sectional study from January-December 2016 in five blood bank laboratories across the country. Routinely-collected programme data were analyzed; blood donors were tested with rapid diagnostic tests-HBsAg for HBV, anti-HCV antibody for HCV, antibodies HIV1&2 for HIV and TPHA for syphilis.
RESULTS
There were 16807 blood samples analysed, with 80% from males; 2285 (13.6%) tested positive for at least one of the four pathogens. Overall prevalence was: 9.7% hepatitis B; 1.0% hepatitis C; 2.8% HIV; 0.8% syphilis. Prevalence was higher among samples from rural blood banks, the difference most marked for hepatitis C. The proportion of voluntary donors was 12%. Family replacement donors had a higher prevalence of hepatitis B, C and HIV than volunteers.
CONCLUSION
A high prevalence of blood-borne pathogens, particularly hepatitis B, was revealed in Sierra Leone blood donors. The study suggests the country should implement the prevention of mother-to-child transmission of hepatitis B and push to recruit more volunteer, non-remunerated blood donors.
Transmissible blood-borne infections are a serious threat to blood transfusion safety in West African countries; and yet blood remains a key therapeutic product in the clinical management of patients. Sierra Leone screens blood donors for blood-borne infections but has not implemented prevention of mother-to-child transmission for hepatitis B. This study aimed to describe the overall prevalence of hepatitis B and C, HIV and syphilis among blood donors in Sierra Leone in 2016 and to compare the differences between volunteer versus family replacement donors, as well as urban versus rural donors.
METHODS
Retrospective, cross-sectional study from January-December 2016 in five blood bank laboratories across the country. Routinely-collected programme data were analyzed; blood donors were tested with rapid diagnostic tests-HBsAg for HBV, anti-HCV antibody for HCV, antibodies HIV1&2 for HIV and TPHA for syphilis.
RESULTS
There were 16807 blood samples analysed, with 80% from males; 2285 (13.6%) tested positive for at least one of the four pathogens. Overall prevalence was: 9.7% hepatitis B; 1.0% hepatitis C; 2.8% HIV; 0.8% syphilis. Prevalence was higher among samples from rural blood banks, the difference most marked for hepatitis C. The proportion of voluntary donors was 12%. Family replacement donors had a higher prevalence of hepatitis B, C and HIV than volunteers.
CONCLUSION
A high prevalence of blood-borne pathogens, particularly hepatitis B, was revealed in Sierra Leone blood donors. The study suggests the country should implement the prevention of mother-to-child transmission of hepatitis B and push to recruit more volunteer, non-remunerated blood donors.
Journal Article > ResearchFull Text
Antimicrob Agents Chemother. 2014 March 24; Volume 58 (Issue 6); 3182-90.; DOI:10.1128/AAC.02379-13
Bhatt NB, Barau C, Amin A, Baudin E, Meggi B, et al.
Antimicrob Agents Chemother. 2014 March 24; Volume 58 (Issue 6); 3182-90.; DOI:10.1128/AAC.02379-13
This is a substudy of the Agence Nationale de Recherches sur le Sida et les Hépatites Virales (ANRS) Comparison of Nevirapine and Efavirenz for the Treatment of HIV-TB Co-infected Patients (ANRS 12146-CARINEMO) trial, which assessed the pharmacokinetics of rifampin or isoniazid with or without the coadministration of nonnucleoside reverse transcriptase inhibitor-based HIV antiretroviral therapy in HIV-tuberculosis-coinfected patients in Mozambique. Thirty-eight patients on antituberculosis therapy based on rifampin and isoniazid participated in the substudy (57.9% males; median age, 33 years; median weight, 51.9 kg; median CD4(+) T cell count, 104 cells/μl; median HIV-1 RNA load, 5.5 log copies/ml). The daily doses of rifampin and isoniazid were 10 and 5 mg/kg of body weight, respectively. Twenty-one patients received 200 mg of nevirapine twice a day (b.i.d.), and 17 patients received 600 mg of efavirenz once a day (q.d.) in combination with lamivudine and stavudine from day 1 until the end of the study. Blood samples were collected at regular time-dosing intervals after morning administration of a fixed-dose combination of rifampin and isoniazid. When rifampin was administered alone, the median maximum concentration of drug in serum (Cmax) and the area under the concentration-time curve (AUC) at steady state were 6.59 mg/liter (range, 2.70 to 14.07 mg/liter) and 27.69 mg · h/liter (range, 11.41 to 109.75 mg · h/liter), respectively. Concentrations remained unchanged when rifampin was coadministered with nevirapine or efavirenz. When isoniazid was administered alone, the median isoniazid Cmax and AUC at steady state were 5.08 mg/liter (range, 1.26 to 11.51 mg/liter) and 20.92 mg · h/liter (range, 7.73 to 56.95 mg · h/liter), respectively. Concentrations remained unchanged when isoniazid was coadministered with nevirapine; however, a 29% decrease in the isoniazid AUC was observed when isoniazid was combined with efavirenz. The pharmacokinetic parameters of rifampin and isoniazid when coadministered with nevirapine or efavirenz were not altered to a clinically significant extent in these severely immunosuppressed HIV-infected patients. Patients experienced favorable clinical outcomes. (This study has been registered at ClinicalTrials.gov under registration no. NCT00495326.).