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A feasible laboratory-strengthening intervention yielding a sustainable clinical bacteriology sector within 18-months of implementation in a large referral hospital in Ethiopia || Oral Presentation #O0734


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Background Access to clinical bacteriology in low resource settings (LRS) is a key bottleneck preventing individual patient management of treatable severe infections, detection and control of antimicrobial resistance (AMR), and epidemiologic surveillance. We sought to demonstrate the feasibility of a practical bundle of interventions aimed at implementing sustainable clinical bacteriology services at Tikur Anbessa Specialized Hospital in Addis Ababa, Ethiopia, and report on cost and intensity of supervision. Materials/methods A minimal intervention bundle based on the CLSI QMS01-A guideline was established, consisting of (i) an initial needs assessment, (ii) development of key SOPs, (iii) adaptation of processes for LRS, (iv) training and supervision of laboratory staff via consultant visits and existing online resources, and (v) implementation of a practical quality systems approach. A guiding principle of the bundle was sustainability of all interventions post implementation. Results An initial investment of Can$ 35,000 for laboratory reagents, and a total of 50 visit days per year from 3 Canadian microbiologists were committed. Twelve SOPs, including antimicrobial susceptibility testing, were adapted, and an automated blood culture platform was donated (bioMerieux). In the first 18 months of implementation of the intervention, the average volume of specimens analyzed in the lab went from 15/day to 75 specimens /day. The number of blood cultures tested increased from an average of 2/day to over 20/day. Standardized antimicrobial susceptibility testing with cumulative antibiograms were generated for the institution. Quality control was implemented for all procedures and quality assurance tools implemented included external quality assurance and proficiency testing of 5 technologists with longitudinal follow-up. At present the laboratory is applying for SLIPTA certification by ASLM. Reagent costs, staff training and retention, and engagement of clinical personnel with the lab proved to be manageable challenges. Key external challenges include in-country supply-chain management issues related to lack of competition among distributors and foreign-currency exchange distortions. Conclusions Using a relatively low-intensity intervention based on existing training tools and accreditation schemes, we demonstrate that establishment of sustainable high-quality clinical bacteriology is not only within reach but also a critical step towards assessing the burden of AMR in settings like this one.
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feasible laboratory-strengthening intervention
yielding a sustainable clinical bacteriology sector
within 18-months of implementation in a large
referral hospital in Ethiopia
Cedric P Yansouni
, Daniel Seifu, Michael Libman, Solomon Gizaw, Mequanint
Mitiku, Getachew Seyoum, Freyhiwot Tekle-Haimanot, Mane Asres, Øystein H
Johansen, Workeabeba Abebe,
Makeda Semret
28th ECCMID 2018 -Madrid, Spain 21-24 April 2018
The authors have received in-kind research support from BD Molecular Diagnostics
and bioMérieux in the last 2 years.
This project receive in-kind support from bioMérieux in the form of a BactiAlert 3D
blood culture instrument
Clinical bacteriology in LRS can no longer be regarded as optional
Maputo declaration meeting 2008, Annex C:
unavailable in
Clinical bacteriology in LRS can no longer be regarded as optional
AMR Non-malarial febrile illness
malaria transmission è
↑ alternative illnesses that
have to be considered
2 roles for diagnostics:
pathogen-specific treatment
discontinuation of
unnecessary antimicrobials
when bacterial disease is
ruled out
>10-15% of hospitalized
patients develop
healthcare -associated
infections in LMIC
oAMR ↑ in LRS
oHAI ↑ in LRS
oAMR ↑ impact of HAI
Infections (HAI)
O’Neill J. HM Government and the
Wellcome Trust, May 2016.
Glob Heart 2014; 9: 347-358.
Lancet 2011; 377: 228-241.
Bull World Health Organ 2011; 89: 757-765.
Lancet Infect Dis 2018; 10.1016/s1473-3099(18)30101-4.
2009: AAU-McGill Infectious
Diseases subspecialty training
2015: Funded project
– “Burden of hospital-acquired infections in the
largest referral hospital in Ethiopia, and impact
of a sustainable laboratory intervention on
antimicrobial prescribing practices
2017: AMP-ID collaboration
Objective of this talk:
Report on the laboratory-
strengthening intervention
towards a sustainable clinical
bacteriology sector
Also from this project at ECCMID 2018:
• “Alarming rates of drug-resistance in gram-negative blood stream infections among
hospitalized patients in Ethiopia: an urgent call to strengthen diagnostic bacteriology
and antimicrobial stewardship in low-resource settings” (P0947)
• “Opportunities and barriers to implementing Antibiotic Stewardship in Low-Resource
Settings: lessons from a mixed-methods study in a tertiary care hospital in Ethiopia”
1. initial needs assessment
2. development of key SOPs
3. adaptation of processes for LRS
4. training and supervision of
laboratory staff via consultant
visits and existing online
5. implementation of a practical
quality systems approach
Exploratory visits late 2015
Very low volume of specimens
Problematic quality!
50-bottle automated blood culture
platform donated, but infrequent use
Variable staff proficiency
Support from Norwegian cooperation
Few SOPs
Little relationship with clinicians
1. initial needs assessment
2. development of key SOPs
3. adaptation of processes for LRS
4. training and supervision of
laboratory staff via consultant
visits and existing online
5. implementation of a practical
quality systems approach
Decision to prioritize BSI
12 core SOP were adapted
from MUHC protocols
No epi to guide SOP content
PLoS Negl Trop Dis 2016; 10: e0005053.
1. initial needs assessment
2. development of key SOPs
3. adaptation of processes for LRS
4. training and supervision of
laboratory staff via consultant
visits and existing online
5. implementation of a practical
quality systems approach
Tota l of 50 visit-days/year from 3
McGill microbiologists committed
(i.e. 4-5 x 2-wk visits)
Training sessions
Daily plate rounds
Formal lectures
Strong promotion of SOP awareness
Outside resources
Online weekly proficiency testing
program from UBC, Canada
1. initial needs assessment
2. development of key SOPs
3. adaptation of processes for LRS
4. training and supervision of
laboratory staff via consultant
visits and existing online
5. implementation of a practical
quality systems approach
Promoting the quality mindset
QC implemented for all procedures
QA approaches implemented
EQA participation (EPHI, nascent)
Proficiency testing of 7 techs (tailor-made
Online weekly proficiency testing (
more used as training tool)
Selected QA audits (mostly analytical)
Path to accreditation
Results so far
Initial investment of Can$ 35,000 for laboratory reagents
In the first 18 months of implementation:
Specimens received 15/day è75 /day.
Blood cultures tested 2/day è>20/day.
Standardized AST with cumulative antibiograms generated
Aiming for SLIPTA certification by ASLM èISO 15189.
Results so far
In the first 18 months of
Specimens received 15/day è
75 /day.
Blood cultures tested 2/day è
Standardized AST with cumulative
antibiograms generated
Aiming for SLPTA certification by
ASLM èISO 15189.
Standardizing practice
Addressing misconceptions among staff
Earning trust of entire team
Overcoming local supply
and ForEx issues
Engagement from hospital &
university community toward
importance of lab sector
Attractiveness of microbiology as
a career path without
institutional prestige
Attractiveness of ID as
subspecialty given lower
revenue compared to procedural
Generating demand from clinicians
Quality specimen
Requisition neglect
mislabled specimens è
Main Challenges
No telephone system in hospital!
No in-hospital LIS and connectivity to individual
ordering physicians
Data analysis responsibility
Strengthening relationship with clinicians in
absence of MD homologue in lab
Strengthening synergies with tiered lab network
Overcoming post-analytical obstacles
connectivity to users using off-the-shelf commercial tools
Local cumulative antibiograms Real-time locally adapted treatment guidelines
Screenshots from
Next steps
Accreditation SLMTA, ISO
New technologies
Improving individual
patient care
resistance with OUR
actions each day
Getting in-hospital LIS
connectivity to individual
ordering physicians
Strengthening relationship with
Updating empiric guidelines
according to local data
Working better with today’s tools
Smarter application of
current tools
Enabling quality assurance
and quality improvement
Using connectivity and
transport innovations
The Lancet Infectious Diseases. 2018.
Clin Microbiol Infect. 2017;23(7):426-33.
M Semret, M Ndao, J Jacobs & CP Yansouni; Clin Microbiol Infect 2018 (in press)
Point-of-care and point-of-“can”:
Leveraging reference-laboratory capacity for integrated diagnosis of fever
syndromes in the tropics
Evaluating new tools for bacteriology in low-resource settings
many options for bacterial identification, very few for AST
Liu et al; J Clin Microbiol 2016;54:49-58
Roche gobbles Smarticles. Nat Biotechnol. 2015;33(10):1012.
MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hopital
Principal de Dakar, Senegal (West Africa). PLoS One. 2015;10(12):e0145889.
Usefulness of MALDI-TOF Mass Spectrometry for Routine Identification of Candida
Species in a Resource-Poor Setting. Mycopathologia. 2015;180(3-4):173-9.
Multiplex/serial monoplex
NAAT approaches MALDI-TOF MS Innovative new approaches for rapid PHENOTYPIC
antimicrobial susceptibility testing
1. Reliable bacteriology and AST are now implemented at TASH
2. For sustainability optimists:
Current budget for staff and reagents can be sustained locally
Institutional buy-in: hospital now has a head of quality-management
Clinician buy-in: results are used, specimens are sent, and post-analytical efforts are
bearing fruit
Many tools used were off-the-shelf commercially available, or adapted from existing ones
3. For sustainability pessimists, many obstacles outside of lab:
Foreign exchange distortions
Supply chain challenges and distributor monopolies
4. Availability has lead to recognition of critical importance of bacteriology
Funding and key partners
... • Prioritizing Blood Culture processing to diagnose Blood Stream Infection • Implementation of 12 core SOPs including standardized identification and susceptibility testing • Training and supervising of laboratory personnel via consultant visits and existing online training • Implementation of a practical Quality approach (169). ...
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This review provides an update on the factors fuelling antimicrobial resistance and shows the impact of these factors in low-resource settings. We detail the challenges and barriers to integrating clinical bacteriology in hospitals in low-resource settings, as well as the opportunities provided by the recent capacity building efforts of national laboratory networks focused on vertical single-disease programmes. The programmes for HIV, tuberculosis and malaria have considerably improved laboratory medicine in Sub-Saharan Africa, paving the way for clinical bacteriology. Furthermore, special attention is paid to topics that are less familiar to the general medical community, such as the crucial role of regulatory frameworks for diagnostics and the educational profile required for a productive laboratory workforce in low-resource settings. Traditionally, clinical bacteriology laboratories have been a part of higher levels of care, and, as a result, they were poorly linked to clinical practices and thus underused. By establishing and consolidating clinical bacteriology laboratories at the hospital referral level in low-resource settings, routine patient care data can be collected for surveillance, antibiotic stewardship and infection prevention and control. Together, these activities form a synergistic tripartite effort at the frontline of the emergence and spread of multi-drug resistant bacteria. If challenges related to staff, funding, scale, and the specific nature of clinical bacteriology are prioritized, a major leap forward in the containment of antimicrobial resistance can be achieved. The mobilization of resources coordinated by national laboratory plans and interventions tailored by a good understanding of the hospital microcosm will be crucial to success, and further contributions will be made by market interventions and business models for diagnostic laboratories. The future clinical bacteriology laboratory in a low-resource setting will not be an “entry-level version” of its counterparts in high-resource settings, but a purpose-built, well-conceived, cost-effective and efficient diagnostic facility at the forefront of antimicrobial resistance containment.
Full-text available
Background Routine microbiology results are a valuable source of antimicrobial resistance (AMR) surveillance data in low- and middle-income countries (LMICs) as well as in high-income countries. Different approaches and strategies are used to generate AMR surveillance data. Objectives We aimed to review strategies for AMR surveillance using routine microbiology results in LMICs and to highlight areas that need support to generate high quality AMR data. Sources We searched papers that used routine microbiology to describe the epidemiology of AMR and drug resistant infections in LMICs in PubMed. We also included papers that, from our perspective, were critical in highlighting the biases and challenges or employed specific strategies to overcome these in reporting AMR surveillance in LMICs. Content Topics covered included strategies of identifying AMR cases (including case-finding based on isolates from routine diagnostic specimens and case-based surveillance of clinical syndromes), of collecting data (including cohort, point-prevalence survey, and case-control), of sampling AMR cases (including lot quality assurance surveys), and of processing and analysing data for AMR surveillance in LMICs. Implications The various AMR surveillance strategies warrant a thorough understanding of their limitations and potential biases to ensure maximum utilization and interpretation of local routine microbiology data across time and space. For instance, surveillance using case-finding based on results from clinical diagnostic specimens is relatively easy to implement and sustain in LMIC settings but the estimates of incidence and proportion of AMR is at risk of biases due to underuse of microbiology. Case-based surveillance of clinical syndrome generates informative statistics that can be translated to clinical practices but needs financial and technical support, and locally-tailored trainings to sustain. Innovative AMR surveillance strategies that can be easily implemented and sustained with minimal costs will be useful for improving AMR data availability and quality in LMICs.
Full-text available
Intense antibiotic consumption in Low- and Middle-Income Countries (LMICs) is fueled by critical gaps in laboratory infrastructure and entrenched syndromic management of infectious syndromes. Few data inform the achievability and impact of antimicrobial stewardship interventions, particularly in Sub-Saharan Africa. Our goal was to demonstrate the feasibility of a pharmacist-led laboratory-supported intervention at Tikur Anbessa Specialized Hospital in Addis Ababa, Ethiopia, and report on antimicrobial use and clinical outcomes associated with the intervention. Methods: This was a single-center prospective quasi-experimental study conducted in two phases: (i) an intervention phase (November 2017 to August 2018), during which we implemented weekly audit and immediate (verbal and written) feedback sessions on antibiotic prescriptions of patients admitted in 2 pediatric and 2 adult medicine wards, and (ii) a post-intervention phase (September 2018 to January 2019) during which we audited antibiotic prescriptions but provided no feedback to the treating teams. The intervention was conducted by an AMS team consisting of 4 clinical pharmacists (one trained in AMS) and one ID specialist. Our primary outcome was antimicrobial utilization (measured as days of therapy (DOT) per 1,000 patient-days and duration of antibiotic treatment courses); secondary outcomes were length of hospital stay and in-hospital all-cause mortality. A multivariable logistic regression model was used to explore factors associated with all-cause in-hospital mortality. Results: We collected data on 1,109 individual patients (707 during the intervention and 402 in the post-intervention periods). Ceftriaxone, vancomycin, cefepime, meropenem, and metronidazole were the most commonly prescribed antibiotics; 96% of the recommendations made by the AMS team were accepted. The AMS team recommended to discontinue antibiotic therapy in 54% of cases during the intervention period. Once the intervention ceased, total antimicrobial use increased by 51.6% and mean duration of treatment by 4.1 days/patient. Mean LOS stay as well as crude mortality also increased significantly in the post-intervention phase (LOS: 24.1 days vs. 19.8 days; in hospital death 14.7 vs. 6.9%). The difference in mortality remained significant after adjusting for potential confounders. Conclusions: A pharmacist-led AMS intervention focused on duration of antibiotic treatment was feasible and had good acceptability in our setting. Cessation of audit-feedback activities was associated with immediate and sustained increases in antibiotic consumption reflecting a rapid return to baseline (pre-intervention) prescribing practices, and worse clinical outcomes (increased length of stay and in-hospital mortality). Pharmacist-led audit-feedback activities can effectively reduce antimicrobial consumption and result in better-quality care, but require organizational leadership's commitment for sustainable benefits.
Full-text available
Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p<0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05-2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p<0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication. Funding: DFID-MRC-Wellcome Trust Joint Global Health Trial Development Grant, National Institute of Health Research Global Health Research Unit Grant.