Implementation and Evaluation of Antimicrobial Resistance Surveillance Systems in Sub-Saharan Africa

Abstract

EXECUTIVE SUMMARY

The thesis aims to enhance the understanding of antimicrobial resistance (AMR) patterns in Sub-Saharan Africa and evaluate existing laboratory capacities for AMR surveillance in the region. It comprises two comprehensive cross-sectional studies. The first, conducted between November 2013 and March 2017, analyses clinical specimens from febrile patients hospitalized in Burkina Faso, Gabon, Ghana, and Tanzania, with focus on key AMR concerns highlighted by the World Health Organization, including carbapenem-resistant and extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales, fluoroquinolone-resistant Salmonella enterica, and methicillin-resistant Staphylococcus aureus. Notable variations in susceptibility patterns were found, with Burkina Faso exhibiting high prevalence in ESBL production and ciprofloxacin resistance, emphasizing the importance of region-specific AMR surveillance and improved reporting for targeted interventions. The study found no resistance to carbapenems, indicating their potential as an effective option against infections caused by ESBL-producing bacteria, despite their cost and limited availability. However, the thesis advocates for sustained vigilance in detecting emerging carbapenemase-producing pathogens to ensure timely response and management.

Paper two assessed a convenience sample of healthcare facilities in Kenya, encompassing public and private sectors, rural and urban settings, as well as national, county and community units. The assessment was conducted through online surveys of laboratory managers between October 5th and 8th, 2020, with the aim of evaluating laboratory capacity for AMR surveillance and identifying areas for improvement. A scoring scheme was applied to evaluate indicators of quality assurance, management and dissemination of AMR data, material and equipment, staffing, microbiology competency, biosafety and certification. Gaps in laboratory information management technology, quality assurance, data management, and resources were identified, especially in rural areas. Interestingly, facilities performing bacterial cultures only and those conducting antimicrobial susceptibility testing (AST) were found to have similar capacities, except in terms of equipment. This implies that investing in equipment could enhance the capabilities of facilities conducting cultures only to also perform ASTs, presenting a noteworthy opportunity for expanding AMR diagnostics and improving healthcare delivery within Kenya and potentially beyond its borders.

The thesis advances AMR knowledge in Sub-Saharan Africa, providing a roadmap for tailored policies, strengthened surveillance systems, and improved capacities in health laboratories. The findings can serve as a basis to gauge potential impacts of future interventions and the applied scoring tool can be utilized in similar contexts. Furthermore, the evaluation tool in the current research stands as a valuable resource for facilities to independently assess their capacities and practices, contributing to ongoing development efforts in combating AMR.

ABSTRACT

Aim: To enhance the understanding of antimicrobial resistance patterns in Sub-Saharan Africa and evaluate existing laboratory capacity for AMR surveillance in the region. Methods: The thesis comprises two cross-sectional studies: a quantitative approach in [I] and a mixed methods approach in [II]. In Paper I, clinical specimens were collected from febrile patients aged ≥30 days and ≤15 years in Burkina Faso, Gabon, Ghana, and Tanzania. Antimicrobial susceptibility testing was performed on Enterobacterales and Staphylococcus aureus using the disk diffusion method. ESBL production was confirmed via a double-disk diffusion test and gene detection. Multilocus sequence typing was conducted on ESBL-producing Escherichia coli, Klebsiella pneumoniae, ciprofloxacin-resistant Salmonella enterica, and Staphylococcus aureus. Ciprofloxacin-resistant Salmonella enterica isolates were screened for plasmid-mediated resistance genes and mutations. S. aureus isolates were tested for mecA and Panton-Valentine Leukocidin (PVL) presence and spa-typed. In Paper II, health facilities in Kenya were conveniently sampled. Online surveys were conducted with laboratory managers to assess quality assurance, data management, resources, staffing, competency, biosafety, and certification. Facility capacities were evaluated using a 0-1 scoring scheme and compared across facility types, settings, and governance levels. Results: The study analyzed 4,052 specimens from 3,012 patients, finding 219 positive cultures. Prevalence of ESBL-producing Enterobacterales varied: highest in Burkina Faso (45.2%), followed by Gabon (25.8%) and Ghana (15.1%), while Tanzania had none. ESBL-positive Salmonella was found in Burkina Faso and methicillin-resistant S. aureus in Ghana. ST131 dominated ESBL E. coli, and ESBL K. pneumoniae had diverse sequence types. Ciprofloxacin-resistant Salmonella were common in Burkina Faso (50%), carrying qnrB genes. PVL was found in 81.3% of S. aureus (I). Among 219 participating facilities, most did not offer bacterial culture testing (n= 135, 61.6%), while 47 (21.5%) provided culture services only, and 37 (16.9%) conducted antimicrobial susceptibility testing (AST). Major gaps in AST facilities were poor access to laboratory information management technology (LIMT) (score: 45.9%) and low participation in external quality assessment (EQA) programs (score of 67.7%). Urban facilities had more than two-fold higher access to laboratory technology compared to rural facilities (58.6% vs. 25.0%). Laboratories lacking culture services showed significant infrastructural gaps (average score 59.4%), whereas facilities performing cultures only and AST had notably high and similar scores (Average scores: 83.6%. & 82.9%). Lack of equipment was the main challenge for susceptibility testing in 46.8% of laboratories (II). Conclusions: The findings highlight distinct susceptibility patterns in the study regions and underscore the need for local AMR surveillance and reporting. The study also identified gaps in laboratory information management technology, external quality assurance, and equipment in the surveyed health facilities in Kenya. The findings suggest that by investing in equipment, facilities performing cultures can be successfully upgraded to provide additional antimicrobial susceptibility testing, presenting a chance for a leap toward improved AMR diagnostics and surveillance in the country.