Diagnostic Bacteriology in District Hospitals in Sub-Saharan Africa: At the Forefront of the Containment of Antimicrobial Resistance

Abstract

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.

Keywords: Sub-Saharan Africa; antimicrobial resistance (AMR); antimicrobial stewardship (AMS); clinical and bacteriology; infection prevention and control (IPC); low-resource settings (LRS).

Figure 1

Benin, West-Africa: mobile hand washing facility. The water in the reservoir is a 0.05% chlorine solution which was added when the reservoir was nearly empty. Two containers with liquid soap (top and right side of the reservoir) were topped-up when needed. Simple swabbing of the tap and semi-quantitative culture of the soap (calibrated loop) was performed on standard culture media (MacConkey agar). Tap and soap were heavily contaminated with multidrug resistant Klebsiella pneumoniae. Simple control measures (daily cleaning and drying of the reservoir (system of alternating two reservoirs), replacing the containers instead of topping-up) stopped the contamination. Follow-up cultures were done during the implementation phase of the control measures. Written informed consent was obtained from the individual for the publication of this image.

Figure 2

The integrated Tiered Laboratory Network with focus on test menus relevant to clinical bacteriology at different levels-of-care. Clinical bacteriology has recently moved from Level ≥ 3 to Level 2, i.e., the district or referral hospital. Adapted from Unicef and WHO (37), Best and Sakande (39), WHO (47), Centers for Disease Control and Prevention (48), Unitaid (24), and WHO (49), which provide complementary information for the tiered work-up of HIV, tuberculosis and malaria and other diagnostics. CBL, clinical bacteriology laboratory; GLASS, Global Antimicrobial Resistance Surveillance System; RDT, rapid diagnostic test.

Figure 3

During so-called “Plate Rounds,” clinicians and laboratory staff meet in the laboratory and discuss selected cases of infections in a didactic setting. Culture plates including AST results are shown and discussed (e.g., de-escalation of antibiotic treatment (84). Moreover, Plate Rounds can be connected to remote expert advice by telemedicine (180). Originally conceived as a training tool applied in academic medical centers, Plate Rounds provide excellent opportunities for diagnostic and antibiotic stewardship and create liaisons between clinicians and laboratory staff, trainees and in case pharmacists and IPC team (84). The pictures above are “Plate Rounds” set-up during the short course “Hospital-based Interventions to Contain Antibiotic Resistance in Low-resource Settings” at the Institute of Tropical Medicine. Participants of the microbiology track demonstrate case-based laboratory cultures to their colleagues from the antibiotic stewardship and infection prevention and control tracks (181). Written informed consent was obtained from the individuals for the publication of this image.