The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents

Abstract

Background: In sub-Saharan Africa, acute respiratory infections (ARI), acute gastrointestinal infections (GI) and acute febrile disease of unknown cause (AFDUC) have a large disease burden, especially among children, while respective aetiologies often remain unresolved. The need for robust infectious disease surveillance to detect emerging pathogens along with common human pathogens has been highlighted by the ongoing novel coronavirus disease 2019 (COVID-19) pandemic. The African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA) is a sentinel surveillance study on the aetiology and clinical characteristics of ARI, GI and AFDUC in sub-Saharan Africa.

Methods: ANDEMIA includes 12 urban and rural health care facilities in four African countries (Côte d'Ivoire, Burkina Faso, Democratic Republic of the Congo and Republic of South Africa). It was piloted in 2018 in Côte d'Ivoire and the initial phase will run from 2019 to 2021. Case definitions for ARI, GI and AFDUC were established, as well as syndrome-specific sampling algorithms including the collection of blood, naso- and oropharyngeal swabs and stool. Samples are tested using comprehensive diagnostic protocols, ranging from classic bacteriology and antimicrobial resistance screening to multiplex real-time polymerase chain reaction (PCR) systems and High Throughput Sequencing. In March 2020, PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and analysis of full genomic information was included in the study. Standardised questionnaires collect relevant clinical, demographic, socio-economic and behavioural data for epidemiologic analyses. Controls are enrolled over a 12-month period for a nested case-control study. Data will be assessed descriptively and aetiologies will be evaluated using a latent class analysis among cases. Among cases and controls, an integrated analytic approach using logistic regression and Bayesian estimation will be employed to improve the assessment of aetiology and associated risk factors.

Discussion: ANDEMIA aims to expand our understanding of ARI, GI and AFDUC aetiologies in sub-Saharan Africa using a comprehensive laboratory diagnostics strategy. It will foster early detection of emerging threats and continued monitoring of important common pathogens. The network collaboration will be strengthened and site diagnostic capacities will be reinforced to improve quality management and patient care.

Keywords: Acute febrile disease of unknown cause; Acute gastrointestinal infections; Acute respiratory tract infections; Aetiologies; Antimicrobial resistance; COVID-19; Outbreak detection; SARS-CoV-2; Sentinel surveillance; Sub-Saharan Africa.

Fig. 1

ANDEMIA study sites. Legend: CHR, Centre Hospitalier Regional; CHU, Centre Hospitalier et Universitaire; CS, Centre de Santé; CSU, Centre de Santé Urbain; CMA, Centre Médical avec Antenne chirurgicale; HGR, Hospital General Regional. Map taken from NASA, Public domain

Fig. 2

ANDEMIA study design. Sentinel hospital sites are located along gradients from rural to urban, as well as dry to tropical climate to account for the various effects that demography, climate and biodiversity may have on local pathogen compositions. Image edited with Adobe Photoshop CS6

Fig. 3

Case definitions decision tree. Legend: *respiratory symptoms are cough, expectoration, dyspnoea, pulmonary consolidation, chest pain; **other than acute neurological disease or arbovirosis, evident causes are soft tissue infection (including dental abscess, severe gum or mouth infection) or muscle infection, severe surgical condition or surgical abdomen, kidney or urinary tract infection, HIV Opportunistic Diseases (WHO, 2010b) and Acute Retroviral Syndrome. ARI, acute respiratory infection; AFDUC, acute febrile disease of unknown cause; GI, acute gastrointestinal infection