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Africa CDC Institute of Pathogen Genomics (IPG) was launched in November 2019 and operates under the Division of Laboratory Systems and Networks.
IPG coordinate the implementation of molecular diagnostics, pathogen genomics and bioinformatics in National Public Health Institutions (NPHIs) and/or Re
...
fe-
-rence Laboratories (NRLs) across Africa.
Africa CDC and APHF are coordinating a continental initiative to maximize the benefits of molecular approaches and pathogen genomics for more effective
outbreak preparedness, prevention, response, and for the control and elimination of endemic diseases in Africa. One of Africa CDC’s flagship initiative is the Africa
Pathogen Genomics Initiative (Africa PGI), a partnership that aims to strengthen laboratory systems and enhance genomic surveillance by equipping the continent’s
public health institutions with the tools, training, and data infrastructure.
About the Project
In 2023, 166 outbreaks and public health events were reported in Africa. This calls for a resilient laboratory systems for timely detection and reporting of current and future outbreaks. This project aims to scale up molecular diagnostic and genomic sequencing-based detection and characterization of outbreaks.
Africa CDC is working with Member States to develop guidance, diagnostic algorithm, training and capacity building to enable outbreak detection, and reporting to inform public health response.
more
6 July 2021. The “WHO consolidated guidelines on tuberculosis. Module 3: Diagnosis - Rapid diagnostics for tuberculosis detection 2021 update” is the latest document replacing the one issued in 2020. Three new nucleic acid amplification test (NA
...
AT) classes are endorsed by WHO and included in the latest consolidated guideline
more
Early detection, assessment and response to acute public health events:
Accessed June 2018 - Détection, la confirmation et de la gestion des épidémies de choléra
Tsetse Control and Gambian Sleeping Sickness; Implications for Control Strategy
Tirados, I.; Esterhuizen, J.; Kovacic, V.; Mangwiro, TNC.; Vale, GA
PLOS Neglected Tropical Diseases
(2015)
CC
Sleeping sickness is controlled by case detection and treatment but this often only reaches less than 75% of the population. Vector control is capable of completely interrupting HAT transmission but is not used because of expense. We conducted a ful
...
l scale field trial of a refined vector control technology. From preliminary trials we determined the number of insecticidal tiny targets required to control tsetse populations by more than 90%. We then carried out a full scale, 500 km2 field trial covering two HAT foci in Northern Uganda (overall target density 5.7/km2). In 12 months tsetse populations declined by more than 90%. A mathematical model suggested that a 72% reduction in tsetse population is required to stop transmission in those settings. The Ugandan census suggests population density in the HAT foci is approximately 500 per km2. The estimated cost for a single round of active case detection (excluding treatment), covering 80% of the population, is US$433,333 (WHO figures). One year of vector control organised within country, which can completely stop HAT transmission, would cost US$42,700. The case for adding this new method of vector control to case detection and treatment is strong. We outline how such a component could be organised.
more
Protocol for the use of rapid tests for the detection of antibodies against SARS - COV-2/COVID-19
Antimicrobial resistance (AMR) surveillance plays an important role in the early detection of resistant strains of public health importance and prompt response to outbreaks in hospitals and the community. Surveillance findings are needed to inform m
...
edical practice, antibiotic stewardship, and policy and interventions to combat AMR. Appropriate use of antimicrobials, informed by surveillance, improves patients’ treatment outcomes and reduces the emergence and spread of AMR. This protocol describes the steps and procedures to establish/enhance AMR surveillance in Latin America and the Caribbean.
more
Advances in the treatment of pediatric cancer have made it possible to expand initiatives beyond cure and cover aspects such as early detection, continuity of treatment and reduction in toxicity. All this has paved the way for a more comprehensive v
...
ision of patient care, which means better chances of healing and a fuller life - objectives of the World Initiative against Childhood Cancer. Within this comprehensive care, psychosocial care includes the social, psychological, spiritual and functional dimensions of the disease process of patients. This series includes guidelines and standards based on evidence that guarantee the quality of said care. The standards are the result of discussion and review by different professionals from Latin America and the Caribbean. Module 1 focuses on psychosocial evaluation as a strategy to support the objectives of the World Initiative against Childhood Cancer, and as a tool for health professionals to gather the necessary information to offer these patients a comprehensive approach focused on well-being, adaptation to the disease process, and adherence to treatment.
more
Health ministries currently lack effective tools for monitoring and evaluation of schistosomiasis control programmes. Egg detection can be used, but the cost, challenges of obtaining samples, and the need for trained personnel and equipment limit th
...
e frequency of monitoring. The purpose of this TPP is to guide the development of new diagnostic tools to reliably measure when prevalence is above or below a cut-off of 10% in school-aged children. Communities remaining above 10% require annual MDA, while communities below 10% can reduce MDA frequency as long as < 10% prevalence can be maintained. However, the lack of a reliable test has hindered the development of maintenance strategies. The test is also needed to track changes of prevalence > 10% to ensure that annual MDA is reducing overall prevalence.
more
SARS-COV-2 antigen rapid diagnostic tests are an alternative option for diagnosing active SARS-CoV-2 infection through detection of viral proteins. Rapid antigen tests revolutionize the response to COVID-19 by providing accurate test results in 10 t
...
o 20 minutes instead of days, allowing tests to be done at point of care, and dramatically lowering the price of the tests.
Proper training on the safe use and implementation of antigen tests is vital to ensuring quality testing. A comprehensive training package around safety, sample collection, testing, reporting and management of antigen tests can be found below.
The training package includes facilitators’ guides for master trainers and trainers, training presentations, and supplementary materials to aid in the delivery of this training.
more
The document presents Cameroon's National Response Plan for the 2018 cholera outbreak, covering August to October 2018. It highlights the epidemiological situation, with outbreaks reported in the North and Central regions and a total of 109 suspected cases and 9 deaths by July 2018. The plan outline
...
s strategies for controlling the epidemic, including epidemiological surveillance, improved access to clean water, sanitation, mass vaccination, community awareness campaigns, and hospital and community-based treatment.
The response is coordinated by the Ministry of Public Health, WHO, and various partners, focusing on early detection, rapid response, and multi-sectoral collaboration. Challenges include poor sanitation, limited healthcare infrastructure, and cross-border disease transmission risks. The plan emphasizes resource mobilization, monitoring, and evaluation to contain the outbreak and prevent future cases.
more
La coordination de la surveillance épidémiologique aux points d'entrée et avec les systèmes nationaux est un processus essentiel pour la détection précoce des risques sanitaires internationaux et la protection de la santé publique mondiale. E
...
lle repose sur la collaboration entre les pays, l'échange rapide d'informations via des canaux officiels, et l'application des directives du Règlement Sanitaire International (RSI). Des mécanismes de communication et d'alerte efficaces, ainsi que des plans de riposte coordonnés, permettent de transformer les données de surveillance en actions concrètes pour prévenir la propagation des maladies.
more
The objective of the study was the validation and implementation of GeneXpert MTB/RIF for routine use in the rapid detection of tuberculosis and sensitivity to rifampicin in clinical samples; for this, 1592 respiratory samples were collected and ana
...
lyzed in the laboratory of Instituto Nacional de Investigación en Salud Pública Guayaquil. The analysis of the results of GeneXpert in comparison with smear microscopy showed an initial sensitivity of 99.8% and specificity of 93.2%; The analysis of discrepancies using the results of the culture as a reference method showed that the GeneXpert results considered false negatives turned out to be true negatives, the same happens with the false positives that correspond to true positives. Recalculated the sensitivity and specificity of the GeneXpert was 99.8% and 100% correspondingly. The comparison with the drugs susceptibility test showed a sensitivity of 91.4% and a specificity of 95.5% for the GeneXpert MTB/RIF system. It is concluded that the implementation of the GeneXpert system allows solution to certain problems associated with the application of conventional diagnostic methodologies, decreasing the waiting times, and increasing the sensitivity and specificity in the diagnosis of drug-resistant tuberculosis, thus generating a valuable opportunity for early diagnosis.
more
A set of 5 training videos on child mental health created by the Ethiopian Federal Ministry of Health.
The research team produced five short training videos, modelling an HEW interviewing mothers of children with autism or intellectual disability to demonstrate skills in early
...
detection, supportive counselling and problem solving. The videos are produced in Amharic (the official Ethiopian language) – a version with English transcripts and subtitles is also available.
In addition, a ‘Mental Health Guide’ was produced that reinforces the training provided in the associated HEAT module, and extends training in childhood developmental and mental health problems.
more
This document is intended to serve as a reference for national public health policy-makers. It outlines the scope of potential meningitis surveillance strategies that make it possible to obtain the data required for epidemic detection, monitoring of
...
epidemiological and microbiological trends, evaluation of meningitis control strategies and assessment of the impact of Nm A conjugate vaccine. Ultimately, it provides information that can be used to decide on a surveillance strategy that is tailored to the needs and capacity of a country.
more
This manual focuses on the availability and clinical use of oxygen therapy in children in health facilities by providing the practical aspects for health workers, biomedical engineers, and administrators. It addresses the need for appropriate detection
...
of hypoxaemia, use of pulse oximetry, clinical use of oxygen and delivery systems and monitoring of patients on oxygen therapy.
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Skin-related neglected tropical diseases, or “skin NTDs”, are historically neglected because active case detection, individual case management, significant resources and intensive effort are required to control, eliminate and eradicate them. Int
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egrated control and management of skin NTDs offers a pathway to overcome some of these past challenges.
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