Effectiveness of COVID-19 vaccine against SARS-CoV-2 infection among symptomatic COVID-19 patients in Uganda.

Background: COVID-19 vaccines significantly reduce severe disease outcomes, but uncertainty remains about long-term protection. We investigated vaccine effectiveness (VE) against SARS-CoV-2 infection over extended periods in the World Health Organisation AFRO-MoVE network studies in Africa.

Methods: Participants with COVID-19-like symptoms were recruited between 2023 and 2024 for a test-negative case-control study conducted across 19-healthcare centres in Uganda.

COVID-19 vaccination status and associated factors among patients presenting with COVID-19-like symptoms in Uganda.

Introduction: The emergence of new SARS-CoV-2 variants threatens the effectiveness of global vaccination campaigns. This study examines the vaccination status and associated factors among patients presenting with COVID-19-like symptoms at 19 healthcare facilities in Uganda.

Materials And Methods: A cross-sectional analysis was conducted using data collected at health facilities to evaluate the effectiveness of COVID-19 vaccines in Uganda from March 2023 to March 2024.

Factors associated with mortality among patients aged 12 years and above requiring hospitalization for severe respiratory illness (SRI): Findings from the COVID-19 vaccine effectiveness evaluation in Kenya and Mali, 2022-2023.

Background: Mortality attributed to respiratory illnesses is well characterized in children <5 years. However, there is paucity of data among older populations. Here, we leveraged data from the COVID-19 Vaccine Effectiveness Evaluation to establish the factors associated with mortality among patients with severe respiratory illness (SRI) in Kenya and Mali.

A decade of rotavirus vaccination in the World Health Organization African Region: An in-depth analysis of vaccine coverage from 2012 to 2023.

Background: Significant progress has been achieved in the introduction of rotavirus vaccines in the World Health Organization, African Region (WHO/AFR), with only 19% (9/47) of the countries yet to introduce the vaccines. Despite this achievement, a considerable number of eligible children in Africa still lack access to these lifesaving rotavirus vaccines.

Methodology: We performed in-depth data exploration and analysis on the WHO/UNICEF rotavirus vaccine uptake estimates of vaccine coverage to document progress and estimated the number of children missing vaccination through under- or un-vaccination between 2012 and 2023.

Emerging SARS-CoV-2 Variants in Uganda in the Era of COVID-19 Vaccination.

The emergence of SARS-CoV-2 variants has heightened concerns about vaccine efficacy, posing challenges in controlling the spread of COVID-19. As part of the COVID-19 Vaccine Effectiveness and Variants (COVVAR) study in Uganda, this study aimed to genotype and characterize SARS-CoV-2 variants in patients with COVID-19-like symptoms who tested positive on a real-time PCR. Amplicon deep sequencing was performed on 163 oropharyngeal/nasopharyngeal swabs collected from symptomatic patients.

Establishing the African region monitoring vaccine effectiveness (AFRO-MoVE) network for respiratory pathogens.

Population-level vaccination with newly developed vaccines to respond to the COVID-19 pandemic created a need to monitor vaccine effectiveness (VE) in the context of emerging SARS-CoV-2 variants and changing epidemiology. WHO and partners launched the African Region Monitoring Vaccine Effectiveness (AFRO-MoVE) Network in March 2021 to assess the performance of COVID-19 vaccines in real-world conditions in Africa. The Network aimed to facilitate and support comparable COVID-19 vaccine effectiveness studies in the African region, to provide a platform of scientific expertise and infrastructure, encourage the use of robust similar study designs to enable pooling to produce regional VE estimates and to build a sustainable network of hospitals, institutions, and experts to evaluate vaccines against pandemic and endemic respiratory pathogens.

Pulmonary non-tuberculous mycobacteria in colonisation and disease in The Gambia.

The clinical relevance of pulmonary non-tuberculous mycobacteria (PNTM) in The Gambia is unknown. The aim of this study was to estimate the prevalence of non-tuberculous mycobacteria (NTM) in colonisation, and the burden of clinically relevant pulmonary NTM (PNTM) disease in The Gambia. This was a cross-sectional study of the prevalence of NTM in participants aged ≥ 15 years, in a nationwide tuberculosis (TB) prevalence survey between December 2011 and January 2013.

Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci.

The isolation of Streptococcus pneumoniae serotypes in systemic tissues of patients with invasive disease versus the nasopharynx of healthy individuals with asymptomatic carriage varies widely. Some serotypes are hyper-invasive, particularly serotype 1, but the underlying genetics remain poorly understood due to the rarity of carriage isolates, reducing the power of comparison with invasive isolates. Here, we use a well-controlled genome-wide association study to search for genetic variation associated with invasiveness of serotype 1 pneumococci from a serotype 1 endemic setting in Africa.

Genomic diversity and antimicrobial resistance among non-typhoidal associated with human disease in The Gambia.

Non-typhoidal associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal collected from 93 patients in 2001 from the eastern, and in 2006-2018 from the western regions of The Gambia respectively.

Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints.

The transmission dynamics of in sub-Saharan Africa are poorly understood due to a lack of adequate epidemiological and genomic data. Here we leverage a longitudinal cohort from 21 neighbouring villages in rural Africa to study how closely related strains of are shared among infants. We analysed 1074 pneumococcal genomes isolated from 102 infants from 21 villages.

Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.

Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 . isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016.

Carriage Dynamics of Pneumococcal Serotypes in Naturally Colonized Infants in a Rural African Setting During the First Year of Life.

(the pneumococcus) carriage precedes invasive disease and influences population-wide strain dynamics, but limited data exist on temporal carriage patterns of serotypes due to the prohibitive costs of longitudinal studies. Here, we report carriage prevalence, clearance and acquisition rates of pneumococcal serotypes sampled from newborn infants bi-weekly from weeks 1 to 27, and then bi-monthly from weeks 35 to 52 in the Gambia. We used sweep latex agglutination and whole genome sequencing to serotype the isolates.

Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.

Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting.

Etiology of Pediatric Meningitis in West Africa Using Molecular Methods in the Era of Conjugate Vaccines against Pneumococcus, Meningococcus, and Type b.

Despite the implementation of effective conjugate vaccines against the three main bacterial pathogens that cause meningitis, , type b (Hib), and serogroup A, the burden of meningitis in West Africa remains high. The relative importance of other bacterial, viral, and parasitic pathogens in central nervous system infections is poorly characterized. Cerebrospinal fluid (CSF) specimens were collected from children younger than 5 years with suspected meningitis, presenting at pediatric teaching hospitals across West Africa in five countries including Senegal, Ghana, Togo, Nigeria, and Niger.

Evolution of Mycobacterium tuberculosis complex lineages and their role in an emerging threat of multidrug resistant tuberculosis in Bamako, Mali.

In recent years Bamako has been faced with an emerging threat from multidrug resistant TB (MDR-TB). Whole genome sequence analysis was performed on a subset of 76 isolates from a total of 208 isolates recovered from tuberculosis patients in Bamako, Mali between 2006 and 2012. Among the 76 patients, 61(80.

Pediatric Bacterial Meningitis Surveillance in Niger: Increased Importance of Neisseria meningitidis Serogroup C, and a Decrease in Streptococcus pneumoniae Following 13-Valent Pneumococcal Conjugate Vaccine Introduction.

Background: Meningitis is endemic in Niger. Haemophilus influenzae type b (Hib) vaccine and the 13-valent pneumococcal conjugate vaccine (PCV13) were introduced in 2008 and 2014, respectively. Vaccination campaign against Neisseria meningitidis serogroup A was carried out in 2010-2011.

Changes in the Molecular Epidemiology of Pediatric Bacterial Meningitis in Senegal After Pneumococcal Conjugate Vaccine Introduction.

Background: Bacterial meningitis is a major cause of mortality among children under 5 years of age. Senegal is part of World Health Organization-coordinated sentinel site surveillance for pediatric bacterial meningitis surveillance. We conducted this analysis to describe the epidemiology and etiology of bacterial meningitis among children less than 5 years in Senegal from 2010 and to 2016.

Declining Trends of Pneumococcal Meningitis in Gambian Children After the Introduction of Pneumococcal Conjugate Vaccines.

Background: Acute bacterial meningitis remains a major cause of childhood mortality in sub-Saharan Africa. We document findings from hospital-based sentinel surveillance of bacterial meningitis among children <5 years of age in The Gambia, from 2010 to 2016.

Methods: Cerebrospinal fluid (CSF) was collected from children admitted to the Edward Francis Small Teaching Hospital with suspected meningitis.

Hospital-based Surveillance Provides Insights Into the Etiology of Pediatric Bacterial Meningitis in Yaoundé, Cameroon, in the Post-Vaccine Era.

Background: Meningitis is endemic to regions of Cameroon outside the meningitis belt including the capital city, Yaoundé. Through surveillance, we studied the etiology and molecular epidemiology of pediatric bacterial meningitis in Yaoundé from 2010 to 2016.

Methods: Lumbar puncture was performed on 5958 suspected meningitis cases; 765 specimens were further tested by culture, latex agglutination, and/or polymerase chain reaction (PCR).

Declines in Pediatric Bacterial Meningitis in the Republic of Benin Following Introduction of Pneumococcal Conjugate Vaccine: Epidemiological and Etiological Findings, 2011-2016.

Background: Pediatric bacterial meningitis (PBM) remains an important cause of disease in children in Africa. We describe findings from sentinel site bacterial meningitis surveillance in children <5 years of age in the Republic of Benin, 2011-2016.

Methods: Cerebrospinal fluid (CSF) was collected from children admitted to Parakou, Natitingou, and Tanguieta sentinel hospitals with suspected meningitis.

Pediatric Bacterial Meningitis Surveillance in the World Health Organization African Region Using the Invasive Bacterial Vaccine-Preventable Disease Surveillance Network, 2011-2016.

Background: Bacterial meningitis is a major cause of morbidity and mortality in sub-Saharan Africa. We analyzed data from the World Health Organization's (WHO) Invasive Bacterial Vaccine-preventable Diseases Surveillance Network (2011-2016) to describe the epidemiology of laboratory-confirmed Streptococcus pneumoniae (Spn), Neisseria meningitidis, and Haemophilus influenzae meningitis within the WHO African Region. We also evaluated declines in vaccine-type pneumococcal meningitis following pneumococcal conjugate vaccine (PCV) introduction.

Pediatric Bacterial Meningitis Surveillance in Nigeria From 2010 to 2016, Prior to and During the Phased Introduction of the 10-Valent Pneumococcal Conjugate Vaccine.

Background: Historically, Nigeria has experienced large bacterial meningitis outbreaks with high mortality in children. Streptococcus pneumoniae (pneumococcus), Neisseria meningitidis (meningococcus), and Haemophilus influenzae are major causes of this invasive disease. In collaboration with the World Health Organization, we conducted longitudinal surveillance in sentinel hospitals within Nigeria to establish the burden of pediatric bacterial meningitis (PBM).

Etiology of Bacterial Meningitis Among Children <5 Years Old in Côte d'Ivoire: Findings of Hospital-based Surveillance Before and After Pneumococcal Conjugate Vaccine Introduction.

Background: Bacterial meningitis remains a major disease affecting children in Côte d'Ivoire. Thus, with support from the World Health Organization (WHO), Côte d'Ivoire has implemented pediatric bacterial meningitis (PBM) surveillance at 2 sentinel hospitals in Abidjan, targeting the main causes of PBM: Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Neisseria meningitidis (meningococcus). Herein we describe the epidemiological characteristics of PBM observed in Côte d'Ivoire during 2010-2016.