Cohort profile: the potentially preventable burden of community-acquired pneumonia in South African adults in the era of widespread PCV13 immunisation and antiretroviral therapy roll-out, before and during the COVID-19 pandemic - the multicentre, multimethod PotPrev Study.

Purpose: In the setting of an established childhood pneumococcal vaccination programme with immediate initiation and treatment of antiretroviral therapy (ART) for people living with HIV (PLWH), the risk of adult pneumococcal community-acquired pneumonia (CAP) is not recently described. We aimed to investigate CAP incidence, recurrence, mortality, risk factors and microbiology before and during the COVID-19 pandemic.

Participants: Adults aged ≥18 years were enrolled in three South African provinces from March 2019 to October 2021, with a brief halt during the initial COVID-19 lockdown.

Genomic Analysis of Virulent, Multidrug Resistant Klebsiella pneumoniae and Klebsiella oxytoca from Bloodstream Infections, South Africa.

Unlabelled: The study investigated the resistome, virulome and mobilome of multidrug resistant (MDR) Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates.

Methods: A total of 46 suspected Klebsiella species (spp.) were collected from blood cultures within the uMgungundlovu District in the KwaZulu-Natal Province.

Costs of Influenza Illness and Acute Respiratory Infections by Household Income Level: Catastrophic Health Expenditures and Implications for Health Equity.

Background: Seasonal influenza illness and acute respiratory infections can impose a substantial economic burden in low- and middle-income countries (LMICs). We assessed the cost of influenza illness and acute respiratory infections across household income strata.

Methods: We conducted a secondary analysis of data from a prior systematic review of costs of influenza and other respiratory illnesses in LMICs and contacted authors to obtain data on cost of illness (COI) for laboratory-confirmed influenza-like illness and acute respiratory infection.

A Global Collaborative Comparison of SARS-CoV-2 Antigenicity Across 15 Laboratories.

Setting up a global SARS-CoV-2 surveillance system requires an understanding of how virus isolation and propagation practices, use of animal or human sera, and different neutralisation assay platforms influence assessment of SARS-CoV-2 antigenicity. In this study, with the contribution of 15 independent laboratories across all WHO regions, we carried out a controlled analysis of neutralisation assay platforms using the first WHO International Standard for antibodies to SARS-CoV-2 variants of concern (source: NIBSC). Live virus isolates (source: WHO BioHub or individual labs) or spike plasmids (individual labs) for pseudovirus production were used to perform neutralisation assays using the same serum panels.

A generalised catalytic model to assess changes in risk for multiple reinfections with SARS-CoV-2.

Background: Monitoring trends in multiple infections with SARS-CoV-2, following several pandemic waves, provides insight into the biological characteristics of new variants, but also necessitates methods to understand the risk of multiple reinfections.

Objectives: We generalised a catalytic model designed to detect increases in the risk of SARS-CoV-2 reinfection, to assess the population-level risk of multiple reinfections.

Methods: The catalytic model assumes the risk of reinfection is proportional to observed infections and uses a Bayesian approach to fit model parameters to the number of nth infections among individuals that occur at least 90 days after a previous infection.

Molecular epidemiology of invasive group B Streptococcus in South Africa, 2019-2020.

Background: Group B Streptococcus (GBS) is a leading cause of neonatal meningitis and sepsis and an important cause of disease in adults. Capsular polysaccharide and protein-based GBS vaccines are currently under development.

Methods: Through national laboratory-based surveillance, invasive GBS isolates were collected from patients of all ages between 2019 and 2020.

Development of a luminex-based assay for the detection of anti-capripoxvirus and rift valley fever virus antibodies in domestic ruminants.

The three members of the genus capripoxvirus (CaPV), lumpy skin disease virus (LSDV), sheeppox virus (SPPV), and goatpox virus (GTPV) have common hosts and areas of overlapping geographical distribution with Rift Valley fever virus (RVFV). Hence, to ensure more cost-effective disease surveillance we developed and evaluated a Luminex assay for the simultaneous detection of antibodies against CaPV and RVFV in domestic ruminants. In cattle, the assay had a sensitivity (Se) of 98.

The importance of microbiology reference laboratories and adequate funding for infectious disease surveillance.

Microbiology reference laboratories perform a crucial role within public health systems. This role was especially evident during the COVID-19 pandemic. In this Viewpoint, we emphasise the importance of microbiology reference laboratories and highlight the types of digital data and expertise they provide, which benefit national and international public health.

Global impact of ten-valent and 13-valent pneumococcal conjugate vaccines on invasive pneumococcal disease in all ages (the PSERENADE project): a global surveillance analysis.

Background: Pneumococcal conjugate vaccines (PCVs) that are ten-valent (PCV10) and 13-valent (PCV13) became available in 2010. We evaluated their global impact on invasive pneumococcal disease (IPD) incidence in all ages.

Methods: Serotype-specific IPD cases and population denominators were obtained directly from surveillance sites using PCV10 or PCV13 in their national immunisation programmes and with a primary series uptake of at least 50%.

Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa.

The role of genomics in public health surveillance has been accentuated by its crucial contributions during the COVID-19 pandemic, demonstrating its potential in addressing global disease outbreaks. While Africa has made strides in expanding multi-pathogen genomic surveillance, the integration into foodborne disease (FBD) surveillance remains nascent. Here we highlight the critical components to strengthen and scale-up the integration of whole genome sequencing (WGS) in foodborne disease surveillance across the continent.

SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study.

Background: In low- and middle-income countries (LMICs) such as South Africa, there is paucity of data on SARS-CoV-2 infections among children attending school, including seroprevalence and transmission dynamics.

Objective: This pilot study aims to assess (1) the prevalence of self-reported or confirmed SARS-CoV-2 prior infections, COVID-19 symptoms (including long COVID), seroprevalence of SARS-CoV-2 antibodies, and general/mental health, (2) longitudinal changes in SARS-CoV-2 seroprevalence, and (3) SARS-CoV-2 acute infections, immune responses, transmission dynamics, and symptomatic versus asymptomatic contacts in a unique cohort of unvaccinated primary school learners, their parents, teachers, and close contacts in semirural primary school settings.

Methods: Learners (grades 1-7) from primary schools in KwaZulu-Natal, South Africa, their parents, and teachers will be invited to enroll into the COVID kids school study (CoKiDSS).

Neprilysin-Mediated Amyloid Beta Clearance and Its Therapeutic Implications in Neurodegenerative Disorders.

Neprilysin (NEP) is a neutral endopeptidase, important for the degradation of amyloid beta (Aβ) peptides and other neuropeptides, including enkephalins, substance P, and bradykinin, in the brain, that influences various physiological processes such as blood pressure homeostasis, pain perception, and neuroinflammation. NEP breaks down Aβ peptides into smaller fragments, preventing the development of detrimental aggregates such as Aβ plaques. NEP clears Aβ plaques predominantly by enzymatic breakdown in the extracellular space.

Recommendations for the optimal introduction of novel antibiotics to treat uncomplicated gonorrhoea in the face of increasing antimicrobial resistance: a case study with zoliflodacin.

New, first-in-class oral antibiotics like zoliflodacin, developed in a public-private partnership, require an optimal introduction strategy while ensuring antibiotic stewardship. Zoliflodacin, given as a single dose for uncomplicated urogenital gonorrhoea, recently demonstrated non-inferiority to ceftriaxone plus azithromycin and safety in a phase 3 randomised controlled trial. Following regulatory approval, zoliflodacin could improve sexually transmitted infection (STI) management and help address the threat of untreatable gonorrhoea, as levels of resistance to current first-line treatments increase.

Structure-based drug designing for potential antiviral activity of selected natural product against Monkeypox (Mpox) virus and its host targets.

Unlabelled: (MPV/MPXV/hMPXV) is a zoonotic infection that is a causative agent of monkeypox disease, which is mainly endemic in West and Central Africa regions, but recent trends suggested that the virus is transmitted around 116 countries worldwide and is still spreading in multiple non-endemic countries, causing global outbreaks. The current therapeutic options for Mpox are limited, with the WHO temporarily recommending smallpox drugs. This suggests an urgent need to discover new therapeutics that may target both viral and host markers involved in the virus life cycle.

Exploring polyamine metabolism of the yeast-like fungus, Emergomyces africanus.

Emergomyces africanus is a thermally dimorphic pathogen causing severe morbidity and mortality in immunocompromized patients. Its transition to a pathogenic yeast-like phase in the human host is a notable virulence mechanism. Recent studies suggest polyamines as key players in dimorphic switching, yet their precise functions remain enigmatic.

The epidemiology of laboratory-confirmed Hepatitis B Virus infection in the general population of South Africa, 2016-2018.

Introduction: despite the introduction of the Hepatitis B Virus (HBV) vaccine in South Africa in 1995, HBV remains endemic. South Africa's HBV vaccine coverage for the third dose was 71% in 2015. Information on the HBV prevalence in South Africa in recent years is limited, therefore, we estimated HBV prevalence and described annual trends.

Vaccine safety surveillance in South Africa through COVID-19: A journey to systems strengthening.

Background: Surveillance systems for monitoring and reporting adverse events following immunisation (AEFI) and adverse events of special interest (AESI) are vital in understanding safety profiles of post-marketed vaccines. Evaluation of surveillance systems is necessary for systems strengthening. We conducted the first evaluation of the South African AEFI surveillance system in its current form, established in 2018.

Safety, effectiveness and immunogenicity of heterologous mRNA-1273 boost after prime with Ad26.COV2.S among healthcare workers in South Africa: The single-arm, open-label, phase 3 SHERPA study.

Limited studies have been conducted on the safety and effectiveness of heterologous COVID-19 vaccine boosting in lower income settings, especially those with high-HIV prevalence., The Sisonke Heterologous mRNA-1273 boost after prime with Ad26.COV2.

Novel polymorphic and copy number diversity in the antibody IGH locus of South African individuals.

The heavy chain of an antibody is crucial for mediating antigen binding. IGHV genes, which partially encode the heavy chain of antibodies, exhibit vast genetic diversity largely through polymorphism and copy number variation (CNV). These genetic variations impact population-level expression levels.

Clostridioides difficile hypervirulent strain ST1 isolated from clinical stool specimens obtained from three Provinces in South Africa.

Objectives: Clostridioides difficile infection is a serious healthcare-associated infection linked to antimicrobial use. The severity of the disease can be associated with hypervirulent ribotypes such as RT027. The study aimed to investigate the molecular epidemiology and genomic characteristics of C.