Rotavirus genotypes in children under five years hospitalized with diarrhea in low and middle-income countries: Results from the WHO-coordinated Global Rotavirus Surveillance Network.

Rotavirus is the most common pathogen causing pediatric diarrhea and an important cause of morbidity and mortality in low- and middle-income countries. Previous evidence suggests that the introduction of rotavirus vaccines in national immunization schedules resulted in dramatic declines in disease burden but may also be changing the rotavirus genetic landscape and driving the emergence of new genotypes. We report genotype data of more than 16,000 rotavirus isolates from 40 countries participating in the Global Rotavirus Surveillance Network.

Tuberculosis testing patterns in South Africa to identify groups that would benefit from increased investigation.

The National Health Laboratory Service (NHLS) collects all public health laboratory test results in South Africa, providing a cohort from which to identify groups, by age, sex, HIV, and viral suppression status, that would benefit from increased tuberculosis (TB) testing. Using NHLS data (2012-2016), we assessed levels and trends over time in TB diagnostic tests performed (count and per capita) and TB test positivity. Estimates were stratified by HIV status, viral suppression, age, sex, and province.

The genomic epidemiology of shigellosis in South Africa.

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei.

Genomics for public health and international surveillance of antimicrobial resistance.

Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome.

manogepix susceptibility testing of South African , and clinical isolates.

We performed antifungal susceptibility testing of manogepix against the yeast phase of 78 , 2 and 5 isolates using a reference broth microdilution method following Clinical and Laboratory Standards Institute recommendations. All three pathogens had low minimum inhibitory concentrations ranging from <0.0005 to 0.

Transient increased risk of influenza infection following RSV infection in South Africa: findings from the PHIRST study, South Africa, 2016-2018.

Background: Large-scale prevention of respiratory syncytial virus (RSV) infection may have ecological consequences for co-circulating pathogens, including influenza. We assessed if and for how long RSV infection alters the risk for subsequent influenza infection.

Methods: We analysed a prospective longitudinal cohort study conducted in South Africa between 2016 and 2018.

Three novel sequencing types from seventeen genomes isolated from dairy cows milk in the Free State Province of South Africa.

is one of the major pathogens causing bovine mastitis, which results in huge economic losses in the dairy industry worldwide. Here, we report genome sequences of 17 . strains, with three novel sequencing types (ST8495, ST8500, and ST8501) isolated from the milk of dairy cows with subclinical mastitis.

Characterization of Salmonella enterica serovar Isangi from South Africa, 2020-2021.

Background: We describe the genotypic characteristics and antimicrobial resistance (AMR) determinants of Salmonella enterica serovar Isangi (Salmonella Isangi) clinical isolates in South Africa from 2020 through 2021.

Methods: During the years 2020 to 2021, the Centre for Enteric Diseases of the National Institute for Communicable Diseases, a national reference centre in South Africa for human infections resulting from enteric bacterial pathogens, investigated a total of 3549 clinical isolates of Salmonella species. Whole genome sequencing (WGS) was performed using Illumina NextSeq Technology.

Association of HIV Exposure and HIV Infection With In-hospital Mortality Among Hospitalized Infants <1 Year of Age, South Africa, 2016-2018.

We enrolled 1323 hospitalized infants aged <1 year in 2016-2018, and examined the association between HIV status and in-hospital mortality. After controlling for confounders, HIV-exposed uninfected infants did not have an increased risk of mortality, whereas infants living with HIV had 4 times greater risk compared with HIV-uninfected infants.

Vaccine value profile for norovirus.

Norovirus is attributed to nearly 1 out of every 5 episodes of diarrheal disease globally and is estimated to cause approximately 200,000 deaths annually worldwide, with 70,000 or more among children in developing countries. Noroviruses remain a leading cause of sporadic disease and outbreaks of acute gastroenteritis even in industrialized settings, highlighting that improved hygiene and sanitation alone may not be fully effective in controlling norovirus. Strengths in global progress towards a Norovirus vaccine include a diverse though not deep pipeline which includes multiple approaches, including some with proven technology platforms (e.

More Frequent HIV Viral Load Testing With Point-Of-Care Tests Detects Elevated Viral Load Earlier in Postpartum HIV-Positive Women in a Randomized Controlled Trial in Two Clinics in Johannesburg, South Africa.

Background: Elevated maternal HIV viral load (VL) increases vertical transmission risk for breastfeeding children. This randomized controlled trial in Johannesburg primarily evaluated whether 3-monthly point-of-care testing, with laboratory-based standard-of-care testing (arm 2), compared with 6-monthly laboratory-based VL testing (arm 1) in postpartum women living with HIV receiving first-line tenofovir-emtricitabine-efavirenz antiretroviral treatment improved VL suppression, factors associated with nonsuppression, and drug resistance in those with virologic failure.

Methods: Mother-child pairs were enrolled July 2018-April 2019 at the child's 6/10/14-week clinic visit.

Antimicrobial susceptibility profile of from patients attending a medical laboratory, Institut Pasteur de Madagascar between 2014 and 2020: phenotypical and genomic characterisation in a subset of isolates.

Objectives: Antimicrobial-resistant (NG) is a concern. Little is known about antimicrobial susceptibility profiles and associated genetic resistance mechanisms of NG in Madagascar. We report susceptibility data of NG isolates obtained by the medical laboratory (CBC) of the Institut Pasteur de Madagascar, Antananarivo, Madagascar, during 2014-2020.

Homologous Ad26.COV2.S vaccination results in reduced boosting of humoral responses in hybrid immunity, but elicits antibodies of similar magnitude regardless of prior infection.

The impact of previous SARS-CoV-2 infection on the durability of Ad26.COV2.S vaccine-elicited responses, and the effect of homologous boosting has not been well explored.

Exploring the potential of village community banking as a community-based financing system for house improvements and malaria vector control in rural Tanzania.

House improvement is associated with remarkable reductions in indoor mosquito bites and disease incidences, even in typical rural houses. However, its exploitation remains extremely poor in Tanzania and other endemic countries due to limited financial resources. Nevertheless, village community banks (VICOBA), practiced in Tanzania for nearly two decades, have proven to provide financial services to rural communities that would otherwise not be able to get them from formal financial institutions.

Scaling artificial light at night and disease vector interactions into socio-ecological systems: a conceptual appraisal.

There is burgeoning interest in how artificial light at night (ALAN) interacts with disease vectors, particularly mosquitoes. ALAN can alter mosquito behaviour and biting propensity, and so must alter disease transfer rates. However, most studies to date have been laboratory-based, and it remains unclear how ALAN modulates disease vector risk.

Risks of Adverse Outcomes for Hospitalized COVID-19 Patients during the Four Waves in Brazil According to SARS-CoV-2 Variants, Age Group, and Vaccine Status.

Brazil was hit with four consecutive waves of COVID-19 until 2022 due to the ancestral SARS-CoV-2 (B.1 lineage), followed by the emergence of variants/subvariants. Relative risks of adverse outcomes for COVID-19 patients hospitalized during the four waves were evaluated.

Integrating Molecular Diagnostics and GIS Mapping: A Multidisciplinary Approach to Understanding Tuberculosis Disease Dynamics in South Africa Using Xpert MTB/RIF.

An investigation was carried out to examine the use of national Xpert MTB/RIF data (2013-2017) and GIS technology for MTB/RIF surveillance in South Africa. The aim was to exhibit the potential of using molecular diagnostics for TB surveillance across the country. The variables analysed include () positivity, the mycobacterial proportion of rifampicin-resistant (RIF), and probe frequency.

Characterisation of Milk Microbiota from Subclinical Mastitis and Apparently Healthy Dairy Cattle in Free State Province, South Africa.

Bovine mastitis is an inflammation of the udder tissue of the mammary gland brought on by microbial infections or physical damage. It is characterised by physical, chemical, and biological changes in the udder and milk. While several different bacterial species have been identified as causative agents of mastitis, many subclinical mastitis (SCM) cases remain culture-negative.

Heterogeneous genetic architectures and evolutionary genomics of prostate cancer in Sub-Saharan Africa.

Men of African descent have the highest prostate cancer (CaP) incidence and mortality rates, yet the genetic basis of CaP in African men has been understudied. We used genomic data from 3,963 CaP cases and 3,509 controls recruited in Ghana, Nigeria, Senegal, South Africa, and Uganda, to infer ancestry-specific genetic architectures and fine-mapped disease associations. Fifteen independent associations at 8q24.

Vaccinating people living with HIV: a fast track to preventive and therapeutic HIV vaccines.

Globally, the number of new HIV infections remains unacceptably high, and urgent new approaches are needed to advance HIV vaccine science. However, the development of a preventive HIV vaccine has proven to be an intractable scientific challenge. Recent advances in HIV immunogen design have taken the field a step closer to triggering the rare precursors of broadly neutralising antibodies, which are widely assumed to be necessary for a vaccine.

Evaluation of the accuracy of the Asanté assay as a point-of-care rapid test for HIV-1 recent infections using serum bank specimens from blood donors in South Africa, July 2018 - August 2021.

Background: Point-of-care (POC) rapid recency testing can be used as a cost-effective tool to identify recently infected individuals (i.e. infected within the last 12 months) in near-real time, support epidemic control and identify hotspots for transmission as part of recent infection surveillance.

Genotype-Phenotype Characterization of Serial Mycobacterium tuberculosis Isolates in Bedaquiline-Resistant Tuberculosis.

Background: Emerging resistance to bedaquiline (BDQ) threatens to undermine advances in the treatment of drug-resistant tuberculosis (DRTB). Characterizing serial Mycobacterium tuberculosis (Mtb) isolates collected during BDQ-based treatment can provide insights into the etiologies of BDQ resistance in this important group of DRTB patients.

Methods: We measured mycobacteria growth indicator tube (MGIT)-based BDQ minimum inhibitory concentrations (MICs) of Mtb isolates collected from 195 individuals with no prior BDQ exposure who were receiving BDQ-based treatment for DRTB.

Geospatial based model for malaria risk prediction in Kilombero valley, South-eastern, Tanzania.

Background: Malaria continues to pose a major public health challenge in tropical regions. Despite significant efforts to control malaria in Tanzania, there are still residual transmission cases. Unfortunately, little is known about where these residual malaria transmission cases occur and how they spread.