Additional file 1: Details of the search strategy. S1.1. Database search strategy. S1.1.2. Updated database search strategy. S1.2. Google scholar search strategy. S1.2.2. Updated google scholar search strategy. S1.3. Google engine search strategy.

Abstract Background The COVID-19 pandemic has highlighted the importance of evidence-based clinical decision-making. Clinical management guidelines (CMGs) may help reduce morbidity and mortality by improving the quality of clinical decisions. This systematic review aims to evaluate the availability, inclusivity, and quality of pandemic influenza CMGs, to identify gaps that can be addressed to strengthen pandemic preparedness in this area. Methods Ovid Medline, Ovid Embase, TRIP (Turning Research Into Practice), and Guideline Central were searched systematically...

OBJECTIVE: We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection. METHODS: We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within...

OBJECTIVE: We aimed to compare clinical severity of Omicron BA.4/BA.5 infection with BA.1 and earlier variant infections among laboratory-confirmed SARS-CoV-2 cases in the Western Cape, South Africa, using timing of infection to infer the lineage/variant causing infection. METHODS: We included public sector patients aged ≥20 years with laboratory-confirmed COVID-19 between 1-21 May 2022 (BA.4/BA.5 wave) and equivalent prior wave periods. We compared the risk between waves of (i) death and (ii) severe hospitalization/death (all within...

Additional file 1: Table S1. Summary of treatment guidelines in South Africa during the Registry period. Table S2. Pre-2021 Treatment outcome definitions used in this study. Table S3. Patient disposition in the South African Registry study. Table S4. Propensity score sensitivity analysis for risk of mortality (EDRWeb data only, end of treatment). Figure S1. Effect of a bedaquiline-based regimen on A treatment success and B mortality (EDRWeb data only, end of treatment) for patient subgroups...

Additional file 2: Data extraction form. S2.1. Data extraction form.

Abstract Background This retrospective cohort study assessed benefits and risks of bedaquiline treatment in multidrug-resistant-tuberculosis (MDR-TB) combination therapy by evaluating safety, effectiveness, drug utilization and emergence of resistance to bedaquiline. Methods Data were extracted from a register of South African drug-resistant-tuberculosis (DR-TB) patients (Electronic DR-TB Register [EDRWeb]) for newly diagnosed patients with MDR-TB (including pre-extensively drug-resistant [XDR]-TB and XDR-TB and excluding rifampicin-mono-resistant [RR]-TB, as these patients are by definition not multidrug-resistant), receiving either a bedaquiline-containing...

Background: South Africa has the highest tuberculosis incidence globally (781/100,000), with an estimated 4.3% of cases being rifampicin resistant (RR). Control and elimination strategies will require detailed spatial information to understand where drug-resistant tuberculosis exists and why it persists in those communities. We demonstrate a method to enable drug-resistant tuberculosis monitoring by identifying high-burden communities in the Western Cape Province using routinely collected laboratory data. Methods and findings: We retrospectively identified cases of microbiologically confirmed...

Additional file 3: Additional figure Figure S3.1. PRISMA diagram

Additional file 3: Additional figure Figure S3.1. PRISMA diagram

Additional file 1: Details of the search strategy. S1.1. Database search strategy. S1.1.2. Updated database search strategy. S1.2. Google scholar search strategy. S1.2.2. Updated google scholar search strategy. S1.3. Google engine search strategy.

While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the...

Objectives: To investigate prevalence of cervical human papillomavirus (HPV) genotypes to inform HPV vaccination strategy in South Africa and to study factors associated with HPV prevalence. Methods: Sexually active, HIV-negative women, aged 16-22 years recruited from Soweto (n=143) and Cape Town (n=148) were tested for cervical HPV and other genital infections. Results: Overall HPV prevalence was 66.7% (194/291) in young women. Cape Town women were more likely to have multiple HPV infections than the Soweto...

Additional file 4: Additional tables Table S4.1. Characteristics of identified CMGs. Table S4.2. CMG recommendations for treatment and supportive care. Table S4.3. Oseltamivir treatment and chemoprophylactic doses for children and infants.

Additional file 1: Table S1. Summary of treatment guidelines in South Africa during the Registry period. Table S2. Pre-2021 Treatment outcome definitions used in this study. Table S3. Patient disposition in the South African Registry study. Table S4. Propensity score sensitivity analysis for risk of mortality (EDRWeb data only, end of treatment). Figure S1. Effect of a bedaquiline-based regimen on A treatment success and B mortality (EDRWeb data only, end of treatment) for patient subgroups...

Background: South Africa has a large burden of rifampicin-resistant tuberculosis (RR-TB), with 18,734 patients diagnosed in 2014. The number of diagnosed patients has increased substantially with the introduction of the Xpert MTB/RIF test, used for TB diagnosis for all patients with presumptive TB. Routine aggregate data suggest a large treatment gap (pre-treatment loss to follow up) between the numbers of laboratory confirmed RR-TB patients and those reported to have started second-line treatment. We aimed to...

The final results from this multi-dose, 90-day inhalation toxicology study in the rat with life-time post-exposure observation have shown a significant fundamental difference in pathological response and tumorgenicity between brake dust generated from brake pads manufactured with chrysotile or from chrysotile alone in comparison to the amphiboles, crocidolite and amosite asbestos. The groups exposed to brake dust showed no significant pathological or tumorigenic response in the respiratory track compared to the air control group at...

Abstract Background This retrospective cohort study assessed benefits and risks of bedaquiline treatment in multidrug-resistant-tuberculosis (MDR-TB) combination therapy by evaluating safety, effectiveness, drug utilization and emergence of resistance to bedaquiline. Methods Data were extracted from a register of South African drug-resistant-tuberculosis (DR-TB) patients (Electronic DR-TB Register [EDRWeb]) for newly diagnosed patients with MDR-TB (including pre-extensively drug-resistant [XDR]-TB and XDR-TB and excluding rifampicin-mono-resistant [RR]-TB, as these patients are by definition not multidrug-resistant), receiving either a bedaquiline-containing...

Additional file 2: Data extraction form. S2.1. Data extraction form.

Additional file 4: Additional tables Table S4.1. Characteristics of identified CMGs. Table S4.2. CMG recommendations for treatment and supportive care. Table S4.3. Oseltamivir treatment and chemoprophylactic doses for children and infants.

Abstract Background The COVID-19 pandemic has highlighted the importance of evidence-based clinical decision-making. Clinical management guidelines (CMGs) may help reduce morbidity and mortality by improving the quality of clinical decisions. This systematic review aims to evaluate the availability, inclusivity, and quality of pandemic influenza CMGs, to identify gaps that can be addressed to strengthen pandemic preparedness in this area. Methods Ovid Medline, Ovid Embase, TRIP (Turning Research Into Practice), and Guideline Central were searched systematically...