Nutrient pollution in South African estuaries is described using a Driver-Pressure-State-Impact-Response framework. The root cause ('driver') of deteriorating water quality is rapid population growth ...that leads to increasing inputs from wastewater treatment works (WWTWs), stormwater run-off and agricultural return flow ('pressures'). Nationally, half of the country's estuaries are affected by nutrient pollution ('state'). This has elicited marked primary producer and secondary (hypoxia, fish kills, loss of ecosystem services) responses ('impact'). The Sundays and Swartkops Estuaries are eutrophic with phytoplankton blooms (>20 µg l−1) and bottom-water hypoxia. Similarly, the nationally important Knysna Estuary experiences eutrophic conditions associated with macroalgal blooms, whereas the Wildevoëlvlei and Zeekoe systems have transitioned to alternate stable states characterised by toxic cyanobacteria blooms, as a result of WWTW inputs and increased water residence times. The health of the St Lucia Estuary, a UNESCO World Heritage site, is under threat from agricultural inputs from the uMfolozi system. Nationally, better treatment and recycling of WWTW inputs is required to improve and restore estuary health. Owing to excessive WWTW effluent volumes, treatment to South Africa's uniform effluent standards no longer prevent eutrophication. Other urgent interventions needed are compliance monitoring, engineering solutions to reduce stormwater and wastewater input, and prudent application of agricultural fertilisers.
Rapid degradation of ecosystems and loss of ecosystem services have sparked interest in developing approaches to report and integrate such change with socio-economic information systems, such as the ...System of National Accounts. Here we describe an approach and application of ecosystem accounting for individual estuaries, building on approaches previously applied at national and bay levels. Using the Swartkops Estuary as a case study, the focus is on physical accounts for ecosystem extent and condition, as well as accounts for two important ecosystem services (carbon sequestration and recreational use). Pressure accounts are also introduced to demonstrate the value of identifying key areas for management and restoration interventions in response to changes in extent and/or condition accounts. Greater resolution in these account reports, achieved through zoning, provides spatially explicit information on ecosystem assets and their services within an estuary to also inform management decision-making at local level. Further, these accounts can also inform local restoration prioritisation, in support of the UN Decade on Ecosystem Restoration (2021-2030), for example offsetting irreversibly degraded areas in one zone with restoration or maintenance of similar habitats in another.Significance: • This study is the first to apply the ecosystem accounting approach at the individual estuary level. • We provide spatially explicit information on ecosystem assets and their services in support of resource management. • Physical accounts include extent and condition, as well as ecosystem service and pressure accounts. • These accounts inform estuary management and restoration at the local governance level.
This report presents the Consolidated Standards of Reporting Trials (CONSORT) extension for the stepped wedge cluster randomised trial (SW-CRT). The SW-CRT involves randomisation of clusters to ...different sequences that dictate the order (or timing) at which each cluster will switch to the intervention condition. The statement was developed to allow for the unique characteristics of this increasingly used study design. The guideline was developed using a Delphi survey and consensus meeting; and is informed by the CONSORT statements for individual and cluster randomised trials. Reporting items along with explanations and examples are provided. We include a glossary of terms, and explore the key properties of the SW-CRT which require special consideration in their reporting.
Background: Limited evidence supports the efficacy of antimicrobial prophylaxis (AP) in prevention of gunshot woundrelated (GSW-related) infection in resource restricted areas. At Tygerberg Hospital, ...South Africa, it is standard care for GSW patients to receive one dose of broad-spectrum AP. For various reasons, this protocol is not consistently followed. This study aimed to assess the efficacy of AP in the reduction of in-hospital GSW-related infection and to identify opportunities for practice improvement.Methods: All patients admitted with GSW over a three-month period were eligible for inclusion. Patients who did and did not receive AP were identified retrospectively the morning of admission; thereafter, data was collected prospectively. Data regarding circumstances of the incident, injury characteristics, type of AP and surgery was obtained. The occurrence of in-hospital GSW-related infection was recorded over 30 days or until discharge. Propensity score matching (PSM) and inverse probability weighting (IPW) methods were utilised to assess the effect of AP on the prevention of GSW-related infection.Results: 165 consecutive patients were assessed, of which 103 received AP according to protocol within 12 hours of admission. PSM showed a reduced in-hospital GSW infection risk of 12% (95% CI, 0.2–24%, p = 0.046) with AP. IPW showed that AP reduced the risk for infection by 14% (95% CI, 3–27%, p = 0.015).Conclusions: Providing AP to GSW patients in a civilian setting appeared to result in a modest but clinically relevant lower risk of in-hospital GSW-related infection. In this study setting, optimisation of AP for all patients with GSWs should significantly lower the burden of wound infection.
The Interrupted Time Series (ITS) is a robust design for evaluating public health and policy interventions or exposures when randomisation may be infeasible. Several statistical methods are available ...for the analysis and meta-analysis of ITS studies. We sought to empirically compare available methods when applied to real-world ITS data.
We sourced ITS data from published meta-analyses to create an online data repository. Each dataset was re-analysed using two ITS estimation methods. The level- and slope-change effect estimates (and standard errors) were calculated and combined using fixed-effect and four random-effects meta-analysis methods. We examined differences in meta-analytic level- and slope-change estimates, their 95% confidence intervals, p-values, and estimates of heterogeneity across the statistical methods.
Of 40 eligible meta-analyses, data from 17 meta-analyses including 282 ITS studies were obtained (predominantly investigating the effects of public health interruptions (88%)) and analysed. We found that on average, the meta-analytic effect estimates, their standard errors and between-study variances were not sensitive to meta-analysis method choice, irrespective of the ITS analysis method. However, across ITS analysis methods, for any given meta-analysis, there could be small to moderate differences in meta-analytic effect estimates, and important differences in the meta-analytic standard errors. Furthermore, the confidence interval widths and p-values for the meta-analytic effect estimates varied depending on the choice of confidence interval method and ITS analysis method.
Our empirical study showed that meta-analysis effect estimates, their standard errors, confidence interval widths and p-values can be affected by statistical method choice. These differences may importantly impact interpretations and conclusions of a meta-analysis and suggest that the statistical methods are not interchangeable in practice.
The first critically ill patient admitted to our hospital in Cape Town, South Africa, during the COVID-19 pandemic was co-infected with HIV and SARS-CoV-2. Pneumocystis jirovecii pneumonia (PCP) and ...other respiratory opportunistic infections share many clinical features with severe COVID-19. Our understanding of the nuances of co-management of HIV and COVID-19 is evolving. We describe the diagnostic and therapeutic challenges presented by this case.
BACKGROUNDEmpirical broad-spectrum antibiotics are frequently prescribed to patients with severe COVID-19, motivated by concern about bacterial coinfection. There is no evidence of benefit from such ...a strategy, while the dangers of inappropriate antibiotics are well described. OBJECTIVESTo investigate the frequency, profile and related outcomes of infections by bacterial pathogens in patients admitted to an intensive care unit (ICU) with severe COVID-19 pneumonia. METHODSThis was a prospective, descriptive study in a dedicated COVID-19 ICU in Cape Town, South Africa, involving all adult patients admitted to the ICU with confirmed COVID-19 pneumonia between 26 March and 31 August 2020. We collected data on patient comorbidities, laboratory results, antibiotic treatment, duration of admission and in-hospital outcome. RESULTSWe included 363 patients, who collectively had 1 199 blood cultures, 308 tracheal aspirates and 317 urine cultures performed. We found positive cultures for pathogens in 20 patients (5.5%) within the first 48 hours of ICU admission, while 73 additional patients (20.1%) had positive cultures later during their stay. The most frequently isolated pathogens at all sites were Acinetobacter baumannii (n=54), Klebsiella species (n=13) and coagulase-negative staphylococci (n=9). Length of ICU stay (p<0.001) and intubation (p<0.001) were associated with positive cultures on multivariate analysis. Disease severity (p=0.5), early antibiotic use (p=0.5), diabetes mellitus (p=0.1) and HIV (p=0.9) were not associated with positive cultures. Positive cultures, particularly for tracheal aspirates (p<0.05), were associated with longer ICU length of stay and mortality. Early empirical antibiotic use was not associated with mortality (odds ratio 2.5; 95% confidence interval 0.95 - 6.81). CONCLUSIONSBacterial coinfection was uncommon in patients at the time of admission to the ICU with severe COVID-19. Avoiding early empirical antibiotic therapy is therefore reasonable. Strategies to avoid coinfection and outbreaks in hospital, such as infection prevention and control, as well as the strict use of personal protective equipment, are important to improve outcomes.
Stepped‐wedge cluster randomized trials, which randomize clusters of subjects to treatment sequences in which clusters switch from control to intervention conditions, are being conducted with ...increasing frequency. Due to the real‐world nature of this design, methodological and implementation challenges are ubiquitous. To account for such challenges, more complex statistical models to plan studies and analyze data are required. In this paper, we consider stepped‐wedge trials that accommodate treatment effect heterogeneity across clusters, implementation periods during which no data are collected, or both treatment effect heterogeneity and implementation periods. Previous work has shown that the sequence‐period cells of a stepped‐wedge design contribute unequal amounts of information to the estimation of the treatment effect. In this paper, we extend that work by considering the amount of information available for the estimation of the treatment effect in each sequence‐period cell, sequence, and period of stepped‐wedge trials with more complex designs and outcome models. When either treatment effect heterogeneity and/or implementation periods are present, the pattern of information content of sequence‐period cells tends to be clustered around the times of the switch from control to intervention condition, similarly to when these complexities are absent. However, the presence and degree of treatment effect heterogeneity and the number of implementation periods can influence the information content of periods and sequences markedly.
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