Browsing by Subject "ICU"

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    Investigating expressed RNA variants that are related to disease severity in SARS-CoV-2-infected patients with mild-to-severe disease
    (2022-04-28) Okendo, Javan; Okanda, David
    Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and the understanding of what constitutes expressed RNAseq variants in healthy, convalescent, severe, moderate, and those admitted to the intensive care unit (ICU) is yet to be presented. We characterize the different expressed RNAseq variants in healthy, severe, moderate, ICU, and convalescent individuals. Materials and methods: The bulk RNA sequencing data with identifier PRJNA639275 were downloaded from Sequence Reads Archive (SRA). The individuals were divided into: (1) healthy, n = 34, moderate, n = 8, convalescent, n = 2, severe, n = 16, and ICU, n = 8. Fastqc version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. STAR was used to align reads to the reference genome, and GATK best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines. Results: Our analysis demonstrated that different sets of unique RNAseq variants characterize convalescent, moderate, severe, and those admitted to the ICU. The data show that the individuals who recover from SARS-CoV-2 infection have the same set of expressed variants as the healthy controls. We showed that the healthy and SARS-CoV-2-infected individuals display different sets of expressed variants characteristic of the patient phenotype. Conclusion: The individuals with severe, moderate, those admitted to the ICU, and convalescent display a unique set of variants. The findings in this study will inform the test kit development and SARS-CoV-2 patients classification to enhance the management and control of SARS-CoV-2 infection in our population.
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    Risk factors and outcomes of acute kidney injury in South African critically ill adults: a prospective cohort study
    (2019-12-10) Aylward, Ryan E; van der Merwe, Elizabeth; Pazi, Sisa; van Niekerk, Minette; Ensor, Jason; Baker, Debbie; Freercks, Robert J
    Abstract Background There is a marked paucity of data concerning AKI in Sub-Saharan Africa, where there is a substantial burden of trauma and HIV. Methods Prospective data was collected on all patients admitted to a multi-disciplinary ICU in South Africa during 2017. Development of AKI (before or during ICU admission) was recorded and renal recovery 90 days after ICU discharge was determined. Results Of 849 admissions, the mean age was 42.5 years and mean SAPS 3 score was 48.1. Comorbidities included hypertension (30.5%), HIV (32.6%), diabetes (13.3%), CKD (7.8%) and active tuberculosis (6.2%). The most common reason for admission was trauma (26%). AKI developed in 497 (58.5%). Male gender, illness severity, length of stay, vasopressor drugs and sepsis were independently associated with AKI. AKI was associated with a higher in-hospital mortality rate of 31.8% vs 7.23% in those without AKI. Age, active tuberculosis, higher SAPS 3 score, mechanical ventilation, vasopressor support and sepsis were associated with an increased adjusted odds ratio for death. HIV was not independently associated with AKI or hospital mortality. CKD developed in 14 of 110 (12.7%) patients with stage 3 AKI; none were dialysis-dependent. Conclusions In this large prospective multidisciplinary ICU cohort of younger patients, AKI was common, often associated with trauma in addition to traditional risk factors and was associated with good functional renal recovery at 90 days in most survivors. Although the HIV prevalence was high and associated with higher mortality, this was related to the severity of illness and not to HIV status per se.
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    The costing of COVID-19 intensive care units at a tertiary hospital in Cape Town, South Africa
    (2024) Hood, Kirsten; Joubert, Ivan; Cunnama, Lucy; Peters, Shrikant
    Background: The expansion of Groote Schuur Hospital's (GSH) Intensive Care Unit (ICU) capacity to accommodate an unprecedented number of patients during the COVID-19 pandemic was an expensive undertaking. There are currently no published formal retrospective analyses of the financial costs of running and expanding COVID-ICUs in South Africa. Objectives: To conduct a cost analysis of the COVID-ICU service at a tertiary state hospital in Cape Town, South Africa. This analysis included the cost of COVID-ICU admissions relating to the first four COVID waves. Aims were to estimate total costs, in-patient day costs, and cost drivers for COVID-ICU. Methods: A retrospective cost analysis (quantitative observational study) using a mixed methods costing approach, was conducted across the COVID-ICUs at GSH. The data used included two consecutive hospital financial years, between April 2020 and March 2022. Costs were calculated monthly and then combined to achieve a total cost over the two-year period. COVID-ICU in-patient days were used as the primary allocation factor. Cost inputs included recurrent costs such as human resources, diagnostics, pharmaceuticals, oxygen, enteral feeds, blood products, consumables, and overheads, as well as capital costs including equipment, and building space. Results: The study period covered the four COVID waves that affected GSH ICU units between April 2020 and March 2022. This period included 10 497 COVID-ICU in-patient days resulting from a total of 776 COVID-ICU admissions. The total calculated spending across the two financial years was R262 482 904, resulting in a cost per in-patient day of R25 006, and a utilisation of 4,4% of the total hospital budget during the same period. The median length of stay was nine days, resulting in a median cost per admission of R225 050. The top five cost drivers were human resources (60%), consumables (9%), pharmaceuticals (8%), oxygen (5%), and overheads (5%). Conclusion: This is a retrospective costing study of the COVID-ICUs at a tertiary hospital in Cape Town, throughout the entire portion of the pandemic that required ICU admissions in South Africa. This analysis provides useful financial insights, a potential economic model for ICU budgeting, and creates a platform for future economic analyses and policy planning regarding level-of-care decisions for general ICU admissions or for similar future pandemics within the South African and LMIC hospital setting.