Nadè Claassen, G. van Wyk, S. van Staden, Michiel M.D. Basson
Background The coronavirus disease 2019 (COVID-19) pandemic in tertiary hospitals from South Africa and world wide have been well described, but limited data are published on the findings. This article aimed to describe patients admitted to a large district hospital in Cape Town, South Africa, during the first wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Infections. To compare the clinical features and further investigate survivors and deceased COVID-19 patients. Methods A single centre retrospective review of clinical records and laboratory data of patients admitted with a positive SARS-CoV-2 polymerase chain reaction (PCR) from April 2020 to August 2020. Results A total of 568 patients with a positive SARS-CoV-2 PCR were admitted to the study centre for one night or longer and of these patients 154 (27%) died of COVID-19. The median age of patients who died of COVID-19 was 66 years and 53 years for survivors. Hypertension, diabetes mellitus and obesity were the commonest comorbidities in patients who survived and died of COVID-19. There were no major differences when comparing the severity of infiltrates on chest X-rays (CXR) of COVID-19 survivors with deceased patients. More than half (58%) of deceased patients died within 3 days following admission to hospital. A substantial number of patients who died of COVID-19 had associated acute kidney injury (n = 79, 51%). Conclusion Acute kidney injury had a high prevalence amongst patients who died of COVID-19. Delays in transfer to intensive care unit (ICU), limited ICU capacity and disease severity contributed to a substantial number of patients dying within 3 days of admission.
{"title":"Experiencing COVID-19 at a large district level hospital in Cape Town: A retrospective analysis of the first wave","authors":"Nadè Claassen, G. van Wyk, S. van Staden, Michiel M.D. Basson","doi":"10.4102/sajid.v37i1.317","DOIUrl":"https://doi.org/10.4102/sajid.v37i1.317","url":null,"abstract":"Background The coronavirus disease 2019 (COVID-19) pandemic in tertiary hospitals from South Africa and world wide have been well described, but limited data are published on the findings. This article aimed to describe patients admitted to a large district hospital in Cape Town, South Africa, during the first wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Infections. To compare the clinical features and further investigate survivors and deceased COVID-19 patients. Methods A single centre retrospective review of clinical records and laboratory data of patients admitted with a positive SARS-CoV-2 polymerase chain reaction (PCR) from April 2020 to August 2020. Results A total of 568 patients with a positive SARS-CoV-2 PCR were admitted to the study centre for one night or longer and of these patients 154 (27%) died of COVID-19. The median age of patients who died of COVID-19 was 66 years and 53 years for survivors. Hypertension, diabetes mellitus and obesity were the commonest comorbidities in patients who survived and died of COVID-19. There were no major differences when comparing the severity of infiltrates on chest X-rays (CXR) of COVID-19 survivors with deceased patients. More than half (58%) of deceased patients died within 3 days following admission to hospital. A substantial number of patients who died of COVID-19 had associated acute kidney injury (n = 79, 51%). Conclusion Acute kidney injury had a high prevalence amongst patients who died of COVID-19. Delays in transfer to intensive care unit (ICU), limited ICU capacity and disease severity contributed to a substantial number of patients dying within 3 days of admission.","PeriodicalId":44007,"journal":{"name":"Southern African Journal of Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42460367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bacteriophages (phages) were discovered in the early part of the 20th century, and their ability to eliminate bacterial infections as bacterial viruses gathered interest almost immediately. Bacteriophage therapy was halted in the Western world due to inconclusive results in early experiments and the concurrent discovery of antibiotics. The spread of antibiotic-resistant bacteria has elicited renewed interest in bacteriophages as a natural alternative to conventional antibiotic therapy. Interest in the application of bacteriophages has also expanded to include the environment, such as wastewater treatment, agriculture and aquaculture. Although the complete phage is important in bacteriophage therapy, the focus is shifting to purified phage enzymes. These enzymes are an attractive option for pharmaceutical companies with their patent potential. They can be bio-engineered for enhanced adjuvant properties, such as a broadened spectrum of activity or binding capability. Enzymes also eliminate the concern that the prophage might integrate resistance genes into the bacterial genome. From a clinical perspective, the first randomised clinical controlled phage therapy trial was conducted with more pioneering phase I/II clinical studies on the horizon. In this opinion paper, the authors outline bacteriophages as naturally occurring bactericidal entities, their therapeutic potential against antibiotic-resistant bacteria and compare them to antibiotics. Their potential multipurpose application in the medical field is also addressed, including the use of bacteriophages for vaccination, and utilisation of the antimicrobial enzymes that they produce.
{"title":"Treating bacterial infections with bacteriophages in the 21st century","authors":"C. Opperman, J. Wojno, A. Brink","doi":"10.4102/sajid.v37i1.346","DOIUrl":"https://doi.org/10.4102/sajid.v37i1.346","url":null,"abstract":"Bacteriophages (phages) were discovered in the early part of the 20th century, and their ability to eliminate bacterial infections as bacterial viruses gathered interest almost immediately. Bacteriophage therapy was halted in the Western world due to inconclusive results in early experiments and the concurrent discovery of antibiotics. The spread of antibiotic-resistant bacteria has elicited renewed interest in bacteriophages as a natural alternative to conventional antibiotic therapy. Interest in the application of bacteriophages has also expanded to include the environment, such as wastewater treatment, agriculture and aquaculture. Although the complete phage is important in bacteriophage therapy, the focus is shifting to purified phage enzymes. These enzymes are an attractive option for pharmaceutical companies with their patent potential. They can be bio-engineered for enhanced adjuvant properties, such as a broadened spectrum of activity or binding capability. Enzymes also eliminate the concern that the prophage might integrate resistance genes into the bacterial genome. From a clinical perspective, the first randomised clinical controlled phage therapy trial was conducted with more pioneering phase I/II clinical studies on the horizon. In this opinion paper, the authors outline bacteriophages as naturally occurring bactericidal entities, their therapeutic potential against antibiotic-resistant bacteria and compare them to antibiotics. Their potential multipurpose application in the medical field is also addressed, including the use of bacteriophages for vaccination, and utilisation of the antimicrobial enzymes that they produce.","PeriodicalId":44007,"journal":{"name":"Southern African Journal of Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44643528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
R. Spies, M. Potter, Sudarshan Govender, Luke Kirk, Simon Rauch, J. Black
Background Evidence-based Infection Prevention and Control (IPC) measures are critical in protecting medical doctors from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Concerns surrounding access to personal protective equipment (PPE), compliance with IPC measures and the quality of available PPE have been raised as possible causes for high rates of SARS-CoV-2 infection in medical doctors in high transmission settings. This study aimed to determine the prevalence of SARS-CoV-2 infection and the risk factors for occupational infection in doctors in the hospitals in Nelson Mandela Bay (NMB). Methods We conducted a cross-sectional study wherein we electronically surveyed medical doctors in public-sector NMB hospitals from 01 March 2020 to 31 December 2020. We collected demographic, health, occupational and SARS-CoV-2 infection and exposure data. Categorical data were described as proportions and a multiple variable logistic regression model was used to identify risk factors for SARS-CoV-2 infection. Results The survey was distributed amongst 498 doctors, 141 (28%) of whom replied. Forty-three (31%) participants reported that they had tested positive for SARS-CoV-2 during the study period. Eighty-nine participants (64%) reported inadequate access to PPE whilst only 68 (49%) participants adhered to PPE recommendations when interacting with patients with confirmed or suspected SARS-CoV-2 infection. We were unable to identify any significant predictors of SARS-CoV-2 infection. Conclusion This study demonstrates a high prevalence of SARS-CoV-2 infection in public hospital doctors in NMB. Most participants reported inadequate access to PPE and poor compliance with IPC protocols. These findings suggest an urgent need for the improved implementation of IPC measures to protect doctors from SARS-CoV-2 infection.
{"title":"SARS-CoV-2 infection in public hospital medical doctors in an Eastern Cape metro","authors":"R. Spies, M. Potter, Sudarshan Govender, Luke Kirk, Simon Rauch, J. Black","doi":"10.4102/sajid.v37i1.335","DOIUrl":"https://doi.org/10.4102/sajid.v37i1.335","url":null,"abstract":"Background Evidence-based Infection Prevention and Control (IPC) measures are critical in protecting medical doctors from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Concerns surrounding access to personal protective equipment (PPE), compliance with IPC measures and the quality of available PPE have been raised as possible causes for high rates of SARS-CoV-2 infection in medical doctors in high transmission settings. This study aimed to determine the prevalence of SARS-CoV-2 infection and the risk factors for occupational infection in doctors in the hospitals in Nelson Mandela Bay (NMB). Methods We conducted a cross-sectional study wherein we electronically surveyed medical doctors in public-sector NMB hospitals from 01 March 2020 to 31 December 2020. We collected demographic, health, occupational and SARS-CoV-2 infection and exposure data. Categorical data were described as proportions and a multiple variable logistic regression model was used to identify risk factors for SARS-CoV-2 infection. Results The survey was distributed amongst 498 doctors, 141 (28%) of whom replied. Forty-three (31%) participants reported that they had tested positive for SARS-CoV-2 during the study period. Eighty-nine participants (64%) reported inadequate access to PPE whilst only 68 (49%) participants adhered to PPE recommendations when interacting with patients with confirmed or suspected SARS-CoV-2 infection. We were unable to identify any significant predictors of SARS-CoV-2 infection. Conclusion This study demonstrates a high prevalence of SARS-CoV-2 infection in public hospital doctors in NMB. Most participants reported inadequate access to PPE and poor compliance with IPC protocols. These findings suggest an urgent need for the improved implementation of IPC measures to protect doctors from SARS-CoV-2 infection.","PeriodicalId":44007,"journal":{"name":"Southern African Journal of Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44120190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The coronavirus disease 2019 (COVID-19) pandemic has irrevocably changed every aspect of social, medical and economic life globally. Although our traditional Western consideration of the underlying causes have led to massive strides in prevention and control of spread, a wider more inclusive approach, including principles of African and non-Western causality may facilitate our ability to prevent future outbreaks. Decolonising our traditional thoughts on medical causality may compliment the practice of medicine and enrich our understanding of health.
{"title":"Decolonising medical causality in the COVID-19 pandemic","authors":"A. Visser","doi":"10.4102/sajid.v37i1.347","DOIUrl":"https://doi.org/10.4102/sajid.v37i1.347","url":null,"abstract":"The coronavirus disease 2019 (COVID-19) pandemic has irrevocably changed every aspect of social, medical and economic life globally. Although our traditional Western consideration of the underlying causes have led to massive strides in prevention and control of spread, a wider more inclusive approach, including principles of African and non-Western causality may facilitate our ability to prevent future outbreaks. Decolonising our traditional thoughts on medical causality may compliment the practice of medicine and enrich our understanding of health.","PeriodicalId":44007,"journal":{"name":"Southern African Journal of Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49511011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Background Candidemia is associated with high morbidity and mortality. The epidemiology of candidemia has changed globally over the past 20 years. South African surveillance demonstrated a shift in epidemiology from Candida albicans to non-albicans species including Candida parapsilosis and Candida auris. Hospital-level candidemia incidence from South Africa has not been reported previously. Methods We performed a retrospective laboratory-based analysis of blood cultures with confirmed causative agents of candidemia. Ward type, department, gender and admission to critical care units were captured. Data were analysed in Microsoft Excel, Statistical Package for the Social Sciences (SPSS) and Epitools. Results The incidence of candidemia during the study period was 2.87 per 1000 admissions. The total proportion of non-albicans species causing candidemia was 425/618 (69.7%). Overall, 65.4% of candidemia cases occurred in non-critical care units. There was a significant increase in the proportion of C. auris isolates between 2016 and 2020 (p < 0.001). Isolation of C. auris was associated with admission to critical care units (p < 0.001, odds ration [OR] 3.856, 95% confidence interval [CI]: 2.360–6.300). The proportion of azole-resistant candidemia cases increased from 21/53 (39.6%) in 2016 to 41/59 (69.5%) in 2020 (p = 0.002). Conclusion The incidence of candidemia remained stable over the five-year study period. However, the proportion of C. auris isolates increased significantly during the study period as did the overall proportion of azole-resistant candidemia. Antifungal stewardship and continued hospital-level surveillance are imperative.
{"title":"Incidence of candidemia and prevalence of azole-resistant candidemia at a tertiary South African hospital – A retrospective laboratory analysis 2016–2020","authors":"V. Chibabhai","doi":"10.4102/sajid.v37i1.326","DOIUrl":"https://doi.org/10.4102/sajid.v37i1.326","url":null,"abstract":"Background Candidemia is associated with high morbidity and mortality. The epidemiology of candidemia has changed globally over the past 20 years. South African surveillance demonstrated a shift in epidemiology from Candida albicans to non-albicans species including Candida parapsilosis and Candida auris. Hospital-level candidemia incidence from South Africa has not been reported previously. Methods We performed a retrospective laboratory-based analysis of blood cultures with confirmed causative agents of candidemia. Ward type, department, gender and admission to critical care units were captured. Data were analysed in Microsoft Excel, Statistical Package for the Social Sciences (SPSS) and Epitools. Results The incidence of candidemia during the study period was 2.87 per 1000 admissions. The total proportion of non-albicans species causing candidemia was 425/618 (69.7%). Overall, 65.4% of candidemia cases occurred in non-critical care units. There was a significant increase in the proportion of C. auris isolates between 2016 and 2020 (p < 0.001). Isolation of C. auris was associated with admission to critical care units (p < 0.001, odds ration [OR] 3.856, 95% confidence interval [CI]: 2.360–6.300). The proportion of azole-resistant candidemia cases increased from 21/53 (39.6%) in 2016 to 41/59 (69.5%) in 2020 (p = 0.002). Conclusion The incidence of candidemia remained stable over the five-year study period. However, the proportion of C. auris isolates increased significantly during the study period as did the overall proportion of azole-resistant candidemia. Antifungal stewardship and continued hospital-level surveillance are imperative.","PeriodicalId":44007,"journal":{"name":"Southern African Journal of Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49397360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A terrific journey for which I have great gratitude","authors":"L. Bekker","doi":"10.4102/sajid.v37i2.400","DOIUrl":"https://doi.org/10.4102/sajid.v37i2.400","url":null,"abstract":"","PeriodicalId":44007,"journal":{"name":"Southern African Journal of Infectious Diseases","volume":" ","pages":""},"PeriodicalIF":0.9,"publicationDate":"2022-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42233703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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