Molecular epidemiology and mechanism of resistance of invasive quinolone-resistant South African isolates of Salmonella enterica, 2004-2006

The molecular epidemiology and mechanism of quinolone resistance of South African human isolates of Salmonella Typhi for the period 2003-2007, Salmonella Enteritidis, Salmonella Isangi and Salmonella Typhimurium for the period 2004-2006, received by the Enteric Diseases Reference Unit (EDRU) of the National Institute for Communicable Diseases was investigated. Molecular epidemiology was investigated using pulsed-field gel electrophoresis (PFGE) analysis for all four serotypes, as well as multiple-locus variable-number tandem-repeats analysis (MLVA) for Salmonella Typhi and Salmonella Typhimurium. Three probable mechanisms for quinolone resistance were investigated which included: amino acid mutations in the quinolone resistance determining regions (QRDRs) of DNA gyrase (gyrA/gyrB) and topoisomerase IV (parC/parE), active efflux of antibiotic out the bacterial cell and plasmid-mediated resistance encoded by qnr genes. For the period 2003-2007, 498 human isolates of Salmonella Typhi were received by the EDRU, of which 27 were resistant to nalidixic acid (MICs, ≥32 μg/ml). Only 19 Salmonella Typhi quinolone-resistant isolates were available for analysis. For the period 2004-2006, 329 human isolates of Salmonella Enteritidis, 1005 human isolates of Salmonella Isangi and 2624 human isolates of Salmonella Typhimurium were received by the EDRU. Of these isolates, 119 Salmonella Enteritidis, 143 Salmonella Isangi and 532 Salmonella Typhimurium were invasive, nalidixic acid-resistant. Only 116 Salmonella Enteritidis, 137 Salmonella Isangi and 516 Salmonella Typhimurium invasive, nalidixic acid-resistant isolates were available for analysis. For each respective serotype the isolates were genetically diverse as they could be differentiated into many PFGE types, suggesting that quinolone-resistant strains have emerged independently of one another for all four serotypes. The use of MLVA for Salmonella Typhi and Salmonella Typhimurium also illustrated the genetic diversity of the isolates by differentiating the isolates in various MLVA types. The investigation into the contributory mechanisms of resistance showed that an over-active efflux system in combination with mutations in both gyrA and parC play a major role in facilitating quinolone resistance in Salmonella Typhi, Salmonella Enteritidis and Salmonella Isangi. These very same mechanisms were also found to be responsible for the quinolone resistance in the majority of the Salmonella Typhimurium isolates along with the rarely isolated mechanism of resistance, a qnr plasmid. This is the first report of any kind identifying the presence of qnr genes in South African Enterobacteriaceae isolates. Our study also highlights the need for further work to establish the link amongst the various mechanisms of resistance as their interactions remains unclear

A systematic review on mobile health applications for foodborne disease outbreak management

BACKGROUND : Foodborne disease outbreaks are common and notifiable in South Africa; however, they are rarely reported and poorly investigated. Surveillance data from the notification system is suboptimal and limited, and does not provide adequate information to guide public health action and inform policy. We performed a systematic review of published literature to identify mobile application-based outbreak response systems for managing foodborne disease outbreaks and to determine the elements that the system requires to generate foodborne disease data needed for public action. METHODS : Studies were identified through literature searches using online databases on PubMed/Medline, CINAHL, Academic Search Complete, Greenfile, Library, Information Science & Technology. Search was limited to studies published in English during the period January 1990 to November 2020. Search strategy included various terms in varying combinations with Boolean phrases “OR” and “AND”. Data were collected following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Statement. A standardised data collection tool was used to extract and summarise information from identified studies. We assessed qualities of mobile applications by looking at the operating system, system type, basic features and functionalities they offer for foodborne disease outbreak management. RESULTS : Five hundred and twenty-eight (528) publications were identified, of which 48 were duplicates. Of the remaining 480 studies, 2.9% (14/480) were assessed for eligibility. Only one of the 14 studies met the inclusion criteria and reported on one mobile health application named MyMAFI (My Mobile Apps for Field Investigation). There was lack of detailed information on the application characteristics. However, based on minimal information available, MyMAFI demonstrated the ability to generate line lists, reports and offered functionalities for outbreak verification and epidemiological investigation. Availability of other key components such as environmental and laboratory investigations were unknown. CONCLUSIONS : There is limited use of mobile applications on management of foodborne disease outbreaks. Efforts should be made to set up systems and develop applications that can improve data collection and quality of foodborne disease outbreak investigations.http://www.biomedcentral.com/bmcpublichealtham2022Medical VirologySchool of Health Systems and Public Health (SHSPH

The intersection of age, sex, race and socio-economic status in COVID-19 hospital admissions and deaths in South Africa.

Older age, male sex, and non-white race have been reported to be risk factors for COVID-19 mortality. Few studies have explored how these intersecting factors contribute to COVID-19 outcomes. This study aimed to compare demographic characteristics and trends in SARS-CoV-2 admissions and the health care they received. Hospital admission data were collected through DATCOV, an active national COVID-19 surveillance programme. Descriptive analysis was used to compare admissions and deaths by age, sex, race, and health sector as a proxy for socio-economic status. COVID-19 mortality and healthcare utilisation were compared by race using random effect multivariable logistic regression models. On multivariable analysis, black African patients (adjusted OR [aOR] 1.3, 95% confidence interval [CI] 1.2, 1.3), coloured patients (aOR 1.2, 95% CI 1.1, 1.3), and patients of Indian descent (aOR 1.2, 95% CI 1.2, 1.3) had increased risk of in-hospital COVID-19 mortality compared to white patients; and admission in the public health sector (aOR 1.5, 95% CI 1.5, 1.6) was associated with increased risk of mortality compared to those in the private sector. There were higher percentages of COVID-19 hospitalised individuals treated in ICU, ventilated, and treated with supplemental oxygen in the private compared to the public sector. There were increased odds of non-white patients being treated in ICU or ventilated in the private sector, but decreased odds of black African patients being treated in ICU (aOR 0.5; 95% CI 0.4, 0.5) or ventilated (aOR 0.5; 95% CI 0.4, 0.6) compared to white patients in the public sector. These findings demonstrate the importance of collecting and analysing data on race and socio-economic status to ensure that disease control measures address the most vulnerable populations affected by COVID-19.Significance:• These findings demonstrate the importance of collecting data on socio-economic status and race alongside age and sex, to identify the populations most vulnerable to COVID-19.• This study allows a better understanding of the pre-existing inequalities that predispose some groups to poor disease outcomes and yet more limited access to health interventions.• Interventions adapted for the most vulnerable populations are likely to be more effective.• The national government must provide efficient and inclusive non-discriminatory health services, and urgently improve access to ICU, ventilation and oxygen in the public sector.• Transformation of the healthcare system is long overdue, including narrowing the gap in resources between the private and public sectors

Corrigendum: The intersection of age, sex, race and socio-economic status in COVID-19 hospital admissions and deaths in South Africa

The following terminology was erroneously reported: “non-white race” should be “people of colour”, or “black African, coloured and people of Indian descent”

Corrigendum: The intersection of age, sex, race and socio-economic status in COVID-19 hospital admissions and deaths in South Africa

Original article: https://doi.org/10.17159/sajs.2022/13323 The following terminology was erroneously reported: “non-white race” should be “people of colour”, or “black African, coloured and people of Indian descent”

The intersection of age, sex, race and socio-economic status in COVID-19 hospital admissions and deaths in South Africa (with corrigendum)

Older age, male sex, and non-white race have been reported to be risk factors for COVID-19 mortality. Few studies have explored how these intersecting factors contribute to COVID-19 outcomes. This study aimed to compare demographic characteristics and trends in SARS-CoV-2 admissions and the health care they received. Hospital admission data were collected through DATCOV, an active national COVID-19 surveillance programme. Descriptive analysis was used to compare admissions and deaths by age, sex, race, and health sector as a proxy for socio-economic status. COVID-19 mortality and healthcare utilisation were compared by race using random effect multivariable logistic regression models. On multivariable analysis, black African patients (adjusted OR [aOR] 1.3, 95% confidence interval [CI] 1.2, 1.3), coloured patients (aOR 1.2, 95% CI 1.1, 1.3), and patients of Indian descent (aOR 1.2, 95% CI 1.2, 1.3) had increased risk of in-hospital COVID-19 mortality compared to white patients; and admission in the public health sector (aOR 1.5, 95% CI 1.5, 1.6) was associated with increased risk of mortality compared to those in the private sector. There were higher percentages of COVID-19 hospitalised individuals treated in ICU, ventilated, and treated with supplemental oxygen in the private compared to the public sector. There were increased odds of non-white patients being treated in ICU or ventilated in the private sector, but decreased odds of black African patients being treated in ICU (aOR 0.5; 95% CI 0.4, 0.5) or ventilated (aOR 0.5; 95% CI 0.4, 0.6) compared to white patients in the public sector. These findings demonstrate the importance of collecting and analysing data on race and socio-economic status to ensure that disease control measures address the most vulnerable populations affected by COVID-19. Significance: These findings demonstrate the importance of collecting data on socio-economic status and race alongside age and sex, to identify the populations most vulnerable to COVID-19. This study allows a better understanding of the pre-existing inequalities that predispose some groups to poor disease outcomes and yet more limited access to health interventions. Interventions adapted for the most vulnerable populations are likely to be more effective. The national government must provide efficient and inclusive non-discriminatory health services, and urgently improve access to ICU, ventilation and oxygen in the public sector. Transformation of the healthcare system is long overdue, including narrowing the gap in resources between the private and public sectors

Outbreak of Listeriosis in South Africa Associated with Processed Meat

International audienceBackgroundAn outbreak of listeriosis was identified in South Africa in 2017. The source was unknown.MethodsWe conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018.ResultsA total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case–control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections.ConclusionsThis investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source