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

Detection of Campylobacter species in stool specimens from patients with symptoms of acute flaccid paralysis in South Africa

Introduction: Guillain-Barré Syndrome (GBS) is an autoimmune disease characterized by acute or subacute symmetrical ascending motor weakness, areflexia, and mild-to-moderate sensory abnormalities. Campylobacter jejuni is reported to be the most common bacterium associated with GBS cases. Despite the eradication of polio, the number of reported GBS cases remains considerably high in South Africa with the causative agents not being well described. Methodology: The aim of the study was to investigate the proportion of Campylobacter spp. detected in stool specimens from patients with symptoms of acute flaccid paralysis (AFP). Stool specimens from patients presenting with AFP, that were negative for polio and non-polio enteroviruses (NPENT), were processed and screened for the presence of Campylobacter spp. using quantitative PCR (qPCR). Results: Of the 512 stool specimens screened between October 2014 to December 2015, 12% (62/512) were positive for Campylobacter spp. Of these 62 Campylobacter infections: 77.4% (48/62) was C. jejuni; 19.4% (12/62) was Campylobacter coli; 3.2% (2/62) was mixed infections of C. jejuni and C. coli. Conclusions: True association of the disease with Campylobacter spp. will enable the proportion of Campylobacter-induced GBS to be better described in South Africa; this can only be done through systematic studies that include bacterial culture and serology together with molecular methodologies

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”

Trends in cases, hospitalizations, and mortality related to the Omicron BA.4/BA.5 subvariants in South Africa

BACKGROUND : In this study, we compared admission incidence risk and the risk of mortality in the Omicron BA.4/BA.5 wave to previous waves. METHODS : Data from South Africa’s SARS-CoV-2 case linelist, national COVID-19 hospital surveillance system, and Electronic Vaccine Data System were linked and analyzed. Wave periods were defined when the country passed a weekly incidence of 30 cases/ 100 000 population. In-hospital case fatality ratios (CFRs) during the Delta, Omicron BA.1/BA.2, and Omicron BA.4/BA.5 waves were compared using post-imputation random effect multivariable logistic regression models. RESULTS : The CFR was 25.9% (N=37 538 of 144 778), 10.9% (N=6123 of 56 384), and 8.2% (N=1212 of 14 879) in the Delta, Omicron BA.1/BA.2, and Omicron BA.4/BA.5 waves, respectively. After adjusting for age, sex, race, comorbidities, health sector, and province, compared with the Omicron BA.4/BA.5 wave, patients had higher risk of mortality in the Omicron BA.1/BA.2 wave (adjusted odds ratio [aOR], 1.3; 95% confidence interval [CI]: 1.2–1.4) and Delta wave (aOR, 3.0; 95% CI: 2.8–3.2). Being partially vaccinated (aOR, 0.9; 95% CI: .9–.9), fully vaccinated (aOR, 0.6; 95% CI: .6–.7), and boosted (aOR, 0.4; 95% CI: .4–.5) and having prior laboratory-confirmed infection (aOR, 0.4; 95% CI: .3–.4) were associated with reduced risks of mortality. CONCLUSIONS : Overall, admission incidence risk and in-hospital mortality, which had increased progressively in South Africa’s first 3 waves, decreased in the fourth Omicron BA.1/BA.2 wave and declined even further in the fifth Omicron BA.4/BA.5 wave. Mortality risk was lower in those with natural infection and vaccination, declining further as the number of vaccine doses increased.https://academic.oup.com/cid/am2024Human NutritionSDG-03:Good heatlh and well-bein

Trends in COVID-19 admissions and deaths among people living with HIV in South Africa : analysis of national surveillance data

DATA SHARING : Aggregated data are available on request to the South African National Institute for Communicable Diseases. The data dictionary is available on request to the corresponding author, [email protected] : In 2021, the HIV prevalence among South African adults was 18% and more than 2 million people had uncontrolled HIV and, therefore, had increased risk of poor outcomes with SARS-CoV-2 infection. We investigated trends in COVID-19 admissions and factors associated with in-hospital COVID-19 mortality among people living with HIV and people without HIV. METHODS : In this analysis of national surveillance data, we linked and analysed data collected between March 5, 2020, and May 28, 2022, from the DATCOV South African national COVID-19 hospital surveillance system, the SARS-CoV-2 case line list, and the Electronic Vaccination Data System. All analyses included patients hospitalised with SARS-CoV-2 with known in-hospital outcomes (ie, who were discharged alive or had died) at the time of data extraction. We used descriptive statistics for admissions and mortality trends. Using post-imputation random-effect multivariable logistic regression models, we compared characteristics and the case fatality ratio of people with HIV and people without HIV. Using modified Poisson regression models, we compared factors associated with mortality among all people with COVID-19 admitted to hospital and factors associated with mortality among people with HIV. FINDINGS : Among 397 082 people with COVID-19 admitted to hospital, 301 407 (75·9%) were discharged alive, 89 565 (22·6%) died, and 6110 (1·5%) had no recorded outcome. 270 737 (68·2%) people with COVID-19 had documented HIV status (22 858 with HIV and 247 879 without). Comparing characteristics of people without HIV and people with HIV in each COVID-19 wave, people with HIV had increased odds of mortality in the D614G (adjusted odds ratio 1·19, 95% CI 1·09–1·29), beta (1·08, 1·01–1·16), delta (1·10, 1·03–1·18), omicron BA.1 and BA.2 (1·71, 1·54–1·90), and omicron BA.4 and BA.5 (1·81, 1·41–2·33) waves. Among all COVID-19 admissions, mortality was lower among people with previous SARS-CoV-2 infection (adjusted incident rate ratio 0·32, 95% CI 0·29–0·34) and with partial (0·93, 0·90–0·96), full (0·70, 0·67–0·73), or boosted (0·50, 0·41–0·62) COVID-19 vaccination. Compared with people without HIV who were unvaccinated, people without HIV who were vaccinated had lower risk of mortality (0·68, 0·65–0·71) but people with HIV who were vaccinated did not have any difference in mortality risk (1·08, 0·96–1·23). In-hospital mortality was higher for people with HIV with CD4 counts less than 200 cells per μL, irrespective of viral load and vaccination status. INTERPRETATION : HIV and immunosuppression might be important risk factors for mortality as COVID-19 becomes endemic.South African National Institute for Communicable Diseases, the South African National Government, and the United States Agency for International Development.http://www.thelancet.com/hiv2025-02-01hj2024Human NutritionSDG-03:Good heatlh and well-bein

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

Abstract 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 &amp; 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. </jats:sec

Additional file 1 of A systematic review on mobile health applications for foodborne disease outbreak management

Additional file 1