Characterisation and epidemiological subtyping of Shiga toxin-producing Escherichia coli isolated from the beef production chain in Gauteng, South Africa.

In South Africa, there is a shortage of epidemiologic data on Shiga toxin-producing Escherichia coli (STEC) in the beef production chain. This study was conducted to characterise STEC isolates originating from three studies conducted in a cattle feedlot, beef abattoirs and retail outlets in Gauteng province, South Africa. Polymerase chain reaction was used to detect virulence genes, the Epsilometer test to assess antimicrobial susceptibility, pulsed-field gel electrophoresis (PFGE) to investigate genetic relatedness of isolates, and conventional serotyping for phenotypic identification.

Identifying gaps in hand hygiene practice to support tailored target audience messaging in Soweto: A cross-sectional community survey.

Effective risk communication is essential for outbreak mitigation, as recently highlighted during the coronavirus disease 2019 (COVID-19) pandemic. Hand hygiene is one of the proposed public health interventions to protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) acquisition and transmission along with social distancing, improved ventilation, environmental cleaning, and wearing of masks. Improving hand hygiene practices in the community requires an understanding of the socio-behavioural context.

Associations Between Eight Earth Observation-Derived Climate Variables and Enteropathogen Infection: An Independent Participant Data Meta-Analysis of Surveillance Studies With Broad Spectrum Nucleic Acid Diagnostics.

Diarrheal disease, still a major cause of childhood illness, is caused by numerous, diverse infectious microorganisms, which are differentially sensitive to environmental conditions. Enteropathogen-specific impacts of climate remain underexplored. Results from 15 studies that diagnosed enteropathogens in 64,788 stool samples from 20,760 children in 19 countries were combined.

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.

Epidemiology of Clostridioides difficile in South Africa.

Background: Clostridioides difficile (CD) is the most common healthcare-associated enteric infection. There is currently limited epidemiological evidence on CD incidence in South Africa.

Aim: To estimate the burden of CD infection (CDI) in the South African public sector between 1 July 2016 and 30 June 2017.

Epidemiological investigation of a typhoid fever outbreak in Sekhukhune District, Limpopo province, South Africa - 2017.

Background: Typhoid fever remains a public health concern in South Africa, where the risk of transmission is high because of poor access to safe water and sanitation. This study describes the investigation of typhoid fever outbreak in Limpopo province.

Methodology: Following notification of laboratory-confirmed cases, a descriptive study was conducted at Sekhukhune District, Limpopo province.

A decade of rotavirus vaccination in Africa - Saving lives and changing the face of diarrhoeal diseases: Report of the 12 African Rotavirus Symposium.

The African Rotavirus Network organised the 12 African Rotavirus Symposium (ARS) from 30 July to 1 August 2019 in Johannesburg, South Africa. The symposium theme "A decade of rotavirus vaccination in Africa - Saving lives and changing the face of diarrhoeal diseases", included sessions aimed at sharing ideas and expertise on prevention and control of diarrhoeal disease in Africa. Inter alia, the delegates reviewed global and regional epidemiological trends on rotavirus diarrhoea, progress and experiences on rotavirus vaccine introduction, including vaccine safety monitoring and impact in Africa, scientific advances in developing newer rotavirus vaccines, surveillance and research on other diarrhoeal pathogens, and providing an enabling environment for networking.

Circulation of classic and recombinant human astroviruses detected in South Africa: 2009 to 2014.

Background: Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA).

Whole-genome sequencing to investigate two concurrent outbreaks of Enteritidis in South Africa, 2018.

serotype Enteritidis ( Enteritidis) is a major cause of foodborne disease outbreaks worldwide. In 2018, two concurrent outbreaks of Enteritidis gastroenteritis in one district of South Africa were investigated. We describe the use of whole-genome sequencing (WGS) analysis of bacterial isolates to assist with the investigation of these outbreaks.

Investigation of two suspected diarrhoeal-illness outbreaks in Northern Cape and KwaZulu-Natal provinces, South Africa, April-July 2013: The role of rotavirus.

Background: Suspected diarrhoeal-illness outbreaks affecting mostly children < 5 years were investigated between May and July 2013 in Northern Cape province (NCP) and KwaZulu-Natal (KZN) province. This study describes the epidemiological, environmental and clinical characteristics and diarrhoeal-illnesses causative agent(s).

Methods: A descriptive cross-sectional study was conducted.

Characterisation of isolates from the 2009, 2010 and 2016 cholera outbreaks in Lusaka province, Zambia.

Introduction: In 2009 and 2010, more than 6,000 cholera cases were recorded during these outbreaks with more than 80% of cases recorded in Lusaka province. After a five-year break, in 2016 an outbreak occurred in Lusaka, causing more than 1,000 cases of cholera. This study will strengthen the epidemiological information on the changing characteristics of the cholera outbreaks, for treatment, prevention and control of the disease.

Outbreak of Listeriosis in South Africa Associated with Processed Meat.

Background: An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown.

Methods: We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type isolates.

Molecular epidemiology of human bocavirus infection in hospitalized children with acute gastroenteritis in South Africa, 2009-2015.

Human bocavirus (HBoV) is known to be associated with a variety of clinical manifestation including acute gastroenteritis (AGE). Despite their global prevalence, no data is available on the epidemiology of HBoV associated with AGE in South Africa (SA). Between April 2009 and April 2015, 3765 stool specimens were collected from children less than 5 years of age hospitalized with diarrhea.

Prevalence and antibiotic susceptibility patterns of enteric bacterial pathogens in human and non-human sources in an urban informal settlement in Cape Town, South Africa.

Background: In light of rampant childhood diarrhoea, this study investigated bacterial pathogens from human and non-human sources in an urban informal settlement. Meat from informal abattoirs (n = 85), river water (n = 64), and diarrheic stool (n = 66) were collected between September 2015 and May 2016. A duplex real-time PCR, gel-based PCR, and CHROMagar™STEC were used to screen Tryptic Soy Broth (TSB) for diarrheic E.

Virulence Characteristics and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Humans in South Africa: 2006-2013.

Shiga toxin-producing (STEC) isolates (N = 38) that were incriminated in human disease from 2006 to 2013 in South Africa were characterized by serotype, virulence-associated genes, antimicrobial resistance and pulsed-field gel electrophoresis (PFGE). The isolates belonged to 11 O:H serotypes. STEC O26:H11 (24%) was the most frequent serotype associated with human disease, followed by O111:H8 (16%), O157:H7 (13%) and O117:H7 (13%).

Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa.

Background: In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for species, species and . For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections.

Objectives: To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region.

Laboratory characterisation of Salmonella enterica serotype Typhi isolates from Zimbabwe, 2009-2017.

Background: Typhoid fever remains a major public health problem in Zimbabwe with recurrent outbreaks reported since 2009. To provide guidance on appropriate treatment choice in order to minimise the morbidity and mortality of typhoid fever and prevent large scale outbreaks, we investigated the antimicrobial susceptibility patterns, prevalence of Salmonella enterica serotype Typhi (S. Typhi) H58 haplotype and molecular subtypes of S.

Outbreak of in South Africa, 2017-2018: Laboratory Activities and Experiences Associated with Whole-Genome Sequencing Analysis of Isolates.

In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of s isolates associated with this outbreak.

Molecular characterization of an outbreak of enterovirus-associated meningitis in Mossel Bay, South Africa, December 2015-January 2016.

Background: Human enteroviruses (HEVs) are common causal agents of aseptic meningitis in young children. Laboratory and syndromic surveillance during December 2015 and January 2016 noted an unusually high number of paediatric aseptic meningitis cases at a hospital in Mossel Bay, Western Cape Province, South Africa. HEV was detected in clinical samples, prompting an outbreak investigation.

Epidemiology of human astroviruses among children younger than 5 years: Prospective hospital-based sentinel surveillance in South Africa, 2009-2014.

Background: The epidemiology of human astroviruses (HAstVs) in hospitalised patients less than 5 years of age from selected sites in South Africa was investigated. Diarrheagenic stool specimens collected from April 2009 to May 2014 were screened retrospectively for selected viruses, bacteria and parasites.

Method: Patient data were analysed to identify epidemiologic factors most frequently detected with HAstV infections.

The Burden of Typhoid Fever in South Africa: The Potential Impact of Selected Interventions.

Typhoid fever is notifiable in South Africa but clinical notification is notoriously poor. South Africa has an estimated annual incidence rate of 0.1 cases per 100,000 population of culture-confirmed typhoid fever, decreased from 17 cases per 100,000 population in the 1980s.

Characterisation of STEC and other diarrheic E. coli isolated on CHROMagar™STEC at a tertiary referral hospital, Cape Town.

Background: Shiga toxin producing E. coli (STEC) is an emerging zoonotic pathogen that can cause acute renal failure, especially in children. Clinical microbiology laboratories may fail to detect STEC and other diarrhoeic E.

The Integrity and Yield of Genomic DNA Isolated from Whole Blood Following Long-Term Storage at -30°C.

Long-term storage of whole blood can affect the integrity of DNA if it is not done under optimal conditions. The aim of this study was to determine whether long-term storage (2-19 years) of whole blood samples at -30°C had a negative effect on the quality or quantity of genomic DNA that could be recovered at extraction. Genomic DNA was isolated from 2758 whole blood samples collected in 4 mL EDTA vacutainers from 1997 to 2012.