The Centre for Enteric Diseases (CED) focuses on the surveillance of pathogens associated with diarrhoea and enteric fevers, and actively assists with the investigation and response to enteric disease outbreaks (including food- and water-borne disease outbreaks). The CED also provides specialised reference laboratory testing for enteric bacteria and viruses, including potential causes of food- and water-borne outbreaks.
The centre staff provide policy advice, scientific and technical support to the government, and the necessary expertise for strengthening outbreak preparedness and response to public health emergencies in line with International Health Regulations (IHR). The CED, in addition, contributes to the training of medical professionals, including medical scientists, medical technologists, epidemiologists, public health workers, nurses and registrars.
The objectives of CED are:
- Conducting surveillance for pathogens associated with diarrhoea and enteric fever;
- Providing reference laboratory functions and specialised laboratory testing for enteric bacteria and viruses;
- Supporting enteric disease outbreak investigation and response activities;
- Being a source of local and regional expertise on enteric diseases;
- Training laboratorians and healthcare workers in relevant laboratory and epidemiologic skills to build local and regional capacity; and
- Engaging in directed and relevant research to answer questions related to regional challenges associated with enteric diseases.
The centre performs surveillance activities for a wide range of enteric bacteria, viruses and parasites. It functions as a reference laboratory for several enteric bacterial pathogens, including Salmonella species, Shigella species, Campylobacter species, Vibrio cholerae, Listeria monocytogenes and diarrhoeagenic Escherichia coli. Viruses associated with diarrhoea (rotavirus, norovirus, sapovirus, astrovirus and adenovirus) are monitored to track strain diversity and the emergence of any potential outbreak strains.
The centre coordinates PulseNet Africa, a regional network of PulseNet International, a global network concerned with global surveillance and molecular subtyping of bacterial enteric pathogens (http://www.pulsenetinternational.org/).
The CED actively supports enteric disease outbreak investigations countrywide. This includes a steadily increasing number of food- and water-borne disease outbreaks.
During the national listeriosis outbreak of 2017 to 2018 the centre played a leading role in outbreak investigation and response, providing critical specialised laboratory testing and epidemiological support to the National Department of Health (NDoH) during what became the largest listeriosis outbreak ever recorded. The CED collated and analysed data on laboratory-confirmed cases and issued publically available weekly situation updates and provided technical expertise to the NDoH to guide and support outbreak investigation activities. The centre was also instrumental in guiding and actively participating in the investigation activities, as well as the subsequent laboratory testing which ultimately confirmed the outbreak source. An integral component of the investigation was the use of whole genome sequencing (WGS) data for clinical, food and environmental isolates; through close collaboration with the Sequencing Core Facility of the NICD, WGS was successfully used in real-time to guide outbreak investigation activities and identify the source. The centre was actively engaged in media interviews during the course of the outbreak, providing a source of scientifically correct information and important health promotion messaging to the public. In addition, the centre assisted with phenotypic confirmatory testing and WGS of clinical isolates from other African countries that were suspected to be linked with the outbreak.
The CED laboratories provide specialised testing for enteric bacteria and viruses, including serotyping, pathotyping, biotyping and PCR where relevant. Molecular epidemiological testing, including PFGE, MLVA and more recently WGS, are utilised to characterise isolates and determine relatedness. This is of critical importance in outbreak investigations and outbreak source attribution
The CED contributes to the training of medical professionals, including medical scientists, medical technologists, epidemiologists, nurses, registrars, and public health officials.
The centre co-hosts WHO training workshops for the Southern African region, to build laboratory and epidemiologic capacity in other African countries for enteric and foodborne disease outbreak investigations. The centre actively participates in PulseNet training workshops for molecular subtyping and whole-genome sequencing of bacterial enteric pathogens.
The CED partners with the national Notifiable Medical Conditions (NMC) surveillance system, which is tasked with providing timely, accurate data of diseases that are of public health importance. These diseases may pose significant public health risks that can result in disease outbreaks or epidemics with high case fatality rates both nationally and internationally.
Whole-genome sequencing (WGS) analysis of microorganisms is poised to transform public health microbiology. WGS is a ‘one-stop technology’, a ‘one technology takes all’, a universal technology applicable to all microorganisms. WGS is particularly useful surrounding activities related to surveillance, epidemiology and response to communicable disease threats including outbreaks.
WGS has the potential to replace all current methodologies used in the clinical microbiology laboratory and WGS data can be interrogated to provide information on microbial identification (genus/species/serotype), antimicrobial susceptibility and presence of antimicrobial resistance genes (determinants), virulence potential and presence of virulence genes, etc. In particular, interrogation of WGS data and comparative genomics are extremely useful in investigations surrounding surveillance and epidemiology, where the genetic relatedness of microbial isolates can be investigated and evolutionary relationships can be inferred.
The Centre for Enteric Diseases (CED) has secured grant funding to perform WGS on ~5000 microbial isolates over the years 2020 to 2021. The focus of the sequencing will be on the family of Enterobacteriaceae. Importantly, sequencing data for isolates need to be complemented with good epidemiological (explanatory) data, as WGS data often needs to be interpreted within the epidemiological context. This sequencing project will mostly have a prospective focus, so that relevant and up-to-date epidemiological data can be collected, to facilitate a ‘real-time’ analysis. We aim to investigate how WGS analysis can support and augment the current methodologies used in laboratory investigations at the NICD. In addition, WGS analysis will strengthen surveillance activities at the NICD and in particular, outbreak response and investigation.
CED will partner with the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses to sequence pathogens which form part of routine GERMS-SA surveillance activities. CED will sequence all isolates of Salmonella species, Shigella species, Campylobacter species, Escherichia coli and Vibrio cholerae O1. CHARM will sequence selected isolates of carbapenemase-producing Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus and Candida auris.
Prof Anthony Smith is the Acting Head of the Centre for Enteric Diseases. His PhD is in Molecular Microbiology from the University of the Witwatersrand, and he holds joint appointments with the University of Pretoria (Extraordinary Professor) and the University of the Witwatersrand (Senior Research Officer).
As a researcher who enjoys considerable international recognition from his peers for the high quality and impact of his recent research outputs, he holds a rating of ‘B2’ with the National Research Foundation of South Africa.
He is a steering committee member of PulseNet International. The Focus Group on Foodborne Disease Genomic Surveillance, Pathogen Genomics Initiative (PGI), and Africa CDC include him on their steering committee. He is a consortium member and partner of SEQAFRICA, a group aimed at building African capacity for whole-genome sequencing (WGS) and bioinformatics.
Among his current activities is the surveillance and epidemiology of enteric pathogenic bacteria in South Africa. Teaching and lecturing about molecular techniques in the clinical microbiology laboratory, including techniques related to laboratory identification and characterisation of bacterial enteric pathogens is one of his specialities. WGS analysis of bacterial pathogens and metagenomics analysis are some of his specialities. Additionally, he supervises postgraduate students and trains intern medical scientists. He has authored 104 peer-reviewed publications.