OVERVIEW
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.
OBJECTIVES
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.
FUNCTIONS
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, 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.
Dr Anthony Smith is a steering committee member of 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 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.
During the 2023 cholera outbreak, the centre supported the DOH in cholera case investigation, field investigation, and contact tracing activities, including in-depth face-to-face interviews with confirmed cases and contacts, the collection of stool specimens from symptomatic contacts, and testing the stool specimens at the CED laboratory. The CED produced several technical guidance documents, which were placed on the NICD website and circulated by the DOH to healthcare facilities. These included a clinical management summary guide, a specimen collection guide, a treatment flow chart, and an advisory for all NHLS labs on the processing of samples for cholera investigation.
The CED laboratories provide specialised testing for enteric bacteria and viruses, including serotyping, biotyping and PCR where relevant. Molecular epidemiological testing, including 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.
https://www.nicd.ac.za/wp-content/uploads/2018/11/NMC-information-pamphlet.pdf
CURRENT PROJECTS
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) performs routine WGS analysis on all isolates of Salmonella species, Listeria monocytogenes, Shiga toxin-producing Escherichia coli (STEC), Vibrio cholerae O1 and any other bacterial species associated with outbreaks.
Participants of any age presenting for the treatment of diarrhoea (as defined by the World Health Organization (WHO); any duration) at selected sentinel hospitals and clinics are approached for enrolment. Enrolment is conducted systematically from Monday to Friday (08:00 – 17:00), after informed consent is obtained from the patient or a parent or guardian.
Demographic, clinical and outcome data are collected in a structured questionnaire by dedicated surveillance officers in participants residing in the site catchment area for at least seven days prior to illness. Stool specimens are collected from participants within 48 hours of enrolment and submitted to the Centre for Enteric Diseases for testing. Specimens are screened for rotavirus (commercial EIA and standardized characterization protocols) and other bacterial and viral enteric pathogens (commercial molecular detection kits and in-house real-time detection assays).
The centre has been conducting rotavirus surveillance since 2009, primarily monitoring rotavirus prevalence post-vaccine introduction. In addition, the laboratory has participated in rotavirus vaccine trials conducted in South Africa, screening specimens for rotavirus and characterising any strains detected. The laboratory was recently approached to perform enzyme-linked immunosorbent assays (ELISA) measuring rotavirus IgA and IgG antibodies in patient sera. With the assistance of a small grant from PATH, senior laboratory staff have been trained at the Christian Medical College, Vellore, India and the Cincinnati Children’s Hospital Medical Centre (CCHMC), USA.
In addition, the laboratory has procured a plate reader and washer, and a computer for data analysis as well as appropriate reagents and consumables to set-up the assays and run a bridging panel with CCHMC. The next phase of the implementation will include additional local development with procurement of rabbit anti-rotavirus capture antibody, growth of virus stocks as well as further bridging runs to ensure that results are comparable between CED and CCHMC. With the assays harmonised and standard operating procedures established at CED, the reagents will be shared with partner laboratories operating in Africa (Malawi, Zambia and Ghana).
Nicola Page is a principal medical scientist, leading the Virology Division and currently acting head of the Centre for Enteric Diseases at the National Institute for Communicable Diseases. She also holds extra-ordinary professor positions within the Department of Medical Virology and the School of Health Systems and Public Health at the University of Pretoria. She completed her undergraduate training at the University of Pretoria in 1995 (cum laude), following up with an Honours degree in 1997. She moved to the Medical University of South Africa, under the guidance of Prof Duncan Steele and competed an MSc(Med) in Medical Virology in 2001 and a PhD in 2005.
She has also subsequently completed the SA-FETP training program (2014-2015) and obtained an MPH in Field Epidemiology at the University of Pretoria, graduating cum laude in 2016. She is a registered medical scientist (Virology) with the Health Professionals Council of South Africa (HPCSA) and has a C1 National Research Foundation (NRF) rating. She serves as a member of the institutional biosafety and biosecurity committee and recently became a certified biosafety professional.
She has authored or co-authored more than 70-refereed articles in scientific journals, worked on the WHO Manual of rotavirus detection and characterization and was a guest editor on the Journal of Infectious Diseases – Rotavirus in Africa supplement.
Secretary
Mzikazi Dickmolo
Tel: +27 11 386 6477
Email: mzikazid@nicd.ac.za
Principal Medical Scientist
Prof Anthony Smith
Email: anthonys@nicd.ac.za
Bacteriology Laboratory Manager
Hlengiwe Mimmy Ngomane
Email: mimmyn@nicd.c.za
Centre Senior Pathologist
Dr Keeren Lutchminarain
Email: keerenl@nicd.ac.za
Centre Epidemiologist
Phuti Sekwadi
Email: phutis@nicd.ac.za
