Research and Surveillance

GERMS-SA laboratory-based surveys for antibiotic-resistant bacteria

  • Provides a platform for generation of reliable AMR data from different geographical regions
  • Bacterial isolates from patients with bloodstream infections are submitted to the Centre for reference laboratory characterisation
  • Surveys include a rota of bacterial pathogens
    • Klebsiella pneumoniae (2010-2012)
    • Pseudomonas aeruginosa (2014-2015)
    • Staphylococcus aureus (2012-2017)
    • Carbapenem-resistant Enterobacteriaceae (2015-2017)
    • Acinetobacter baumannii (2017-)
  • An array of molecular assays (real time and conventional PCR) are performed for the detection of various mechanisms of resistance
    • The presence of the methicillin resistance determinants mecA and mecC are investigated in aureus along with the linezolid resistance gene (cfr) and the Panton-Valentine leukocidin (PVL) toxin
    • In Gram-negative organisms, the following antibiotic resistance genes are investigated: extended spectrum beta-lactamases (ESBLs) blaTEM, blaSHV and blaCTX-M; carbapenemase-producing genes: blaNDM, blaVIM, blaIMP, blaOXA-48 & Variants, blaKPC and blaGES; plasmid mediated ampC and colistin resistance (mcr-1, 2, 3) genes and VEB-1. Porin loss (OprD) and efflux pumps are also investigated
  • Molecular typing/ characterization techniques also include SCCmec element and spa typing in aureus and multilocus sequence typing (MLST) and pulsed field gel electrophoresis (PFGE) in various organisms.

GERMS-SA enhanced surveillance for Staphylococcus aureus

  • The aim of this project is to determine the prevalence of antimicrobial resistance and molecular epidemiology of aureus bacteraemia at enhanced surveillance sentinel sites in two provinces for guideline/ policy formulation and antimicrobial stewardship activities
  • A case is defined as an individual diagnosed with culture-confirmed aureus bacteraemia at any sentinel site. A new episode is defined if an individual had a positive culture >21 days after the first culture.
  • At sentinel public-sector hospitals, nurse surveillance officers collect clinical data from admitted case patients by interview or chart review.


GERMS-SA enhanced surveillance for carbapenem-resistant Enterobacteriaceae

  • The Enterobacteriaceae are part of the commensal human gut flora and are a cause of community- and healthcare-associated infections
  • Over the last decade, Enterobacteriaceae have increasingly developed resistance to all beta-lactam antibiotics including carbapenems, fluoroquinolones and aminoglycosides
  • The mechanism of resistance to carbapenems in the Enterobacteriaceae is complex and mediated by several different mechanisms such as over-production of ampC enzymes, extended-spectrum β-lactamases (ESBLs), carbapenemases, efflux pumps and loss of porin channels
  • The aim of this project is to estimate the burden of laboratory-confirmed CRE bacteraemia at sentinel sites in South Africa and to describe the epidemiological characteristics to support development of guidelines for antimicrobial use


GERMS-SA national and enhanced surveillance for candidaemia

  • In 2009 and 2010, the first national surveillance for candidaemia was conducted which described the species distribution and baseline antifungal susceptibility profiles of the most common Candida species in the public- and private-sector
  • In that survey, Candida albicans was the most common species isolated from 906 cases in the public sector followed by parapsilosis, C. glabrata, C. tropicalis, C. krusei and other Candida species. In contrast, C. parapsilosis was the dominant species among private-sector cases, accounting for 53% of all reported cases. In 2014, the initial emergence of Candida auris in South Africa was described.
  • Five years on from the first survey, national surveillance with the aim of describing changes to the epidemiology of candidaemia was re-initiated.
  • In addition, enhanced surveillance at all GERMS sentinel hospitals and for the first time, at three private facilities in Johannesburg and Pretoria to determine the clinical epidemiology of disease, was set up.


One health project on AMR on a pig farm

  • South Africa has high-density industrial farming of food animals, including cattle, poultry and pigs
  • Routine use of antibiotics for therapeutic, prophylactic and growth promotion on these farms is worrying as antibiotics in food animals have been linked to increases in clinical resistance in human medicine
  • There is limited regulation on antibiotics administered to animals, with overlapping classes of antibiotics used for farming and human therapy
  • Antimicrobial resistance has been detected in farms; however, the extent of resistance and spill-over between agricultural and human medicine sectors remains largely unknown. Hence, investigating the transmission of resistance between animal feed and humans is important.
  • This project aims to describe antibiotic resistance genes present in food animals and livestock workers which may result in a reservoir from which spill-over may occur into the community and/or hospital environments.


Implementation of a public health intervention: cryptococcal antigen screening and pre-emptive treatment

  • Cryptococcal meningitis, a common AIDS-defining fungal opportunistic infection, has a fatal outcome in >50% of cases in routine care in South Africa.
  • In 2014, 5772 new cases of laboratory-confirmed cryptococcal disease were detected by the NICD
  • In randomised clinical trials, cryptococcal antigen (CrAg) screening of HIV-infected persons with a baseline CD4 count <200 cells/µL and pre-emptive antifungal treatment resulted in a ~30% relative reduction in 12-month mortality on ART
  • Two laboratory-based CrAg screening approaches have been evaluated in South Africa.
  • Detailed clinical guidance for the screen-and-treat intervention was included in the 2015 national consolidated guidelines for HIV and in the updated standard treatment guidelines/ essential medicine lists for primary healthcare and hospital levels.
  • In 2016, the National Department of Health made a decision to implement reflex laboratory CrAg screening across the country
  • The Centre is currently evaluating the impact of this programme on cryptococcal meningitis-related deaths


Emergence of a cluster of novel dimorphic fungal pathogens in humans

  • At least seven new species of Emmonsia-like fungi, with phylogenetic and clinical similarities to Blastomyces dermatitidis and Histoplasma capsulatum, have emerged over the last 50 years as causes of systemic human mycoses worldwide
  • They differ from classical Emmonsia species by producing a thermally-dependent yeast-like phase rather than adiaspores, causing disseminated infections, predominantly in immunocompromised patients, and often with high case-fatality rates
  • Such differences will be important for clinicians to consider in diagnosis and patient management, and for microbiologists who may encounter these fungi with increasing frequency
  • Researchers in the Centre are involved in investigating the environmental reservoir, new diagnostic assays and antifungal susceptibility of these novel pathogens

Interventions to reduce deaths associated with advanced HIV

Advanced HIV Position Statement