Laboratory-based antimicrobial resistance surveillance for nosocomial bacteria (LARS)
Laboratory surveillance for antimicrobial resistance (AMR) provides a platform for generation of reliable AMR data from different geographical regions. A limited number of nosocomial bacterial pathogens such as Staphylococcus aureus, Klebsiella pneumoniae (2010-2012), and Pseudomonas aeruginosa (2014-2015) were chosen to monitor trends in resistance at NHLS sentinel sites over the period. Baseline antimicrobial resistance data on other ESKAPE organisms and tests for genes implicated in emerging resistance will also be conducted in future.
Molecular testing includes an array of assays (real time and conventional PCRs) for the detection of various mechanisms of resistance including antibiotic resistance genes, efflux pumps and porin loss. The presence of the methicillin resistance determinants mecA and mecC were investigated in Staphylococcus aureus along with the linezolid resistance gene (cfr) and the Panton-Valentine Leukocidin (pvl) toxin. In Gram-negative organisms, the following antibiotic resistance genes were investigated: extended spectrum beta-lactamases (ESBLs) blaTEM, blaSHV and blaCTX-M; carbapenemase-producing genes: blaNDM, blaVIM, blaIMP, blaOXA-48 & Variants, blaKCP andblaGES; plasmid mediated ampC and colistin resistance (mcr-1) genes and VEB-1. Porin loss (OprD) and efflux pumps were also investigated. Molecular characterization techniques also include SCCmec element and spa typing in Staphylococcus aureus and Multilocus Sequence Typing (MLST) and Pulsed Field Gel Electrophoresis (PFGE) in various organisms.
Collaborators: Andrew Whitelaw, Adriano Duse, Anwar Hoosen, Catherine Samuel, Colleen Bamford, Mark Nicol, Jeannette Wadula, Preneshni Naicker, Ranmini Kularatne, Sharona Seetharam, Trusha Nana, Norma Bosman, Nontombi Mbelle, Ruth Lekalakala, Halima Dawood, Sumayya Haffejee, Koleka Mlisana, Yacoob Coovadia, K. SweSwe Han, P. Ramjathan, P Bohla
Antimicrobial resistance prevalence and transmission between animal feed and humans
Given that antimicrobial resistance is a major global health concern, and that South Africa has high-density industrial farming of food animals, including cattle, poultry and pigs, the 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 has been little regulation of antibiotics administered to animals, with overlaps in the classes of antibiotics used for farming and human therapy. These animals, animal products, farm workers and the farming environment itself are potential reservoirs for resistance determinants. Antimicrobial resistance has been detected in farms; however, the extent of resistance and spillover in the country remain largely unknown. Hence, the transmission of resistance between animal feed and humans is important and requires investigation. We aim to describe the antibiotic resistance genes present in food animals and livestock workers which results in a reservoir from which spillover may occur into the community and/or hospital environments.
Collaborators: Professor Moritz Van Vuuren (vet); Dr Deryn Petty (vet).
Carbapenemase characterization in Klebsiella pneumoniae
Carbapenem non-susceptible isolates obtained during sentinel surveillance from four provinces were confirmed at the NICD and further characterization for carbapenemase genes and plasmid mediated ampC were performed.
Collaborators: LARS members
Enhanced Surveillance for Hospital versus Community Associated Infections by Methicillin-Resistant Staphylococcus aureus
The epidemiology of S. aureus is changing. Staphylococcus aureus is one of the most significant pathogens responsible for causing both nosocomial and community-associated infections, particularly Methicillin-Resistant Staphylococcus aureus (MRSA), which has a high prevalence worldwide, as well as a high morbidity and mortality rate. Previously MRSA was considered as a nosocomial pathogen, now it is recovered from patients at admission in hospitals. This community-associated MRSA (CA-MRSA) occurs either from patients that have never been exposed to healthcare settings or from patients that have been exposed to recent hospital admissions or any interventions in healthcare settings. Since the introduction of antimicrobial agents, bacterial antimicrobial resistance has become a global problem, and as the use of antimicrobial drugs increases the complexity of resistance mechanisms demonstrated by bacterial pathogens becomes increasingly important. Due to the increase in antibiotic resistance, the prevalence of hospital- and community-acquired infections is high with a significant number of deaths. As S. aureus is a causative agent for a wide variety of infections and diseases varying from less serious episodes of food poisoning to more serious wound infections and life-threatening conditions such as bacteraemia, necrotizing pneumonia and endocarditis, there is a need for epidemiological characterization of the organism. MRSA has spread increasingly to the community over the past three decades becoming endemic in most countries. The aim of this project is to identify virulence factors and evolution patterns of S. aureus, in order to determine the prevalence and extent of these nosocomial and community-acquired infections that result in antimicrobial resistance in the South African setting.
Collaborators:Ranmini Kularatne, Trusha Nana, Ruth Lekalakala, Catherine Samuel, Andrew Whitelaw, Preneshni R Naicker, Colleen Bamford,
Enhanced Surveillance for Carbapenem Resistant Enterobacteriaceae
The Enterobacteriaceae are part of the commensal human gut flora and are the cause of community and healthcare-associated infections. Over the last decade, Enterobacteriaceae have increasingly developed resistance to all beta-lactam antibiotics, fluoroquinolones and aminoglycosides. Of concern are carbapenem resistant Enterobacteriaceae (CREs) that have become a threat to healthcare and patient safety worldwide. The LARS project aims to gather information about the spread of CPEs in South Africa from sentinel site at public healthcare facilities.
Collaborators: Colleen Bamford, P.Bohla, Norma Bosman, VindanaChibabhai, Yacoob Coovadia Halima Dawood,Adrian Duse, Sumayya Haffejee, K. SweSweHan,AnwarHoosen, Nontombi Mbelle, Yesholata Mahabeer, Motlatji Maloba, Caroline Maluleka, Koleka Mlisana,Preshni Naicker, Maphoshane Nchabeleng, Sibongile Mahlangu,P. Ramjathan, Sharona Seetharam,Teena Thomas Jeannette Wadula, Andrew Whitelaw
Pneumocystis jirovecii pneumonia (PCP) in hospitalized patients with severe acute respiratory infections (SARI) using an existing surveillance network in South Africa
Surveillance is being done for PCP in adults and children at sentinel sites in North West and KwaZulu-Natal provinces. The relative contribution of PCP to the burden of severe acute respiratory infections is being determined together with the Centre for Respiratory Diseases and Meningitis, NICD. Because colonisation, rather than infection, can confound the interpretation of molecular detection of P. jirovecii, an attempt is being made to correlate gene copy number with serum β-D-glucan levels and clinical findings in enrolled patients.
Sentinel surveillance for parasitic causes of diarrhoea in hospitalised children
Five sentinel sites provide stool samples from under-five children with diarrhoea, as part of a rotavirus surveillance programme; residual samples are screened for bacterial and parasitic pathogens. Of 3443 samples received, 12.4% contained pathogenic parasites; the vast majority (>95%) wereCryptosporidium species. Genotyping has previously shown that these are predominantly C. hominis. This human-specific species is therefore emerging as an important cause of childhood diarrhoea in South Africa. Molecular detection of microsporidial species in these samples has started. These organisms are probablyunderappreciated as diarrhoeal agents, because they are difficult to detect by conventionallaboratory methods.
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 <100 cells/µL and pre-emptive antifungal treatment resulted in a ~30% relative reduction in 6-12 month mortality on ART. Two laboratory-based CrAg screening approaches have been evaluated in South Africa. Reflex laboratory CrAg testing was implemented at 3 NHLS CD4 laboratories serving 199 healthcare facilities in 4 districts of Gauteng and Free State; this was paired with intensive health worker training and prospective monitoring and evaluation. From September 2012 through to September 2015, 53 241 patients were screened, 1971 (3.7%) of whom tested positive for cryptococcal antigenaemia. In parallel, provider-initiated laboratory CrAg screening was implemented at all ART facilities in 5 Western Cape districts with no specific health worker training: from 2012 through to 2013, of 4395 eligible patients, only 26.6% were screened, 2.1% of whom screened CrAg-positive. In this province, unscreened patients were nearly twice as likely to develop disseminated cryptococcal disease compared to screened patients. 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. Both screening strategies are included in national guidelines. In order to inform the decision-making processes within the National Department of Health, we developed a decision analytic model to compare reflex and provider-initiated CrAg screening in terms of programmatic and health outcomes (number screened, number identified for pre-emptive treatment, lives saved, and discounted years of life saved) and screening and treatment costs (2015 USD). We estimated a base case with prevalence and other parameters based on data collected during CrAg screening pilot projects integrated into routine HIV care in Gauteng, Free State, and Western Cape Provinces. We conducted sensitivity analyses to explore how results change with underlying parameter assumptions. Reflex screening compared to provider-initiated screening saves more lives and is likely to be cost saving or have low additional costs per additional year of life saved. In 2016, the National Department of Health made a decision to implement reflex laboratory CrAg screening across the country and the national cryptococcal disease technical working group has been tasked to compile an implementation plan. If properly implemented, this intervention has the potential to directly reduce deaths associated with cryptococcal disease.
Programme partners: Department of Health, USAID, CDC, PEPFAR partners, Boston University
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. It remains unclear whether this cluster of Emmonsia-like species only emerged recently as human pathogens, or whether previous infections were merely under-appreciated. Support for the latter hypothesis comes from South Africa, where the introduction of molecular identification protocols resulted in a dramatic increase in the number of cases of disseminated Emmonsia disease, commensurate with a decline in cases of histoplasmosis. Preliminary phylogenetic analyses suggest that most of the new species of Emmonsia-like fungi form a single, derived clade in the Ajellomycetaceae, while agents of adiaspiromycosis (or classic emmonsiosis) appear to be polyphyletic.
Collaborators: Prof C Kenyon (University of Cape Town), Dr Ilan Schwartz (University of Antwerp), Prof Sybren de Hoog (CBS) and others
Surveillance for candidaemia
Patients with candidaemia were identified through active laboratory-based surveillance at sentinel hospitals in 7 provinces (except Gauteng and Western Cape where surveillance was conducted in previous years) from January 2014 through to December 2015. In January 2016, surveillance was expanded to public- and private-sector laboratories in all provinces. The objective of this expanded surveillance project is to compare Candida species distribution and antifungal resistance with baseline data collected through national surveillance 5 years ago (2009-2010). An incident case of candidaemia was defined as the isolation of Candida species from the first submitted blood culture. Detailed clinical information was collected including underlying diseases and in-hospital mortality. Identification of isolates and antifungal susceptibility testing was performed at the Centre. The Centre has assisted with investigation of a series of outbreaks of candidaemia at a sentinel hospital. During 2014, 80/118 (68%) cases of candidaemia (all Candida species), occurred in the neonatal intensive care unit (NICU) of this sentinel hospital; 48 neonatal cases due to Candida krusei were detected July through October, of 589 admissions in the NICU (attack rate 8.1%). Overlapping collection dates for the first positive specimen suggested a propagated outbreak. Risk factors, which were significantly associated with C. Krusei candidaemia, included necrotizing enterocolitis (NEC), birth weight <1500 g and being admitted during the months of July and August. Neonates weighing 1000 g to 1500 g at birth were 7 times more likely to develop candidaemia than those with BW >2500 g. At the time of audit, the patient census was 12% above the ward’s bed capacity and staff adherence to hand washing protocols was 76%. C. krusei was not isolated from the environment.
Collaborators: GERMS-SA network