title: Antimicrobial susceptibility testing in predicting the presence of carbapenemase genes in Enterobacteriaceae in South Africa.
abstract: BACKGROUND
  Carbapenem-resistant Enterobacteriaceae (CRE) is a concern in South Africa and worldwide. It is therefore important that these organisms be accurately identified for infection prevention control purposes.
  
  
  METHODS
  In this study 1193 suspected CREs from 46 laboratories from seven provinces in South Africa were assessed to confirm the prevalence of carbapenemase genes from our referral diagnostic isolates for the period 2012 to 2015. We compared the antimicrobial susceptibility testing method used in the reference laboratory to the polymerase chain reaction (PCR) which is used as the gold standard. Organism identification and antimicrobial susceptibility testing were performed using automated systems and DNA was extracted using a crude boiling method. The presence of carbapenemase-producing genes (blaNDM,blaKPC,blaOXA-48&variants,blaGES,blaIMPand blaVIM) was screened for using a multiplex real-time PCR.
  
  
  RESULTS
  Sixty-eight percent (n = 812) of the isolates harboured a carbapenemase-producing gene; the three most common genes included: blaNDM,blaOXA-48&variants and blaVIM. Majority of the carbapenemase producing Enterobacteriaceae (CPE) isolates were Klebsiella species (71 %). The Microscan® Walkaway system used for the screening of carbapenemase production was 98 % sensitive with a minimal inhibitory concentration (MIC) breakpoint of less than 0.5 as susceptible for ertapenem and a low specificity (13 %).
  
  
  CONCLUSIONS
  From this study we can conclude that carbapenemase-producing Enterobacteriaceae is increasing in South Africa and the use of phenotypic methods for detection of CPEs showed good sensitivity but lacked specificity.
authors.affiliation: Division of the National Health Laboratory Service, National Institute for Communicable Diseases, 1 Modderfontein Road, Sandringham, 2131, Johannesburg, South Africa. AshikaS@nicd.ac.za.
authors.forename: Ashika
authors.initials: A
authors.lastname: Singh-Moodley
authors.affiliation: Division of the National Health Laboratory Service, National Institute for Communicable Diseases, 1 Modderfontein Road, Sandringham, 2131, Johannesburg, South Africa.|University of Witwatersrand, South Africa, Private Bag 3, Wits 2050, Johannesburg, South Africa.
authors.forename: Olga
authors.initials: O
authors.lastname: Perovic
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000235:genetics*; D024881:Drug Resistance, Bacterial; D004755:Enterobacteriaceae / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D000077727:Ertapenem; D006801:Humans; D008826:Microbial Sensitivity Tests; D060888:Real-Time Polymerase Chain Reaction; D013019:South Africa; D001618:beta-Lactamases / Q000235:genetics*; D047090:beta-Lactams / Q000494:pharmacology
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D047090:beta-Lactams; D001618:beta-Lactamases; C063912:carbapenemase; D000077727:Ertapenem
keywords: Antimicrobial susceptibility testing; Carbapenemase-producing Enterobacteriaceae; Carbapenemases; Resistance genes