Ashika Singh-Moodley

Prevalence and trends of Staphylococcus aureus bacteraemia in hospitalized patients in South Africa, 2010 to 2012 : laboratory-based surveillance mapping of antimicrobial resistance and molecular epidemiology

Introduction We aimed to obtain an in-depth understanding on recent antimicrobial resistance trends and molecular epidemiology trends of S. aureus bacteraemia (SAB). Methods Thirteen academic centres in South Africa were included from June 2010 until July 2012. S. aureus susceptibility testing was performed on the MicroScan Walkaway. Real-time PCR using the LightCycler 480 II was done for mecA and nuc. SCCmec and spa-typing were finalized with conventional PCR. We selected one isolate per common spa type per province for multilocus sequence typing (MLST). Results S. aureus from 2709 patients were included, and 1231 (46%) were resistant to methicillin, with a significant decline over the three-year period (p-value = 0.003). Geographical distribution of MRSA was significantly higher in Gauteng compared to the other provinces (P<0.001). Children <5 years were significantly associated with MRSA with higher rates compared to all other age groups (P = 0.01). The most prevalent SCCmec type was SCCmec type III (531 [41%]) followed by type IV (402 [31%]). Spa-typing discovered 47 different spa-types. The five (87%) most common spa-types were t037, t1257, t045, t064 and t012. Based on MLST, the commonest was ST612 clonal complex (CC8) (n = 7) followed by ST5 (CC5) (n = 4), ST36 (CC30) (n = 4) and ST239 (CC8) (n = 3). Conclusions MRSA rate is high in South Africa. Majority of the isolates were classified as SCCmec type III (41%) and type IV (31%), which are typically associated with hospital and community- acquired infections, respectively. Overall, this study reveals the presence of a variety of hospital-acquired MRSA clones in South Africa dominance of few clones, spa 037 and 1257. Monitoring trends in resistance and molecular typing is recommended to detect changing epidemiological trends in AMR patterns of SAB.

Antimicrobial susceptibility testing in predicting the presence of carbapenemase genes in Enterobacteriaceae in South Africa

BackgroundCarbapenem-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.MethodIn 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,blaIMP and blaVIM) was screened for using a multiplex real-time PCR.ResultsSixty-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 %).ConclusionFrom 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.

Colistin-resistant Acinetobacter baumannii as a cause of neonatal ventriculitis

Acinetobacter baumannii causes invasive paediatric infections, including bacteraemia and meningitis, but neonatal meningitis and ventriculitis is uncommon. The treatment of multidrug resistant (MDR) Acinetobacter infections often relies on colistin, a polymyxin antibiotic, as a last resort. Increased use of this drug has led to the emergence of colistin resistance. An unusual case of colistin-resistant Acinetobacter baumannii ventriculitis in a premature neonate managed with intraventricular colistin is described.

Phenotypic and genotypic correlation of carbapenememase-producing Enterobacteriaceae and problems experienced in routine screening

BACKGROUND The emergence and transmission of carbapenem-resistant Enterobacteriaceae (CRE) is a concern in both the clinical and public health arenas. Reliable and accurate detection of these organisms is required for patient management and infection prevention and control purposes. In the routine laboratory, phenotypic methods are utilised for identification of CRE. OBJECTIVES To investigate the phenotypic profiles of suspected carbapenemase-producing Enterobacteriaceae (CPE) isolates generated by the automated MicroScan Walkaway system making use of the Clinical and Laboratory Standards Institute (CLSI) guidelines, and correlate these with carbapenemase production by molecular methods. METHODS Antimicrobial susceptibility testing was performed using the MicroScan Walkaway system, and the presence of six carbapenemase genes (blaNDM, blaVIM, blaIMP, blaOXA-48and variants, blaGESand blaKPC) was screened for using a multiplex real-time polymerase chain reaction. RESULTS A total of 2 678 isolates were evaluated. Klebsiella pneumoniae accounted for 62.9% of the isolates (n=1 685), followed by Enterobacter cloacae (n=361, 13.5%). Carbapenemases accounted for 75.2% of isolates; blaOXA-48 and its variants predominated (n=978, 36.5%), followed by blaNDM (n=904, 33.8%), blaVIM (n=108, 4.0%), blaIMP (n=35, 1.3%), blaGES (n=24, 0.9%) and blaKPC (n=18, 0.7 %). CONCLUSIONS A considerable number of isolates expressing a carbapenemase or carbapenemases (the majority of which were blaOXA-48 producing) were susceptible to third-and fourth-generation cephalosporins and carbapenems, demonstrating that confirmed carbapenemase-producing isolates are not presenting as possible carriers of carbapenemases using routine diagnostic methods. Similar results were obtained when CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST) clinical breakpoints were applied and are suitable for the purpose of patient management. However, since genotyping assays are costly, it is suggested that routine laboratories first perform comprehensive phenotypic screening for CPE.

Draft Genome Sequence of a Multidrug-Resistant Serratia marcescens Strain, Isolated from a Patient with Peritoneal Cancer in South Africa

ABSTRACT We report here the draft genome sequence of Serratia marcescens ML2637, isolated from a South African pediatric patient in the intensive care unit with peritoneal cancer. The genome comprised 5,718,350 bp, with a 59.1% G+C content. There were 5,594 predicted genes, including 5,301 protein-coding genes, 199 pseudogenes, and 94 RNA genes.

Discrepancies in the identification of methicillin-resistant Staphylococcus aureus and the absence of mecC in surveillance isolates in South Africa

We investigated instances of phenotypic and genotypic discrepancies in the identification of methicillin-resistant Staphylococcus aureus in a reference laboratory in South Africa. Organism identification and antimicrobial susceptibility testing were performed using automated systems; and, the detection of mecA, mecC and nuc was performed using real-time and conventional PCR methods. Staphylococcal cassette chromosome mec (SCCmec) typing was done using conventional typing methods. Ninety-nine percent of phenotypic and genotypic results correlated; however, there were some discrepancies. The mecC gene was not detected in any of isolates tested. Although modest in number, the awareness of potential discrepancies is important and should be noted. However, our findings suggest that such discrepancies are rare and that phenotypic identification methods are acceptable.