Carbapenem-resistant Enterobacteriaceae in patients with bacteraemia at tertiary hospitals in South Africa, 2015 to 2018.

Enhanced surveillance for CREs was established at national sentinel sites in South Africa. We aimed to apply an epidemiological and microbiological approach to characterise CREs and to assess trends in antimicrobial resistance from patients admitted to tertiary academic hospitals. A retrospective analysis was conducted on patients of all ages with CRE bacteraemia admitted at any one of 12 tertiary academic hospitals in four provinces (Gauteng, KwaZulu-Natal, Western Cape and Free State) in South Africa. The study period was from July 2015 to December 2018. A case of CRE bacteraemia was defined as a patient admitted to one of the selected tertiary hospitals where any of the Enterobacteriaceae was isolated from a blood culture, and was resistant to the carbapenems (ertapenem, meropenem, imipenem and/or doripenem) or had a positive result for the Modified Hodge Test (MHT) according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. A positive blood culture result obtained after 21 days of the last blood culture result was regarded as a new case. To distinguish hospital-acquired (HA) from the community-acquired (CA) bacteraemia, the following definitions were applied: the HA CRE bacteraemia was defined as a patient with CRE isolated from blood culture ≥ 72 h of hospital admission or with any prior healthcare contact, within 1 year prior to the current episode or referral from a healthcare facility where the patient was admitted before the current hospital. A case of the CA CRE bacteraemia was defined as a patient with CRE isolated from blood culture < 72 h of hospital admission and with no prior healthcare contact. The majority of carbapenem-resistant Enterobacteriaceae (CRE) (70%) were hospital-acquired (HA) with Klebsiella pneumoniae being the predominant species (78%). In-hospital mortality rate was 38%. The commonest carbapenemase genes were bla-OXA-48 (52%) and bla-NDM (34%). The high mortality rate related to bacteraemia with CRE and the fact that most were hospital-acquired infections highlights the need to control the spread of these drug-resistant bacteria. Replacement with OXA-48 is the striking finding from this surveillance analysis. Infection control and antibiotic stewardship play important roles in decreasing the spread of resistance.

A small proportion of community-associated methicillin-resistant Staphylococcus aureus bacteraemia, compared to healthcare-associated cases, in two South African provinces.

We compared the proportion of cases of community-associated and healthcare-associated methicillin-resistant Staphylococcus aureus (CA-MRSA and HA-MRSA, respectively) bacteraemia among patients at five hospitals in the Gauteng and Western Cape provinces in South Africa and described the molecular characteristics and antimicrobial susceptibility trends. This was a cross-sectional study using data collected by enhanced surveillance for S. aureus bacteraemia. A total of 2511 cases of S. aureus bacteraemia were identified from January 2013 to January 2016. Among 1914 cases of S. aureus, 557 (29.1%) cases were identified as MRSA infection. Forty-four cases (44/1914 [2.3%] of all S. aureus cases) were considered CA-MRSA infection and 513/1914 (26.8% of all cases) had HA-MRSA infection; the majority were neonates. CA-MRSA constituted 7.9% (44/557) of all cases of MRSA infection. Staphylococcus aureus isolates demonstrated significantly reduced susceptibility to the following classes of antimicrobial agents: macrolides, tetracyclines, aminoglycosides and cotrimoxazole, in 2015 compared to 2013 (p < 0.05). Of the 557 MRSA isolates, 484 (87%) were typed for SCCmec elements and spa types: the most common SCCmec type was type III (n = 236, 48.76%), followed by type IV (n = 144, 29.76%). The most common spa types were t037 (n = 229, 47.31%) and t1257 (n = 90, 18.60%). Of 28 isolates selected for multilocus sequence typing (MLST), the most common sequence types (STs) were ST239 and ST612 of clonal complex 8 (CC8) (n = 8 each) and a novel ST (ST4121) was obtained for one isolate. This study demonstrates that S. aureus bacteraemia is common in South African academic centres and characterised by HA-MRSA SCCmec types III and IV. A small proportion of CA-MRSA cases were caused by a few different sequence types.

Analysis and comparison of cumulative antibiograms for the Charlotte Maxeke Johannesburg Academic Hospital adult intensive care and high-care units, 2013 and 2017.

BACKGROUND: Infection is a common complication for patients in intensive care units (ICUs), and increasing antimicrobial resistance (AMR) is a major concern. It is therefore crucial to monitor AMR patterns in order to support clinical decision-making and antimicrobial stewardship strategies. Clinical microbiologists should provide annual cumulative antibiogram reports, which can be used to guide initial empirical antimicrobial therapy for the management of infections. OBJECTIVES: To analyse the cumulative antibiograms for the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) combined adult multidisciplinary ICU and high-care unit (HCU) for 2013 and 2017, compare the antimicrobial susceptibility testing (AST) patterns between the 2 years, and analyse the subset of blood culture isolates. METHODS: A retrospective descriptive analysis was performed of routine bacterial and fungal culture and AST data extracted from the National Health Laboratory Service laboratory information system for the ICU/HCU. Only the first diagnostic isolate of a given species per patient per year was included in the analysis. All analysis and reporting were done in accordance with the applicable Clinical and Laboratory Standards Institute guidelines. RESULTS: Enterobacteriaceae predominated in first-isolate cultures in 2013 (60%) and 2017 (56%). There was an overall decrease in extended-spectrum beta-lactamase-producing Enterobacteriaceae from 2013 (42%) to 2017 (30%) (p=0.013), accompanied by an increase in carbapenem-resistant Enterobacteriaceae from 2013 (4%) to 2017 (11%) (p=0.24). Although the total percentage of Acinetobacter spp. decreased in 2017 (p=0.021), the proportion of extensively drug-resistant isolates doubled to 68% in 2017 (p<0.001). The percentage of methicillin-resistant Staphylococcus aureus decreased significantly from 49% to 14% (p<0.001), along with a significant decrease in vancomycin-resistant enterococci from 17% to 0% (p=0.001). Candida auris increased from 0% in 2013 to 11% in 2017 (p=0.002), and non-albicans Candida spp. predominated (80%) in blood cultures in 2017 (p=0.023). CONCLUSIONS: Appropriate selection of empirical antimicrobial therapy should be guided by the ICU-specific antibiogram. The recommended empirical antimicrobial therapy at the CMJAH ICU/HCU based on the antibiogram analysis would include ertapenem to cover the Enterobacteriaceae. Amikacin is recommended for empirical treatment of suspected pseudomonal infections. Additional empirical antimicrobial therapy for Gram-positive organisms is not routinely advocated, and empirical antifungal therapy with amphotericin B or micafungin is only appropriate in patients at high risk for invasive candidiasis.