Candida auris is an invasive healthcare-associated fungal pathogen. Cases of candidemia, defined as illness in patients with Candida cultured from blood, were detected through national laboratory-based surveillance in South Africa during 2016–2017. We identified viable isolates by using mass spectrometry and sequencing. Among 6,669 cases (5,876 with species identification) from 269 hospitals, 794 (14%) were caused by C. auris . The incidence risk for all candidemia at 133 hospitals was 83.8 (95% CI 81.2–86.4) cases/100,000 admissions. Prior systemic antifungal drug therapy was associated with a 40% increased adjusted odds of C. auris fungemia compared with bloodstream infection caused by other Candida species (adjusted odds ratio 1.4 [95% CI 0.8–2.3]). The crude in-hospital case-fatality ratio did not differ between Candida species and was 45% for C. auris candidemia, compared with 43% for non– C. auris candidemia. C. auris has caused a major epidemiologic shift in candidemia in South Africa.

Introduction Candida auris is a multidrug-resistant fungal pathogen endemic in South African hospitals. Materials and methods We tested bloodstream C. auris isolates that were submitted to a reference laboratory for national laboratory-based surveillance for candidaemia, 2016-2017. We confirmed species identification by phenotypic/molecular methods. We tested susceptibility to amphotericin B, anidulafungin, caspofungin, micafungin, itraconazole, posaconazole, voriconazole, fluconazole and flucytosine using broth microdilution (BMD) and Etest. We interpreted minimum inhibitory concentrations (MICs) using tentative breakpoints. We sequenced the genomes of a subset of isolates and compared to the C. auris B8441 reference strain. Results Of 400 C. auris isolates, 361 (90%) were resistant to at least one antifungal agent, 339 (85%) to fluconazole alone (MIC of ≥32 mg/L), 19 (5%) to fluconazole and amphotericin B (MIC ≥2 mg/L) and one (0.3%) to amphotericin B alone. Two (0.5%) isolates from a single patient were pan-resistant (fluconazole, amphotericin B, echinocandins). Of 93 isolates selected for whole genome sequencing, 78 clustered in clade III including the pan-resistant isolates, 13 in clade I and two in clade IV. Eighty-four of these (91%) were resistant to at least one antifungal agent; both resistant and susceptible isolates had mutations. The common substitutions identified across the different clades were VF125AL, Y132F, K177R, N335S, E343D in ERG11 ; N647T in MRR1; A651P, A657V, S195G in TAC1b; S639P in FKS1; and S58T in ERG3 genes. Conclusions Most South African C. auris isolates were resistant to azoles, though resistance to polyenes and echinocandins was less common. We observed mutations in resistance genes even in phenotypically-susceptible isolates.

Candidemia is a major cause of healthcare-associated infections. We describe a large outbreak of Candida krusei bloodstream infections among infants in Gauteng Province, South Africa, during a 4-month period; a series of candidemia and bacteremia outbreaks in the neonatal unit followed. We detected cases by using enhanced laboratory surveillance and audited hospital wards by environmental sampling and epidemiologic studies. During July–October 2014, among 589 patients, 48 unique cases of C. krusei candidemia occurred (8.2% incidence). Risk factors for candidemia on multivariable analyses were necrotizing enterocolitis, birthweight <1,500 g, receipt of parenteral nutrition, and receipt of blood transfusion. Despite initial interventions, outbreaks of bloodstream infection caused by C. krusei, rarer fungal species, and bacterial pathogens continued in the neonatal unit through July 29, 2016. Multiple factors contributed to these outbreaks; the most functional response is to fortify infection prevention and control.

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.

Candida auris is an invasive healthcare-associated fungal pathogen. Cases of candidemia, defined as illness in patients with Candida cultured from blood, were detected through national laboratory-based surveillance in South Africa during 2016-2017. We identified viable isolates by using mass spectrometry and sequencing. Among 6,669 cases (5,876 with species identification) from 269 hospitals, 794 (14%) were caused by C. auris. The incidence risk for all candidemia at 133 hospitals was 83.8 (95% CI 81.2-86.4) cases/100,000 admissions. Prior systemic antifungal drug therapy was associated with a 40% increased adjusted odds of C. auris fungemia compared with bloodstream infection caused by other Candida species (adjusted odds ratio 1.4 [95% CI 0.8-2.3]). The crude in-hospital case-fatality ratio did not differ between Candida species and was 45% for C. auris candidemia, compared with 43% for non-C. auris candidemia. C. auris has caused a major epidemiologic shift in candidemia in South Africa.

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During a one year prospective study of Haemophilus influenzae infections in patients treated in hospitals in the metropolitan area of Cape Town. H. influenzae type b accounted for 81.7% of 126 invasive isolates, whereas 86.1% of the 280 non-invasive isolates were non-typeable. Ampicillin resistance was detected among 10.8% of strains of which all but one produced beta-lactamase. All strains were susceptible to cefotaxime as were more than 95% to chloramphenicol, rifampicin, tetracycline but 20.4% were resistant to co-trimoxazole and 87.2% to erythromycin.

The reasons for the dramatic emergence of C. auris as a pathogen in healthcare settings are not clear. We know that East Asia, South Asia, Africa and South America have unique C. auris clades separated from other clades by tens of thousands of single nucleotide polymorphisms. 10 This is consistent with the hypothesis that C. auris emerged independently and simultaneously on several continents. While C. auris is likely to have an environmental reservoir outside the healthcare setting, this has yet to be established. Several intrinsic properties of the pathogen probably facilitated its rapid spread in hospitals. C. auris produces biofilms. 11,12,13 While this fungus Candida auris has been detected at almost 100 South African hospitals, causing large outbreaks in some facilities, and this pathogen now accounts for approximately 1 in 10 cases of candidaemia. The objective of this guideline is to provide updated, evidence-informed recommendations outlining a best-practice approach to prevent, diagnose and manage C. auris disease in public-and private-sector healthcare settings in South Africa. The 18 practical recommendations cover five focus areas: laboratory identification and antifungal susceptibility testing, surveillance and outbreak response, infection prevention and control, clinical management and antifungal stewardship.