In Vitro Antifungal Resistance of Candida auris Isolates from Bloodstream Infections, South Africa

Abstract

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.

In Vitro Antifungal Activity of Manogepix and Other Antifungal Agents against South African Candida auris Isolates from Bloodstream Infections

“…Of the 400 isolates confirmed as C. auris at NICD, 394 isolates cultured from 340 cases had manogepix MICs determined; the remaining six isolates were contaminated during storage before manogepix MICs could be determined. Of the 340 cases, 45 cases had more than one isolate tested ( 16 ).…”

“…Of 83 fluconazole-resistant C. auris isolates and a single fluconazole-susceptible isolate which had their genomes sequenced, as well as 35 fluconazole-susceptible isolates for which WGS was not analyzed in the current study, all had mutations in the ERG11 genes. All these isolates also had low manogepix MICs with no differences in manogepix MIC between fluconazole-resistant and -susceptible isolates ( 16 ).…”

“…Echinocandins are recommended for treatment of bloodstream C. auris infection ( 14 , 15 ). A large proportion of South African C. auris isolates, dominated by clade III, are resistant to fluconazole but variably resistant to amphotericin B and echinocandins ( 16 ). For comparison, 90% of 350 Indian C. auris isolates collected between 2009 and 2017 and dominated by clade I were resistant to fluconazole and lower proportions were resistant to echinocandins (2%) and amphotericin B (8%) ( 17 ).…”

Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades

“…Clade II harbors the greatest percentage of drug-susceptible isolates [ 2 ], while clade I has the greatest reported percentage of MDR and pan-resistant isolates and is commonly resistant to fluconazole [ 2 , 13 , 18 ] and amphotericin B [ 2 , 13 ]. Clade III isolates are most often resistant to fluconazole, but resistance to amphotericin B is rare [ 2 , 19 ]. Clade IV isolates have the highest percentage of echinocandin resistance, which only sporadically occurs in clades I and III [ 2 ].…”

“…Although ITS sequencing was reliable to differentiate three out of four clades, it showed less resolution compared to microsatellite typing, as C. auris clade I and clade III show no variation within the ITS region [ 31 ]. Typing of C. auris clades has a role in molecular epidemiology, allowing tracing the origins of nosocomial transmission [ 2 , 19 , 32 , 33 ], while this might also confer a clinical value, as it can help to estimate virulence, transmission, and resistance tendencies [ 2 , 33 ].…”