Multilocus sequence typing of azole-resistant Candida auris strains, South Africa

Rindidzani Magobo; Mabatho Mhlanga; Craig Corcoran; Nelesh P Govender

doi:10.4102/sajid.v35i1.116

Multilocus sequence typing of azole-resistant Candida auris strains, South Africa

S Afr J Infect Dis. 2020 Mar 23;35(1):116. doi: 10.4102/sajid.v35i1.116. eCollection 2020.

Authors

Rindidzani Magobo^{1

2}, Mabatho Mhlanga¹, Craig Corcoran², Nelesh P Govender¹

Affiliations

¹ Centre for Healthcare-associated Infections, Antimicrobial Resistance and Mycoses, Division of the National Health Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa.
² Ampath National Reference Laboratory, Pretoria, South Africa.

Abstract

Background: Candida auris is an emerging multidrug-resistant fungal pathogen associated with high mortality.

Methods: We investigated the genetic relatedness of clinical C. auris isolates from patients admitted to either public- or private-sector hospitals, which were submitted to a reference laboratory from 2012 to 2015. Patient demographics and clinical details were recorded. We performed antifungal susceptibility testing, sequencing of the hotspot 1 and 2 regions of the FKS1 and FKS2 genes for all isolates with an echinocandin minimum inhibitory concentration (MIC) of ≥1 µg/mL and cluster analysis using multilocus sequence typing.

Results: Eighty-five isolates were confirmed as C. auris. The median patient age was 59 years [inter-quartile range (IQR): 48-68 years], with male patients accounting for 68% of cases. Specimen types included urine (29%), blood (27%), central venous catheter tips (25%), irrigation fluid (7%), tissue (5%), respiratory tract specimens (4%) and other (3%). Ninety-seven per cent of isolates were resistant to fluconazole, 7% were resistant to both fluconazole and voriconazole, 8% were resistant to both fluconazole and echinocandins (considered multidrug resistant) and all were susceptible to amphotericin B. Of the 15 randomly selected fluconazole-resistant isolates, 14 isolates had an isavuconazole MIC ≤ 1 µg/mL. No FKS mutations were detected. Multilocus sequence typing (MLST) analysis grouped isolates into two clusters: cluster 1 and cluster 2 comprising 83 and 2 isolates, respectively.

Conclusions: Azole-resistant C. auris strains circulating in South African hospitals were related by MLST, but the possibility of nosocomial transmission should be explored using a more discriminatory technique, for example, whole genome sequencing.

Keywords: Candida auris; FKS sequencing; South Africa; azole resistant; multilocus sequence typing.