Molecular Characterization of Candida auris Isolates at a Major Tertiary Care Center in Lebanon

Abstract

BackgroundThe globally emerging Candida auris pathogens poses heavy burden to the healthcare system. Their molecular analyses assist in understanding their epidemiology, dissemination, treatment, and control. This study was warranted to describe the genomic features and drug resistance profiles using whole genome sequencing (WGS) among C. auris isolates from Lebanon.MethodsA total of 28 C. auris clinical isolates, from different hospital units, were phenotypically identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and tested for antifungal resistance using Vitek-2 system and E test. The complete genomes were determined by WGS using long reads sequencing (PacBio) to reveal the clade distribution and antifungal resistance genes.ResultsCandida auris revealed uniform resistance to fluconazole and amphotericin B, with full susceptibility to echinocandins. Among key resistance genes studied, only two mutations were detected: Y132F in ERG11 gene and a novel mutation, D709E, found in CDR1 gene encoding for an ABC efflux pump. Phylogenetically, C. auris genomes belonged to South Asian clade I and showed limited genetic diversity, suggesting person to person transmission.ConclusionThis characterization of C. auris isolates from Lebanon revealed the exclusivity of clade I lineage together with uniform resistance to fluconazole and amphotericin B. The control of such highly resistant pathogen necessitates an appropriate and rapid recovery and identification to contain spread and outbreaks.

COVID-19 and C. auris: A Case-Control Study from a Tertiary Care Center in Lebanon

“…The reported antifungal susceptibilities on 28 C. auris isolates are shown in Table 6 [ 22 ]. C. auris was considered to be uniformly resistant to fluconazole, and 100% of the isolates demonstrated specified breakpoints of resistance (MIC ≥ 2 ug/mL) for amphotericin B.…”

“…C. auris was considered to be uniformly resistant to fluconazole, and 100% of the isolates demonstrated specified breakpoints of resistance (MIC ≥ 2 ug/mL) for amphotericin B. On the contrary, there was a uniform susceptibility of the isolates for micafungin and caspofungin [ 22 ].…”

“…C. auris colonies were phenotypically identified by Matrix-Assisted Laser Desorption/Ionization-Time of Flight MALDI-TOF (Bruker Daltonik, GmbH, Bremen, Germany) and by the VITEK-2 system (bioMérieux, Marcy l’Étoile, France). Samples were saved and referred for genome sequencing analysis in order to reveal the clade distribution and antifungal resistance genes [ 22 ]. This was done by AUBMC microbiology laboratory team in collaboration with the Faculty of Medicine and University Hospital in Plzen Czechia [ 22 ].…”

“…Samples were saved and referred for genome sequencing analysis in order to reveal the clade distribution and antifungal resistance genes [ 22 ]. This was done by AUBMC microbiology laboratory team in collaboration with the Faculty of Medicine and University Hospital in Plzen Czechia [ 22 ]. Antifungal susceptibility testing was done using VITEK-2 and E-test antimicrobial susceptibility tests.…”

“…Due to the financial issues in view of the economic crisis in Lebanon and the COVID-19 pandemic, susceptibility tests could not be performed on several patients. Genomes were determined by whole genome sequencing (WGS) using long reads sequencing (PacBIO) to identify the antifungal resistance genes and the clade distribution [ 22 ].…”