Emergence of Clonally-Related South Asian Clade I Clinical Isolates of Candida auris in a Greek COVID-19 Intensive Care Unit

Abstract

Candida auris has recently emerged as a multidrug-resistant yeast implicated in various healthcare-associated invasive infections and hospital outbreaks. In the current study, we report the first five intensive care unit (ICU) cases affected by C. auris isolates in Greece, during October 2020–January 2022. The ICU of the hospital was converted to a COVID-19 unit on 25 February 2021, during the third wave of COVID-19 in Greece. Identification of the isolates was confirmed by Matrix Assisted Laser Desorption Ionization Time of Flight mass spectroscopy (MALDI-TOF]. Antifungal susceptibility testing was performed by the EUCAST broth microdilution method. Based on the tentative CDC MIC breakpoints, all five C. auris isolates were resistant to fluconazole (≥32 μg/mL), while three of them exhibited resistance to amphotericin B (≥2 μg/mL). The environmental screening also revealed the dissemination of C. auris in the ICU. Molecular characterization of C. auris clinical and environmental isolates was performed by MultiLocus Sequence Typing (MLST) of a set of four genetic loci, namely ITS, D1/D2, RPB1 and RPB2, encoding for the internal transcribed spacer region (ITS) of the ribosomal subunit, the large ribosomal subunit region and the RNA polymerase II largest subunit, respectively. MLST analysis showed that all isolates possessed identical sequences in the four genetic loci and clustered with the South Asian clade I strains. Additionally, PCR amplification and sequencing of the CJJ09_001802 genetic locus, encoding for the “nucleolar protein 58” that contains clade-specific repeats was performed. Sanger sequence analysis of the TCCTTCTTC repeats within CJJ09_001802 locus also assigned the C. auris isolates to the South Asian clade I. Our study confirms that C. auris is an emerging yeast pathogen in our region, especially in the setting of the ongoing COVID-19 worldwide pandemic. Adherence to strict infection control is needed to restrain further spread of the pathogen.

Candida auris: Outbreak, surveillance and epidemiological monitoring in Northern Greece

“…1 ) within the South Asian lineage (Clade I), similarly to other strains from Greece until today. 7 , 40 Monitoring is ongoing, with new strains being added daily to the Mycology Lab's collection but with no differentiation of the total image until now (same sensitivity profile and phylogeny).…”

Potential Environmental Reservoirs of Candida auris: A Systematic Review

“…Sixteen studies used swabs [48][49][50][51][52][53][55][56][57][58]60,63,65,[68][69][70], while two used gauze [54,59], and one used both direct contact plates and swab techniques [61]. Six studies did not report the methods of sample collection [13,47,62,64,66,67]. Among the studies that employed swabs, only 12 reported the material, of which 9 were sponges [48,55,58,60,63,65,[68][69][70] and 3 were cotton [49,51,53].…”

“…Additionally, 13 studies reported the presence of this yeast in areas outside the patient's rooms, such as keyboards, sinks, and air vents [48,50,[53][54][55][57][58][59][60]64,65,69,70]. The clade of C. auris was determined by WGS and analyzed by fifteen studies, of which twelve studies found the South Asian clade [13,[48][49][50][51][52][55][56][57]62,63,66] and three studies detected the African clade [47,61,64].…”

“…Eleven studies tried to understand the relationship between clinical and environmental samples [13,47,48,50,51,57,60,61,63,64,66]. Five studies proved that they were similar [13,57,60,63,66], four that there was a close relationship between them [47,48,51,61], and two mentioned that there was a difference of between 1 and 160 SNPs between clinical and environmental samples [50,64].…”

Candida auris Outbreaks: Current Status and Future Perspectives

“…Although clinical cut-off values for C. auris antifungal susceptibility tests have not yet been reported, it is known that high MICs for some antifungal agents, such as azoles, indicate that these compounds are not a viable therapeutic option for most clinical cases [34]. However, tentative CDC MIC breakpoints have been used for the following antifungal agents: fluconazole (≥32 µg/mL), voriconazole (≥2 µg/mL), posaconazole (≥2 µg/mL), itraconazole (≥2 µg/mL), anidulafungin (≥4 µg/mL), micafungin (≥4 µg/mL), caspofungin (≥4 µg/mL), and amphotericin B (≥2 µg/mL) [87]. According to these breakpoints, around 90% of C. auris isolates in the US are resistant to azoles, 30% are resistant to amphotericin B, and 3-5% are resistant to echinocandins.…”