Table 1.
Candida auris: nosocomial outbreaks that have incorporated genotypic methods to investigate isolate relatedness.
| Country, Year (Reference) | Setting | No. Patients/No. Outbreak Isolates Analyzed | Typing Method | Genetic Diversity | Drug-Resistance Genes and Mutations |
|---|---|---|---|---|---|
| USA 2017 [76] |
Single centre New Jersey (NJ), single centre Illinois (IL) | 2/2 NJ 2/2 IL |
WGS | NJ: 2 isolates assigned to clade I (separated by <10 SNPs) IL: 2 isolates assigned to clade IV (separated by <10 SNPs) |
Not reported |
| UK 2018 [77] |
Neurosciences ICU (over 3 years) | 70/72 | WGS | All outbreak isolates formed a single genetic cluster (clade III) comprising 72 isolates from 37 patients and 6 temperature-probe isolates (separated by <30 SNPs between isolates); close matches between patient and temperature-probe samples |
Not reported |
| Saudi Arabia 2020 [78] |
Single centre, various wards | 7/7 | WGS | All 7 isolates assigned to clade I but 2 sub-clusters (for both clusters, isolates within separated by <10 SNPs) | Not reported |
| USA 2020 [79] |
Surgical ICU, liver transplant |
5/5 | WGS | All 5 isolates assigned to clade I (separated by <16 SNPs) | Not reported |
| Italy 2021 [80] |
COVID ICU | 10/10 | WGS | All 10 isolates assigned to clade I (separated by mean/median SNPs 7) | All isolates resistant to fluconazole and amphotericin B ERG11 K143R mutation all isolates TACB1 A640V mutation all isolates |
| Hong Kong 2021 [81] | Single centre | 15/19 | WGS | All 19 isolates assigned to clade I (separated by <13 SNPs) | Not reported |
| USA 2021 [82] |
Single centre; COVID-19 ward, non-COVID-19 wards | 15/15 12 in COVID-19 ward, 3 in non-COVID-19 ward |
WGS | 12 isolates with spatio-temporal link: all assigned to clade III (separated by ≤5 SNPs); 3 non-COVID ward isolates with no spatio-temporal link also closely related to COVID ward isolates (≤5 SNPs) |
Not reported |
| USA 2021 [83] |
Single institution | 14/20 | WGS | All 20 isolates assigned to clade III (separated by 1–9 SNPs); however, unable to distinguish 5 outbreak isolates from non-epidemiologically unliked isolates (n = 15) |
Not reported |
| USA 2021 [84] |
Multiple LTACH/vSNFs in region (9 facilities) | 182/81 | WGS | 81 isolates assigned to clade III (separated by <11 SNPs); suggesting significant spread among these facilities in the region |
Not reported |
| Canada 2021 [85] |
ICU of community health facility | 4/4 | WGS | All 4 isolates assigned to clade I (separated by ≤15 SNPs) | ERG11 Y132F mutation all isolates |
| UK 2022 [86] |
Single hospital (ICU, cardiothoracic, cardiac medical) | 16/21 | WGS | 18 isolates assigned to clade I (separated by mean of 4 SNP); 4 environmental isolates also belonged to clade I; 3 isolates assigned to Clade III (separated by mean 12 SNPs); 3 introductions to hospital, with subsequent spread |
ERG11 Y132F mutation-in clade I isolates (n = 18 clinical and 4 environmental isolates), ERG11 F126L mutation in clade III isolates (n = 3) |
| France 2022 [87] | Burn ICU | 2/2 | WGS | Both isolates assigned to clade I (separated by ≤12 SNPs) | Not reported |
| Iran 2022 [88] |
5 isolates from Iran (different settings) | 5/5 | STR and WGS | New clade identified (clade V) (with isolates within separated by <100 SNPs) and separated by >200,000 SNPs from other clades |
ERG11 Y132F mutation (n = 1), ERG11 I466L mutation (n = 1), TAC1b D599G mutation (n = 1) |
| Lebanon 2022 [83] |
Single centre (ICU, resp care, CCU neuro ICU, ED) | 21/28 | WGS | 28 isolates assigned to clade I (separated by 1–6 SNPs) | All fluconazole and amphotericin B resistant ERG11 Y132F mutation all isolates CDR1 D709E mutation all isolates |
| Italy 2023 [89] |
ICU | 503/60 | WGS | All 60 isolates assigned to clade Ic (separated by median of 8 SNPs, IQR 5–12); in comparison, non-epidemiologically linked “control” isolates reported as less related (separated by median of 14 SNPs, IQR 12–16) |
All 60 isolates resistant to fluconazole 2 isolates resistant to caspofungin Gene mutations identified in azole-resistant isolates: CDR1 (V704L substitution), ERG1 (K143R), TAC1B (A640V) HMG1 (P238H) |
| Qatar 2023 [90] |
9 major hospitals | 65/76 | WGS | All 76 isolates assigned to clade I (separated by ≤21 SNPs) |
ERG11 Y132F mutation (n = 120), K143R (n = 2) CDR1 E709D mutation (n = 12), V704L (n = 2) FKS1 S639F mutation (n = 2) and S639Y (n = 1) One pan-resistant isolate also harboured a premature stop codon in ERG3 and novel mutations in CDR2 |
| Venezuela 2016 [91] |
ICU, single centre |
18/18 | AFLP | All isolates (n = 18) clustered together with overall similarity of 85% with two sub-clusters; cluster was distantly related to strain type of C. auris. | Not reported |
| UK 2016 [92] |
Cardiothoracic ICU single centre |
50/15 | AFLP | All isolates (n = 15) formed a distinct cluster with high degree of relatedness; clearly separated from isolates (n = 48), not linked to cluster |
Not reported |
| Spain 2018 [93] |
Single centre ICU | 140/58 | AFLP | All isolates (n = 58) in a single cluster, with overall genetic similarity of >96% | Not reported |
| Kuwait 2020 [94] | HDU of secondary care hospital (long-term care) | 71/71 | 12-locus short tandem repeat (STR) analysis | With exception of 4 isolates from a single patient which differed only at a single locus, all outbreak isolates (n = 71) and environmental isolates (n = 7) had identical STR patterns and belonged to clade Ic; control clade I isolates not linked to outbreak also differed from outbreak isolates at one locus only |
ERG11 Y123F mutation present in nearly all isolates; 4 isolates (one patient) had the ERG11 K143R mutation. |
| Brazil 2021 [95] |
Single centre ICU | 6/6 | Microsatellite analysis | All 6 isolates belonged to clade I but were of three different STRs, signifying three different strains (~85% related) | Not reported |
AFLP, amplified fragment length polymorphisms; CCU, coronary care unit; ED, Emergency Department; HDU, high-dependency unit; ICU, intensive care unit; LTACH, long-term acute care hospital; neuro, neurosurgical; resp, respiratory; SNP, single-nucleotide polymorphism; STR, short tandem repeat; vSNFs, ventilator skilled nursing facilities; WGS, whole genome sequencing.