References
- LockhartSRSimultaneous emergence of multidrug resistant Candida auris on three continents confirmed by whole genome sequencing and epidemiological analysesClin. Infect. Dis.201764 134 14010.1093/cid/ciw691
- LamothFLockhartSRBerkowELCalandraTChanges in the epidemiological landscape of invasive candidiasisJ. Antimicrob. Chemother.201873i4i1310.1093/jac/dkx444
- ArendrupMCPrakashAMeletiadisJSharmaCChowdharyAComparison of EUCAST and CLSI reference microdilution MICs of eight antifungal compounds for Candida auris and associated tentative epidemiological cutoff valuesAntimicrob. Agents Chemother.201761e00485175444165
- Calvo, B. et al. First report of Candida auris in America: clinical and microbiological aspects of 18 episodes of candidemia. J. Infect.73, 369–374 (2016).
- SarmaSCandidemia caused by amphotericin B and fluconazole resistant Candida aurisIndian J. Med. Microbiol.201331909110.4103/0255-0857.108746
- MagoboRECorcoranCSeetharamSGovenderNPCandida auris-associated candidemia, South AfricaEmerg. Infect. Dis.2014201250125110.3201/eid2007.1317654073876
- LockhartSRBerkowELChowNWelshRMCandida auris for the clinical microbiology laboratory: not your grandfather’s Candida speciesClin. Microbiol. Newsl.2017399910310.1016/j.clinmicnews.2017.06.0035831145
- SatohKCandida auris sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospitalMicrobiol. Immunol.200953414410.1111/j.1348-0421.2008.00083.x
- ChowdharyANew clonal strain of Candida auris, Delhi, IndiaEmerg. Infect. Dis.2013191670167310.3201/eid1910.1303933810747
- LeeWGFirst three reported cases of nosocomial fungemia caused by Candida aurisJ. Clin. Microbiol.2011493139314210.1128/JCM.00319-113165631
- Schelenz, S. et al. First hospital outbreak of the globally emerging Candida auris in a European hospital. Antimicrob. Resist. Infect. Control5, 35 (2016). 10.1186/s13756-016-0132-5
- Ben-AmiRMultidrug-resistant Candida haemulonii and C. auris, Tel Aviv, Israel.Emerg. Infect. Dis20172319520310.3201/eid2302.1614865324804
- SchwartzISHammondGWFirst reported case of multidrug-resistant Candida auris in CanadaCan. Commun. Dis. Report.20174315015310.14745/ccdr.v43i78a02
- PrakashAEvidence of genotypic diversity among Candida auris isolates by multilocus sequence typing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and amplified fragment length polymorphismClin. Microbiol. Infect.201622277.e1910.1016/j.cmi.2015.10.022
- MohsinJThe first cases of Candida auris candidaemia in OmanMycoses20176056957510.1111/myc.12647
- AraúzABIsolation of Candida auris from 9 patients in Central America: importance of accurate diagnosis and susceptibility testingMycoses201861444710.1111/myc.12709
- LockhartSRThinking beyond the common Candida species: need for species-level identification of Candida due to the emergence of multidrug-resistant Candida aurisJ. Clin. Microbiol.2017553324332710.1128/JCM.01355-175703798
- ChowdharyAMultidrug-resistant endemic clonal strain of Candida auris in IndiaEur. J. Clin. Microbiol. Infect. Dis.20133391992610.1007/s10096-013-2027-1
- AsadzadehMAhmadSAl-SweihNKhanZMolecular fingerprinting studies do not support intrahospital transmission of Candida albicans among candidemia patients in KuwaitFront. Microbiol.2017824710.3389/fmicb.2017.002475318450
- LitvintsevaAPWhole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infectionsJ. Clin. Microbiol.2014523216322210.1128/JCM.00936-144313140
- EtienneKAWhole genome sequence typing to investigate the Apophysomyces outbreak following a tornado in Joplin, Missouri, 2011PLoS ONE20127e4998910.1371/journal.pone.00499893507928
- EngelthalerDMNext-generation sequencing of Coccidioides immitis Isolated during cluster investigationEmerg. Infect. Dis.20111722723210.3201/eid1702.1006203204756
- Quick, J. et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16, 114 (2015).
- Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature530, 228–232 (2016).
- ButlerGEvolution of pathogenicity and sexual reproduction in eight Candida genomesNature200945965766210.1038/nature080642834264
- ChatterjeeSDraft genome of a commonly misdiagnosed multidrug resistant pathogen Candida aurisBMC Genom.20151611610.1186/s12864-015-1863-z
- SharmaCKumarNPandeyRMeisJFChowdharyAWhole genome sequencing of emerging multidrug resistant Candida auris isolates in India demonstrates low genetic variationNew Microbes New Infect.201613778210.1016/j.nmni.2016.07.0035006800
- JeffaresDCThe genomic and phenotypic diversity of Schizosaccharomyces pombeNat. Genet.20154723524110.1038/ng.32154645456
- LitiGPopulation genomics of domestic and wild yeastsNature200945833734110.1038/nature077432659681
- Cuenca-EstrellaMAntifungal drug resistance mechanisms in pathogenic fungi: from bench to bedsideClin. Microbiol. Infect.201420545910.1111/1469-0691.12495
- ArendrupMCPattersonTFMultidrug-resistant candida: epidemiology, molecular mechanisms, and treatmentJ. Infect. Dis.2017216S445S45110.1093/infdis/jix131
- Jimenez-Ortigosa, C., Moore, C., Denning, D. W. & Perlin, D. S. Emergence of echinocandin resistance due to a point mutation in the fks1 gene of Aspergillus fumigatus in a patient with chronic pulmonary Aspergillosis. Antimicrob. Agents Chemother. AAC.01277–17–15. 10.1128/AAC.01277-17 (2017).
- Ben-AmiRFitness and virulence costs of Candida albicans FKS1 hot spot mutations associated with echinocandin resistanceJ. Infect. Dis.201120462663510.1093/infdis/jir3513144175
- DodgsonARDodgsonKJPujolCPfallerMASollDRClade-specific flucytosine resistance is due to a single nucleotide change in the FUR1 gene of Candida albicansAntimicrob. Agents Chemother.2004482223222710.1128/AAC.48.6.2223-2227.2004415630
- PaponNMolecular mechanism of flucytosine resistance in Candida lusitaniae: contribution of the FCY2, FCY1, and FUR1 genes to 5-fluorouracil and fluconazole cross-resistanceAntimicrob. Agents Chemother.20075136937110.1128/AAC.00824-06
- MorioFLogeCBesseBHennequinCLe PapePScreening for amino acid substitutions in the Candida albicans Erg11 protein of azole-susceptible and azole-resistant clinical isolates: new substitutions and a review of the literatureDiagn. Microbiol. Infect. Dis.20106637338410.1016/j.diagmicrobio.2009.11.006
- ChowdharyAA multicentre study of antifungal susceptibility patterns among 350 Candida auris isolates (2009–17) in India: role of the ERG11 and FKS1 genes in azole and echinocandin resistanceJ. Antimicrob. Chemother.201813e10062909
- Jeffery-SmithACandida auris: a review of the literatureClin. Microbiol. Rev.201831e0002917
- Ruiz GaitánACNosocomial fungemia by Candida auris: first four reported cases in continental EuropeRev. Iberoam. Micol.201734232710.1016/j.riam.2016.11.002
- SanguinettiMMechanisms of azole resistance in clinical isolates of Candida glabrata collected during a hospital survey of antifungal resistanceAntimicrob. Agents Chemother.20054966867910.1128/AAC.49.2.668-679.2005547307
- WhaleySGAzole antifungal resistance in Candida albicans and emerging non-albicans Candida speciesFront. Microbiol.20177112210.3389/fmicb.2016.02173
- Garcia-EffronGLeeSParkSClearyJDPerlinDSEffect of Candida glabrata FKS1 and FKS2 mutations on echinocandin sensitivity and kinetics of 1,3-beta-d-glucan synthase: implication for the existing susceptibility breakpointAntimicrob. Agents Chemother.2009533690369910.1128/AAC.00443-092737881
- Berkow, E. L. & Lockhart, S. R. Activity of CD101, a long-acting echinocandin, against clinical isolates of Candida auris. Diagn. Microbiol. Infect. Dis.10.1016/j.diagmicrobio.2017.10.021 (2017).
- Rex, J. H., Alexander, B. D., Andes, D. & Arthington-Skaggs, B. Reference Method for Broth Dilution Antifungal Susceptibility Testing of Yeasts. Approved Standard. 3rd edn (M27-A3) (Clinical and Laboratory Standards Institute (CLSI), Wayne, PA, 2008).
- WatsonMpoRe: an R package for the visualization and analysis of nanopore sequencing dataBioinformatics20153111411510.1093/bioinformatics/btu590
- BorodovskyMMcIninchJGENMARK: parallel gene recognition for both DNA strandsComput. Chem.19931712313310.1016/0097-8485(93)85004-V
- BairochAApweilerRThe SWISS-PROT protein sequence database and its supplement TrEMBL in 2000Nucleic Acids Res.200028454810.1093/nar/28.1.4510592178
- KanehisaMGotoSKEGG: Kyoto encyclopedia of genes and genomesNucleic Acids Res.200028273010.1093/nar/28.1.27102409
- FinnRDClementsJEddySRHMMER web server: interactive sequence similarity searchingNucleic Acids Res.201139W29W3710.1093/nar/gkr3673125773
- FinnRDPfam: the protein families databaseNucleic Acids Res.201442D222D23010.1093/nar/gkt1223
- HaftDHSelengutJDWhiteOThe TIGRFAMs database of protein familiesNucleic Acids Res.20033137137310.1093/nar/gkg128165575
- LoweTMEddySRtRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequenceNucleic Acids Res.19972595596410.1093/nar/25.5.0955146525
- LagesenKRNAmmer: consistent and rapid annotation of ribosomal RNA genesNucleic Acids Res.2007353100310810.1093/nar/gkm1601888812
- Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (2013). arXiv:1303.3997
- LiHThe sequence alignment/map format and SAMtoolsBioinformatics2009252078207910.1093/bioinformatics/btp3522723002
- McKennaAThe genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing dataGenome Res.2010201297130310.1101/gr.107524.11020644199
- Smit, A., Hubley, R., & Green, P. RepeatMasker Open-4.0. 2013–2015 (2015).
- RhodesJA population genomics approach to assessing the genetic basis of within-host microevolution underlying recurrent Cryptococcal meningitis infectionG3201771165117610.1534/g3.116.037499
- RambautALamTTMax CarvalhoLPybusOGExploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)Virus Evol.20162vew00710.1093/ve/vew0074989882
- PfallerMADiekemaDJProgress in antifungal susceptibility testing of Candida spp. by use of clinical and laboratory standards institute broth microdilution methods, 2010 to 2012J. Clin. Microbiol.2012502846285610.1128/JCM.00937-123421803