Use of Rolling Circle Amplification to Rapidly Identify Species of Cladophialophora Potentially Causing Human Infection Hossein Hamzehei • Seyed Amir Yazdanparast • Mehrnaz Mohammad Davoudi • Sadegh Khodavaisy • Mitra Golehkheyli • Saham Ansari • G. S. de Hoog • Hamid Badali Received: 31 August 2012 / Accepted: 21 January 2013 / Published online: 8 March 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract The genus Cladophialophora comprises etiologic agents of disease in immunocompetent patients, ranging from mild cutaneous colonization to cerebral encephalitis, in addition to saprobic species. Due to the high degree of phenotypic similarity between closely related species of the genus, identification problems are imminent. In the present study, we described rapid and sensitive rolling circle amplification (RCA) method based on species- specific padlock probes targeted for the internal transcribed spacer regions of rDNA. ITS regions of 12 Cladophialophora species were sequenced, and subsequently, 10 specific padlock probes were designed for the detection of single nucleotide poly- morphisms. The majority of circularizable padlock probes were designed based on single nucleotide polymorphisms (SNPs), while for C. bantiana, C. immunda and C. devriesii were characterized by two or more nucleotides. Individual species-specific probes correctly identified in all ten Cladophialophora species correctly by visualization on 1.2 % agarose gels used to verify specificity of probe-template binding; no cross-reactivity was observed. Simplicity, sensitivity, robustness and low costs provide RCA a H. Hamzehei Laboratory Research Center, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran S. A. Yazdanparast Department of Medical Parasitology and Mycology, School of Allied Medicine, Tehran University of Medical Sciences, Tehran, Iran M. Mohammad Davoudi Student Research Center/Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran S. Khodavaisy Department of Medical Parasitology and Mycology, Kurdistan University of Medical Sciences, Sanandaj, Iran S. Khodavaisy Department of Medical Mycology and Parasitology, School of public health, Tehran University of Medical Sciences, Tehran, Iran M. Golehkheyli Department of Microbiology, Damghan Branch Islamic Azad University, Damghan, Iran S. Ansari  H. Badali Department of Medical Mycology and Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran G. S. de Hoog CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands H. Badali (&) Invasive Fungi Research Center (IFRC)/Molecular and Cell Biology Research Center (MCBRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran e-mail: badalii@yahoo.com 123 Mycopathologia (2013) 175:431–438 DOI 10.1007/s11046-013-9630-7