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Journal of Clinical Microbiology, November 2007, p. 3647-3654, Vol. 45, No. 11
0095-1137/07/$08.00+0     doi:10.1128/JCM.00619-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

MP1 Homologue-Based Multilocus Sequence System for Typing the Pathogenic Fungus Penicillium marneffei: a Novel Approach Using Lineage-Specific Genes

Patrick C. Y. Woo,^1,2,3, Candy C. Y. Lau,^3, Ken T. K. Chong,³ Herman Tse,^1,2,3 Dominic N. C. Tsang,⁴ Rodney A. Lee,⁵ Cindy W. S. Tse,⁶ Tak-lun Que,⁷ Liliane M. W. Chung,³ Antonio H. Y. Ngan,³ Wai-ting Hui,³ Samson S. Y. Wong,^1,2,3 Susanna K. P. Lau,^1,2,3 and Kwok-yung Yuen^1,2,3*

State Key Laboratory of Emerging Infectious Diseases,¹ Research Centre of Infection and Immunology,² Department of Microbiology, The University of Hong Kong,³ Department of Pathology, Queen Elizabeth Hospital,⁴ Department of Pathology, Pamela Youde Hospital,⁵ Department of Pathology, Kwong Wah Hospital,⁶ Department of Pathology, Tuen Mun Hospital, Hong Kong⁷

Received 20 March 2007/ Returned for modification 2 June 2007/ Accepted 7 September 2007

A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of Penicillium marneffei, the most important thermal dimorphic fungus causing respiratory, skin, and systemic mycosis in Southeast Asia. The sequences of 11 housekeeping genes were identical among 10 strains of P. marneffei, but those of MP1 and its 13 homologues, a novel superfamily of mannoproteins in the subdivision Pezizomycotina of Ascomycetes, mostly species of Penicillium and Aspergillus, showed significant variations. Therefore, a multilocus sequence typing (MLST) system for P. marneffei was constructed using MP1 (549 bp) and the four of its homologues (MPLP4 [337 bp], MPLP7 [347 bp], MPLP10 [546 bp], and MPLP13 [422 bp]) that showed the greatest variations. Among the 2,201 bp of the five loci, 183 polymorphic sites were observed in 44 strains of P. marneffei. The median number of alleles at each locus was five (range, 5 [MPLP4, MPLP7, and MPLP13] to 15 [MPLP10]). Four of the five genes had nonsynonymous substitution/synonymous substitution (d_n/d_s) ratios of >1. A total of 35 different sequence types (STs) were assigned to the 44 P. marneffei isolates, with 28 of the 35 STs identified only once. The discriminatory power was 0.9884. MP1 and its homologues were better than housekeeping genes for MLST in P. marneffei. Due to their more rapid evolutionary rates, lineage-specific genes may be better candidates than housekeeping genes for sequence-based typing, especially in microbes that evolve slowly or have evolved recently.

Published ahead of print on 19 September 2007.

P. C. Y. Woo and C. C. Y. Lau contributed equally to the manuscript.