title: MP1 homologue-based multilocus sequence system for typing the pathogenic fungus Penicillium marneffei: a novel approach using lineage-specific genes.
abstract: 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.
authors: State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong.
authors: Patrick C Y
authors: PC
authors: Woo
authors: Candy C Y
authors: CC
authors: Lau
authors: Ken T K
authors: KT
authors: Chong
authors: Herman
authors: H
authors: Tse
authors: Dominic N C
authors: DN
authors: Tsang
authors: Rodney A
authors: RA
authors: Lee
authors: Cindy W S
authors: CW
authors: Tse
authors: Tak-Lun
authors: TL
authors: Que
authors: Liliane M W
authors: LM
authors: Chung
authors: Antonio H Y
authors: AH
authors: Ngan
authors: Wai-Ting
authors: WT
authors: Hui
authors: Samson S Y
authors: SS
authors: Wong
authors: Susanna K P
authors: SK
authors: Lau
authors: Kwok-Yung
authors: KY
authors: Yuen
mesh_terms: D000328:Adult; D000368:Aged; D001483:Base Sequence; D002675:Child, Preschool; D016521:Electrophoresis, Gel, Pulsed-Field; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D016533:Mycological Typing Techniques / Q000379:methods*; D010407:Penicillium / Q000145:classification* / Q000235:genetics; D017422:Sequence Analysis, DNA