Talaromyces marneffei genomic, transcriptomic, proteomic and metabolomic studies reveal mechanisms for environmental adaptations and virulence

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Comparative mitogenomic and phylogenetic characterization on the complete mitogenomes of <i>Talaromyces</i> (<i>Penicillium</i>) <i>marneffei</i>

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Polyketides, Toxins and Pigments in Penicillium marneffei

Penicillium marneffei (synonym: Talaromyces marneffei) is the most important pathogenic thermally dimorphic fungus in China and Southeastern Asia. The HIV/AIDS pandemic, particularly in China and other Southeast Asian countries, has led to the emergence of P. marneffei infection as an important AIDS-defining condition. Recently, we published the genome sequence of P. marneffei. In the P. marneffei genome, 23 polyketide synthase genes and two polyketide synthase-non-ribosomal peptide synthase hybrid genes were identified. This number is much higher than those of Coccidioides immitis and Histoplasma capsulatum, important pathogenic thermally dimorphic fungi in the Western world. Phylogenetically, these polyketide synthase genes were distributed evenly with their counterparts found in Aspergillus species and other fungi, suggesting that polyketide synthases in P. marneffei did not diverge from lineage-specific gene duplication through a recent expansion. Gene knockdown experiments and ultra-high performance liquid chromatography-photodiode array detector/electrospray ionization-quadruple time of flight-mass spectrometry analysis confirmed that at least four of the polyketide synthase genes were involved in the biosynthesis of various pigments in P. marneffei, including melanin, mitorubrinic acid, mitorubrinol, monascorubrin, rubropunctatin, citrinin and ankaflavin, some of which were mycotoxins and virulence factors of the fungus.published_or_final_versio

Intra-genomic internal transcribed spacer region sequence heterogeneity and molecular diagnosis in clinical microbiology

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study.published_or_final_versio

Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region

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Human oropharynx as natural reservoir of Streptobacillus hongkongensis

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Identification of a novel bat papillomavirus by metagenomics

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Burkholderia pseudomallei in soil samples from an oceanarium in Hong Kong detected using a sensitive PCR assay

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Clinical spectrum of Exophiala infections and a novel Exophiala species, Exophiala hongkongensis

Poster PresentationBackground: Exophiala species are saprophytic fungi which have been isolated from environments rich in hydrocarbons or from hot, humid, and oligotrophic environments. These fungi are considered as dematiaceous moulds; and due to their phenotypic characteristics at the beginning of colony formation, they are also often referred to as ‘black yeasts’, a misnomer which sometimes may mislead the choice of antifungal agents. When the cultures mature, brown hyphae are formed bearing conidiogenous cells referred to as annellides, a typical characteristic of this fungal genus. Although Exophiala species are environmental fungi, they should not be disregarded as contaminants when they are isolated from clinical specimens. These fungi are causative agents of skin and subcutaneous tissue infections and of systemic infections, such as prosthetic valve endocarditis, dialysis-associated peritonitis, and disseminated infections, especially in immunocompromised patients. Unfortunately, Exophiala species can often only be identified to the genus level by phenotypic characterisation. Objectives: The aims of this study were to study the clinical spectrum of Exophiala infections in Queen Mary Hospital, Hong Kong by a polyphasic approach, and to characterise a potentially novel Exophiala species, Exophiala hongkongensis (ex-type strain HKU32T). Methods: All Exophiala strains characterised in this study were isolated from patients during a 15-year period (1998-2012) and were retrieved from the collection in the clinical microbiology laboratory at Queen Mary Hospital, Hong Kong. The strains were characterised phenotypically by microscopic examination of fungal structure using the agar block smear preparation method and phylogenetically using the internal transcribed spacer (ITS) region and Rpb1 gene. In addition, a unique strain, HKU32T, was further characterised phenotypically by scanning electron microscopy, enzyme activity test using the API-ZYM system, and growth tests on different temperatures and culture media. HKU32T was also further phylogenetically characterised using β-tubulin and β-actin genes. All the phylogenetic analyses were performed by the maximum likelihood method using MEGA 5.0.5. Results: Microscopic examination of the young cultures of all the 12 strains showed subspherical, budding, yeast-like cells. Sequencing of the ITS region and partial Rpb1 gene showed 11 of the 12 strains were known Exophiala species, including E. oligosperma [n = 3], E. jeanselmei [n = 2], E. lecanii-corni [n = 2], E. bergeri [n = 1], E. cancerae [n = 1], E. dermatitidis [n = 1], and E. xenobiotica [n = 1]). As for HKU32T, it displayed unique morphological features and was positive for eight enzymes in the API-ZYM test. Optimal growth was observed at 30°C on potato dextrose agar or at 24°C on cornmeal agar. HKU32T also occupied unique phylogenetic positions in all the phylogenetic analyses, with Exophiala nishimurae being the most closely related species. Clinical spectrum of Exophiala infections in Hong Kong included chronic skin infection, colonisation of gastrointestinal tract, continuous ambulatory peritoneal dialysis (CAPD) peritonitis, onychomycosis, pneumonia, tinea pedis, and wrist or finger nodule. Conclusion: Exophiala species could cause a wide range of infections and the most frequent species isolated from patients in Hong Kong was Exophiala oligosperma. Exophiala hongkongensis sp. nov. is proposed to describe the unique strain HKU32T