Trichosporon austroamericanum Infections among Hospitalized Patients, France, 2022-2024

Abstract

During 2022-2024, six cases of invasive fungal infection occurred among immunocompromised patients at Marseille University Hospital, Marseille, France. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry initially identified Trichosporon inkin fungi. However, phylogenetic analysis of intergenic spacer region 1 and whole-genome sequences revealed the genetically distinct species T. austroamericanum. Analysis of core genome and mitogenome from 6 patient isolates and 1 environmental isolate revealed substantial genetic diversity among T. austroamericanum strains, indicating a polyclonal outbreak. Furthermore, the mitochondrial genome emerged as a potential marker for intraspecies differentiation, which potentially could aid in epidemiologic investigations. Identified in 2024 but potentially underestimated, T. austroamericanum has since been reported in case clusters from hospital settings in France, highlighting the need for accurate fungal identification and suggesting previously identified T. inkin cases should be re-evaluated for T. austroamericanum. Clinical T. austroamericanum is emerging in hospital settings and should be included in the differential diagnosis of fungal infections.

Keywords: France; Trichosporon austroamericanum; Trichosporonosis; emerging disease; fungi; opportunistic agents; outbreak; yeast.

Figure 1

Maximum-likelihood phylogenetic tree of IGS1 sequences from study of Trichosporon austroamericanum infections among hospitalized patients, France, 2022–2024. The tree includes strains isolated from 6 patients (red font) and 1 environmental sample (L0453, blue font), mapped against T. austroamericanum and related species from GenBank (https://www.ncbi.nlm.nih.gov/genbank) and the CBS culture collection (https://wi.knaw.nl/fungal_table). Bold font indicates reference strain CBS 17435. The clustering confirms that the patient and environmental strains belong to T. austroamericanum and form a distinct clade. The tree also shows the relationships between other Trichosporon species, such as T. inkin, T. caseorum, and T. ovoides, and other T. austroamericanum reference strains from the National Reference Center for Invasive Mycoses and Antifungals at Institut Pasteur (https://www.pasteur.fr). Bootstrap values are indicated at the nodes. Scale bar indicates nucleotide substitutions per site. IGS, intergenic spacer region.

Figure 2

Core-genome phylogenetic relationships and single-nucleotide polymorphism (SNP) distance matrix from study of Trichosporon austroamericanum infections among hospitalized patients, France, 2022–2024. A) Phylogenetic tree based on the core genome of the analyzed strains showing the evolutionary relationship between strains. Distance between branches reflects the degree of genetic divergence on the basis of SNP variations in the core genome. Scale bar indicates nucleotide substitutions per site. B) Core-genome SNP distance matrix. Each value represents the number of SNPs that differ between genome pairs. Darker shades indicate greater distance.

Figure 3

Whole-genome single-nucleotide polymorphism (SNP)–based phylogeny and distance matrix from study of Trichosporon austroamericanum infections among hospitalized patients, France, 2022–2024. A) Whole-genome phylogenetic tree of the analyzed strains. Blue font indicates reference strain; blue font indicates environmental strain. Scale bar indicates nucleotide substitutions per site. B) Whole-genome SNP distance matrix. Each value represents the number of SNPs that differ between genome pairs. Darker shades indicate greater distance.

Figure 4

Single-nucleotide polymorphism (SNP) map and phylogenetic analysis of mitogenomes from investigation of Trichosporon austroamericanum infections among hospitalized patients, France, 2022–2024. A) SNP map of mitochondrial genomes from T. austroamericanum isolates. The SNP alignment highlights 3 key positions in the mitochondrial genome (at positions 22240 in the cox3 gene, 31837 in the apocytochrome b gene, and 39897 in the trnL [tRNA-Leu] gene). B) Phylogenetic placement of clinical isolates (red font), the environmental strain (blue font), and strains from the National Reference Centre for Invasive Mycoses and Antifungals at Institut Pasteur (https://www.pasteur.fr). Scale bar indicates nucleotide substitutions per site.

Figure 5

Maximum-likelihood phylogenetic tree and BLAST ring of isolates from a study of Trichosporon austroamericanum infections among hospitalized patients, France, 2022–2024. A) Maximum-likelihood phylogenetic tree of the mitochondrial genome, showing the relationship between T. inkin, T. asahii, T. austroamericanum reference strain (bold font), and T. austroamericanum isolates from this study. Scale bar indicates nucleotide substitutions per site. B) Mitogenome alignment of T. austroamericanum isolates against T. inkin (MT801082), obtained by using BLAST Ring Image Generator (https://github.com/happykhan/BRIG).