IMA Fungus, Год журнала: 2024, Номер 15(1)
Опубликована: Сен. 11, 2024
Язык: Английский
Microbiology Spectrum, Год журнала: 2024, Номер 12(4)
Опубликована: Март 6, 2024
Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale phylogenetics (phylogenomics) species and populations to reconstruct evolutionary relationships in dense data set 710 fungal genomes from the biomedically technologically important genus Aspergillus. To do so, generated novel 1,362 high-quality markers specific for Aspergillus provided profile Hidden Markov Models each, facilitating their use by others. Examining resulting phylogeny helped resolve ongoing controversies, identified new ones, revealed extensive strain misidentification (7.59% strains were previously misidentified), underscoring importance population-level sampling classification. These findings corroborated using current standard, taxonomically informative loci. suggest that phylogenomics can facilitate accurate classifications reconstructions Tree Life.IMPORTANCEIdentification relies markers. Advances genomic technologies have made it possible sequence genome any strain, making assignment (and discovery ones). We examined usefulness limitations large publicly available multiple biomedically, agriculturally, industrially Our nearly 8% misidentified. work highlights systematic biology suggests sequencing strains, including reference (e.g., type strains), will be required reduce errors public databases.
Язык: Английский
Процитировано
16
Microbial Genomics, Год журнала: 2024, Номер 10(1)
Опубликована: Янв. 16, 2024
Candida glabrata is a commensal yeast of the gastrointestinal tract and skin humans. However, it causes opportunistic infections in immunocompromised patients, second most common pathogen causing bloodstream infections. Although there are many studies on epidemiology C. infections, fine- large-scale geographical nature remain incompletely understood. Here we investigated both population structure through genome sequencing 80 clinical isolates obtained from six tertiary hospitals Qatar by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within Qatari identified signatures recombination, inbreeding clonal expansion between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to recombination at level, MATa MATα alleles were detected indicating potential sexual reproduction environments. Comparisons samples showed that was very similar those other parts world, consistent significant role recent anthropogenic activities shaping its structure. Genome-wide association known novel genomic variants associated reduced susceptibilities fluconazole, 5-flucytosine echinocandins. Together, our diversity, patterns antifungal drug resistance mechanisms as well relationships world.
Язык: Английский
Процитировано
8
BMC Bioinformatics, Год журнала: 2025, Номер 26(1)
Опубликована: Янв. 13, 2025
Язык: Английский
Процитировано
1
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июнь 28, 2024
Fungal infections are difficult to prevent and treat in large part due strain heterogeneity. However, the genetic mechanisms driving pathogen variation remain poorly understood. Here, we determined extent which
Язык: Английский
Процитировано
5
Nature Communications, Год журнала: 2024, Номер 15(1)
Опубликована: Сен. 28, 2024
Язык: Английский
Процитировано
5
mBio, Год журнала: 2025, Номер unknown
Опубликована: Май 12, 2025
ABSTRACT Fungal infections are difficult to prevent and treat in large part due strain heterogeneity, which confounds diagnostic predictability. Yet, the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined extent Starships —giant transposons capable of mobilizing numerous fungal genes—generate phenotypic variability opportunistic human pathogen Aspergillus fumigatus . We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology multiple isolates same reference strain, reveal 20 distinct that generating genomic heterogeneity over timescales relevant for experimental reproducibility. Starship -mobilized genes encode functions, known biofilm-related virulence factors biosynthetic gene clusters, many differentially expressed during infection antifungal exposure a strain-specific manner. These findings support new model evolution wherein help generate genome structure, content, expression among strains. Together, our results demonstrate previously hidden mechanism genotypic and, turn, major pathogen. IMPORTANCE No “one size fits all” option exists treating Accounting is thus fundamental developing efficacious treatments strategies safeguarding health. report significant progress toward achieving this goal by uncovering : giant transposons, called , span dozens kilobases mobilize as cargo. By conducting systematic investigation these unusual single species, their contributions population-level at genome, pangenome, transcriptome levels. The compendium develop will not only predict introduced elements laboratory experiments but serve foundational resource determining how impact clinically phenotypes, such resistance pathogenicity.
Язык: Английский
Процитировано
0
Critical Reviews in Microbiology, Год журнала: 2024, Номер unknown, С. 1 - 14
Опубликована: Июль 1, 2024
and
Процитировано
3
Mycopathologia, Год журнала: 2024, Номер 189(4)
Опубликована: Июль 3, 2024
The genus Aspergillus consists of a vast number medically and environmentally relevant species. species classified in series Versicolores are ubiquitous the environment include opportunistic pathogen sydowii, which is associated with onychomycosis superficial skin infections. Despite frequent clinical reports A. sydowii related species, antifungal susceptibility data scarce, hampering optimal treatment choices subsequent patient outcomes. Here, we employed testing (AFST) based on microbroth dilution set 155 strains using common antifungals amphotericin B, itraconazole, voriconazole, posaconazole, isavuconazole micafungin addition luliconazole olorofim. All were identified partial calmodulin gene sequencing, 145 being seven creber three versicolor, latest taxonomic insights. Overall, tested potent against entire strain collection. In comparison to fumigatus, azole B MICs slightly elevated for some strains. AFST olorofim, here reported first time, displayed highest vitro activity, making these interesting alternative drugs but studies warranted future therapeutic use.
Язык: Английский
Процитировано
3
Current Protocols, Год журнала: 2024, Номер 4(11)
Опубликована: Окт. 30, 2024
Abstract Multiple sequence alignments and phylogenetic trees are rich in biological information fundamental to research biology. PhyKIT is a tool for processing analyzing the content of multiple trees. Here, we describe how use diverse analyses, including (i) constructing phylogenomic supermatrix, (ii) detecting errors orthology inference, (iii) quantifying biases data sets, (iv) identifying radiation events or lack resolution using gene support frequencies, (v) conducting evolution‐based screens facilitate function prediction. Several functions that streamline alignment processing—such as renaming FASTA entries tree tips—are also discussed. These protocols demonstrate simple command‐line operations unified framework analysis processing, from supermatrix construction diagnosis gaining clues about function. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 : Installing syntax usage 2 Constructing 3 Detecting anomalies relationships 4 Quantifying matrices related measures 5 Identifying polytomies 6 Assessing gene‐gene coevolution genetic screen
Язык: Английский
Процитировано
3
Communications Biology, Год журнала: 2024, Номер 7(1)
Опубликована: Сен. 4, 2024
Язык: Английский
Процитировано
1