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Fungi are vital microbes present throughout the biosphere. Many species are essential decomposers in the ecosystem, breaking down organic materials and nourishing other lives. Moreover, some have directly influenced human civilization by providing beneficial products, such as edible mushrooms, brewer's yeast, baker's yeast, and antibiotics. However, it's important to note that this group of organisms can also have a "dark side". Each year, fungal pathogens cause approximately 150 million severe infections and 1.7 million deaths. The high rate of infection is compounded by the limited availability of antifungal drugs and the increasing prevalence of antifungal resistance. In response to the global burden of fungal diseases, the World Health Organization published a list of priority fungal pathogens in 2022 and highlighted strategies such as surveillance, sustainable research investments, and public health interventions to combat the increasing fungal threats. My PhD research has focused on surveillance and genomic analyses of several human fungal pathogens, particularly Candida auris. Candida auris is an emerging multidrug-resistant yeast that causes systemic infections with high mortality rates. While initially recognized as a nosocomial pathogen, our genomic analyses of strains isolated from clinical environments, tropical wetlands, fruit surfaces, and dog ears revealed potential transmission routes between diverse environments and patients, including a potential driver for the prevalence of antifungal resistance. Furthermore, our research indicated limited genetic exchange within and between lineages of Candida auris. Through genome-wide association analyses of global Candida auris strains, several known and novel genomic variants were identified associated with susceptibility to azoles, echinocandins, and amphotericin B. Overall, our studies underscore the importance of continuous surveillance to understand potential routes of Candida auris transmission and the urgent need for innovative approaches to treat multidrug-resistant Candida auris infections. / Thesis / Doctor of Philosophy (PhD)

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The honey bee (Apis mellifera) is important both ecologically, as a generalist pollinator, and economically by pollinating our crops and producing honey. Honey bees use plants for foraging for pollen and nectar, which together constitute their entire diet. Yet, as flowering times of plants vary during the summer, so do the floral resources available. Honey bees are known to be selective for their food sources. Thus, their specificity in plant choices could vary according to the availability of flower sources, showing a differing usage of plant diversity in different timepoints. Alternatively, the honey bees selectivity to fulfill their nutrient needs could lead to a constant usage of diversity. The taxonomic origin of the plant DNA found in honey can be identified and used to investigate the plant taxa the bees have collected nectar and pollen from. This study asks whether the diversity of plants which honey bees use varies during summer (June, July, and August). I used two diversity indices as response variables: 1) the Shannon-Wiener diversity index and 2) the number of plant genera identified in the DNA in the honey. I used data gathered from 41 hives from 14 Finnish beekeepers. An ANOVA test revealed no significant difference among the three timepoints in either response variable, indicating honey bees select a constant diversity of plants throughout the season. The result suggest that different plants can fulfill honey bees’ requirements at different parts of the summer. Honey bees are generalists, but selective, producing a relatively constant usage of plants throughout the season.

No / Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

Yes / Aeromonas hydrophila is a well-known waterborne pathogen that recently was found to infect humans. Here, we report the draft genome of a freshwater isolate from a Malaysian waterfall, A. hydrophila strain M023, which portrays N-acylhomoserine lactone-dependent quorum sensing. / University of Malaya via High Impact Research Grants (UM C/625/1/HIR/MOHE/CHAN/01, A-000001-50001, and UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027)

Yes / Pantoea stewartii strain M073a is a Gram-negative bacterium isolated from a tropical waterfall. This strain exhibits quorum-sensing activity. Here, the assembly and annotation of its genome are presented. / High Impact Research Grants from the University of Malaya (UM.C/625/1/HIR/MOHE/CHAN/01, grant no. A-000001-50001 and UM-MOHE HIR Grant UM.C/625/1/HIR/MOHE/ CHAN/14/1, no. H-50001-A000027)

Yes / Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In this study, the genome of marine Bacillus sp. strain G3(2015) was sequenced using MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome annotation. / University of Malaya through HIR grants (UM-MOHE HIR grant UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027; UM-MOHE HIR grant UM C/625/1/HIR/MOHE/CHAN/01, A000001- 50001); Postgraduate Research grant PG083-2015B

No / Background: Phylogenetic studies of bacteria have been based so far either on a single gene (usually the 16SrRNA) or on concatenated housekeeping genes. For what concerns the genus Mycobacterium these approaches support the separation of rapidly and slowly growing species and the clustering of most species in well-defined phylogenetic groups. The advent of high-throughput shotgun sequencing leads us to revise conventional tax-onomy of mycobacteria on the light of genomic data. For this purpose we investigated 88 newly sequenced species in addition to 60 retrieved from GenBank and used the Average Nucleotide Identity pairwise scores to reconstruct phylogenetic relationships within this genus.Results:Our analysis confirmed the separation of slow and rapid growers and the intermediate position occupied by the M. terrae complex. Among the rapid growers, the species of the M. chelonae-abscessus complex belonged to the most ancestral cluster. Other major clades of rapid growers included the species related to M. fortuitum and M. smegmatis and a large grouping containing mostly environmental species rarely isolated from humans. The members of the M. terrae complex appeared as the most ancestral slow growers. Among slow growers two deep branches led to the clusters of species related to M. celatum and M. xenopi and to a large group harboring most of the species more frequently responsible of disease in humans, including the major pathogenic mycobacteria (M.tuberculosis,M. leprae,M. ulcerans). The species previously grouped in the M. simiae complex were allocated in a number of sub-clades; of them, only the one including the species M. simiae identified the real members of this complex. The other clades included also species previously not considered related to M. simiae. The ANI analysis,in most cases supported by Genome to Genome Distance and by Genomic Signature-Delta Difference, showed that a number of species with standing in literature were indeed synonymous.Conclusions:Genomic data revealed to be much more informative in comparison with phenotype. We believe that the genomic revolution enabled by high-throughput shotgun sequencing should now be considered in order to revise the conservative approaches still informing taxonomic sciences.