The incidence of candidemia in healthcare centers is associated with high morbidity and mortality. Frequency varies significantly among regions, with some species being more prevalent than others in Latin America. In this study, 191 clinical Candida isolates were collected from a major hospital in Ecuador from January 2019 to February 2020 aiming to assess their prevalence and distribution. After data processing, 168 isolates characterized by the VITEK 2 system were subsequently identified by ITS sequencing. Results showed diverse Candida species distributions, with C. albicans and C. tropicalis being the most prevalent across different clinical sources. In hospitalized individuals, C. tropicalis (38%) and C. albicans (37%) were the most prevalent, followed by, C. parapsilosis (16%), C. glabrata (5%), and other non-Candida albicans (NCA) species (6%). Conversely, C. parapsilosis (48%), C. albicans (20%), and C. glabrata (14%), associated with candidemia, were the most common in blood and CSF. Additionally, uncommon NCA species such as C. haemulonii, C. kefyr, and C. pelliculosa were identified in Ecuador for the first time. Discrepancies in species identification were observed between the VITEK 2 system and ITS sequencing, coinciding at 85%. This highlights the need for ongoing surveillance and identification efforts in Ecuador’s clinical and epidemiological settings.

Carbapenem resistance in Enterobacteriaceae poses a major threat to public health because of the limited therapeutic options. The dissemination of the bla _KPC gene, which encodes KPC carbapenemases, typically occurs through Tn 4401 transposons and plasmids that facilitate its transmission. In this study, we analysed 802 genomes of ESKAPE pathogens and other Enterobacteriaceae from Ecuador, including both clinical and non-clinical isolates, to determine the prevalence and genetic context of bla _KPC-2 and bla _KPC-3 and their associated mobile genetic elements. Whole-genome analysis revealed several isolates carrying bla _KPC , with bla _KPC-3 restricted to Klebsiella pneumoniae . While most isolates harboured the Tn 4401a transposon, we identified a novel variant, Tn 4401l , in two K. pneumoniae isolates collected between 2020 and 2021. Additionally, two putative plasmids carrying Tn 4401a were reconstructed: pECU0072020, a mosaic multidrug-resistant plasmid with a unique genetic organization, and pECU0062021, a more compact structure carrying only bla _KPC-2 . The findings demonstrate the wide distribution of bla _KPC within diverse bacterial hosts across multiple regions of Ecuador, the emergence of a novel Tn 4401l variant and the presence of putative plasmids that could potentially accelerate multidrug resistance dissemination. This study highlights the need for continuous genomic surveillance and coordinated strategies and practices regarding the use of antibiotics to mitigate the risk of outbreaks and interspecies transmission of carbapenem resistance.

Wickerhamomyces anomalus, also known as Candida pelliculosa, has emerged as an opportunistic yeast implicated in invasive infections and hospital outbreaks, especially among neonatal and immunocompromised individuals. Despite its clinical relevance, the genomic determinants underlying the pathogenesis and virulence remain poorly understood. Here, we report the first high-quality nuclear and complete mitochondrial genome derived from a clinical isolate of W. anomalus. The nuclear genome spans 13.9 Mb with 34.5% GC content and contains 6305 protein-coding genes, 8235 coding sequences, and 147 tRNAs, with 98.1% completeness by BUSCO. The mitochondrial genome (47.6 kb) encodes 19 protein-coding genes, 26 tRNAs, two rRNAs, and exhibits atypical structural features, including inverted repeats and three LAGLIDADG (LD)-type homing endonuclease ORFs. We further assembled mitochondrial genomes from 12 additional clinical isolates and compared them with CpEC_UEES and publicly available W. anomalus mitochondrial genomes. Size, gene content and synteny were highly conserved, with structural variations largely limited to the LD ORFs. Phylogenetic analysis of 48 nuclear assemblies showed that clinical isolates are not monophyletic but are interspersed with environmental isolates across the tree. These assemblies provide the first comprehensive clinical genomic resources for W. anomalus, offering a reference framework for comparative and functional studies. The genomic innovations, together with a high content of repetitive and non-coding elements, suggest enhanced plasticity that may underpin metabolic flexibility and survival under host-associated stresses. These rearrangements represent an underappreciated mechanism of adaptation in emerging fungal pathogens, contributing to the clinical relevance of W. anomalus. These genomic resources facilitate rigorous comparative analyses to identify determinants of pathogenicity, virulence, and antifungal resistance, accelerating the development of improved diagnostics, surveillance, and management strategies for W. anomalus infections