Fernando Gónzález‐Candelas

HaloClassifier: integrating coding-signature features and k-mer composition for plasmid-chromosome discrimination in haloarchaeal genomes

HaloClassifier distinguishes plasmid and chromosome contigs in haloarchaeal genomes with high accuracy, enabling plasmidome reconstruction in fragmented assemblies.

Multihospital expansion of vancomycin-resistant Enterococcus faecium ST117-CT7799 and transmission of linear plasmids co-carrying vanA and linezolid resistance genes, Comunitat Valenciana, Spain (2022-2024)

The paper characterizes the spread and resistance mechanisms of vancomycin-resistant Enterococcus faecium in Spanish hospitals, identifying a dominant lineage and plasmid-mediated resistance gene transmission.

Integrative mobilizable elements are pervasive throughout Pseudomonadota

The paper identifies and characterizes PIMEs, a widespread family of integrative mobilizable elements in Pseudomonadota, revealing their role in horizontal transfer and immune system reservoirs.

Complete genomes reveal the full extent of Mycobacterium tuberculosis complex diversity across evolutionary scales

The paper uses long-read sequencing to generate complete genomes of Mycobacterium tuberculosis complex isolates, revealing increased genomic diversity and improved resolution in transmission analysis.

A new typing scheme demonstrates high discriminatory power for Treponema pallidum subspecies

This paper introduces a new MLST scheme for Treponema pallidum subspecies with high discriminatory power, validated using global clinical samples and showing distinct genetic clusters.

Long-term evolution of prokaryotic genomes in a chemolithotrophic cave over 5.5 million years of isolation

This study examines prokaryotic genome evolution in the Movile Cave over 5.5 million years, finding reduced gene diversity, increased pseudogenization, and limited horizontal gene transfer.

Short-Term Evolution and Dispersal Patterns of fluconazole-resistance in Candida auris clade III

This study analyzes global Candida auris genomes to identify fluconazole-resistant subgroups and their dispersal patterns, revealing rapid evolution and global spread since 2010.

Improved prediction of antimicrobial resistance in Klebsiella pneumoniae using machine learning

This study uses machine learning to improve antimicrobial resistance prediction in Klebsiella pneumoniae for antibiotics where rule-based methods fail, identifying new resistance determinants.

Genotypic and phenotypic characterization of a nosocomial outbreak of Candida auris in Spain during five years

The paper characterizes a Candida auris outbreak in Spain over five years, finding all isolates belong to clade III, share resistance mutations, and are phenotypically identical, suggesting a single origin and transmission.

VIPERA: Viral Intra-Patient Evolution Reporting and Analysis

VIPERA analyzes intra-patient SARS-CoV-2 sequence evolution to track viral ancestry and trajectories.

One is not enough: on the effects of reference genome for the mapping and subsequent analyses of short-reads

This paper evaluates how choosing different reference genomes affects short-read mapping and subsequent analyses in five bacterial species, finding significant biases in SNP calling, recombination rates, and phylogenetic trees.

Ancient bacterial genomes reveal a formerly unknown diversity of Treponema pallidum strains in early modern Europe

This study identifies previously unknown Treponema pallidum strains in early modern Europe, suggesting a complex history of treponemal diseases.

Gene expression models based on a reference laboratory strain are bad predictors of Mycobacterium tuberculosis complex transcriptional diversity.

The paper shows that gene expression models based on the H37Rv strain poorly predict transcriptional diversity in Mycobacterium tuberculosis complex strains.