Biology subjects

Ugalde, J. A.

Publications and source records attributed to Ugalde, J. A..

9 recordsLinked to original sources

bioRxiv2026

Prophage {Phi}ESI promotes competitive dominance in the emergent Salmonella serovar Infantis lineage

The global spread of multidrug-resistant Salmonella enterica serovar Infantis has been largely attributed to the pESI megaplasmid, yet additional factors underlying the ecological success of this lineage remain unclear. Here, we characterize {Phi}ESI (phage of emergent Salmonella Infantis), a temperate bacteriophage discovered during coculture of an emergent pESI-positive strain (PM57) and a non-emergent strain (DR006). Phage {Phi}ESI shows a siphovirus morphotype with a long tail and an elongated head, with a genome of 46,490 bp, which is integrated as a prophage in the 3-end of an Arg-tRNA gene in PM57, but is absent in DR006, which is susceptible to the {Phi}ESI-mediated lysis. The screening of {Phi}ESI genes across 20,429 global Salmonella Infantis genomes revealed an almost exclusive association of {Phi}ESI and {Phi}ESI-like phages with the emergent pESI-positive Salmonella Infantis lineage. Further bioinformatic analyses of complete chromosomes revealed diverse {Phi}ESI insertion profiles showing geographic clustering, and the presence of large-scale chromosomal inversions flanked by {Phi}ESI genes. Competition assays showed that PM57 outcompeted DR006 in coculture, coinciding with high viral loads that selectively targeted DR006, and susceptibility assays showed that strains lacking {Phi}ESI/{Phi}ESI-like prophages were susceptible to {Phi}ESI-mediated lysis. Together, our findings identify {Phi}ESI as a competitive factor associated with emergent Salmonella Infantis, able to selectively eliminate susceptible competitors. Our findings suggest that {Phi}ESI/{Phi}ESI-like prophages contributed to the persistence and global dissemination of the emergent Salmonella Infantis lineage. ImportanceEmergent multidrug-resistant Salmonella enterica serovar Infantis strains carrying pESI megaplasmids have spread worldwide, posing a global public health threat and a significant economic burden. Nevertheless, the factors contributing to the success of this foodborne pathogen, beyond pESI, remain poorly understood. Here, we describe {Phi}ESI, a novel temperate bacteriophage carried by the emergent lineage as a chromosomally integrated prophage. We show that {Phi}ESI provides a competitive advantage to emergent strains by selectively killing non-emergent competitors while protecting lysogens from reinfection. Our findings uncover the contribution of {Phi}ESI/{Phi}ESI-like bacteriophages to the success of emergent Salmonella Infantis, highlighting how lineage-associated prophages can shape the ecological success of pathogenic bacteria.

microbiology↗

bioRxiv2026

NanoVI: a Bayesian variational inference Nextflow pipelinefor species-level taxonomic classification from full-length16S rRNA Nanopore reads

SummaryNanoVI is a Nextflow pipeline for species-level taxonomic classification of full-length 16S rRNA Oxford Nanopore reads. Unlike existing tools that rely on expectation-maximization (EM) algorithms, NanoVI employs Bayesian variational inference with a Dirichlet-Categorical conjugate model, yielding abundance estimates accompanied by Bayesian 95% credible intervals that quantify estimation uncertainty, along with automatic shrinkage that suppresses spurious taxa. NanoVI integrates the Genome Taxonomy Database (GTDB) r226, providing phylogenetically consistent taxonomy while maintaining compatibility with NCBI-style databases. Benchmarked against a standardized mock community, NanoVI achieves species-detection metrics comparable to Emu, with 25-62% lower execution time and fewer false-positive assignments. Validation on 20 clinical vaginal microbiome samples confirms reproducibility against previously published Emu-based analyses. Availability and implementationNanoVI is implemented in Nextflow DSL2 with Docker containerization and is freely available at https://github.com/microbialds/NanoVI under an open-source license.

bioinformatics↗

bioRxiv2026

Emergence of a multidrug-resistant Salmonella enterica serovar Amager lineage carrying the blaCTX-M-65-positive pESI megaplasmid

The spread of extended-spectrum {beta}-lactamase (ESBL)-producing and fluoroquinolone-resistant Salmonella pose a global public health challenge in addition to the high burden of infections associated with this foodborne pathogen. In this study we aimed to characterize a multidrug-resistant strain of Salmonella serovar Amager isolated from a Chilean river in October 2023. Antimicrobial susceptibility testing revealed a resistance phenotype against multiple antibiotic families, including fluoroquinolones and {beta}-lactams, showing ESBL production. Hybrid genome sequencing allowed the identification of a 311,303 bp plasmid carrying the aadA1, aph(4)-Ia, aac(3)-IVa, floR, sul1, tet(A), and blaCTX-M-65 genes, sharing 99.98% sequence identity with the Salmonella Infantis pESI-like megaplasmid. In addition, the qnrB19 gene was found in a {approx}2.7 kbp plasmid of widespread distribution. Population structure and temporal phylogenetic analysis at the global scale revealed the emergence of a Salmonella Amager lineage from the HC20_35565 cluster, carrying the Salmonella Infantis blaCTX-M-65-positive pESI-like megaplasmid and causing human infections in the United States and the United Kingdom. Our work describes the emergence of a Salmonella lineage with resistance against first-line antibiotics used for treating severe infections, underscoring the relevance of environmental surveillance as a means for detecting emergent pathogens and anticipating human infections.

genomics↗

bioRxiv2025

Mitochondrial genome rearrangements and virulence-associated features in a clinical isolate of the emerging pathogen Wickerhamomyces anomalus

BackgroundWickerhamomyces anomalus, also known as Candida pelliculosa, traditionally regarded as an environmental yeast, 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. ResultsHere, we report the first high-quality nuclear and complete mitochondrial genome assemblies from a clinical isolate of W. anomalus. The nuclear genome spans 13.9 Mb with 34.5% GC content and contains 6,305 protein-coding genes, 8,235 coding sequences, and 147 tRNAs, with 98.1% completeness by BUSCO. The mitochondrial genome (47.6 kb) encodes 19 protein-coding genes, 26 tRNAs, and two rRNAs. Remarkably, it exhibits atypical rearrangements, including inverted repeats and atp9 duplications. ConclusionsWe provide the first de novo nuclear genome from a clinical W. anomalus isolate, along with the first complete mitochondrial genome for this species, establishing a high-quality reference for this emerging pathogen. 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 indentify determinants of pathogenicity, virulence, and antifungal resistance, accelerating the development of improved diagnostics, surveillance, and management strategies for W. anomalus infections

genetics↗

bioRxiv2025

A global perspective on the genomics of Moraxella catarrhalis

2.Moraxella catarrhalis is an opportunistic pathogen of the human respiratory tract, primarily associated with otitis media in children and exacerbations of chronic obstructive pulmonary disease (COPD) in adults. Despite its clinical importance, the genomic diversity and functional specialization of M. catarrhalis remain insufficiently characterized. This study aimed to analyze the global genetic diversity of M. catarrhalis using whole-genome sequencing to identify phylogenetic lineages, antimicrobial resistance patterns, and key virulence factors. Phylogenomic analysis of 345 publicly available genomes identified three phylogroups, of which one exhibited significant genomic divergence and was excluded from further analyses due to its potential classification as a separate species. The remaining two phylogroups corresponded to previously described seroresistant and serosensitive lineages. Phylogroup B exhibited a higher prevalence of antimicrobial resistance genes, particularly bro-1 and bro-2, while Phylogroup A exhibited unique metabolic adaptation, including genes encoding for the DppB-DppC-DppD dipeptide transport system. Both phylogroups shared crucial virulence factors, including UspA1 and UspA2, which facilitate adhesion and immune evasion. Potential therapeutic targets were identified, including PilQ, essential for type IV pilus biogenesis, and CopB, which plays a key role in iron acquisition and immune evasion. Overall, these findings highlight the significance of phylogenomics approaches to elucidate the genetic mechanisms underlying pathogenicity and resistance in M. catarrhalis, providing insights for future therapeutic and preventive strategies. 3. Impact statementThis study presents a comprehensive phylogenomic analysis of M. catarrhalis, expanding current knowledge of its genetic diversity, antimicrobial resistance, and virulence factors. By analyzing 345 global genomes, we identified three distinct phylogroups, one of which shows substantial genomic divergence, suggesting it may represent a novel species within the Moraxella genus. Our findings confirm the existence of seroresistant and serosensitive lineages, providing new insights into their metabolic adaptations and differential antibiotic resistance profiles. Notably, phylogroup B harbors a higher prevalence of {beta}-lactam resistance genes, while phylogroup A exhibits unique peptide transport systems. This work strengthens the evidence that phylogenomic approaches are essential to understand the evolutionary dynamics and pathogenic potential of M. catarrhalis. The identification of conserved virulence factors and potential therapeutic targets, such as PilQ and CopB, underscores the relevance of this pathogen in respiratory infections and the need for targeted interventions. Our results not only clarify the population structure of M. catarrhalis but also provide a valuable genomic framework for future studies on antimicrobial resistance and vaccine development, with broad utility for microbiologists, clinicians, and public health researchers. 4. Data summaryThe authors confirm all supporting data, code, and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2025

Profiling of Vaginal Microbial Communities in Chilean Women Via Self-sampling and Full-length 16S rRNA Sequencing

The vaginal microbiota is a dynamic ecosystem that plays a crucial role in womens health, with Lactobacillus species predominating in healthy individuals. Disruptions in this microbiota can lead to dysbiosis, increasing susceptibility to infections such as bacterial vaginosis and other reproductive health complications. While most studies on the vaginal microbiome have been conducted in North American and European populations, data from Latin America, particularly Chile, remain scarce. This study presents a comprehensive analysis of the vaginal microbiota in Chilean women using full-length 16S rRNA gene sequencing with Oxford Nanopore Technology (ONT). We implemented a self-sampling methodology and a bioinformatics pipeline to achieve species-level resolution of microbial communities. Taxonomic profiling using Emu revealed that Lactobacillus was the dominant genus in most samples, while others exhibited microbial compositions consistent with Community State Type (CST) IV, characterized by higher diversity and lower Lactobacillus abundance. Alpha and beta diversity analyses further demonstrated distinct microbial clustering patterns across CSTs, with species-level resolution providing enhanced classification accuracy. Our findings highlight the potential of long-read sequencing and self-sampling for improving vaginal microbiome studies, particularly in underrepresented populations. This research contributes valuable insights into the composition and diversity of the vaginal microbiota in Chilean women, paving the way for more precise diagnostics and targeted interventions in reproductive health.

microbiology↗

bioRxiv2025

BugBuster: A novel automatic and reproducible workflow for metagenomic data analysis

SummaryIn metagenomic sequencing, large volumes of data are obtained with all the genetic information present in a sample, allowing valuable data to be obtained about microbial communities. The software and processes necessary to obtain quality results have become increasingly complex and sophisticated, limiting the accessibility of biologists who try to use them. To facilitate the analysis of this data, a modular and reproducible workflow was developed using the Nextflow workflow orchestrator named BugBuster. The pipeline is easy to implement because all its dependencies are provided within containers, it is reproducible, modular and portable. BugBuster consists of different processes that allow data analysis at the level of reads, contigs and MAGs, also including modules for resistome characterization and taxonomic profiling. Availability and implementationBugBuster was written in Nextflow DSL2 Syntaxis. The program applications, user manual, exemplary data and code are freely available at https://github.com/gene2dis/BugBuster.

bioinformatics↗

bioRxiv2018

Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis

Microbial community analysis can be biased by multiple technical factors, such as storage conditions, DNA extraction, or amplification conditions. In a high-throughput laboratory that relies on samples obtained from thousands of different subjects, knowledge of the extent of subject-introduced sampling and storage variation on the outcome of the inferred microbiome, as well as the effect of laboratory-introduced variation caused by reagent batches, equipment, or operator on the consistency of these processes within the laboratory is paramount. Here, we analyzed the effect of sampling from different parts of the same stool specimen or on different consecutive days, as well as short-term storage of samples at different temperatures on microbiome profiles obtained by 16S rRNA gene amplification. Each of these factors had relatively little effect on the microbial composition. In addition, replicate amplification of 44 stool samples showed reproducible results. Finally, 363 independent replicate extractions and amplifications of a single human homogenized stool (HS) specimen showed reproducible results (average Lins correlation = 0.95), with little variation introduced by HS batch, operator, extraction equipment, or DNA sequencer. In all cases, variations between replicates were significantly smaller than those between individual samples; subject identity always was the largest determinant. We propose that homogenized stool specimens could be used as quality control to routinely monitor the laboratory process and to validate new methods.

microbiology↗

bioRxiv2017

A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis

The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a womans reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive womens health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 32 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 4 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, healthy ranges were determined in a group of 50 self-reported healthy women. The hrHPV portion of the test was evaluated against the Digene High-Risk HPV HC2 DNA test with vaginal samples obtained from 185 women. Results were concordant for 181/185 of the samples (overall agreement of 97.83%, Cohens kappa = 0.93), with sensitivity and specificity values of 94.74% and 98.64%, respectively. Two discrepancies were caused by the Digene assays known cross-reactivity with low-risk HPV types, while two additional samples were found to contain hrHPV not detected by Digene. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.

microbiology↗