Biology subjects

Guerrero-Araya, E.

Publications and source records attributed to Guerrero-Araya, E..

5 recordsLinked to original sources

bioRxiv2025

Identification of Novel Cryptic and Classical Clades in Clostridioides difficile

Clostridioides difficile is a major cause of nosocomial infections and antimicrobial-associated diarrhea, with significant global health implications. While five classical clades (C1 to C5) have traditionally encompassed most pathogenic strains, recent genomic studies have uncovered several highly divergent cryptic clades (C-I to C-V), suggesting greater taxonomic and evolutionary complexity. In this study, we performed a comprehensive whole-genome analysis of 25,144 publicly available C. difficile genomes, supplemented with 21 novel isolates from Costa Rica and Brazil. Using average nucleotide identity (ANI), recombination-corrected core-genome phylogenies, we confirmed the presence of all known classical and cryptic clades and identified two novel classical clades (C6 and C7) and two previously undescribed cryptic clades (C-VI and C-VII). We further detected evidence for bifurcation within cryptic clade C-III, supporting its division into two lineages C-IIIa and C-IIIb. ANI comparisons revealed that cryptic clades share less than 95% identity with classical C. difficile strains but remain more similar to C. difficile than to any other Peptostreptococcaceae species, reinforcing their placement within the species boundary. Core-genome recombination analyses revealed limited gene flow between cryptic and classical clades, except for Clade C7, which exhibited intermediate recombination patterns and may represent a transitional lineage. These findings expand the known diversity of C. difficile, provide a revised genomic framework for clade classification, and underscore the evolutionary depth and ecological breadth of cryptic lineages with potential clinical relevance.

microbiology↗

bioRxiv2025

Phylogenomic analysis of the collagen-like BclA proteins in Clostridioides difficile

Clostridioides difficile is a Gram-positive, anaerobic, spore-forming bacterium and a major nosocomial pathogen, notable for its high genetic diversity. C. difficile has been classified into five classical phylogenetic clades (C1 to C5) and five cryptic clades (C-I to C-V), reflecting its extensive genome plasticity. In addition, C. difficile spores are considered essential for the onset, persistence and transmission of the disease, and their exosporium layer has hair-like projections formed by the BclA-family of proteins (BclA1, BclA2 and BclA3). Previous work in C1 and C2 strains has demonstrated that the absence of these proteins affects spore germination, pathogenesis, persistence, and recurrence of CDI. Nevertheless, the conservation of BclAs across different C. difficile clades remains unclear. In this work, genomics analysis in more than 25,000 C. difficile genomes revealed that the prevalence and variability of the BclAs was not conserved across classical and cryptic clades. The most represented clade on the dataset was C1, where roughly 50% of the genomes possessed all three bclA genes. Pseudogenization of bclA1 or all bclAs was observed in C2 and C3, respectively. Additionally, the absence of bclA1 in C4 and of both bclA1 & bclA3 in C5, further demonstrates the divergence of BclAs among C. difficile clades. Subsequent analysis revealed high variability in the central collagen-like region (CLR) of all three BclAs, and a highly conserved bclA1 pseudogenization event in most members of C2. Overall, the extensive variability of bclA, attributed to the CLR, prevalence of a bclA1 pseudogenization and complete absence of bclAs in certain clades, is likely to impact spore morphogenesis and pathogenesis across different C. difficile clades.

microbiology↗

bioRxiv2020

FastMLST: A multi-core tool for multilocus sequence typing of draft genome assemblies

Multilocus Sequence Typing (MLST) is a precise microbial typing approach at the intra-species level for epidemiological and evolutionary purposes. It operates by assigning a sequence type (ST) identifier to each specimen, based on a combination of allelic sequences obtained for multiple housekeeping genes included in a defined scheme. The use of MLST has multiplied due to the availability of large numbers of genomic sequences and epidemiological data in public repositories. However, data processing speed has become problematic due to datasets massive size. Here, we present FastMLST, a tool that is designed to perform PubMLST searches using BLASTn and a divide-and-conquer approach. Compared to mlst, CGE/MLST, MLSTar, and PubMLST, FastMLST takes advantage of current multi-core computers to simultaneously type thousands of genome assemblies in minutes, reducing processing times by at least 16-fold and with more than 99.95% consistency. Availability and ImplementationThe source code, installation instructions and documentation are available at https://github.com/EnzoAndree/FastMLST

bioinformatics↗

bioRxiv2020

The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies

Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI-III. The emergence of these three novel genomospecies predates clades C1-5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work impacts the diagnosis of CDI worldwide.

microbiology↗

bioRxiv2020

Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery

Sellimonas intestinalis is a Gram positive and anaerobic bacterial species previously considered as uncultivable. Although little is known about this Lachnospiraceae family member, its increased abundance has been reported in patients who recovered intestinal homeostasis after dysbiosis events. In this context, the aim of this work was taken advantage of a culturomics protocol that allowed the recovery species extremely oxygen-sensitive from faecal samples, which led to the establishment of an S. intestinalis isolate. Whole genome sequencing and taxonomic allocation confirmation were the base to develop comparative analyses including 11 public genomes closely related. Phylogeographic analysis revealed the existence of three lineages (linage-I including isolates from Chile and France, linage-II from South Korea and Finland, and linage-III from China and one isolate from USA). Pangenome analysis on the established dataset revealed that although S. intestinalis seems to have a highly conserved genome (with 50.1% of its coding potential being part of the coregenome), some recombination signals were evidenced. The identification of cluster of orthologous groups revealed a high number of genes involved in metabolism, including amino acid and carbohydrate transport as well as energy production and conversion, which matches with the metabolic profile previously reported for healthy microbiota. Additionally, virulence factors and antimicrobial resistance genes were found (mainly in linage-III), which could favour their survival during antibiotic-induced dysbiosis. These findings provide the basis of knowledge about this species with potential as a bioindicator of intestinal homeostasis recovery and contribute to advance in the characterization of gut microbiota members with beneficial potential.

microbiology↗