Biology subjects

Almagro-Moreno, S.

Publications and source records attributed to Almagro-Moreno, S..

5 recordsLinked to original sources

bioRxiv2024

Modular small RNA drives the emergence of virulence traits and environmental trade-offs in Vibrio cholerae

The sole gain of laterally acquired virulence genes does not fully explain the transition of environmental strains into human pathogens. To date, the specific molecular drivers and fitness trade-offs that enable some strains within a population to undergo this process remain enigmatic. Here, we describe a small RNA (sRNA) with a unique modular structure that shapes the evolution of toxigenic Vibrio cholerae, the agent of cholera. The sRNA comprises of a highly variable 5 module located within the ompU ORF and a conserved 3 one downstream from the gene. This atypical location confers a distinct bimodular structure to the OmpU-encoded sRNA (OueS), generating allelic variants that differentially contribute to the emergence of virulence potential in some strains and associated fitness trade-offs between human infection and environmental survival. Unlike environmental counterparts, the OueS allele from toxigenic strains controls phenotypes essential during host colonization: a) stringently inhibits biofilm formation via a novel sRNA-sRNA interaction by suppressing the iron-responsive sRNA RyhB, and b) confers resistance against intestinal bacteriophages by activating the recently discovered CBASS phage defense system. Toxigenic OueS is also required for successful intestinal colonization and, as the first known example of its kind, acts as a functional surrogate of the master virulence regulator ToxR, controlling over 84% of its regulome. On the other hand, isogenic strains encoding environmental alleles of OueS exhibit higher competitive fitness than those harboring toxigenic ones during colonization of natural reservoirs such as crustaceans and phytoplankton. Our findings provide critical insights into the evolution of toxigenic V. cholerae and reveal specific molecular mechanisms and fitness costs associated with the emergence of pathogenic traits in bacteria.

microbiology↗

bioRxiv2023

Modular small RNA drives pathogen emergence

Pathogen emergence is a poorly understood complex phenomenon. To date, the molecular mechanisms that allow strains within a bacterial population to emerge as human pathogens remain mostly enigmatic. We recently uncovered that toxigenic Vibrio cholerae encode preadaptations to host colonization, what we term virulence adaptive polymorphisms (VAPs), however, the molecular mechanisms driving them are not known. ompU is a VAP-encoding gene that is associated with the production of the major outer membrane porin OmpU. Here, we show that the ompU ORF also encodes a modular small RNA overlapping its 3 terminus that plays a major role in V. cholerae physiology. We determined that the OmpU-encoded sRNA (OueS) strongly suppresses biofilm formation, a phenotype that is essential for host intestinal colonization, via repression of iron uptake. OueS controls over 84% of the genes regulated by ToxR, a major virulence regulator, and plays an integral role during the infection process. We demonstrate that OueS is critical for intestinal colonization and its bimodular nature dictates the virulence potential of V. cholerae. Overall, our study reveals specific molecular mechanisms leading to the emergence of pathogenic traits in bacteria unveiling the hidden genetics associated with this process. We propose a scenario where a limited number of modular genes could explain the emergence of novel phenotypic traits in biological systems.

microbiology↗

bioRxiv2022

Allelic diversity uncovers protein domains contributing to the emergence of antimicrobial resistance

Antimicrobial resistance (AMR) remains a major threat to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here, we developed a framework that exploits genetic diversity from environmental bacterial populations to decode emergent phenotypes such as AMR. OmpU, is a porin that makes up to 60% of the outer membrane of Vibrio cholerae, the cholera pathogen. This porin is directly associated with the emergence of the bacterium and confers resistance to numerous host antimicrobials. In this study, we examined naturally occurring allelic variants of OmpU in environmental V. cholerae and established associations that connected genotypic variation with phenotypic outcome. We covered the landscape of gene variability and found that the porin forms two major phylogenetic clusters with striking genetic diversity. We generated 14 isogenic mutant strains, each encoding a unique ompU allele, and found that divergent genotypes lead to convergent antimicrobial resistance profiles. We identified and characterized functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Specifically, we identified four conserved domains that are linked with resistance to bile and host-derived antimicrobial peptides. Mutant strains for these domains exhibit differential susceptibility patterns to these and other antimicrobials. Interestingly, a mutant strain in which we exchanged the four domains of the clinical allele for those of a sensitive strain exhibits a resistance profile closer to a porin deletion mutant. Finally, using phenotypic microarrays, we uncovered novel functions of OmpU and their connection with allelic variability. Our findings highlight the suitability of our approach towards dissecting the specific protein domains associated with the emergence of AMR and can be naturally extended to other bacterial pathogens and biological processes. AUTHOR SUMMARYAntimicrobial resistance (AMR) is one of the major threats to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here we developed an approach that uses genetic diversity from environmental populations to decode emergent phenotypes such as AMR. Specifically, we examined naturally occurring allelic variants of an outer membrane porin, OmpU, in Vibrio cholerae and established associations between genotype and phenotype. Using this approach, we identified and characterized the functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Our perspective towards disentangling the emergence of AMR can be naturally extended to other proteins and bacterial pathogens.

microbiology↗

bioRxiv2022

Cluster-driven evolution and modularity uncover paths of cholera emergence

Cholera, an acute secretory diarrhea, is caused by strains from a phylogenetically confined group within the Vibrio cholerae species, the pandemic cholera group (PCG). To date, the molecular and evolutionary factors that enable the isolated emergence of toxigenic V. cholerae from environmental populations remain mostly enigmatic. Comprehensive analyses of over 1,100 V. cholerae genomes, including novel environmental isolates from this study, reveal that the species consists of four major clades and several minor ones. PCG belongs to a large clade located within a lineage shared with environmental strains, the pandemic cholera lineage. This hierarchical classification provided us with a framework to unravel the eco-evolutionary dynamics of the genetic determinants associated with the emergence of toxigenic V. cholerae. Our analyses indicate that this phenomenon is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. We determined that certain PCG-associated alleles are essential for successful colonization whereas others provide a non-linear competitive advantage, acting as a critical bottleneck that elucidates the isolated emergence of PCG. For instance, toxigenic strains encoding non-PCG alleles of a) tcpF or b) a sextuple allelic exchange mutant for genes tcpA, toxT, VC0176, VC1791, rfbT and ompU, lose their ability to colonize the intestine. Interestingly, these alleles do not play a role in the colonization of model environmental reservoirs. Our study uncovers the evolutionary roots of toxigenic V. cholerae and offers a tractable approach for investigating the emergence of pathogenic clones within an environmental population. SIGNIFICANCEThe underlying factors that lead to specific strains within a species to emerge as human pathogens remain mostly enigmatic. Toxigenic clones of the cholera agent, Vibrio cholerae, are encompassed within one phylogenomic clade, the pandemic cholera group (PCG). Here, we investigate the molecular and evolutionary factors that explain the confined nature of this group. Our analyses determined that the emergence of PCG is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. These allelic variations act as a critical bottleneck that elucidates the isolated emergence of PCG and provides a tractable blueprint for the study of the emergence of pathogenic clones within an environmental population.

microbiology↗

bioRxiv2019

Waterborne, abiotic and other indirectly transmitted (W.A.I.T.) infections are defined by the dynamics of free-living pathogens and environmental reservoirs

While the ecology of infectious disease is a rich field with decades worth of empirical evidence and theory, there are aspects that remain relatively under-examined. One example is the importance of the free-living survival stage of certain pathogens, and especially is cases where they are transmitted indirectly between hosts through an environmental reservoir intermediate. In this study, we develop an integrated, broadly applicable mathematical method to examine diseases fitting this description--the waterborne, abiotic and other indirectly transmitted (W.A.I.T.) infection framework. To demonstrate its utility, we construct realistic models of two very different epidemic scenarios: cholera in a densely populated setting with limited access to clean drinking water and hepatitis C virus in an urban setting of injection-drug users. Using these two exemplars, we find that the W.A.I.T. model fortifies the centrality of reservoir dynamics in the "sit and wait" infection strategy, and provides a way to simulate a diverse set of intervention strategies.

systems biology↗