Biology subjects

Ibarra-Chavez, R.

Publications and source records attributed to Ibarra-Chavez, R..

5 recordsLinked to original sources

bioRxiv2026

Antimicrobial-resistance plasmids encode Evangelion, a widespread DUF4062 anti-phage defence family

Mobile genetic elements have profoundly shaped the evolution of bacterial anti-phage immunity, yet much of this defence repertoire remains undiscovered. Antimicrobial-resistance plasmids are well known for disseminating antibiotic-resistance genes, but whether they also serve as reservoirs of previously unrecognised antiviral immunity remains poorly understood. Here, we identify Evangelion, a widespread family of single-gene anti-phage defence systems, through phenotype-guided interrogation of a naturally occurring methicillin-resistant Staphylococcus aureus plasmid. Eva01, the founding member of the family, protects against lytic Silviavirus phages and is built around a conserved DUF4062 core coupled to a highly diversified auxiliary region that is essential for defence activity. Evangelion systems are enriched on antimicrobial-resistance plasmids but are distributed across diverse bacterial hosts and mobile genetic elements, revealing an evolutionarily conserved defence framework that has diversified through horizontal gene transfer and adaptation to distinct phage environments. Genetic, structural and functional analyses support a model in which Eva01 senses intracellular phage replication-associated processes and couples activation of a DUF4062 effector to NAD depletion and abortive infection. Together, our findings define a previously unrecognised family of mobile anti-phage defence systems, establish DUF4062 proteins as a new component of the bacterial anti-phage repertoire, and demonstrate that phenotype-guided interrogation of mobile genetic elements provides a powerful strategy for discovering defence systems beyond the reach of current computational approaches.

molecular biology↗

bioRxiv2025

Prophage and SaPI diversity in local clinical Staphylococcus aureus reveal hidden drivers of virulence.

Prophages are key drivers of bacterial evolution, genomic variability, virulence, and ecological adaptation. Here, we examined the prophage diversity of 109 Staphylococcus aureus clinical isolates from four tertiary care hospitals in Mexico City, integrating comparative analyses with 993 international genomes. Prophages were detected in 97% of the local strains, mirroring the near-ubiquitous presence (99%) observed globally. We identified 216 genomic regions encoding putative prophage functional elements. Using Mitomycin C induction, we recovered 17 temperate phages, 12 of which were functionally active and capable of lysogeny-lysis switching and reinfection. Induced phages lacked virulence or antibiotic resistance genes, in contrast to 55% of the predicted prophages in local S. aureus isolates that harbored known virulence factors. Moreover, 19% of the predicted prophages were phage-inducible chromosomal islands (PICIs) related to SaPI1, SaPI2, and SaPIpt1028. These PICIs encode anti-phage defense systems (63%) and virulence genes (27%), such as tsst-1 and hlb. Our findings reveal a complex prophage and PICI landscape in S. aureus circulating in Mexican hospitals, with implications for phage- host dynamics, horizontal gene transfer, and the evolution of pathogenic potential across geographically diverse populations. ImportanceStaphylococcus aureus is a major hospital pathogen whose evolution is driven by mobile genetic elements including prophages and phage-inducible chromosomal islands (PICIs). Although computational analyses predict prophages in nearly all S. aureus genomes, we demonstrate that only a small fraction is functionally active. Through experimental induction of clinical isolates from Mexican hospitals, we recovered active prophages that surprisingly lacked virulence genes, in contrast to the predicted prophages that frequently harbor virulence factors. Importantly, we discovered that many predicted "prophages" are PICIs carrying anti-phage defenses and toxins. These findings challenge the current prophage prediction methods and reveal the complex prophage-PICI landscape that shapes horizontal gene transfer and pathogenic evolution in clinical S. aureus populations.

microbiology↗

bioRxiv2025

Immune-deficient bacteria serve as gateways to genetic exchange and microbial evolution

Horizontal gene transfer plays a key role in bacterial evolution, yet its efficiency under natural conditions, especially between genetically distinct strains, remains unclear. Using Staphylococcus aureus as a model, we found that gene transfer via various mechanisms is significantly restricted between strains from different clonal complexes (CCs), with the notable exception of lateral transduction, which occurs at high frequency. Interestingly, some strains exhibited a "promiscuous" ability to accept diverse mobile genetic elements. These strains were defective in the key immune defences of S. aureus, specifically the Type I restriction-modification systems that normally protect against foreign DNA. A broader analysis revealed that such immune-deficient mutants are widespread within S. aureus populations. Our study uncovered a trade-off that explains their persistence in nature: although these mutants are more susceptible to phage attack, they gain an evolutionary advantage by acquiring beneficial genes - such as those conferring antibiotic resistance - which enhance survival under selective pressure. These immune-deficient cells act as gateways for foreign DNA, which, once integrated and advantageous, can spread within the same CC. Our findings highlight an unexpected role for immune-deficient bacteria in facilitating the emergence of novel virulence factors and antibiotic resistance, emphasising their importance in shaping bacterial evolution.

microbiology↗

bioRxiv2025

Hidden in plain sight: Bacterial genomes reveal thousands of lytic phages with therapeutic potential

Phages are typically classified as temperate, integrating into host genomes, or lytic, replicating and killing bacteria. Lytic phages are not expected in bacterial genome sequences, yet our analysis of 3.6 million bacterial assemblies from 1,226 species revealed >100,000 complete lytic phage genomes, which we term Bacterial Assembly-associated Phage Sequences (BAPS). This represents a [~]five-fold increase in the number of phages with known hosts and fundamentally reshapes our understanding of phage biology. Identifying BAPS has enabled the discovery of entirely novel phage clusters, including clusters distantly related to Salmonella Goslarviruses in E. coli, and Shigella, while significantly expanding known genera such as Seoulvirus (from 16 to >300 members). Notably, close relatives of therapeutic lytic phages were also detected, suggesting clinical isolate sequencing unknowingly archives viable phage candidates. The discovery of complete, lytic phage genomes within bacterial assemblies challenges long-standing assumptions and reveals a vast, untapped reservoir of phages.

microbiology↗

bioRxiv2019

Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria

Emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. We established a series of CRISPR-Cas13a-based antibacterial nucleocapsid, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus through promiscuous RNA cleavage after recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs were generated by packaging CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibited strong bacterial killing activities upon recognizing target genes regardless of their location. The antimicrobials treatment efficacy was confirmed using a Galleria mellonella larvae model. Further, we demonstrated that the CapsidCas13a(s) can assist in bacterial gene detection without employing nucleic acid amplification and optical devices.

microbiology↗