Recent News 22 : Phage-Mediated Dissemination of Virulence Determinants in Salmonella enterica: A Global Genomic Analysis and the Emergence of Bacterial Countermeasures

Phage-Mediated Dissemination of Virulence Determinants in Salmonella enterica: A Global Genomic Analysis and the Emergence of Bacterial Countermeasures

Abstract

The global health burden of Salmonella enterica, a leading agent of foodborne illness, continues to rise despite advances in detection, hygiene, and therapeutic interventions. Recent evidence points to an underappreciated yet crucial force in its evolution: bacteriophages. These viruses, long known for their roles in bacterial mortality and horizontal gene transfer, are now implicated in the worldwide dissemination of virulence factors that directly affect Salmonella pathogenicity, persistence, and host adaptation. A major international study, analyzing over 466,000 bacterial genomes and more than 5,000 phage sequences, reveals a dynamic virome acting as a conduit for the spread of key virulence genes. Unexpectedly, this study also uncovers an intrinsic genetic defense—centered on the bacterial csrA gene—that modulates phage activity and constrains virulence gene mobility. This review synthesizes these findings in the broader context of microbial evolution, phage biology, and potential translational applications, particularly with respect to phage therapy and biosecurity in food production systems.

Introduction

The evolutionary arms race between bacteriophages and bacteria has shaped microbial genomes for billions of years. While traditionally viewed as killers of bacteria, phages also serve as genetic couriers, transferring genes between hosts in processes such as generalized and specialized transduction. In pathogenic bacteria, this phenomenon has far-reaching consequences for virulence, antibiotic resistance, and ecological plasticity.

Salmonella enterica, an enteric pathogen responsible for an estimated 93.8 million illnesses and 155,000 deaths globally each year, represents a compelling model to study phage-driven evolution. Its genetic variability, host range, and capacity for long-term environmental persistence make it especially prone to the influence of mobile genetic elements, including prophages embedded within its genome.

Experiments to validate the effect of csrA on phage cyclization and cI repressor. Credit: iMeta (2025). DOI: 10.1002/imt2.70042

Global Surveillance of Phage-Encoded Virulence Genes

In a landmark study published in iMeta in 2025, Tianjing She et al. conducted the most extensive genomic surveillance to date of phage-associated virulence gene flow in S. enterica. Drawing from global databases, the authors examined 466,343 bacterial genomes alongside 5,084 phage sequences from a range of environmental, clinical, and animal sources.

The analysis revealed that phages routinely carry and disseminate genes implicated in host colonization, intracellular survival, and immune evasion. Among the most notable genes identified were:

• fliC, encoding flagellin, a key motility and immune recognition factor;

• iacP, an invasion-associated chaperone protein;

• mgtB, involved in magnesium transport under intracellular conditions;

• misL, an autotransporter protein associated with adhesion to host tissues.

Phylogenetic congruence between phage-encoded and chromosomal variants of these genes, often with >98% nucleotide identity, provided compelling evidence of recent horizontal gene transfer events. Many of these phages exhibited genomic signatures of lysogeny, suggesting long-term integration and potential co-evolution with their Salmonella hosts.

Mechanistic Insights into Phage-Mediated Virulence Dissemination

The majority of virulence-associated phages belonged to the Caudoviricetes order, with the Siphoviridae and Myoviridae families being especially prominent. These phages possess specialized transduction mechanisms, enabling the excision and packaging of host genes adjacent to phage integration sites. Functional annotations revealed intact promoters and ribosome-binding sites upstream of the virulence genes, confirming their potential for expression in newly infected hosts.

Interestingly, over 28% of analyzed prophage genomes encoded transcriptional activators homologous to bacterial sigma factors, potentially enhancing the transcription of adjacent bacterial genes during lysogenic cycles. This integration of virulence expression into phage regulatory circuitry underscores the mutualistic potential of such relationships.

The csrA Regulatory Axis: A Bacterial Countermeasure

Perhaps the most striking aspect of the study was the identification of the csrA gene as a potent endogenous regulator of phage activity. csrA is a global post-transcriptional regulator known for its role in carbon storage regulation, motility, and biofilm formation in various Gram-negative bacteria. However, its antiviral function in Salmonella was previously unknown.

Overexpression experiments revealed that csrA modulates the expression of the cI repressor, a phage-derived gene that governs the lytic-to-lysogenic switch. Elevated cI levels inhibit the induction of the lytic cycle, thereby stabilizing prophages and preventing the packaging and release of virulence-encoding phage particles.

By acting as a regulatory feedback loop, csrA effectively restricts the horizontal spread of harmful traits within bacterial populations, representing a form of population-level self-regulation. This also suggests evolutionary pressure on Salmonella populations to maintain genomic integrity and minimize the deleterious consequences of phage-mediated hypervirulence.

Public Health and Therapeutic Implications

The revelation that bacteriophages can serve as vehicles for virulence gene dissemination has profound implications for both the management of Salmonella outbreaks and the development of novel antimicrobials.

In food safety contexts, where phage biocontrol is increasingly explored as an alternative to antibiotics, the presence of prophage-borne virulence genes poses a serious risk. Without careful screening, therapeutic phages could inadvertently exacerbate pathogenicity or promote gene transfer events that lead to super-virulent strains.

To mitigate this risk, phage therapy protocols must incorporate whole-genome sequencing and functional annotation of candidate phages, ensuring they are devoid of undesirable gene cargo. Additionally, synthetic biology approaches may be used to engineer phages with specific deletions in recombination hotspots or transduction modules, reducing their capacity for horizontal gene transfer.

On the other hand, the csrA-mediated antiviral mechanism offers a potential avenue for therapeutic development. Modulating the csrA–cI axis through small molecules, RNA interference, or CRISPR-based gene regulation may serve to suppress prophage activation in vivo, curbing the spread of virulence traits during infection.

Broader Evolutionary Perspectives

The role of phages in the dissemination of virulence genes is not unique to Salmonella. Similar phenomena have been observed in Vibrio cholerae, Shigella flexneri, and Escherichia coli O157:H7, where phage-encoded toxins and adhesins are critical to pathogenesis. This points to a broader paradigm in microbial evolution, in which phages act as evolutionary accelerants, increasing the adaptive potential of their hosts.

Yet, the discovery of intrinsic countermeasures like csrA underscores a key evolutionary tension: the need to harness phage benefits (e.g., novel genes, immunity to superinfection) while minimizing their costs (e.g., host lysis, uncontrolled gene flow). This dynamic interplay shapes not only individual bacterial genomes but also the structure and function of entire microbial communities.

Conclusion

The 2025 iMeta study offers a sobering yet illuminating glimpse into the hidden dynamics of bacterial evolution. By functioning as both weapons and messengers, bacteriophages are reshaping the virulence landscape of Salmonella enterica on a global scale. In parallel, the discovery of regulatory pathways like the csrA–cI axis opens new frontiers in our understanding of bacterial defense and evolutionary restraint.

Future efforts must balance the promise of phage therapy with the imperative to understand and control phage-mediated gene transfer. As metagenomic databases grow and tools for viral genome annotation improve, a clearer picture of the global phage-bacteria network will emerge—one that may ultimately inform both the containment of pathogens and the design of next-generation microbial therapies.

References :

1. She, T., Sun, M., Balcazar, J.L., et al. (2025). Phage-mediated horizontal transfer of Salmonella enterica virulence genes with regulatory feedback from the host. iMeta, 4(2), 70042. https://doi.org/10.1002/imt2.70042

2. Brüssow, H., Canchaya, C., Hardt, W.D. (2004). Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev, 68(3), 560–602. https://doi.org/10.1128/MMBR.68.3.560-602.2004

3. Casjens, S.R., Thuman-Commike, P.A. (2011). Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology, 411(2), 393–415. https://doi.org/10.1016/j.virol.2010.12.007
4. Waters, L.S., Storz, G. (2009). Regulatory RNAs in bacteria. Cell, 136(4), 615–628. https://doi.org/10.1016/j.cell.2009.01.043
5. Touchon, M., Rocha, E.P. (2016). Coevolution of the organization and structure of prokaryotic genomes. Cold Spring Harb Perspect Biol, 8(1): a018168. https://doi.org/10.1101/cshperspect.a018168
6. https://www.msn.com/en-us/health/other/caught-in-the-crossfire-how-phages-spread-salmonella-virulence-genes/ar-AA1H6XNy, Copyright, MSN (c) https://www.msn.com/en-us/health/other/caught-in-the-crossfire-how-phages-spread-salmonella-virulence-genes/ar-AA1H6XNy