Mobile integrons encode phage defense systems
Investigation article published in Science
May 8th, 2025
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle for hundreds of antimicrobial resistance genes among key pathogens. These elements also carry gene cassettes of unknown function (gcus) whose role and adaptive value remain unexplored. In this work, we show that gcus encode phage resistance systems, many of which are newly discovered. Bacteriophage resistance integron cassettes (BRiCs) can be combined and mixed with resistance cassettes to produce multiphage or drug and phage resistance. The fitness costs of BRiCs are variable and dependent on the genetic context and can be modulated by changing the order of cassettes in the array. Hence, MIs act as highly mobile, low-cost defense islands.
Integrons are genetic elements fostering bacterial adaptation in changing environments. These recombination platforms facilitate the acquisition of cassettes encoding genes and their storage in arrays of unrelated adaptive functions. The expression of the genes in the array depends on the Pc promoter in the platform and is modulated by polar effects exerted by cassettes upstream. Under stress conditions, integrons can reshuffle cassettes, changing the pattern of expression of the array. Hence, integrons rapidly increase genetic diversity while keeping the fitness cost to a minimum in the absence of stress.
Mobile integrons (MIs) are a subset of these elements that have been mobilized by transposons onto plasmids. They were discovered for their role in the rise of multidrug resistance among Shigella spp. isolates in the 1950s. Currently, they are common among the deadliest Gram-negative pathogens where they are found carrying several antimicrobial resistance cassettes (ARCs). Altogether, MIs have brought almost 200 ARCs from the environment to our hospitals. This has led to the perception that they are almost exclusively devoted to antimicrobial resistance, and the presence in arrays of a small number of gene cassettes of unknown function (gcus) has been generally overlooked.
Integron recombination occurs under stressful conditions, and cassettes are inserted next to the Pc, where expression is highest, to test their functions. Additionally, recombination in integrons is semiconservative (generating recombined and nonrecombined products), allowing for a bet-hedging strategy when acquiring new cassettes. All this suggests that genes found in integron cassettes have provided an adaptive value for the host upon acquisition. Because phage predation is a major threat for bacteria, we wanted to investigate if gcus could encode bacteriophage defense systems.
We have synthesized and built a library of 129 gcus in Escherichia coli. We have tested them against a panel of phage and discovered 47 phage defense systems. These systems are functionally and structurally diverse and confer different levels of resistance either directly or through abortive infection. We characterized in depth 13, showing that they are encoded in bona fide integron cassettes, which we call bacteriophage resistance integron cassettes (BRiCs). BRiCs are mobile, and the systems they encode can also confer resistance in other species of critical importance, such as Klebsiella pneumoniae or Pseudomonas aeruginosa. They also interfere with prophage activation, highlighting that integrons participate in complex interactions between mobile genetic elements. When BRiCs are in first position of the array and their expression is maximal, their impact on host fitness can range from undetectable to toxic, and it is variable across genetic backgrounds. This cost can be circumvented by incorporating cassettes that exert strong polar effects in the array. As part of an integron, a BRiC can be combined with other BRiCs or ARCs to provide multiphage or phage and antibiotic resistance.
MIs act as cost-efficient and highly mobile defense islands at the crossroads of antibiotic and bacteriophage resistance. At the dawn of a second phage therapy era, their role and impact should not be underestimated.
Kieffer N., Hipolito A., Ortiz-Miravalles L., Blanco P., Delobelle T., Vizuete P., Ojeda F., Jove T., Jurenas D., García-Quintanilla M., Carvalho A., Domingo-Calap P. and Escudero JA..
 | Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM). |
| Departamento de Sanidad Animal. Facultad de Veterinaria. Universidad Complutense (UCM). |
 | Université Libre de Bruxelles (ULB). |
 | Université de Limoges (UL). |
 | Centro de Investigación de Enfermedades Infecciosas (CIBERINFEC). Instituto de Salud Carlos III (ISCIII). |
| Instituto de Biología Integrativa de Sistemas (I2SysBio). Consejo Superior de Investigaciones Científicas (CSIC). Universitat de València (UV). | |
 | WEL Research Institute. |
Related news in other media:
- Veterinarios españoles identifican en bacterias nuevos mecanismos de defensa a terapias alternativas a los antibióticos - animalshealth.es
- ¿Qué son los integrones y por qué son una alternativa a los antibióticos? - larazon.es
- Identifican en bacterias nuevos mecanismos de defensa a terapias alternativas a los antibióticos - saludadiario.es
- Descubren una alternativa a los antibióticos que funciona como auténticas “islas de defensa - consalud.es
