Mechanisms and clinical importance of bacteriophage resistance

Abstract

We are in the midst of a golden age of uncovering defense systems against bacteriophages. Apart from the fundamental interest in these defense systems, and revolutionary applications that have been derived from them (e.g. CRISPR-Cas9 and restriction endonucleases), it is unknown how defense systems contribute to resistance formation against bacteriophages in clinical settings. Bacteriophages are now being reconsidered as therapeutic agents against bacterial infections due the emergence of multidrug resistance. However, bacteriophage resistance through defense systems and other means could hinder the development of successful phage-based therapies. Here, we review the current state of the field of bacteriophage defense, highlight the relevance of bacteriophage defense for potential clinical use of bacteriophages as therapeutic agents and suggest new directions of research.

Keywords: adaptive immunity; bacteria; defense; innate immunity; phage resistance; phage therapy.

Figure 1.

Host adaptations leading to phage resistance. (A) Point mutations can lead to a loss or modification of the phage receptors (green rectangles), or to downregulation of their expression. (B) Receptor masking proteins like TraT of Escherichia coli (pink) can bind to the surface-exposed regions of phage receptors, making them unavailable for the phages. (C)Outer-membrane vesicles (OMVs) presenting phage receptors act as decoys to prevent the phages from encountering the bacteria. (D) An increase in the production of extracellular matrix (light green) leads to phage receptors being physically hidden. (E) Phase variation occurs through three mechanisms: site-specific recombination, slipped-strand mispairing and epigenetic modifications. It can regulate the bacterial phenotype, including the expression of surface proteins like phage receptors.

Figure 2.

Host phage defense systems. (A) Multiple defense systems act via nucleic acid interference. R-M systems are generally composed of an MTase that methylates endogenous DNA to distinguish it from exogenous DNA, and of an REase that cleaves the exogenous, non-methylated DNA. DISARM interacts with phage DNA to prevent its circularization, thereby blocking its replication or lysogeny. BREX or Ago systems interact with phage DNA and prevent it from replicating without necessarily cleaving it. CRISPR-Cas systems are known as the adaptive immune system of bacteria. The CRISPR array contains sequences of foreign origin that can be transcribed and processed to act as a guide for the Cas endonuclease, which recognizes and cleaves said sequences upon reentry into the bacteria. (B) Abortive infection comprises a series of mechanisms that lead to bacterial cell suicide. An example in which this can happen is through an imbalance in the concentration of toxins and antitoxins in a cell. Another example is through the action of effector proteins that might get activated directly, like in the case of retrons, or via second messengers, like in the case of CBASS or Thoeris. These effector proteins can lead to cell death in several ways, for instance through inner membrane degradation (CBASS) or through NAD depletion (Thoeris). (C) Bacteria can produce secondary metabolites such as daunorubicin (depicted) that intercalate phage DNA and prevent it from circularizing and replicating. (D) Analysis of genetic defense islands has recently led to the discovery of a series of defense systems that are yet to be fully characterized. These include: Hachiman, Shedu, Gabija, Septu, Lamassu, Zorya, Kiwa, Druantia, Wadjet, RADAR, DRTs, AVAST and pVips, among others.

Figure 3.

Phage-derived defense systems. (A) Superinfection exclusion systems (Sie) are encoded by phages to prevent other phages from infecting their host. Some phages like T5 produce proteins that mask their receptor and make it inaccessible. Other phages, especially prophages, encode membrane-associated proteins that interact with the phage receptor, blocking the DNA entry channel, triggering a conformational change or inhibiting the invading phage's enzymes. (B) Prophages like Panchino of Mycobacteriumsmegmatis can confer resistance to their hosts through the expression of R-M systems or DNA-binding repressor proteins that target the DNA of newly infecting phages. Other prophage-encoded systems, like RexA-RexB or the newly characterized PARIS, can trigger an Abi response upon sensing an invasion by a new phage.