Chapter 7 - Bacteriophage Host Range and Bacterial Resistance
Introduction
Viruses are obligate intracellular parasites of cellular organisms. As such, their basic life cycle involves cooption of cellular metabolism toward production of new virus particles, release of those particles from their cellular confines, and then acquisition of new cells. A virus life cycle consequently is successful only to the extent that those three steps are productively completed. Many things can go wrong in the course of the viral life cycle such that productive infection is never achieved (Fig. 7.1), and we can describe these phenomena in terms of a virus' host range, which for bacteriophages (phages) is an assortment of susceptible bacteria types. Additionally relevant is the range of bacterial types to which phages can transduce DNA.
Phage-resistance mechanisms encoded by bacteria (bacterial resistance) serve to limit phage host range. Though often viewed mainly as blocks on phage adsorption, there are a number of additional bacteria, prophage, and, perhaps most typically, plasmid-encoded mechanisms which interfere with phage infections (Fig. 7.2). Collectively, these mechanisms have been described as making up the “Bacteriophage ‘Resistome’” (Hoskisson and Smith, 2007), and they have been extensively reviewed especially among lactic acid bacteria (LAB; Allison and Klaenhammer, 1998, Daly et al., 1996, Dinsmore and Klenhammer, 1995, Forde and Fitzgerald, 1999, Garvey et al., 1995, Hill, 1993, Klaenhammer and Fitzgerald, 1994). Phages, in turn, employ numerous resistance‐countering and therefore host-range expanding adaptations, as are also discussed in these reviews. See also Ackermann and DuBow, 1987, Nieradko and Los, 2006, Weinbauer, 2004 for further explorations of phage host range and bacterial resistance.
Bacterial resistance mechanisms are usually differentiated into adsorption blocks (Section IV), phage-genome uptake blocks (Section V.A), restriction modification (Section V.B), and abortive infections (Section VI). More recently, CRISPR mechanisms have been added to this list (Section V.C). Here we employ a similar but more broadly applicable scheme which emphasizes phage versus bacterium survival (Fig. 7.3). We find this approach to be more applicable to our interest in phage–host ecological interaction (Abedon, 2006, Abedon, 2008a, Abedon, 2008b, Abedon, 2009a, Abedon, 2010, Abedon and LeJeune, 2005, Breitbart et al., 2005, Hyman and Abedon, 2008) since phage functioning is primarily a product of infection success while bacterial functioning can be viewed largely in terms of survival following phage encounter. This functioning occurs within natural environments (Abedon, 2010, Thingstad et al., 2008, Weinbauer, 2004), industrial ferments (Bogosian, 2006; plus above for LAB ferments), in the course of phage employment to combat nuisance and pathogenic bacteria (phage therapy; e.g., Balogh et al., 2010, Goodridge, 2010, O'Flaherty et al., 2009), etc., and often is antagonistic in terms of phage versus bacterium success. Bacterial resistance thus serves, above all, to assure bacterial survival, but at the same time plays a predominant role in defining phage host range.
Section snippets
Host-Range Determination
The concept of phage host range, as consisting only of those bacteria that a phage can productively infect, is at best an ideal and at worst misleading. This is because measured host ranges are dependent on what techniques and conditions are used in their determination, including plaquing, spot testing, or broth-based measures of phage population growth. In light of the ambiguity associated with different techniques, and their potential to fail to determine the desired productive (i.e.,
Breadth of Host Range
A great deal of effort has been put toward determining phage host ranges, variously defined. These studies can be found in an extensive literature of individual phage characterization as well as numerous studies in which bacterial strains have been differentiated in terms of the phages to which they are susceptible (for the latter, search using the phrase “phage type” or “phage typing”). In all cases reported host ranges can be assumed to be smaller than actual host ranges given that all
Adsorption Resistance
Phage infections can be thwarted at a number of different steps (Fig. 7.2). One of these steps, adsorption, we define narrowly as phage attachment to cognate receptor molecules found on a bacterial cell. Adsorption can be blocked—resulting in what often is described as adsorption inhibition—either by preventing encounters between phages and their receptors (Section IV.A) or through functional receptor elimination (Section IV.B). They serve to limit a phage's adsorptive host range (Table 7.1).
Prevention of Host Takeover
We use the term “restriction” to describe postadsorption resistance mechanisms that prevent irreversible takeover of host metabolism by phages (Figure 7.2, Figure 7.3). Note that the word restriction, when applied to phage–bacteria interactions, commonly is associated with restriction endonucleases (Section V.B), as in host-mediated “restriction or extension of the host range of bacteriophages” (Stent, 1963, p. 377). However, historically the term has also been employed using a broader meaning:
Abortive Infection
With abortive infections, sometimes referred to as phage exclusion mechanisms, phages are unable to successfully infect but the bacterial host dies as well (Figure 7.2, Figure 7.3). Contrasting restriction enzymes which can degrade any unprotected DNA regardless of origin, abortive infection mechanisms may be fairly specific in terms of the phage strains they affect. Because the bacterium is killed but the rest of the population of bacteria are protected from subsequent phage infection, Shub
Concluding Remarks
The experience in the laboratory, following phage exposure to individual bacteria, often is the selection of bacterial strains to which phages cannot adsorb, and otherwise is biased toward bacterial resistance mechanisms that allow the host to continue replicating in the presence of the added phages. This experience has become the paradigm for phage–host coevolution, where bacterial mutation resulting in changes in surface molecules results in the blocking of phage adsorption, whereas
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