What are the disadvantages of using phage therapy?

Bacteriophage therapy is gaining outstanding recognition all over the world due to the emergency of superbugs. Superbugs are bacteria that resist antibiotics, these organisms tend to develop some mechanisms that can protect them from being affected by the drug. Antimicrobial resistance is caused by many factors including using the drug without a diagnosis, using human drugs on animals, overusing antibiotics, and many more. Bacteriophages as a natural enemy of these bacteria tend to evolve as the bacteria evolve to resist it, therefore no superbug without a phage to clear, it just needs time to find a perfect virus for the job. Phage is indeed better than antibiotics if the superbug is the pathogen to concern. But are there disadvantages of using phage therapy?
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List of limitations facing phage therapy (disadvantages of using phage therapy)

Take long to  prepare (cant be used in an emergency)

Bacteriophages need a lot of tests to be done right from their isolation, purification, characterizing, and storage. All these processes together may take days up to weeks, therefore it is not applicable for phage therapy to be applied in an emergency. Some scientists have tried creating phage cocktails so that there is a higher probability of having a sensitive pathogen, therefore, lowering the preparation time. 

Can not be used as a wide-spectrum antibiotics

Bacteriophages are viruses and viruses are specific mostly specific to a certain host cell, meaning that they attack a  specific bacteria group and not the other. This has limited the phage therapy in terms of having multiple bacterial infections where you need a very broad antibacterial agent. Also, this can be solved by using a phage cocktail.

Contribute to the Development of Antibiotic Resistance (Horizontal Transfer of Antibiotic Resistance Genes to the bacteria)

Lysogenic phages incorporate their DNA into the bacterial genome. Consequently, they might be vehicles for the horizontal exchange of genetic material and play a role in the diffusion of antibiotic resistance genes (ARGs). Theoretically, due to transduction, new microbes, or even more resistant bacteria can develop (O’Shea and Boyd, 2002; Brabban et al., 2005; Maiques et al., 2007). However, the real contribution of phages to the diffusion of ARGs is not precisely defined. Most of the studies specifically planned to measure how often phages encode ARGs have suggested that these viruses are reservoirs of ARGs. Genes such as blaTEM (resistance to β-lactams), qnrS (reduced susceptibility to fluoroquinolones), erm B (resistance to macrolides), sulI (resistance to sulphonamides), and tetW (resistance to tetracyclines) have been found in the virome of activated sludge and environmental water samples (Parsley et al., 2010; Marti et al., 2014; Rodriguez-Mozaz et al., 2015; Subirats et al., 2016) and in the phage DNA fraction isolated from the intestinal mucus of wild freshwater fish species (Marti et al., 2018) and human fecal samples (Quirós et al., 2014).

 Moreover, diffusion of ARGs can be significantly favored by the presence in the environment of phage inducers, i.e., substances able to induce the expression of prophage gene products or lead to the excision and spread of temperate BPs. Some antibiotics, such as fluoroquinolones and some anticoagulants, are the most important (Torres-Barceló, 2018b). Treatment of wastewater samples with EDTA or sodium citrate activates the lytic cycle of lysogenic phages and leads to the generation of new phage particles, bacterial lyses, phage release outside the cell, and infection of a greater number of bacteria (Colomer-Lluch et al., 2014).

Finally, great numbers of phages carrying genes associated with antibiotic resistance have been detected in secretions and tissues of patients who suffer from recurrent infections due to antibiotic-resistant pathogens and had been previously repeatedly treated with antimicrobial drugs. One of the best examples in this regard is CF, as evidenced by the study conducted by Fancello et al. (2011). These authors analyzed 1,031 short sequences in the CF virome putatively encoding antibiotic resistance and identified 66 efflux pump genes, 15 fluoroquinolone resistance genes, and 9 β-lactamase genes. This and similar findings led to the supposition that BPs might be vehicles for the adaptation of bacteria to the CF lung environment and the emergence and selection of multidrug-resistant pathogens with chimeric repertoires (Rolain et al., 2011). 

However, a recent reevaluation of previously collected data has suggested that AGR abundance in phages was vastly overestimated and that the risk of transduction, although possible, is lower than previously thought. In several studies, conclusions were misled by the excessive bacterial DNA content of the studied samples. Moreover, inadequate approaches to detect ARGs in phage genomes have been used (Enault et al., 2017). Partially in agreement with these findings were Lekunberri et al. (2017) who carried out an analysis of 33 viromes from human feces, pig feces, raw sewage, and freshwater and marine environments. The human-associated viromes did not carry or rarely carried ARGs, while those deriving from non-human sources harbored a significantly higher prevalence of ARGs.

Reduced Activity Due to Immune System Response

Bacteriophages (BP) and their products are non-self-antigens, and it is not surprising that they can be recognized by the immune system and induce responses that can theoretically reduce the benefit of BP administration. Immune response to BPs has been demonstrated in both experimental animals and humans, although with differences according to the phage strain, the route of administration, and the prior exposure. In animals, BPs were taken up by phagocytic cells a few minutes after the administration and might be destroyed by these cells within 2 h (Kaźmierczak et al., 2014). Moreover, examining the survival of T7 BP in the blood of healthy and immunocompromised mice, it was shown that whereas in animals with severe combined immunodeficiency, BP titers were stable for a long time, in healthy mice 99% of BPs were eliminated within 60 min of the injection. As phage titers remained stable in the B-cell-deficient mouse, the greatest part of phage clearance from blood seemed to be due to specific antibody production (Srivastava et al., 2004).

In humans, Dąbrowska et al. (2014) studied the antigenicity of the proteins forming the E. coli T4 BP head surface has reported that specific antibodies could be detected in more than 80% of enrolled individuals, although none of them had received phage therapy. However, even if not fully demonstrated, it seems likely that the immune response evoked by phages has a marginal or no impact on the potential bacterial killing of phage administration. Bacterial lysis occurs before a specific antibody is evoked. Moreover, with some exceptions, phage administration was generally not associated with tissue damage, an increase in pro-inflammatory cytokines, or increased reactive oxygen species (ROS) production (Park et al., 2014). Miernikiewicz et al. (2013) have shown that phage T4 and its head proteins are given intraperitoneally to mice did not affect the production of cytokines [interleukin (IL)-1α, IL-1β, IL-2, IL-6, IL-10, IL-12 p40/p70, interferon (IFN)-γ, tumor necrosis factor (TNF)-α, monocyte chemoattractant protein (MCP-1), monokine induced by gamma (MIG), RANTES, granulocyte colony-stimulating factor (GCSF), and granulocyte-macrophage colony-stimulating factor (GM-CSF)] or ROS.

Similar findings were reported by Hwang et al. (2016) who studied the safety of an E. coli phage cocktail given by mouth to rats for 4 weeks. Carmody et al. (2010) studied the efficacy of phage therapy given by intranasal inhalation in a mouse model of B. cenocepacia pulmonary infection. Bacterial density, macrophage inflammatory protein 2 (MIP-2), and TNF-α were not increased but, on the contrary, were significantly reduced in the lungs of treated mice compared to untreated controls (p < 0.05). On the other hand, data collected in humans that seem to indicate that BP administration is safe seem to support that, even if present, the immune response to BPs is not clinically important.

The use of bacteriophage therapy seems to be interesting although there are some setbacks that need to be addressed before we apply the therapy at the industrial level/capacity. The advantages of phage therapy are outweighing its limitations, I hope in near future to have over counter phage preparations worldwide. More research is needed

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