Unraveling the Significance of Phage-Derived Enzymes for Treating Secondary Bacterial Infections among COVID-19 Patients

Abstract

The COVID-19 (Corona Virus Disease of 2019) pandemic had a profound impact on humanity, affecting over 200 million people. Among the complications associated with viral respiratory infections in COVID-19 patients, secondary bacterial infections (SBIs) pose a significant threat to the prognosis of COVID-19 patients, leading to increased morbidity and mortality rates. This crisis is exacerbated by the growing antimicrobial resistance in bacteria, which limits our available treatment options. Recently, the use of phage and phage-derived enzymes (PDEs) has emerged as a promising alternative strategy to combat bacterial infections as they possess a natural ability to eliminate bacteria effectively. The primary objective of this chapter is to emphasize the prevalence of SBIs and the significance of PDEs in addressing SBIs among COVID-19 patients. Specifically, phage-derived depolymerases and endolysins showed considerable antivirulence potency and effectively break down the bacterial cell wall. These enzymes have emerged as a promising class of new antibiotics, with their therapeutic efficacy already confirmed in animal models. By exploring this novel approach, we may discover new avenues to improve patient outcomes and combat the challenges posed by bacterial infections in the context of the COVID-19 pandemic.

1. Introduction

The COVID-19 (Corona Virus Disease of 2019) pandemic has had a profound impact on global health, overwhelming healthcare systems and resulting in significant morbidity and mortality rates worldwide [1]. While the primary focus has been on managing the viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it has become increasingly evident that secondary bacterial infections (SBIs) pose an additional challenge in the clinical management of COVID-19 patients [2]. Compared to pneumonia caused by other respiratory pathogens, severe COVID-19, resulting from infection with the severe acute respiratory syndrome SARS-CoV-2, is known to be associated with a prolonged duration of illness and causes SBIs [3]. These secondary infections can complicate the course of the disease, prolong hospital stays, and contribute to adverse patient outcomes. Patients who experience extended hospital stays face an elevated risk of acquiring multidrug-resistant (MDR) bacterial infections within healthcare settings [4]. These infections are often a result of nosocomial transmission and inadequate antibiotic treatment. Furthermore, the widespread and intensive use of antibiotics during the pandemic can contribute to a higher prevalence of MDR bacteria [5]. Conventional antibiotics have been the cornerstone of bacterial infection treatment for decades, but their efficacy is diminishing due to the emergence of antibiotic-resistant bacteria. The urgent need for novel therapeutic approaches has prompted researchers to explore alternative strategies [6]. One such approach gaining traction is the use of phage-derived enzymes (PDEs) as potential tools to combat bacterial infections.

Phage therapy, which utilizes bacteriophages (phages) as natural predators of bacteria, has emerged as a promising avenue for the treatment of bacterial infections [7, 8]. Phages are viruses that specifically target and infect bacteria, ultimately leading to their destruction [9, 10, 11]. Phages have the ability to recognize and attach to bacterial cell surfaces, inject their genetic material into the bacteria, and hijack the host machinery to produce numerous progeny phages. As a result, phage therapy has shown efficacy against a wide range of bacterial pathogens [12]. Phage therapy and PDEs have not been documented in previous viral pandemics. Currently, there are few efforts have been done on the application of phage therapy in COVID-19 patients with secondary carbapenem-resistant Acinetobacter baumannii (CRAB) pneumonia [13]. Adaptive Phage Therapeutics, a clinical-stage biotechnology company, has recently initiated a study to explore the use of phages in treating COVID-19 patients with bacterial co-infections [14]. However, there are also few drawbacks and limitations of using phages as alternatives [15].

In the context of COVID-19, the significance of PDEs (endolysins and depolymerases) in managing SBIs is of particular interest [16]. As COVID-19 patients often experience compromised immune responses and respiratory distress, they are susceptible to SBIs, which can lead to severe complications and worsen patient outcomes [3]. Therefore, understanding the potential role of PDEs in mitigating these secondary infections is crucial for improving therapeutic interventions and patient care. These enzymes have specific mechanisms of action that allow them to target and eliminate bacteria in a highly efficient manner [17, 18, 19, 20].

This chapter aims to unravel the significance of PDEs in SBIs among COVID-19 patients. We will try to shed light on the occurrence of SBIs in COVID-19, factors that can enhance the susceptibility to SBIs. We will provide insights into the advantages and limitations of utilizing PDEs for controlling such infections and a practical work flow for working with PDEs as well. By shedding light on this topic, this chapter seeks to contribute to the growing body of knowledge surrounding the use of PDEs as a novel therapeutic strategy against SBIs in the context of COVID-19.

2. Fundamental concerns about high prevalence of SBIs in COVID-19 patients

COVID-19 has emerged as a potentially life-threatening infectious disease, prompting scientists to intensify their efforts in comprehending its pathogenesis [21]. The significant morbidity and mortality rates associated with COVID-19 primarily stem from the widespread presence of the SARS-CoV-2 and subsequent microbial infections within the respiratory system [22]. The higher rates of SBIs in COVID-19 patients have emerged as a primary concern in the medical community. The correlation between contracting COVID-19 and developing subsequent bacterial infections has already been confirmed. There is a rising trend of simultaneous severe bacterial infections alongside the viral disease in COVID-19 patients, leading to prolonged hospital stays [23]. This scenario can potentially exacerbate the severity of COVID-19 illness and contribute to high mortality rates [24].

The most commonly encountered pathogens causing SBIs in COVID-19 patients include Acinetobacter baumannii (A. baumannii), Pseudomonas aeruginosa (P. aeruginosa), Klebsiella pneumoniae (K. pneumoniae), and Staphylococcus aureus (S. aureus). The isolation ratios of carbapenem-resistant and colistin-resistant strains for these pathogens are as follows: A. baumannii: 83.7% of isolates were carbapenem-resistant and 5.6% were colistin-resistant. For P. aeruginosa: 79.2% of isolates were carbapenem-resistant and 1.7% were colistin-resistant and K. pneumoniae: 42.7% of isolates were carbapenem-resistant and 42.7% were colistin-resistant [25]. While some COVID-19 patients experienced a higher incidence of bloodstream infections (BSI) caused by Enterococcus, this was not a general trend. Whole-genome sequencing of Enterococcus isolates revealed that the increased rate of BSI in these patients could not be solely attributed to nosocomial transmission [26].

In a multicenter study involving 476 COVID-19 participants, the results demonstrated that SBIs were strongly associated with the severity of outcomes [2]. Based on evidence from previous pandemics and seasonal flu outbreaks, it has been suggested that co-infections have the potential to exacerbate viral illnesses. However, it remains unclear whether they definitively impact patient outcomes in the case of COVID-19. During the initial SARS-CoV outbreak in 2003, up to 30% of patients were found to have SBIs, and co-infection was positively associated with disease severity [27]. Another study revealed that bacterial co-infections were found in 2–65% of patients during regular influenza seasons, and these co-infections were associated with elevated levels of illness and mortality [28]. The escalation of bacterial co-infections during seasonal flu emphasizes the importance of investigating the underlying mechanisms of pathogenicity, particularly in the context of COVID-19.

In a retrospective study conducted by Zhou et al., it was reported that during the ongoing COVID-19 pandemic, approximately one in seven hospitalized patients with the illness experienced a potentially life-threatening SBIs. Among the non-survivors, almost half of them (27 out of 54) developed a secondary infection. Additionally, 10 out of 32 patients (31%) developed ventilator-associated pneumonia, which required invasive mechanical ventilation [29]. These findings highlight the significant risk of SBIs in COVID-19 patients, particularly in those who require intensive care and mechanical ventilation. Several studies have indicated that COVID-19 patients experience more severe illness and a higher fatality rate compared to patients with influenza [30]. In fact, the fatality rate among COVID-19 patients has been reported to be approximately three times higher than that of influenza patients [31]. Furthermore, COVID-19 patients exhibited a two-fold increase in patient mortality rates associated with pulmonary SBIs. In comparison to influenza infections, COVID-19 patients require a longer duration from admission to the detection of bacterial growth. These observations highlight the heightened risk and impact of SBIs in the context of COVID-19, underscoring the need for effective management strategies to mitigate their consequences. Based on a meta-analysis of 24 cohort studies involving 3338 hospitalized COVID-19 patients, it was found that 3.5% of patients (with 95% confidence interval (CI) ranging from 0.4% to 6.7%) had bacterial co-infection at the time of presentation. Additionally, 14.3% of patients (with 95% CI ranging from 9.6% to 18.9%) developed SBIs [32]. These findings provide an estimation of the prevalence of bacterial co-infections and SBIs in hospitalized COVID-19 patients, highlighting the need for vigilance in managing these additional complications. According to the results of microbial culture tests, a total of 92 patients (8.7%) had microbiologically confirmed respiratory or circulatory tract infections. Among 61 patients evaluated for respiratory tract infections, 44 patients were identified to have mono-microbial infections, while 17 patients had poly-microbial infections [33]. These findings indicate the presence of both single and multiple bacterial pathogens contributing to respiratory tract infections in a subset of patients. Out of the 94 patients included in the study, a substantial majority, approximately 68%, acquired at least one of the studied SBIs during their stay in the intensive care unit (ICU). Among these patients, nearly two-thirds (65.96%, n = 62) developed secondary pneumonia as a specific type of SBI [34].

COVID-19 patients exhibited higher rates of bacterial infections compared to other pneumonia patients, with rates of 12.6% versus 8.7%, respectively. The duration of bacterial infection was also longer in COVID-19 patients, with a median of 4 (range 1–8) days compared to 1 (range 1–3) day in other pneumonia patients. Notably, Gram-positive infections that developed later (more than 48 hours after admission) were more frequent in COVID-19 patients, accounting for 28% compared to 9.5% in other pneumonia patients [35]. Importantly, for COVID-19 patients, the presence of SBIs was associated with a 2.7-fold increased risk of death. This highlights the significant impact of secondary infections on the prognosis and mortality of COVID-19 patients. According to Zhang et al., their study revealed that 22 out of 38 patients (57.89%) experienced secondary infections. The likelihood of developing secondary infections was higher in patients who underwent invasive mechanical ventilation or were in critical condition (P < 0.0001) [36]. The presence of secondary infections was associated with lower rates of discharge and increased mortality rates. These findings suggest that secondary infections in COVID-19 patients can have a negative impact on patient outcomes, leading to prolonged hospital stays, increased mortality, and potentially hampering the recovery process.

Based on several disease severity markers, it has been observed that COVID-19 patients tend to experience more severe illnesses and have worse outcomes. This is evident from a higher percentage of patients requiring intubation for mechanical ventilation and an increased number of deaths [37]. These markers suggest a greater impact and high severity of COVID-19 compared to other respiratory illnesses. Significantly, COVID-19 patients have been found to have a higher incidence of SBIs than previously described, and these infections have been independently associated with death in COVID-19 cases [5]. These findings suggest that SBIs may play a significant role in the severity of the disease in COVID-19 patients and could even be a potential target for therapeutic interventions.

3. Major factors that can enhance the susceptibility to SBIs in COVID-19 patients

SBIs can cause severe complications in patients with COVID-19 as follows:

3.1 Prolonged hospitalization and invasive procedures

Many severe cases of COVID-19 require hospitalization, often ICUs. Prolonged hospital stays and invasive procedures, such as intubation and mechanical ventilation, central venous catheter insertion, or urinary catheterization, increase the risk of nosocomial (hospital-acquired) bacterial infections [38]. These procedures can introduce bacteria into the body or provide opportunities for bacterial colonization. Additionally, COVID-19 patients who receive immunosuppressive treatments, such as tocilizumab, anakinra, and corticosteroids, have been found to have a higher incidence of BSIs [16]. This has led to increased mortality rates and a greater need for ICU admissions among patients with BSI. Moreover, COVID-19 infection triggers pathological alterations in the body, such as a compromised immune system, dysregulated immune signaling, and diffuse alveolar damage [26]. These factors contribute to the development of SBIs and limit the effectiveness of antibiotic treatments. The combination of COVID-19 induced immune dysfunction and SBIs poses significant challenges in the management of critically ill patients, requiring a multifaceted approach to optimize outcomes.

3.2 Antimicrobial resistance (AMR)

The convergence of AMR crises poses significant threats when dealing with SBIs in COVID-19-affected patients. Antimicrobial usage is crucial in the treatment of infectious diseases. However, the indiscriminate use of antibiotics during the COVID-19 outbreak has exacerbated the problem of AMR. Despite the widespread administration of antibiotic therapy, the increased prevalence of SBIs in COVID-19 patients may be attributed to the presence of AMR bacteria in hospital settings [39]. The most frequently identified infections in blood and mucous samples of COVID-19 patients are associated with ESKAPE pathogens, which include Enterococcus faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter species. In the context of influenza illness, S. aureus pathogens have been known to cause secondary pneumonia. Environmental changes and immunological responses that create favorable conditions for S. aureus infection are considered factors contributing to its spread to the lungs. Additionally, A. baumannii has been associated with long-term respiratory conditions predisposing individuals to influenza-like upper respiratory tract infections [40]. P. aeruginosa is frequently encountered as an opportunistic pathogen in the respiratory system. Nevertheless, it is also acknowledged as the predominant Gram-negative bacterial specie linked to severe hospital-acquired infections in diverse healthcare environments [41]. Its ability to cause infections in hospital environments poses a significant concern due to its inherent resistance to many antibiotics and its propensity for developing resistance mechanisms. Effective control measures and judicious use of antibiotics are essential in mitigating the impact of P. aeruginosa infections in healthcare settings. ICUs and patients with compromised immune systems are particularly susceptible to nosocomial infections caused by Gram-negative bacteria such as A. baumannii and K. pneumoniae, both of which exhibit signs of MDR. Among the microorganisms isolated from blood cultures, coagulase-negative staphylococci accounted for 31% of cases, while A. baumannii was prominent at 27.5%. In respiratory tract cultures, A. baumannii constituted the majority with a rate of 33.3%, followed by S. aureus and K. pneumoniae, each at 9.5%. Notably, A. baumannii exhibited the highest level of resistance, being resistant to all antibiotics except for colistin [33]. This highlights the challenging nature of treating infections caused by MDR A. baumannii and the importance of appropriate infection control measures to prevent their spread in healthcare settings. Indeed, the availability of effective antibiotic options for “superbugs” such as MDR bacteria is limited [16]. Compounding the issue, the use of certain “last-resort” antibiotics, including colistin, is closely regulated due to concerns regarding organ toxicity, disruption of normal microbial flora, and the potential for inducing AMR [42]. This creates a challenging situation in managing infections caused by these highly resistant bacteria, as alternative treatment options are often limited and their use must be carefully considered to minimize adverse effects. This highlights the urgent need for the development of new antimicrobial therapies and the implementation of strategies to combat the spread of AMR.

3.3 Impaired immune response

COVID-19 can suppress the immune system, making individuals more susceptible to SBIs. The viral infection and the resulting inflammatory response can disrupt the normal functioning of immune cells, impairing their ability to fight off bacterial pathogens effectively [43, 44].

3.4 Ventilator-associated pneumonia (VAP)

COVID-19 patients who require mechanical ventilation are at higher risk of developing VAP [45, 46]. VAP caused by bacteria that colonize the respiratory tract and can lead to serious lung infections. The use of ventilators can impair normal lung function and create an environment conducive to bacterial growth, increasing the likelihood of VAP.

3.5 Disruption of the normal microbiota

COVID-19 and its treatments, such as broad-spectrum antibiotics, can disrupt the normal balance of microbial communities in the body [47, 48]. This disruption, known as dysbiosis, can create opportunities for pathogenic bacteria to overgrow and cause infections.

3.6 Pre-existing comorbidities

COVID-19 patients often have pre-existing health conditions, such as diabetes, cardiovascular diseases, or chronic respiratory conditions. These comorbidities can weaken the immune system and impair the body’s ability to combat bacterial infections effectively [49, 50].

3.7 Viral-induced tissue damage

The SARS-CoV-2 virus primarily infects the respiratory tract, causing inflammation and damage to lung tissues. This tissue damage can compromise the local defense mechanisms and create an environment favorable for bacterial colonization and infection [51]. Healthcare professionals take precautions to minimize the risk of SBIs in COVID-19 patients, including appropriate antibiotic use, infection control measures, and monitoring for signs of infection.

4. Harnessing the potential of PDEs as alternative therapeutics

Considering the sluggish pace of new antibiotic discovery, intact phages and their proteins emerge as promising therapeutic options for antibiotic-resistant bacteria [52, 53, 54]. The concept of phage therapy dates back to the early twentieth century, but it has regained interest in recent years due to the rise of AMR. Phage therapy, utilizing phages, has gained attention as a potential alternative to conventional antibiotics [55]. Phages have several advantages over traditional antibiotics, including their specificity to target bacteria, ability to self-replicate, and potential to evolve alongside bacteria. Clinical trials and case studies have demonstrated the efficacy of phage therapy in treating various bacterial infections, including those caused by MDR bacteria [56]. However, there are some potential drawbacks and challenges associated with their use including AMR transfer, emergence of phage-resistant bacteria, immunogenicity and safety concerns, complex biology, and regulatory challenges. In this context, there has been considerable research focused on phage-encoded proteins that show potential in combating bacterial infections. They have shown efficacy against a wide range of bacterial pathogens, including both Gram-positive and Gram-negative bacteria. These enzymes exhibit a high degree of specificity and can rapidly kill bacteria without harming host cells or disrupting the normal microbiota. These PDEs included endolysins and depolymerases, use as potential therapeutic agents [57]. Endolysins are enzymes produced by phages during the lytic cycle. They can hydrolyze the bacterial cell wall, leading to bacterial lysis and death [58]. Depolymerases are enzymes that degrade the extracellular polymeric substances in biofilms, which are protective matrices formed by bacteria (Figure 1) [59].

Figure 1.

A schematic representation of drug-resistant secondary infections that can occur in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Studies have shown that PDEs can effectively eradicate bacterial biofilms, making them potential candidates for treating biofilm-related infections [60]. They have demonstrated activity against antibiotic-resistant bacteria, including methicillin-resistant S. aureus and carbapenem-resistant Enterobacteriaceae [61]. In addition to their direct antimicrobial effects, PDEs can synergize with antibiotics, enhancing their efficacy against bacterial pathogens [62]. These enzymes have shown promising in various applications, including wound healing, food safety, agriculture, and the prevention of bacterial contamination in medical devices [63]. PDEs are generally considered safe, with a low risk of adverse effects. However, more research is needed to fully understand their long-term safety profiles.

However, challenges regarding development and applications of PDEs include regulatory hurdles, formulation optimization, and the potential for bacterial resistance to emerge [64]. Strategies such as engineering enzymes for improved stability and activity, as well as combination therapies with antibiotics or other antimicrobial agents, may help overcome these challenges.

5. PDEs to act as anti-virulence agents: depolymerases & endolysins

PDEs, such as endolysins and depolymerases, possess a unique mechanisms of action to target and eliminate bacterial pathogens (Figure 2). These enzymes have evolved to efficiently disrupt bacterial cell walls or biofilm matrices, ultimately leading to bacterial death.

Figure 2.

Mechanism of action of phage-derived enzymes (PDEs).

5.1 Endolysins

Endolysins are bacteriophage-encoded enzymes that target the peptidoglycan layer of bacterial cell walls. They have a modular structure, typically consisting of two functional domains: an N-terminal catalytic domain and a C-terminal cell wall-binding domain. The catalytic domain possesses enzymatic activity, such as amidase or glycosidase activity, which can cleave specific bonds within the peptidoglycan structure. Once the endolysin binds to the cell wall of susceptible bacteria, the catalytic domain hydrolyzes the peptidoglycan, leading to the rapid breakdown of the cell wall. The loss of structural integrity causes the bacteria to lyse, releasing progeny phages into the surrounding environment [65].

5.2 Depolymerases

Depolymerases are enzymes produced by phages that target the EPS of bacterial biofilms. Biofilms are complex communities of bacteria encased in a self-produced matrix of EPS, which protects them from the immune system and antimicrobial agents. Depolymerases specifically degrade the EPS components, disrupting the biofilm matrix and rendering bacteria more susceptible to clearance by the immune system or antimicrobial treatments. Depending on the specific type of biofilm and bacterial species, depolymerases can degrade various components of the EPS, such as polysaccharides, proteins, or DNA. Capsular depolymerases present a unique form of antibiotic action: rather than killing bacteria outright, they strip the bacteria of their protective polysaccharides, rendering them vulnerable to immune factors. This characteristic provides a potential edge over endolysins, as depolymerases do not cause bacterial lysis, thereby reducing the risk of inflammatory responses caused by endotoxins [66].

To date, there is limited research about in vivo studies of PDEs, but their efficacy has been demonstrated in animal models (Table 1). The results indicate that PDEs have the potential to revolutionize the treatment of secondary infections in COVID-19 patients who are unresponsive to conventional therapies.

Phage	Enzyme	Delivery route	Model	Results	Reference
S. aureus phage SAP-26	LysSAP26	5–80 μg/mL injection	Mouse model	40% survival rate	[67]
S. aureus phage	SAL200	Intranasal	Lethal murine model	40% survival rate	[68]
E. coli K1	Endo Sialidase from Coliphage E	Intraperitoneal injection	Neonatal rat model of bacteremia	100% of animals protected from death	[69]
Salmonella Typhimurium	P22sTsp endorhamnosidase from Salmonella phage P22	Oral administration	Chicken model of gastrointestinal infection	Bacterial cfu reduction of ~ 1 order	[70]
A. baumannii phage PD-6A3	Ply6A3	Intraperitoneal injection	Mouse sepsis model	32.4% killed	[71]
K. pneumoniae	K64dep capsule depolymerase from Klebsiella phage K64-1	Intraperitoneal injection	Mouse model of bacteremia	100% of animals protected from death	[72]
A. baumannii phage vB_AbaP_D2	Abtn-4	Intraperitoneal injection	Mouse sepsis model	A. baumannii were killed by Abtn-4 (5 μM) in 2 h	[73]
P. aeruginosa	LKA1gp49 LPS lyase from Pseudomonas phage LKA1	Injection into the last pro-leg	Galleria mellonella infection model	20% of animals protected from death	[15]
K. pneumoniae	Dep_kpv79 and Dep_kpv767 depolymerase	Intraperitoneal injection, intramuscular injection	Mouse model	80%, 100%	[74]
A. baumannii	depolymerase Dpo71	Injection into the last pro-leg	Galleria mellonella infection model	80%	[75]
A. baumannii	Capsule depolymerase B9gp69	—	Cell line model of human lung	—	[76]
Proteus mirabilis	Phage derived-Depolymerase	Injection into the last pro-leg	Galleria mellonella infection model	20% protected from death	[77]
ESKAPE group bacteria	LysAm24, LysAp22, LysECD7, and LysSi3	Injection	Mouse model	40% of animals	[78]

Table 1.

Applications of phage-derived enzymes in animal models.

6. A practical approach for PDEs regarding COVID-19

To effectively implement phage-derived therapeutics in a COVID-19-designated hospital, a practical workflow involving different functional areas and varying levels of personal protective equipment (PPE) can be established. The following steps outline a feasible workflow.

6.1 Patient care and bacterial culture

Standard patient care and bacterial culture activities will predominantly occur in the patient ward and clinical laboratory, utilizing appropriate PPE for infection control.

6.2 Phage screening and efficiency analysis

Within the clinical laboratory, a dedicated section adhering to BSL-3 lab PPE requirements will be designated for conducting phage screening and efficiency analysis. This specialized area ensures safety during phage-related procedures.

6.3 Phage amplification and vial preparation

Phages will be regularly amplified by cultivating them in the original host bacteria within the standard microbiology laboratory. This process, carried out under appropriate PPE, will result in the production of ready-to-use phage vials.

6.4 Packaging facility

A packaging facility, meeting Good Manufacturing Practice (GMP) certification standards, will be responsible for packaging the phage vials. This controlled environment ensures quality and safety during the packaging process.

6.5 Selection and delivery of therapeutic proteins

Qualified vials containing purified PDEs will be efficiently selected from the packaging facility. These selected vials will be promptly delivered to the patient ward for therapeutic administration. This process follows a controlled material flow, moving from lower BSL lab zones to higher BSL lab zones, accompanied by the necessary information flow.

6.6 Phage-typing and epidemiological analysis

Bacterial isolates will undergo regular phage-typing procedures for epidemiological purposes. This analysis will provide valuable data to inform the development of sufficient quantities of PDEs and the creation of broad-spectrum, fixed-composition cocktails, particularly for emergency situations. By implementing this practicable workflow, a COVID-19-designated hospital can effectively integrate phage-derived therapeutics into its existing healthcare infrastructure, ensuring safety, quality, and expedited delivery of these potential treatments to patients in need (Figure 3).

Figure 3.

This study proposes a workflow for managing COVID-19 (Corona virus disease of 2019) infections [16]. It involves using a pre-established phage library targeted against a specific pathogenic bacterium that has been identified in either a patient or on a hospital surface. The process includes screening the phage library and delivering pre-stocked phage-enzyme vials for application to the patient or the affected environment. PDEs: phage-derived enzyme; PPE: personal protective equipment; BSL: biosafety level; and GMP: good manufacturing practices.

7. Challenges and future prospects

Although PDEs show promise as a therapeutic strategy, several challenges need to be addressed. This section discusses the limitations and obstacles associated with their utilization, including regulatory hurdles, bacterial resistance, and formulation issues. Furthermore, it explores potential future directions and advancements in the field.

7.1 Regulatory hurdles

One of the key challenges in the clinical implementation of PDEs is navigating the regulatory landscape. Regulatory agencies may have limited experience or specific requirements for the approval and use of phage-based therapies, which can impede their widespread adoption. Overcoming these regulatory hurdles requires collaborative efforts between researchers, regulatory bodies, and pharmaceutical companies to establish clear guidelines and streamline the approval process [64, 79].

7.2 Bacterial resistance

As with any antimicrobial treatment, the potential emergence of bacterial resistance to PDEs is a concern. Bacteria can evolve mechanisms to evade the activity of these enzymes, such as modifying their cell surface receptors or producing protective substances. Continued research is needed to understand the mechanisms of bacterial resistance to PDEs and develop strategies to mitigate its occurrence, such as using multiple enzymes or combinations with other antimicrobials [56].

7.3 Formulation and delivery optimization

Effective delivery of PDEs to the target site remains a challenge. Enzymes must be formulated in a way that maintains their stability, activity, and bioavailability. Overcoming barriers such as enzymatic degradation, poor penetration into tissues, and immunogenicity requires innovative delivery systems, including nanoparticles, liposomes, or hydrogels, to ensure optimal enzyme delivery and efficacy [80, 81].

7.4 Clinical trials and evidentiary support

Additional clinical trials are necessary to establish the safety, effectiveness, and ideal dosing protocols of PDEs in treating SBIs among patients with COVID-19. Robust clinical evidence is necessary to demonstrate their effectiveness compared to standard treatments, including antibiotics. Well-designed clinical trials with appropriate control groups and endpoints are crucial for gathering the data required to support the integration of PDEs into clinical practice.

7.5 Personalized and precision medicine

The development of personalized treatment approaches, guided by patient-specific bacterial profiles and susceptibilities, holds promise for optimizing the use of PDEs. Integrating genomics and metagenomics techniques to characterize bacterial populations and predict their response to specific enzymes could enable tailored treatment strategies. Implementing precision medicine principles can help optimize therapy, minimize the emergence of resistance, and improve patient outcomes.

Overall, despite the challenges, the future prospects of PDEs in SBIs among COVID-19 patients are promising. Addressing the regulatory hurdles, understanding and countering bacterial resistance, and delivery systems, generating robust clinical evidence, exploring combination therapy strategies, and embracing personalized medicine approaches will contribute to realizing the full potential of PDEs as valuable therapeutic tools in the management of SBIs in the context of COVID-19 and beyond.

8. Conclusion

The end of the COVID-19 pandemic is expected to be a prolonged process, despite extensive efforts made to control it. Various indicators of disease severity have revealed that certain COVID-19 patients experience more severe illness and worse outcomes. Additionally, our ability to combat MDR bacteria is diminishing as they become more widespread, further exacerbating the complications in COVID-19 patients. Although there have been limited clinical studies on SBIs in COVID-19, the findings suggest that the condition might be treatable. To address challenges like resistance, host specificity, and drug development during the purification and characterization of phage-derived antimicrobials, alternative phage-based treatments can be utilized when the complete phage is not as effective. The significance of PDEs in SBIs among COVID-19 patients cannot be overstated. However, there are certain limitations and important questions surrounding the delivery route of these phage-derived therapies and their impact on the host. This chapter underscores the importance of understanding the mechanisms and applications of PDEs in combating bacterial infections. By harnessing their potential, healthcare professionals can develop targeted interventions to mitigate the burden of SBIs and improve patient outcomes.

Conflicts of interest

There are no conflicts of interest.

Author contributions

A.N. prepared the first draft of the manuscript. L.L., X.Z., Y.L. and Y.C. were responsible for this manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This study was funded by grants from the Natural Science Youth Foundation of Shandong Province (ZR2022QC028); the National Key Research and Development Project (2023YFE0107600); the Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences (CXGC2022E10; CXGC2023F10); the Innovation Capability Improvement Project for Science and Technology SMEs in Shandong Province (2022TSGC2384).