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Article

Exploring Local Reservoirs for Bacteriophages with Therapeutic Potential against ESKAPE Pathogens

by
Alejandra Aidee Loera Piedra
1,2,
Isamar Leticia Becerra Mejía
1,2,
Brenda Luna Galicia
1,
Sergio Francisco Martínez Díaz
3,
Julieta Luna Herrera
2,* and
Ma. Guadalupe Aguilera Arreola
1,*
1
Laboratorio de Bacteriología Médica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11350, Mexico
2
Laboratorio de Inmunoquímica II. Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11350, Mexico
3
Laboratorio de Microbiología y Biología Molecular, Centro Interdisciplinario de Ciencias Marinas, Instituto Politécnico Nacional, La Paz 23096, Mexico
*
Authors to whom correspondence should be addressed.
Microbiol. Res. 2024, 15(3), 1459-1470; https://doi.org/10.3390/microbiolres15030098
Submission received: 11 June 2024 / Revised: 2 August 2024 / Accepted: 2 August 2024 / Published: 8 August 2024
Browse Figure
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Abstract

:
Bacteriophage therapy is a promising strategy used to treat antimicrobial-resistant or persistent bacterial infections. More recently, the clinical utility of bacteriophages has been rediscovered due to the rise of multi-drug resistance and their potential use in clinical practice as an additional treatment option. In this study, local municipal wastewater facilities, hospital wastewater systems, and freshwater reservoirs were evaluated for the presence of lytic bacteriophages. These phages were isolated using conventional phage isolation techniques: water sample collection and processing, pre-enrichment with the host bacteria, the spot test, and the double-layer method. Plaques were selected according to their morphology and lytic activity on the target bacteria. Clinical isolates and reference strains belonging to the ESKAPE group were the targets during phage isolation. A total of 210 lytic plaque morphotypes with activity against ESKAPE strains were isolated from 22 water samples. Each isolate was qualitatively evaluated for its ability to inhibit the growth of its host strain. Thirty-one translucent plaques with apparent lytic activity were selected for purification. Of these, 87.1% were isolated from wastewater samples, and 12.9% were isolated from flowing freshwater. Specifically, the phages isolated from the freshwater samples targeted Staphylococcus aureus strains, and no phage from Enterococcus faecium strains was isolated. In conclusion, wastewater samples are a suitable source for the isolation of exogenous lytic phages; however, freshwater could be considered an alternative source for the isolation of lytic phages.

1. Introduction

The widespread use of antibiotics as therapeutic agents for humans and animals and as growth promoters in agriculture has caused the emergence of multi-drug-resistant (MDR) bacteria, defined as bacteria resistant to more than three antibiotic classes [1]. Critical-priority bacteria, as defined by the World Health Organization (WHO), include a group of life-threatening nosocomial pathogens known as ‘ESKAPE’, an acronym indicating the names of these bacteria and their ability to evade the antimicrobial activity of antibiotics: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. [2,3]. These pathogens, together with Clostridioides difficile, Escherichia coli, Campylobacter spp. (Campylobacter jejuni and Campylobacter coli), Legionella spp., and Salmonella spp., are the most common causes of nosocomial infections [4].
Understanding the real global burden of antimicrobial resistance could lead to the implementation of strategies to solve this problem. Murray et al. [5] estimated that in 2019, around 4.95 million deaths throughout the world were associated with MDR bacteria. The deadliest pathogen associated with resistance was E. coli, followed by S. aureus, K. pneumoniae, Streptococcus pneumoniae, A. baumannii, and P. aeruginosa. In Mexico, according to Red Hospitalaria de Vigilancia Epidemiológica (RHOVE), in the third quarter of 2023, there were 10,603 healthcare-acquired infections (HAIs) in secondary- and tertiary-level hospitals, and the principal agent that caused these HAIs was E. coli, followed by P. aeruginosa, K. pneumoniae, A. baumannii, S. aureus, Staphylococcus epidermidis, and Enterobacter cloacae, among others, such as the yeast Candida albicans [6,7].
Bacteria may become resistant to antibiotics via de novo gene mutation or the acquisition of mobile genetic elements. ESKAPE pathogens have developed resistance mechanisms against oxazolidinones; lipopeptides; macrolides; fluoroquinolones; tetracyclines; β-lactams; β-lactam–β-lactamase inhibitor combinations; and antibiotics that are the last line of defence, including carbapenems, glycopeptides, and clinically unfavorable polymyxins [8,9,10]. Under this scenario, the development of novel therapeutics is urgently needed to treat infections caused by drug-resistant bacteria, especially the ESKAPE pathogens. Alternative therapies such as the use of antibiotics in combination with adjuvants, bacteriophages, antimicrobial peptides, nanoparticles, and photodynamic light therapy have been considered [11].

Bacteriophages

Since the discovery of bacteriophages (also known as phages) about a century ago, their use in clinical applications has increased. Phages are the most abundant biological entities on Earth, with an estimated abundance of at least 1031 virions [12,13,14]. Bacteriophages are natural predators of bacteria and are considered potent antibacterial agents because they can infect their host via a range of biochemically diverse host-surface receptors, including carbohydrates, lipopolysaccharides, and proteins, and they can multiply rapidly inside their host and kill the bacteria through a lytic process [15]. The phage host range is generally determined by how specifically the phage structures interact with the host’s receptors. Recognition of a highly unique region can lead to a narrow host range, where a phage may be capable of infecting only a single host species or strain [16].
There are four common phage life cycles: lytic, lysogenic, pseudolysogenic, and chronic infection. Each cycle involves at least five stages: adsorption via recognition of host-associated receptors (proteins, sugars, and cell-surface structures) in the host bacteria; injection of nucleic acids into the host; replication using the host cell’s molecular machinery; assembly of virus particles; and host cell lysis, in which phage particles are released into the environment to infect other cells [17,18]. Lytic phages immediately start to replicate inside the host cell, whereas lysogenic phages integrate into the host cell’s genome and remain there until their lytic cycle is activated [19,20].
The use of phages in clinical practice is called phage therapy. It involves the successful infection of a prokaryotic host cell to eventually kill it via lysis [21]. Unlike antibiotics, bacteriophages have the characteristics of self-amplification, host specificity, relatively low toxicity, and the ability to disintegrate established biofilms [22]. In recent years, the compassionate use of phage therapy and interest in phage therapy for treating infections caused by MDR ESKAPE pathogens, including cystic fibrosis and chronic lung infection caused by P. aeruginosa and A. baumannii, urinary tract infections and prosthetic infections caused by K. pneumoniae, and cardiothoracic infection related to E. faecium and S. aureus, have increased [23,24,25,26,27].
As a result of the emerging interest in studying phage therapy, private institutions, such as Intralytix, Inc. and Adaptive Phage Therapeutics, Inc., have focused their studies on the development and application of phage therapy in the medical field. The companies have clinical trials available for consultation at https://clinicaltrials.gov/ (accessed on 29 June 2024), in which they evaluate the safety and efficacy of bacteriophages to eliminate specific types of microorganisms. The ShigActiveTM formulation designed by Intralytix was developed to reduce or eliminate Shigella spp., and Adaptive Phage Therapeutics, Inc. has clinical trials to reduce or eliminate E. coli and K. pneumoniae, which cause urinary tract infections. Medical institutions such as the Mayo Clinic in the United States; the University Hospital Montpellier in France; the Copenhagen University Hospital, Hvidovre in Denmark; etc. also have clinical trials evaluating the efficacy and security of phage therapy [28,29].
However, the scenario in phage therapy is not completely encouraging. Some reports in the literature have noted complications in personalized bacteriophage therapy in co-infections caused by K. pneumoniae [30,31,32] or refractory P. aeruginosa bronchopulmonary infection [30,31,32]. Moreover, recently, the failure of phage therapy was reported during the treatment of a patient with an MDR P. aeruginosa prosthetic vascular graft infection who was treated with a cocktail of phages in combination with ceftazidime–avibactam (CZA) [30,31,32]. The failure was apparently due to the development of a resistant phage population of bacteria. Additionally, the authors remarked on the absence of local biobanks of phages for P. aeruginosa, from which specific phages could be selected to provide personalized treatments to patients with complex conditions caused by these bacteria [30,31,32]. In Mexico, research aimed at understanding phage therapy in the context of clinical practice has been very limited. In contrast, researchers have employed phage therapy in aquaculture to eliminate Vibrio species or in agriculture for the biocontrol of Ralstonia solanacearum [33,34,35]. The aim of this study was to identify reservoirs of phages capable of infecting ESKAPE pathogens obtained locally from clinical settings at a tertiary-care hospital in Mexico City.

2. Materials and Methods

2.1. ESKAPE Strains and Growth Conditions

Thirty-two ESKAPE strains were employed in this study. Thirty clinical isolates were recovered from patients with healthcare-acquired infections (HAIs) at a tertiary healthcare center in Mexico City, as well as two American Type Culture Collection (ATCC) strains: P. aeruginosa ATCC 27853 and K. pneumoniae ATCC BAA1705. The ESKAPE strains were preserved at −80 °C in Todd–Hewitt broth (Dibico, Cuautitlán Izcalli, Mexico) with 40% (v/v) glycerol and cultured in Luria–Bertani (LB) broth (Dibico) and LB agar (Dibico) with 222 mg of MgCl2 and CaCl2 at 37 °C [36]. Isolates were identified using the VITEK MS identification system (bioMérieux Inc., Grenoble, France), except for E. cloacae strains, which were identified with the VITEK 2 compact system (bioMérieux Inc., Grenoble, France). Susceptibility tests were carried out with a VITEK 2 compact system according to the manufacturer’s instructions (bioMérieux Inc., Grenoble, France). An AST-N271 card was used for the K. pneumoniae, E. cloacae, and P. aeruginosa IIH strains; XN-05 and XN-08 cards for A. baumannii; AST-GP75 for E. faecium and S. aureus; and the disc diffusion method was used for P. aeruginosa 1, 4, 7, and 10. The antimicrobial profiles are shown in Table 1.

2.2. Water Sample Collection

Twenty-two water samples were collected: nine flowing water samples, three hospital wastewater samples, and ten municipal wastewater samples. The samples were collected in a 1 L flask, with 50 mL transferred for processing. Each sample was sonicated for 30 s and centrifuged at 13,000× g for 10 min. Finally, the sample was filtered using a syringe filter with a pore size of 0.22 μm (Corning, Kaiserslautern, Germany) [37].

2.3. Phage Enrichment, Isolation, and Purification

Phages were enriched according to the standard method [38], with slight modifications. Briefly, 3 mL of the filtered water samples were incubated with 3 mL of 2X LB broth and 100 µL of a combination of four target bacteria and then incubated at 37 °C overnight at 150 rpm. The target strains used in phage isolation are shown in Table 1 [39]. Then, 1% chloroform (Sigma-Aldrich, St. Louis, MO, USA) was added to the culture, and the mixture was centrifuged at 13,000× g for 5 min and filtered using a 0.22 µm syringe filter (Corning, Kaiserslautern, Germany). The filtrates were serially diluted with SM buffer (5.8 g NaCl, 2.0 g MgSO4⋅7H2O, and 50 mL of 1 M Tris–HCl [pH 7.4] in 1 L distilled water [dH2O]) and inoculated in a spot test and double-overlay assay plates to obtain isolated plaques with each target bacterium [37]. Lytic plaques were selected according to their morphological characteristics: size and opacity.

2.4. Preliminary Lytic Activity Evaluation

The selected plaques were individually scraped with a pipette tip and transferred to culture tubes for the respective target bacteria in the LB broth. The tubes were incubated at 37 °C for 5–6 h at 150 rpm [40,41]. Additionally, the plaques that achieved complete lysis of the target bacterium were further purified with 3–5 rounds of serial passages and then propagated in a liquid medium. The obtained phage lysates were filtered using a 0.22 µm syringe filter (Corning, Kaiserslautern, Germany) and stored at 4 °C until their use [42].

3. Results

Twenty-two water samples were analyzed for the presence of lytic phages against 32 ESKAPE strains. From the double-layer assay, lytic plaques of variable sizes were picked (Figure 1): 5–8 mm diameter cleared lytic plaques for K. pneumoniae phages, A. baumannii, and K. pneumoniae lytic plaques surrounded by a clear zone (Figure 1A); 1–2 mm diameter cleared lytic plaques for E. cloacae phages, P. aeruginosa, and A. baumannii bacteriophages (Figure 1B,C); and punctiform to 2 mm diameter cleared lytic plaques for S. aureus bacteriophages (Figure 1D).
Based on this algorithm, a total of 66 plaques against S. aureus, 18 plaques against K. pneumoniae, 99 plaques against A. baumannii, 12 plaques against P. aeruginosa, and 16 plaques against E. cloacae were selected. No phages were isolated for the E. faecium strains (Table 2, Table 3 and Table 4).
From the ten municipal wastewater samples, phages with lytic activity against the S. aureus IIH-145 and IIH-108; K. pneumoniae IIH-97.2, IIH-126, IIH-155, and ATCC BAA 1705; A. baumannii 20/403 and 21/432; P. aeruginosa ATCC27853 and PA10; and E. cloacae IIH 141, IIH142, 04, and 08 strains were selected (Table 2).
From the three hospital wastewater samples, phages with lytic activity against the S. aureus IIH-145 and IIH-108; K. pneumoniae IIH-155 and ATCC BAA 1705; A. baumannii 20/403 and 21/432; P. aeruginosa PA7; and E. cloacae IIH 141, IIH142, 04, and 08 strains were selected (Table 3).
From the nine flowing water samples, phages with lytic activity against the S. aureus IIH-145 and IIH-108, and A. baumannii 20/403 and 21/432 strains were selected. No phages with lytic activity against E. faecium, K. pneumoniae, P. aeruginosa, or E. cloacae were selected (Table 4).
Finally, after the preliminary lytic activity evaluation, eight lytic phages against the S. aureus strains, collected from flowing water (M16 and M19), hospital wastewater (M13), and municipal wastewater (M12) samples; ten lytic phages against the K. pneumoniae strains, collected from municipal wastewater (M1 and M2) and hospital wastewater (M10 and M11) samples; six lytic phages against the A. baumannii strains, collected from municipal wastewater (M1, M3, M5, M7, and M8) and hospital wastewater (M10) samples; two lytic phages against the P. aeruginosa strains, collected from municipal wastewater (M2) samples; and five lytic phages against the E. cloacae strains, collected from municipal wastewater (M2) and hospital wastewater (M10) samples were present.

4. Discussion

At present, some institutions have readily available phages and phage cocktails. However, bacteria in general have a biogeographical structure, and variants of bacterial pathogens can differ among human populations. Therefore, phages isolated from one geographic region are not likely—or are less likely—to be effective against bacterial strains from another geographic area [43,44,45]. Hence, isolating new phages is necessary for current or newly emerging pathogenic strains in different geographic regions [44].
The start of an infection involves bacteriophages being adsorbed into the host cell via interactions between the phage’s binding proteins and the host cell’s receptors. The location of these receptors varies with different phages and hosts, and they can be found on the walls of Gram-positive and Gram-negative bacteria, as well as on bacterial capsules and appendages like pili and flagella. In the present study, the principal challenge was to isolate phages using clinical strains, which represent bacteria from an exogenous niche. Another point to consider in phage isolation is the nature of the receptors, which could be polysaccharides, proteins, or sugar moieties. The diversity in receptors and structures represents the variety of mechanisms developed by phages and their hosts to overcome the evolutionary strategies adopted by their counterparts. More than one receptor may be involved in the adsorption process, giving phages an advantage in finding their cell receptor, especially when isolating phages from exogenous strains. This work ensured the isolation of bacteriophages with lytic activity against different ESKAPE group strains (Table 2, Table 3 and Table 4) [18].
In this work, several lytic plaques were selected according to their size and clarity (opacity); these features allow the lytic activity of different plaques to be selected and evaluated (Figure 1). The selected lytic plaques produced by S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and E. cloacae bacteriophages are circular and clear and have variable sizes, from punctiform to 8 mm (Figure 1A–D), with special features, such as a clear halo surrounding the lytic plaque presented by A. baumannii and K. pneumoniae bacteriophages (Figure 1A). This clear zone is due to the presence of polysaccharide depolymerases (PSDs), which allow phages to degrade bacterial barriers consisting of capsular polysaccharides (CPSs), exopolysaccharides (EPSs), and lipopolysaccharides (LPSs) and allow virions to reach the adsorption receptors found on cell-envelope surfaces [46,47]. Depolymerases are structural components of the adsorption apparatus (tail fibers, tail spikes, baseplates, or neck proteins) and can be divided into two groups, lyases and hydrolases, that are released as free enzymes upon phage-induced lysis from within. It could also be due to the over-production of proteins that do not end up being incorporated into virions or the use of alternative start codons in their translation that result in the production of both soluble and virion-associated forms. Both unincorporated forms can freely diffuse, causing polysaccharide degradation that is phenotypically identified as a halo zone around the plaque [46,48].
Phages control the abundance of bacteria in all habitats so they can impact the diversity of bacterial communities, ensuring ecological equilibrium; thus, phages play major roles in biogeochemical cycling by short-circuiting the flow of carbon through bacterial killing, known as the viral shunt. Phages are also modulators of the human gut, where they predominantly exist in lysogens, which can affect the physiology and metabolism of their host [49,50]. As seen in the present work, most of the isolated phages are presumptively lysogenic (Table 2, Table 3 and Table 4) compared with phages with presumptively lytic activity.
Because phages are dependent on host cells to replicate, they can be found wherever target prokaryotes are found, which could be considered an indirect measure of the presence of a microorganism. Wastewater contains complex consortiums of pathogenic and nonpathogenic microorganisms, chemical compounds, heavy metals, and other potentially hazardous substances [51]. While numerous studies and reviews have examined phages in their natural environments, less attention has been given to the key role of phages in artificial environments, such as wastewater effluents [50].
Pseudomonas spp., Acinetobacter spp., Enterobacter spp., and Staphylococcus spp. are ubiquitous bacterial genera associated with a variety of environmental habitats that encompass species isolated worldwide; for that reason, finding phages in wastewater samples and flowing water is usually easy. These genera comprise species that could cause human infections, specifically P. aeruginosa, A. baumannii, K. pneumoniae, E. cloacae, and S. aureus [52,53,54,55].
Isolate phages from wastewater and flowing water are capable of infecting those microorganisms, meaning that those environments are closely associated with human activity. Additionally, because phages are present in these environments and coexist with their bacterial hosts, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and E. cloacae can also be assumed to be present in the studied environments (Table 3 and Table 4), with these microbial communities potentially impacting human health and the environment upon discharge of wastewater into the receiving environment [56].
The isolation of lysogenic phages against P. aeruginosa, A. baumannii, and S. aureus strains was also achieved in flowing water (Table 4), even though only S. aureus lytic phages were selected; therefore, they can also represent an option for bacteriophage isolation even though groups of researchers have mostly achieved the isolation of bacteriophages against ESKAPE pathogens from wastewater samples.
The failure to isolate E. faecium phages in the water samples of this study may be due to the evolution of strategies by these bacteria to avoid recognition by bacteriophages or to interference with phage replication inside the host. Thus, evaluating the mechanisms that could limit phage adsorption on the cell surface or understanding the defensive strategies that bacteria employ to avoid phage replication becomes necessary. These approaches include abortive infection, assembly interference and capsid piracy, DNA degradation by the RM system, CRISPR-CAS, injection block, or/and prevention of receptor recognition [57,58,59].
To our knowledge, this is the first work in Mexico that intentionally seeks to isolate bacteriophages with lytic activity using strains belonging to the ESKAPE group that have been isolated from patients with healthcare-associated infections in hospitals in Mexico City using water samples collected from Mexico City, Veracruz, Oaxaca, and Guerrero State. The phages isolated in this work are part of a phage library that is being characterized to ensure the safety and security of phages prior to their use in clinical practice. The subsequent steps for advancing the isolated bacteriophages toward clinical application should involve several key considerations. The efficiency of bacterial lysis should be prioritized by selecting phages that demonstrate rapid and effective killing with a high burst size. Only strictly lytic phages should be considered, as temperate phages that integrate into bacterial genomes should be avoided. Stability studies are also required to ensure that phages retain their activity until use. Bioinformatic analyses should be employed to screen for phages devoid of antimicrobial resistance genes and virulence factors. In vivo testing in animal models needs to be conducted to assess the safety, potential immune responses, and optimal dosing regimens. Clinical trials should then be designed to evaluate the efficacy of phages in treating specific infections, with attention paid to infection type, dosage, and administration route [60,61,62]. Addressing regulatory challenges is also crucial, and ongoing efforts should aim to establish standardized methods and guidelines to support the clinical use of phage therapy. These measures are collectively required to ensure that phages are both effective and safe for therapeutic applications [63].

5. Conclusions

The increase in antimicrobial resistance, especially of ESKAPE pathogens, has led to the resumption of studies on "forgotten" techniques such as phage therapy. Thus, to combat these infections, it is necessary to create and increase local biobanks with bacteriophages capable of infecting the microbiota of a given region. To achieve this goal, the exploration of local reservoirs that contribute to the creation of these biobanks is also necessary. We demonstrated that local sources of wastewater could be a suitable source of isolate phages that infect ESKAPE strains isolated from patients in a hospital in Mexico City. Because microorganisms can have a biogeographical structure, it is important to look for local sources from which to isolate phages capable of infecting local pathogens.

Author Contributions

Conceptualization, S.F.M.D., J.L.H. and M.G.A.A.; data curation, A.A.L.P., I.L.B.M., S.F.M.D. and M.G.A.A.; formal analysis, A.A.L.P., I.L.B.M., B.L.G., S.F.M.D., J.L.H. and M.G.A.A.; funding acquisition, M.G.A.A.; methodology, A.A.L.P., I.L.B.M., S.F.M.D. and M.G.A.A.; project administration, M.G.A.A.; supervision, M.G.A.A.; writing—original draft, A.A.L.P. and M.G.A.A.; writing—review and editing, S.F.M.D. and J.L.H. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the ‘Secretaría de Investigación y Posgrado del Instituto Politécnico Nacional’, project numbers 2208, 20221544, 20221693, 20230999, and 20231021, and by the student innovation projects 2021–2022 and 2023–2024. M.G.A.A., J.L.H., and S.F.M.D. received support from COFAA, EDI, and SNI. A.A.L.P., I.L.B.M., and B.L.G. received CONACHyT and/or BEIFI fellowships.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The raw data supporting the conclusions of this article will be made available by the authors on request.

Acknowledgments

The authors thank Norma Velazquez Guadarrama for providing some P. aeruginosa strains and Alejandra Aquino Andrade for providing the E. cloacae and K. pneumoniae strains.

Conflicts of Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Microbiolres 15 00098 g001
Figure 1. Double-layer assay for phage isolation. The plate shows the selected lytic plaque morphotypes. (A) Lytic plaques of K. pneumoniae bacteriophages, with clear plaques surrounded by a clear zone, ranging in size from 5 to 8 mm with well-defined boundaries. (B) Lytic plaques of P. aeruginosa bacteriophages, with clear plaques, ranging in size from 1 to 2 mm with well-defined boundaries. (C) Lytic plaques of E. cloacae bacteriophages, with clear plaques ranging in size from 1 to 3 mm with well-defined boundaries. (D) Lytic plaques of S. aureus bacteriophages, with clear plaques ranging in size from punctiform to 1 mm with well-defined boundaries.
Figure 1. Double-layer assay for phage isolation. The plate shows the selected lytic plaque morphotypes. (A) Lytic plaques of K. pneumoniae bacteriophages, with clear plaques surrounded by a clear zone, ranging in size from 5 to 8 mm with well-defined boundaries. (B) Lytic plaques of P. aeruginosa bacteriophages, with clear plaques, ranging in size from 1 to 2 mm with well-defined boundaries. (C) Lytic plaques of E. cloacae bacteriophages, with clear plaques ranging in size from 1 to 3 mm with well-defined boundaries. (D) Lytic plaques of S. aureus bacteriophages, with clear plaques ranging in size from punctiform to 1 mm with well-defined boundaries.
Microbiolres 15 00098 g001
Table 1. Antimicrobial profiles of the strains used in phage isolation.
Table 1. Antimicrobial profiles of the strains used in phage isolation.
Host SpeciesStrainSource IsolationAntimicrobial Profile
E. faeciumIIH-109.3Catheter tipβ-LacR, CEP-2 gR, CEP-3 gR, NITR MDR
IIH-160Sore skinβ-LacR, CEP-2 gR, CEP-3 gR, GLPR MDR
IIH-41.5Catheter tipβ-LacR, CEP-2 gR, CEP-3 gR, GLPR, NITRMDR
IIH-168.5Catheter tipβ-LacR, AMGR, CEP-2 gR, CEP-3 gR, NITRMDR
IIH-168.2Catheter tipβ-LacR, AMGR, CEP-2 gR, CEP-3 gR, NITRMDR
IIH-132Catheter tipβ-LacR, CEP-2 gR, CEP-3 gR, GLPR, NITRMDR
IIH-98Dialysis fluidβ-LacR, AMGR, CEP-2 gR, CEP-3 gR, GLPR, NITRMDR
IIH-140Catheter tipβ-LacR, CEP-2 gR, CEP-3 gR, GLPR, NITRMDR
S. aureusIIH-107Catheter tipβ-LacR, FQR, MCLR, LICRMDR
IIH-6Dialysis fluidFQRS
IIH-145UlcerFQR, MCLR, LICRMDR
IIH-108Woundβ-LacR, FQR, MCLR, LICR MDR
K. pneumoniaeIIH-126Wound infectionPENR, β-LacRS
IIH-155Bronchial secretionPENR, β-LacRS
IIH-97.2Catheter tipPENRS
ATCC BAA1705UrinePENR, β-LacR, β-Lac/InhR, CEP-1 gR, CEP-2 gR, CEP-3 gR, CEP-4 gR, CARR, AMGR, FQR, NITRMDR
A. baumanniiAB 21/432Data not providedPENR, CEP-2 gR, CEP-3 gR, CEP-4 gR, MONOR, CARR, FQRMDR
AB 20/403Pedriatric neurologyPENR, CEP-2 gR, CEP-3 gR, CEP-4 gR, MONOR, CARRMDR
AB BAA747Ear pusPENR, CEP-1 gR, CEP-2 gR MDR
AB 10/289Coronary Care UnitPENR, CEP-1 gR, CEP-2 gR, CEP-3 gR, CEP-4 gR, CARRMDR
P. aeruginosaPA IIH-97Bronchial secretionAMGR, CEP-3 gR, CEP-4 gRMDR
ATCC27853Blood cultureAMGRS
PA IIH-78Catheter tipAMGR, CEP-3 gR, CEP-4 gRMDR
PA IIH-66Catheter tipAMGR, CEP-3 gR, CEP-4 gRMDR
PA1Surgery serviceAMGR, CARR, CEP-3 gR, FQR, β-Lac/InhR, MCLR, FOSR MDR
PA4UrgencyAMGR, CARR, CEP-3 gR, FQR, β-Lac/InhR, MCLR, FOSRMDR
PA7Pediatric serviceAMGR, CARR, CEP-3 gR, FQR, MCLR, FOSRMDR
PA10Cardiology AMGR, CARR, CEP-3 gR, FQR, MCLR, FOSRMDR
E. cloacaeIIH-41Blood cultureAMGR, CEP-2 gR S
IIH-42Blood cultureAMGR, CEP-2 gRS
04Pediatric serviceAMGR, CEP-2 gR, CEP-3 gR, CARRMDR
08Pediatric serviceAMGR, CEP-2 gR, CEP-3 gR, SFNRMDR
AMG: Aminoglycosides, FQ: Fluoroquinolone, MCL: Macrolide, OZL: Oxazolidinone, GLP: Glycopeptide, TET: Tetracycline, GLC: Glycylcyclines, NIT: Nitrofuran, LIC: Lincosamide, STP: Streptogramins, RIF: Rifamycin, SFN: Sulfonamide, CAR: Carbapenems, PEN: Penicillin, MONO: Monobactams, POLY: Polymyxin, FOS: Phosphonates, CEP-1 g: second-generation Cephalosporins, CEP-2 g: second-generation Cephalosporins, CEP-3 g: third-generation Cephalosporins, CEP-4 g: fourth-generation Cephalosporins, β-Lac: β-lactamic, β-Lac/Inh: β-lactamic/inhibitors of β-lactamases, MDR: multi-drug resistant, S: susceptible.
Table 2. Number of presumptively different bacteriophages per sample obtained from municipal wastewater.
Table 2. Number of presumptively different bacteriophages per sample obtained from municipal wastewater.
SampleStaphylococcus aureusKlebsiella pneumoniaeAcinetobacter baumanniiPseudomonas aeruginosaEnterobacter cloacae
IIH-145IIH-108IIH-97.2IIH-126IIH-155ATCC BAA 170520/40321/432ATCC 27853PA10IIH-141IIH-1420408
M122 3 22
M2 332123222222
M323 24
M423 22
M5 2 23
M623 22
M723 32
M811 22
M923 21
M1223 32
Total152333512223222222
Notes. No phages were isolated for the Enterococcus faecium strains. Only strains that led to the isolation of bacteriophages are presented.
Table 3. Number of presumptively different bacteriophages per sample obtained from hospital wastewater.
Table 3. Number of presumptively different bacteriophages per sample obtained from hospital wastewater.
SampleStaphylococcus aureusKlebsiella pneumoniaeAcinetobacter baumanniiPseudomonas aeruginosaEnterobacter cloacae
IIH-145IIH-108IIH-155ATCC 170520/40321/432Pa7IIH-141IIH-1420408
M10 2212343212
M11113 324
M1312 32
Total2551878
Notes. No phages were isolated for the Enterococcus faecium strains. Only strains that led to the isolation of bacteriophages are presented.
Table 4. Number of presumptively different bacteriophages per sample isolated from flowing water.
Table 4. Number of presumptively different bacteriophages per sample isolated from flowing water.
SampleStaphylococcus aureusAcinetobacter baumannii
IIH-145IIH-10820/40321/432
M141222
M151222
M161323
M171222
M18 22
M19 222
M201132
M211123
M221122
Total7141920
Notes. No phages were isolated for the Enterococcus faecium, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter cloacae strains. Only strains that led to the isolation of bacteriophages are presented.
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Loera Piedra, A.A.; Becerra Mejía, I.L.; Luna Galicia, B.; Martínez Díaz, S.F.; Luna Herrera, J.; Aguilera Arreola, M.G. Exploring Local Reservoirs for Bacteriophages with Therapeutic Potential against ESKAPE Pathogens. Microbiol. Res. 2024, 15, 1459-1470. https://doi.org/10.3390/microbiolres15030098

AMA Style

Loera Piedra AA, Becerra Mejía IL, Luna Galicia B, Martínez Díaz SF, Luna Herrera J, Aguilera Arreola MG. Exploring Local Reservoirs for Bacteriophages with Therapeutic Potential against ESKAPE Pathogens. Microbiology Research. 2024; 15(3):1459-1470. https://doi.org/10.3390/microbiolres15030098

Chicago/Turabian Style

Loera Piedra, Alejandra Aidee, Isamar Leticia Becerra Mejía, Brenda Luna Galicia, Sergio Francisco Martínez Díaz, Julieta Luna Herrera, and Ma. Guadalupe Aguilera Arreola. 2024. "Exploring Local Reservoirs for Bacteriophages with Therapeutic Potential against ESKAPE Pathogens" Microbiology Research 15, no. 3: 1459-1470. https://doi.org/10.3390/microbiolres15030098

APA Style

Loera Piedra, A. A., Becerra Mejía, I. L., Luna Galicia, B., Martínez Díaz, S. F., Luna Herrera, J., & Aguilera Arreola, M. G. (2024). Exploring Local Reservoirs for Bacteriophages with Therapeutic Potential against ESKAPE Pathogens. Microbiology Research, 15(3), 1459-1470. https://doi.org/10.3390/microbiolres15030098

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