Citations

ABSTRACT The optimal phage susceptibility testing (PST) method is unclear. Here, two PST methods were compared using Pseudomonas aeruginosa isolates recovered from patients with cystic fibrosis enrolled in a placebo-controlled clinical trial of a single intravenous dose of a four-phage cocktail (WRAIR-PAM-CF1). In total, 508 P. aeruginosa sputum isolates were evaluated, including isolates collected before or after phage or placebo treatment, isolates from the same trial participants over time, and isolates of different colony morphologies from the same participants at the same time point. Susceptibility to phages PaWRA01Φ11, PaWRA01Φ39, PaWRA02Φ83, and PaWRA02Φ87 and a cocktail of all four phages was assessed using a plaque assay (PA) and a Biolog Omnilog-based liquid assay (LA) with the same bacterial inoculum. A total of 170/508 isolates (33%) and 195/508 isolates (38%) were identified as susceptible to the cocktail by PA and LA, respectively. Among the susceptible isolates, 169/170 (99%; PA) and 187/195 (96%; LA) also tested susceptible to at least one of the four phages in the cocktail. Susceptible percent agreement between the PA and LA ranged from 76% to 100% and non-susceptible percent agreement ranged from 89% to 100% for all phages studied and the cocktail. Phage PaWRA02Φ83 demonstrated the greatest individual activity, with 164/508 (32%) and 188/508 (37%) isolates testing susceptible by PA and LA, respectively. The four-phage cocktail provided numerically broader coverage of P. aeruginosa (i.e., had the highest susceptibility rate) than did any single phage. There was high concordance between PST results by PA and LA. IMPORTANCE Standardization of phage susceptibility testing (PST) methods is essential to support phage therapy trials and any future clinical implementation. There are no standardized PST methods or interpretive criteria for PST. In this study, PST was performed by a plaque assay and a Biolog Omnilog-based liquid assay on Pseudomonas aeruginosa isolates recovered from cystic fibrosis patients enrolled in a clinical trial. Susceptibility of 508 isolates to four phages and a cocktail of all four was evaluated. There was high concordance between susceptibility assessed by plaque and liquid assays and numerically broader coverage of P. aeruginosa by the cocktail compared to any single phage. This manuscript should be of interest to those performing PST.

Abstract Background Staphylococci are the most frequent microorganisms in periprosthetic joint infection (PJI) and treatment remains challenging. Phage is being considered as a potential treatment. Here, the in vitro activity of phages SaMD07FSphi1or SaNSI1469phi1, alone and in combination with vancomycin against staphylococcal biofilms was evaluated. Figure 1 In vitro activity of phage SaMD07FSphi1 against S. aureus and S. epidermidis biofilms Figure 2 In vitro activity of phage SaNSI1469phi1 against S. aureus and S. epidermidis biofilms Methods Biofilms were grown at 37°C on 4 cm stainless steel K-wires in tryptic soy broth (TSB) with 106 cfu/ml of S. epidermidis or S. aureus (8 PJI isolates with phage activity against planktonically-grown bacteria). After 24 h, 3 K-wires were quantitatively cultured to define pre-treatment bacterial loads, with the remaining assigned to one of four treatment groups: TSB, phage (4 x 106 plaque forming units/ml), vancomycin (16 µg/ml) or phage/vancomycin. K-wires were incubated for 6 or 24 h at 37°C, rinsed, sonicated, and quantitatively cultured. Testing was performed in triplicate and on 3 separate days and mean log10 cfu/K-wire reduction factors (LRFs) versus TSB calculated. Results Phage SaMD07FSphi1 (Figure 1) plus vancomycin showed LRFs of 2.8 (p, 0.0003) and 2.3 (p, 0.0177) log10 cfu/K-wire at 24 h for S. aureus IDRL-6121 and S. aureus IDRL-8454, respectively, whereas phage alone showed was 3.1 (p, 0.0003) and 3.0 (p, 0.0003), respectively. All treatments were ≤1.0 log10 cfu/K-wire 24 h LRFs for S. aureus IDRL-6175, S. epidermidis IDRL-5966 and S. epidermidis IDRL-6108.This phage plus vancomycin showed LRFs of 0.6 log10 cfu/K-wire at 6 h for S. epidermidis IDRL-5966 and S. aureus IDRL-6175, with bacterial regrowth at 24 h. Phage SaNSI1469phi1 (Figure 2) plus vancomycin showed 24 h LRFs of 2.0 (p, 0.02) and 3.2 (p, 0.003) log10 cfu/K-wire for S. epidermidis IDRL-6955 and S. aureus IDRL-7299, respectively, whereas phage alone was 0.2 (p, 0.17) and 0.5 (p, 0.03) log10 cfu/K-wire, respectively. All treatments showed ≤1.0 log10 cfu/K-wire 24-hour LRFs log10 cfu/K-wire for S. epidermidis IDRL-10273. This phage alone showed 6 h LRFs of 1.0 and 1.3 for S. epidermidis IDRL-6955 and S. aureus IDRL-7299, with bacterial regrowth at 24 h. Conclusion Phages SaMD07FSphi1 and SaNSI1469phi1 alone and with vancomycin showed activity against staphylococcal biofilms formed by 4 isolates. Increased activity was observed at 6 h in some cases, with bacterial regrowth at 24 h. Disclosures Robin Patel, MD, a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection: a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection|MicuRx Pharmaceuticals and bioMérieux: Grant/Research Support|PhAST, Day Zero Diagnostics, DEEPULL DIAGNOSTICS, S.L., Nostics, HealthTrackRx, bioMérieux and CARB-X: Advisor/Consultant|Up-to-Date and the Infectious Diseases Board Review Course: Honoraria

Background: Phages are being assessed for treatment of periprosthetic joint infection (PJI). Staphylococci are the most common cause of PJI. Phages are traditionally considered to be strain-specific and restricted to specific species. We aimed to assess the in vitro activity of a collection of staphylococcal phages against a selection of clinical Staphylococcus isolates recovered from PJI over a 20-year period. Methods: The activity of 37 staphylococcal phages was evaluated against 204 staphylococcal isolates, including 102 Staphylococcus aureus, 81 Staphylococcus epidermidis , and 21 Staphylococcus lugdunensis , using a tetrazolium dye–based metabolic assay. Standardized inocula of bacteria and phage were incubated over 48 hours. Growth inhibition ≥8 hours was considered indicative of phage activity. Results: A total of 7,548 phage-isolate pairs were assessed. Overall, 31 of 37 phages had activity against at least 1 isolate. The most broadly active phage showed activity against 50 of 195 isolates (26%) tested. Twenty-three phages showed cross-species activity, with 11 phages active against all 3 Staphylococcus species, and 12 phages active against 2 species. Of all S. aureus isolates tested, 61% were susceptible to at least 1 phage, while 31% and 76% of S. epidermidis and S. lugdunensis isolates were susceptible to at least 1 phage, respectively. Conclusions: This is the largest library of phages evaluated against staphylococci from PJI. Results show that staphylococcal phages can have cross-species activity, suggesting that phage libraries may offer cross-species coverage of clinically encountered staphylococcal isolates from PJI. Level of Evidence: Level V . Mechanism-based reasoning. See Instructions for Authors for a complete description of levels of evidence.

ABSTRACT The genomic sequences of seven phages isolated from municipal sewage in Rochester, Minnesota, USA, using Klebsiella pneumoniae strains ( bla KPC carriers) as hosts are reported. These phages are lytic and belong to the Ackermannviridae, Drexlerviridae , and Zobellviridae families. No known antimicrobial resistance or virulence genes were found within their genomes.

ABSTRACT Phage therapy has not been established in the clinical routine, in part due to uncertainties concerning efficacy and immunogenicity. Here, three rabbits were immunized against staphylococcal phage K to assess viral potency in the presence of immunized serum. Three rabbits received weekly intramuscular injections of ~10 10±1 pfu/mL phage K. Phage K-specific IgG formation was measured by an enzyme-linked immunosorbent assay (ELISA); phage inactivation was assessed by calculating K-rates. Using transmission electron microscopy (TEM) and immunogold labeling, antibody binding to phage K was visualized. This was numerically assessed by objective imaging analysis comparing the relative distances of each gold particle to the nearest phage head and tail structure. Immunization led to a strong IgG response, plateauing 7 days after the last phage injection. There was no significant correlation between K-rate and antibody titer over time. TEM showed IgG binding to the head structure of phage K. Image analysis showed a significant reduction in relative distances between antibodies and phage head structures when comparing samples from day 0 and day 28 ( P < 0.0001). These results suggest that while individual serum analysis for antibodies against therapeutic phage bears consideration prior to and with prolonged therapy, during phage application, the formation of specific antibodies against phage may only partially explain decreased phage potency in the presence of immunized serum. Instead, other factors may contribute to an individual’s “humoral receptiveness” to phage therapy. Future investigations should be directed toward the identification of the humoral factors that have the most significant predictive value on phage potency in vivo .

Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA) biofilms can be resilient to the human immune system and antibiotics, a challenge augmented by acquired antimicrobial resistance. Phage therapy is being evaluated for biofilm-associated infections. Methods Here, model phages SaMD07ø1 and SaRB105030ø5 were evaluated against their hosts SaMD07 and SaRB105030, respectively, grown as biofilms in 96-well plates, as biofilms on glass beads and planktonically. Trypticase soy broth (TSB) and phosphate buffered saline (PBS) were evaluated as testing media (Figure 1). Biofilms were incubated with phages in the presence of media containing tetrazolium dye in 96-well plates and assessed for hold times (delays in reaching bacterial log-phase metabolic activity compared to controls) over 48 hours (h) using a Biolog Omnilog® system and by assessing colony forming units (CFUs). Subsequently, using the beads biofilm assay in TSB medium performed on the Omnilog® (BBTO) (Figure 2), test phage SaMD22ø1 was evaluated in quintuplicate against biofilms formed by MRSA isolates IDRL-6130, IDRL-6927, IDRL-6987, IDRL-7381, IDRL-7542 and IDRL-10947, all recovered from periprosthetic joint infection. Test phage K was evaluated against GFP-labelled MRSA AH1263 using BBTO method and simultaneously by fluorescence microscopy.Figure 1.Biofilm phage susceptibility testing methods evaluated (created with BioRender.com)Figure 2.Biofilm phage susceptibility testing using biofilms grown on beads assessed in TSB medium using the Omnilog® (BBTO) method with phage SaMD22ø1. Results A comparison of result of testing of biofilms in wells and on beads and against planktonic bacteria is shown in Figure 3. Phage SaMD07ø1 showed no growth at 4 h; whereas phage SaRB105030ø5 showed ∼1-log decrease in CFUs at 4 h and ∼3-log decrease in CFUs at 8 h (Figure 3). BBTO hold-times of 37, 28 and 15 h were observed for phages SaMD07ø1, SaRB105030ø5 and phage K respectively. Phage SaMD22ø1 had an average hold time of 9 h and showed hold times &gt;6 hours for all isolates tested (Figure 4). Microscopic inspection showed eradication of GFP-labelled MRSA biofilm by phage K (Figure 5).Figure 3.Results of quantitative culture of biofilms treated with phages SaMD07ø1 and SaRB105030ø5 in TSB medium.Panel 1 shows results of phage SaMD07ø1 with biofilms grown in wells (1a), on beads (1b) and planktonically (1c). Panel 2 shows results of phage SaRB105030ø5 with biofilms grown in wells (2a), on beads (2b) and planktonically (2c).Figure 4.Activity of phage SaMD22ø1 against biofilms formed by six MRSA strains determined using the Omnilog® (BBTO) method. The solid blue line indicates a hold time of 8 hours.Figure 5.Efficacy of Phage K to efficiently eradicate GFP-labelled MRSA strain AH1263 observed under the fluorescence microscope at 40X magnification. The authors are thankful to Dr. Alexander Horswill at University of Colorado for providing the GFP-labelled MRSA strain. Conclusion In conclusion, BBTO is a promising method for testing biofilm phage susceptibility although clinical correlation and testing of larger numbers of phage and bacterial isolates are needed. Disclosures Joseph Fackler, n/a, Adaptive Phage Therapeutics, Inc: Employee|Adaptive Phage Therapeutics, Inc: Stocks/Bonds John M. Sowers, n/a, Adaptive Phage Therapeutics: Employee|Adaptive Phage Therapeutics: Stocks/Bonds Robin Patel, MD, Abbott Laboratories: Advisor/Consultant|Adaptive Phage Therapeutics: Grant/Research Support|Adaptive Phage Therapeutics: Mayo Clinic has a royalty-bearing know-how agreement and equity in Adaptive Phage Therapeutics.|BIOFIRE: Grant/Research Support|CARB-X: Advisor/Consultant|ContraFect: Grant/Research Support|Day Zero Diagnostics: Advisor/Consultant|HealthTrackRx: Advisor/Consultant|Mammoth Biosciences: Advisor/Consultant|Netflix: Advisor/Consultant|Oxford Nanopore Technologies: Advisor/Consultant|PhAST: Advisor/Consultant|See details: Patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic|See details: continued, patent on an anti-biofilm substance issued|TenNor Therapeutics Limited: Grant/Research Support|Torus Biosystems: Advisor/Consultant|Trellis Bioscience, Inc.: Advisor/Consultant

ABSTRACT Standardized approaches to phage susceptibility testing (PST) are essential to inform selection of phages for study in patients with bacterial infections. There is no reference standard for assessing bacterial susceptibility to phage. We compared agreement between PST performed at three centers: two centers using a liquid assay standardized between the sites with the third, a plaque assay. Four Pseudomonas aeruginosa phages: PaWRA01ø11 (EPa11), PaWRA01ø39 (EPa39), PaWRA02ø83 (EPa83), PaWRA02ø87 (EPa87), and a cocktail of all four phages were tested against 145 P . aeruginosa isolates. Comparisons were made within measurements at the two sites performing the liquid assay and between these two sites. Agreement was assessed based on coverage probability (CP 8 ), total deviation index, concordance correlation coefficient (CCC), measurement accuracy, and precision. For the liquid assay, there was satisfactory agreement among triplicate measurements made on different days at site 1, and high agreement based on accuracy and precision between duplicate measurements made on the same run at site 2. There was fair accuracy between measurements of the two sites performing the liquid assay, with CCCs below 0.6 for all phages tested. When compared to the plaque assay (performed once at site 3), there was less agreement between results of the liquid and plaque assays than between the two sites performing the liquid assay. Similar findings to the larger group were noted in the subset of 46 P . aeruginosa isolates from cystic fibrosis. Results of this study suggest that reproducibility of PST methods needs further development.

Abstract Clinical research networks conduct important studies that would not otherwise be performed by other entities. In the case of the Antibacterial Resistance Leadership Group (ARLG), such studies include diagnostic studies using master protocols, controlled phage intervention trials, and studies that evaluate treatment strategies or dynamic interventions, such as sequences of empiric and definitive therapies. However, the value of a clinical research network lies not only in the results from these important studies but in the creation of new approaches derived from collaborative thinking, carefully examining and defining the most important research questions for clinical practice, recognizing and addressing common but suboptimal approaches, and anticipating that the standard approaches of today may be insufficient for tomorrow. This results in the development and implementation of new methodologies and tools for the design, conduct, analyses, and reporting of research studies. These new methodologies directly impact the studies conducted within the network and have a broad and long-lasting impact on the field, enhancing the scientific value and efficiency of generations of research studies. This article describes innovations from the ARLG in diagnostic studies, observational studies, and clinical trials evaluating interventions for the prevention and treatment of antibiotic-resistant bacterial infections.

AbstractIn this overview, we describe important contributions from the Antibacterial Resistance Leadership Group (ARLG) to patient care, clinical trials design, and mentorship while outlining future priorities. The ARLG research agenda is focused on 3 key areas: gram-positive infections, gram-negative infections, and diagnostics. The ARLG has developed an innovative approach to clinical trials design, the desirability of outcome ranking (DOOR), which uses an ordinal measure of global outcome to assess both benefits and harms. DOOR was initially applied to observational studies to determine optimal dosing of vancomycin for methicillin-resistant Staphylcococcus aureus bacteremia and the efficacy of ceftazidime-avibactam versus colistin for the treatment of carbapenem-resistant Enterobacterales infection. DOOR is being successfully applied to the analysis of interventional trials and, in collaboration with the US Food and Drug Administration (FDA), for use in registrational trials. In the area of diagnostics, the ARLG developed Master Protocol for Evaluating Multiple Infection Diagnostics (MASTERMIND), an innovative design that allows simultaneous testing of multiple diagnostic platforms in a single study. This approach will be used to compare molecular assays for the identification of fluoroquinolone-resistant Neisseria gonorrhoeae (MASTER GC) and to compare rapid diagnostic tests for bloodstream infections. The ARLG has initiated a first-in-kind randomized, double-blind, placebo-controlled trial in participants with cystic fibrosis who are chronically colonized with Pseudomonas aeruginosa to assess the pharmacokinetics and antimicrobial activity of bacteriophage therapy. Finally, an engaged and highly trained workforce is critical for continued and future success against antimicrobial drug resistance. Thus, the ARLG has developed a robust mentoring program targeted to each stage of research training to attract and retain investigators in the field of antimicrobial resistance research.