Journal: bioRxiv

Article Title: Joint antibiotic and phage therapy: addressing the limitations of a seemingly ideal phage for treating Staphylococcus aureus infections

doi: 10.1101/2020.04.24.060335

Figure Lengend Snippet: A population dynamic model to account for the observed changes in the densities of bacteria and phage in . The variables, W, S and E are, respectively the wildtype S. aureus Newman, small colonies, and the evolved bacteria, cells per ml, and V the PYO Sa phage, particles per ml. The parameters δ W , δ S and δ E are the adsorption rate constants per cell per ml. The parameters β W , β S and βE are the number of phage particles produced per infected cell burst. We assume that β S =0, the S are infected by PYO Sa but the phage but do not replicate or kill these bacteria. The parameters μ SW , μ WS , μ SE and μ ES are the transition rates, per cell per hour, between the different states.

Article Snippet: Unless otherwise noted, all experiments were performed from derivatives of the parent strain S. aureus Newman (ATCC 25904).

Techniques: Bacteria, Adsorption, Produced, Infection

Journal: bioRxiv

Article Title: Joint antibiotic and phage therapy: addressing the limitations of a seemingly ideal phage for treating Staphylococcus aureus infections

doi: 10.1101/2020.04.24.060335

Figure Lengend Snippet: Concentrations of the different antibiotics in μg/ml (RIF 0.02, OXA 3, CIP 0.5, VAN 8, DAP 64, KAN 46), corresponding to minimum bacteriocidal concentrations. A. The ratio of the change in density of S. aureus after 24 hours of exposure to antibiotics, antibiotics and phage, or phage alone. Hash red, the density of S. aureus recovered was below the detection limit, ~10 2 per ml. B. The ratio of the change in the density of PYO Sa after 24 hours of confronting S. aureus Newman in combination with antibiotics or alone.

Article Snippet: Unless otherwise noted, all experiments were performed from derivatives of the parent strain S. aureus Newman (ATCC 25904).

Techniques:

Journal: bioRxiv

Article Title: Joint antibiotic and phage therapy: addressing the limitations of a seemingly ideal phage for treating Staphylococcus aureus infections

doi: 10.1101/2020.04.24.060335

Figure Lengend Snippet: S. aureus antibiotic pharmacodynamics A) Natural log of the change in density of growing cultures of S. aureus Newman exposed to 1.6X and 8X MIC, low and high for 24 hours (1440 minutes). The green and purple lines are experimental changes in density estimated by plating; while the blue and red lines are the results of a linear regression of the changes in density estimated during the first 180 minutes of exposure. B) Changes in the optical density of experimental cultures of S. aureus Newman exposed to 5μg/ml ciprofloxacin, mean and standard error of the ODs for three replicas. In red are cells that were treated with ciprofloxacin and then transferred without the presence of this drug for seven days before the MIC determination was performed. In blue are cells that were treated with ciprofloxacin for one week before the MIC was performed. C, D, E) Simulation Results Common parameters: v MAXS =1.5, v MINS =-0.6,v MAXSR = 1.2, v MINSR =-3, ks=1,kh=1,k=1,e=5.0E-7 C) Changes in the densities of bacteria in serial transfer culture with persistence with parameters in the range estimated for S. aureus in oxacillin. Specific parameters: vp=0.2, MIC S = 1.8, x P =1.0e-4, y P =1E-3, A MAX =3. Exposure to oxacillin does not start until the second transfer (compare to center). D) and E) Heteroresistance for ciprofloxacin MIC S = 0.218, MIC H =1, x= 1E-6, y=1e-3, x P =0, y P =0, A MAX =0.5 Changes in the densities of bacteria in serial transfer culture with heteroresistance with parameters in the range estimated for S. aureus in ciprofloxacin. Exposure to ciprofloxacin doesn’t start until the second transfer (compare to bottom). E) Unique Parameters for E: MIC S = 0.218, MIC H =1, x=1E-6, 1E-3 x P =0, y P =0. Simulation of the changes in the densities of bacteria and average MIC of the antibiotic mixture of the low MIC sensitive and the high MIC heteroresistant populations in serial transfer culture in the absence of the antibiotics.

Article Snippet: Unless otherwise noted, all experiments were performed from derivatives of the parent strain S. aureus Newman (ATCC 25904).

Techniques: Drug discovery, Bacteria

Journal: bioRxiv

Article Title: Joint antibiotic and phage therapy: addressing the limitations of a seemingly ideal phage for treating Staphylococcus aureus infections

doi: 10.1101/2020.04.24.060335

Figure Lengend Snippet: A. Wild type S. aureus and small colony variants visualized. B. Changes in densities of S. aureus Newman and PYO Sa in three independent (red, green, blue) serial transfer experiments diluted 1/100 in fresh media daily. C. Changes in densities of S. aureus Newman and PYO Sa in serial transfer cultures initiated two small colony variants isolated from the 5 th transfer of the cultures with PYO Sa and S. aureus Newman in panel B. D. Changes in densities of S. aureus Newman and PYO Sa in serial transfer cultures initiated with PYO Sa and equal densities of cultures derived from small colonies and the ancestral S. aureus Newman. E. Changes in densities of S. aureus and PYO Sa in serial transfer cultures initiated with PYO Sa and single colonies of evolved (wild-type colony morphology) bacteria isolated from the 5 th transfer of the cultures in panel B. F. Changes in the ratio of bacteria and phage at time 0 and 24 hours. Wild type S. aureus Newman (W), small colony variants (S), and evolved bacteria (E). Three independent replicas.

Article Snippet: Unless otherwise noted, all experiments were performed from derivatives of the parent strain S. aureus Newman (ATCC 25904).

Techniques: Isolation, Derivative Assay, Bacteria

Journal: bioRxiv

Article Title: Joint antibiotic and phage therapy: addressing the limitations of a seemingly ideal phage for treating Staphylococcus aureus infections

doi: 10.1101/2020.04.24.060335

Figure Lengend Snippet: Changes in the densities of bacteria and phage in (1/100) 10 ml serial transfer cultures of S. aureus Newman and PYO Sa and a phage-free control, CON. A) Three independent cultures initiated with S. aureus Newman (W) that had not previously been exposed to PYO Sa . B) Three independent cultures initiated with S. aureus Newman (E) obtained from the 5 th transfer of independent serial passage experiments with S. aureus Newman mixed with PYO Sa .

Article Snippet: Unless otherwise noted, all experiments were performed from derivatives of the parent strain S. aureus Newman (ATCC 25904).

Techniques: Bacteria, Control

Journal: Cell host & microbe

Article Title: Resistin-like molecule α provides vitamin A-dependent antimicrobial protection in the skin

doi: 10.1016/j.chom.2019.04.004

Figure Lengend Snippet: (A,B) S. pyogenes (A) or wild-type or staphyloxanthin-deficient (ΔCRTM) Staphylococcus strains (B) were grown to logarithmic phase and applied on a gauze rectangle to the dorsal skin of Retnla−/− or wild-type mice under occlusion for 2 days. CFU were determined in sections of inoculated skin.

Article Snippet: Relative expression values were determined using the comparative Ct (ΔΔCt) method, and transcript abundances were normalized to Gapdh or 18S transcript abundance. table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-RELMα Life Span Cat# LS-C104472; RRID:AB_2180030 anti-RETN Life Span Cat# LS-C131843–100; RRID:AB_10834395 anti-RELMα Abcam Cat# ab39626, RRID:AB_777652 Alexa Fluor® 594 secondary antibody Thermo Fisher Scientific Cat# {"type":"entrez-nucleotide","attrs":{"text":"R37119","term_id":"794575","term_text":"R37119"}} R37119 , RRID:AB_2556547 Anti-Actin Sigma-Aldrich Cat# A5060, RRID:AB_476738 Bacterial and Virus Strains Staphylococcus aureus ATCC ATCC 25923 Escherichia coli K-12 ATCC ATC-PTA-7555 Pseudomonas aeruginosa ATCC ATCC 27853 Listeria monocytogenes , EGD-e BD Biosciences BD# 237500 Staphylococcus epidermidis , clinical isolate Hooper Lab N/A Streptococcus pyogenes ATCC ATCC12384 Propionibacterium acnes ATCC ATCC 6919 Staphylococcus aureus (parent strain) Dr. George Liu N/A Staphylococcus aureus (ΔCRTM) Dr. George Liu N/A Citrobacter rodentium , DBS100 ATCC ATCC 51459 Biological Samples Human skin tissue-Control samples UT Southwestern Tissue Bank/PI: Ben Chong M.D.

Techniques:

Journal: Cell host & microbe

Article Title: Resistin-like molecule α provides vitamin A-dependent antimicrobial protection in the skin

doi: 10.1016/j.chom.2019.04.004

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Relative expression values were determined using the comparative Ct (ΔΔCt) method, and transcript abundances were normalized to Gapdh or 18S transcript abundance. table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-RELMα Life Span Cat# LS-C104472; RRID:AB_2180030 anti-RETN Life Span Cat# LS-C131843–100; RRID:AB_10834395 anti-RELMα Abcam Cat# ab39626, RRID:AB_777652 Alexa Fluor® 594 secondary antibody Thermo Fisher Scientific Cat# {"type":"entrez-nucleotide","attrs":{"text":"R37119","term_id":"794575","term_text":"R37119"}} R37119 , RRID:AB_2556547 Anti-Actin Sigma-Aldrich Cat# A5060, RRID:AB_476738 Bacterial and Virus Strains Staphylococcus aureus ATCC ATCC 25923 Escherichia coli K-12 ATCC ATC-PTA-7555 Pseudomonas aeruginosa ATCC ATCC 27853 Listeria monocytogenes , EGD-e BD Biosciences BD# 237500 Staphylococcus epidermidis , clinical isolate Hooper Lab N/A Streptococcus pyogenes ATCC ATCC12384 Propionibacterium acnes ATCC ATCC 6919 Staphylococcus aureus (parent strain) Dr. George Liu N/A Staphylococcus aureus (ΔCRTM) Dr. George Liu N/A Citrobacter rodentium , DBS100 ATCC ATCC 51459 Biological Samples Human skin tissue-Control samples UT Southwestern Tissue Bank/PI: Ben Chong M.D.

Techniques: Virus, Recombinant, Protease Inhibitor, Control, Cream, Sample Prep, Reverse Transcription, Purification, Real-time Polymerase Chain Reaction, Chromatin Immunoprecipitation, Expressing, Cloning, Plasmid Preparation, Software, Microscopy