Journal: Antimicrobial Agents and Chemotherapy

Article Title: Unraveling the Gentamicin Drug Product Complexity Reveals Variation in Microbiological Activities and Nephrotoxicity

doi: 10.1128/AAC.00533-20

Figure Lengend Snippet: Microbiological activities of gentamicin congeners against Gram-negative wild-type strains and an isogenic E. coli panel that harbored key aminoglycoside-modifying enzymes

Article Snippet: However, gentamicin C1a had an MIC that was 4-fold more potent than that of the gentamicin mixture, which was significantly different. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Panel Geometric mean MIC value (mg/liter) a Mix b C1a C2 C2a C1 Wild type E. coli ATCC 25922 0.5 0.5 0.5 0.5 0.5 P. aeruginosa ATCC 27853 0.5 0.25 0.25 0.25 1 A. baumannii M2 c 1 0.25 0.5 0.5 2 Isogenic e E. coli ATCC 700926 + empty vector d 0.25 0.125 0.125 0.125 0.125 E. coli ATCC 700926 + aac(6′)-Ib 1 4 0.5 32 0.25 E. coli ATCC 700926 + aac(3)-III 4 2 4 4 32 E. coli ATCC 700926 + aph(3′)-Ia 0.5 0.125 0.25 0.25 0.5 Open in a separate window a MIC values are the geometric mean of multiple independent measurements rounded to the nearest CLSI standard dilution increment. b “Mix” refers to batch of laboratory-grade gentamicin used to purify the gentamicin congeners. c Wild-type A. baumannii M2 has been previously characterized ( 34 ). d Parent E. coli strain containing the empty version of the pBBR1MCS-4 vector ( 35 ) used to carry the aminoglycoside-modifying enzyme genes in the isogenic panel. e Nine additional isogenic E. coli isolates with either aac(6′)-aph(2′′) , aph(3′)-II , aph(3′)-III , aph(3′)-IV , aph(3′)-V , aph(3′)-VII , aac(2′)-I , aac(3)-I , or aac(3)-X were also tested, and the MICs for each congener fell within ±1 log 2 dilution of the gentamicin “Mix” MIC.

Techniques: Plasmid Preparation

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Unraveling the Gentamicin Drug Product Complexity Reveals Variation in Microbiological Activities and Nephrotoxicity

doi: 10.1128/AAC.00533-20

Figure Lengend Snippet: Microbiological activities of laboratory-grade gentamicin compared to artificial mixtures of gentamicin congeners that maximized gentamicin C1 and C2 (artificial mix 1) or minimized gentamicin C1 and C2 (artificial mix 2) within USP allowable ranges

Article Snippet: However, gentamicin C1a had an MIC that was 4-fold more potent than that of the gentamicin mixture, which was significantly different. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Panel Geometric mean MIC value (mg/liter) a Mix b C1a C2 C2a C1 Wild type E. coli ATCC 25922 0.5 0.5 0.5 0.5 0.5 P. aeruginosa ATCC 27853 0.5 0.25 0.25 0.25 1 A. baumannii M2 c 1 0.25 0.5 0.5 2 Isogenic e E. coli ATCC 700926 + empty vector d 0.25 0.125 0.125 0.125 0.125 E. coli ATCC 700926 + aac(6′)-Ib 1 4 0.5 32 0.25 E. coli ATCC 700926 + aac(3)-III 4 2 4 4 32 E. coli ATCC 700926 + aph(3′)-Ia 0.5 0.125 0.25 0.25 0.5 Open in a separate window a MIC values are the geometric mean of multiple independent measurements rounded to the nearest CLSI standard dilution increment. b “Mix” refers to batch of laboratory-grade gentamicin used to purify the gentamicin congeners. c Wild-type A. baumannii M2 has been previously characterized ( 34 ). d Parent E. coli strain containing the empty version of the pBBR1MCS-4 vector ( 35 ) used to carry the aminoglycoside-modifying enzyme genes in the isogenic panel. e Nine additional isogenic E. coli isolates with either aac(6′)-aph(2′′) , aph(3′)-II , aph(3′)-III , aph(3′)-IV , aph(3′)-V , aph(3′)-VII , aac(2′)-I , aac(3)-I , or aac(3)-X were also tested, and the MICs for each congener fell within ±1 log 2 dilution of the gentamicin “Mix” MIC.

Techniques:

Journal: Cell

Article Title: Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity

doi: 10.1016/j.cell.2020.02.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial Strains S. aureus RN4220 Nair et al., 2011 N/A S. aureus Newman Bae et al., 2006 N/A S. aureus TB4 Bae et al., 2006 N/A S. aureus MW2 Baba et al., 2002 N/A E. coli MG1655 ATCC ATCC® 700926 Chemicals, Peptides, and Recombinant Proteins Tryptic Soy Agar Becton Dickinson {"type":"entrez-nucleotide","attrs":{"text":"BD236950","term_id":"33046720","term_text":"BD236950"}} BD236950 Tryptic Soy Broth Becton Dickinson {"type":"entrez-nucleotide","attrs":{"text":"BD211825","term_id":"33021595","term_text":"BD211825"}} BD211825 Luria-Bertani Agar Becton Dickinson {"type":"entrez-nucleotide","attrs":{"text":"BD244520","term_id":"33054290","term_text":"BD244520"}} BD244520 Luria-Bertani Broth Becton Dickinson {"type":"entrez-nucleotide","attrs":{"text":"BD244620","term_id":"33054390","term_text":"BD244620"}} BD244620 Lysostaphin Ambi Products LSPN-50 Gentamicin GIBCO Cat#15710064 Chloramphenicol Sigma-Aldrich C0378 Erythromycin Sigma-Aldrich E5389 Tetracycline Sigma-Aldrich T3383 Kanamycin Sigma-Aldrich K1637 IPTG Invitrogen Cat#15529019 Q5® High-Fidelity DNA polymerase NEB M0491L NEBuilder® HiFi DNA Assembly Master Mix NEB E2621L AMPure XP beads Beckman Coulter A63880 Critical Commercial Assays QIAprep Spin Miniprep Kit QIAGEN Cat#27104 MiSeq Reagent Kit v2 (300-cycles) Illumina MS-102–2002 NextSeq 500/550 High Output Kit v2.5 (75 Cycles) Illumina Cat#20024906 Deposited Data Next-generation sequencing FASTQ files This paper SRA: PRJNA595000 Oligonucleotides See Table S4 This paper N/A Recombinant DNA See Table S4 This paper N/A Software and Algorithms Burrows-Wheeler Alignment tool(BWA) Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Python version 2.7 Python Software Foundation https://www.python.org FIRE Elemento et al., 2007 https://tavazoielab.c2b2.columbia.edu/FIRE/ Open in a separate window KEY RESOURCES TABLE CRISPR adaptation converts genomic DNA into economical genome-wide crRNA libraries Highly comprehensive libraries reveal genetic determinants of antibiotic sensitivity Generation of diverse crRNA libraries in genetically recalcitrant bacteria Dual-crRNA libraries reveal genetic interaction and historical contingency

Techniques: Recombinant, Next-Generation Sequencing, Software

Journal: Cell

Article Title: Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis

doi: 10.1016/j.cell.2019.09.015

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and Virus Strains T3 From Ian Molineux (University of Texas, Austin) N/A E. coli NEB5α New England Biolabs cat no. C2987I E. coli BL21 ATCC ATCC PTA-5073 E. coli BL21 ΔwaaC This paper E. coli BL21–369 E. coli BL21 ΔwaaG This paper E. coli BL21–372 E. coli BL21 PRM01 This paper E. coli BL21 PRM01 E. coli BL21 PRM02 This paper E. coli BL21 PRM02 E. coli BL21 PRM03 This paper E. coli BL21 PRM03 E. coli BL21 PRM04 This paper E. coli BL21 PRM04 E. coli BL21 PRM05 This paper E. coli BL21 PRM05 E. coli BL21 PRM06 This paper E. coli BL21 PRM06 E. coli BL21 PRM07 This paper E. coli BL21 PRM07 E. coli BL21 PRM08 This paper E. coli BL21 PRM08 E. coli MG1655 ATCC ATCC 700926 Yersinia pseudotuberculosis YPIII ATCC ATCC 29833 Chemicals, Peptides, and Recombinant Proteins Lysogeny Broth (LB medium) LabExpress cat no. 3001 LB Agar LabExpress cat no. 3002 Critical Commercial Assays KAPA Biosystems HiFi KAPA Biosystems Kapa/Roche kit code: KK2602 KAPA Biosystems Robust 2G KAPA Biosystems Kapa/Roche kit code: KK5516 KAPA SYBR®FAST qPCR Kit KAPA Biosystems Kapa/Roche kit code: KK4618 TURBO DNase Thermo Fisher cat no. AM2239 Deposited Data NGS data characterizing library diversity This paper Available upon request Spreadsheet summarizing EOP Data in This paper N/A Variable domain of an antibody Protein Data Bank; Harris et al., 1997 PDB ID: 1IGT T7 gp17 crystal structure Protein Data Bank; Garcia-Doval and van Raaij, 2012 PDB ID: 4A0T Experimental Models: Organisms/Strains Mouse: Crl:CD1(ICR) Charles River Strain Code: 022 Oligonucleotides See Table S5 for list of all oligonucleotides used in this study This paper N/A Recombinant DNA pSLM49 This paper (Encodes T3 gene 17) N/A pSLD18 This paper (Recombineering plasmid for making LPS mutants) N/A Software and Algorithms SWISS-MODEL Arnold et al., 2006 https://swissmodel.expasy.org/ seqtk Heng Li, MIT https://github.com/lh3/seqtk FASTAptamer Alam et al., 2015 https://burkelab.missouri.edu/fastaptamer.html Open in a separate window KEY RESOURCES TABLE list-behavior=unordered prefix-word= mark-type=disc max-label-size=0 Vastly diverse phagebody libraries containing 10 7 different members were created Structure-informed engineering of viral tail fibers generated host-range alterations Bacterial resistance to phagebodies was not observed across long timescales Select phagebodies limit bacterial growth in a mouse wound infection model

Techniques: Recombinant, Plasmid Preparation, Software