KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Goat Anti-Human IgG H&L (HRP) | Abcam | ab97175 |
| Goat Anti-Human IgA (HRP) | Southern Biotech | 2050-05 |
| KPL SureBlue Reserve TMB Microwell Peroxidase Substrate | seracare | 5120-0082 |
| Goat Anti-Human IgG Fc (HRP) preadsorbed | Abcam | ab98624 |
| Bacterial and virus strains | ||
| Mycobacterium smegmatis mc2155 | Snapper et al., 1990 | NC_008596 |
| Mycobacterium abscessus patient samples | This paper | National Jewish Health |
| Mycobacteriophage BPsΔ33HTH_HRM10 | Dedrick et al., 2019 | http://phagesdb.org |
| Mycobacteriophage D29_HRMGD40 | Dedrick et al., 2021 | http://phagesdb.org |
| Mycobacteriophage Muddy | Dedrick et al., 2019 | http://phagesdb.org |
| Mycobacteriophage Itos | Dedrick et al., 2021 | http://phagesdb.org |
| Mycobacteriophage BPsΔ33HTH_HRMGD03 | Dedrick et al., 2021 | http://phagesdb.org |
| Mycobacterium abscessus | ATCC | 19977 |
| Biological samples | ||
| Patient serum | This paper | National Jewish Health |
| Patient sputum | This paper | National Jewish Health |
| Patient urine | This paper | National Jewish Health |
| Airway secretions from patient explanted lungs | This paper | National Jewish Health |
| Bronchioalveolar lavage from patient explanted lungs | This paper | National Jewish Health |
| Tissue from patient explanted lungs | This paper | National Jewish Health |
| Chemicals, peptides, and recombinant proteins | ||
| Ringers Solution | Oxoid | Cat# BR0052G |
| 3,3′,5,5′-Tetramethylbenzidine (TMB) Liquid Substrate System for ELISA | Sigma Aldrich | Cat# T0440-1 |
| Ammonium Acetate | SIGMA-ALDRICH | CAS:631-61-8 |
| Octyl Sepharose CL-4B | GE Healthcare | 17-0790-01; CAS: 68652-09-5 |
| n-Propanol | Macron Fine Chemicals | CAS: 71-23-8 |
| n-Hexane | Fisher Chemical | CAS: 110-54-3 |
| Chloroform | EMD Millipore | CAS: 67-66-3 |
| Acetonitrile | SIGMA-ALDRICH | CAS:75-05-8 |
| Trifluoroacetic acid | SIGMA-ALDRICH | CAS: 76-05-1 |
| Trifluoroacetic anhydride | SIGMA-ALDRICH | CAS:407-25-0 |
| D-Arabinose (U-13C5, 99%) CLM-8477-0 | Cambridge Isotope Lab | CAS: NA; PSO 8I-382 |
| (R)-(-)-2-Octanol | SIGMA-ALDRICH | CAS:5978-70-1 |
| Sodium Hydroxide | Fisher Chemical | CAS:1310-73-2 |
| Palmitic-2,2-d2 acid | Cambridge Isotope Lab | CAS: 57-10-3 |
| N-Ethyldiisopropylamine | SIGMA-ALDRICH | CAS: 7087-68-5 |
| 2,3,4,5,6-Pentafluorobenzyl Bromide | SIGMA-ALDRICH | CAS: 1765-40-8 |
| Sulfuric acid | EMD Millipore | CAS: 7664-93-9 |
| Custodial HTK Solution Transport Medium | Essential Pharmaceuticals | |
| Poly-Prep Chromatography Columns | BIO-RAD | Cat. #731-1550 |
| HR GC Column VF-5ms | Agilent Technologies | Part No: CP8944 |
| Carbonate-bicarbonate buffer capsules | Sigma Aldrich | Cat. # C3041 |
| Critical commercial assays | ||
| EndoZyme II | Hyglos GmbH | Cat# 890030 |
| TaqMan™ Gene Expression Master Mix | Thermofisher | Cat # 4369016 |
| LA Taq DNA Polymerase with GC buffers | Takara | Cat # RR02AG |
| Q5 High-Fidelity DNA Polymerase | NEB | Cat # M0491L |
| Nextera XT Index Kit v2 Set A | Illumina | Cat # FC-131-2001 |
| MiSeq Reagent Kit v2 | Illumina | Cat # MS-102-2003 |
| Deposited data | ||
| Bacterial isolate whole genome sequences | This paper | PRJNA319839 |
| Video files incorporating a complete set of axial, coronal and sagittal reconstructions of high-resolution computerized tomography (CT) scans from each timepoint illustrated in Figure 3 (2 days prior to phage, post-phage therapy day 81, and post-phage day 229) | This paper | DOI: 10.17632/jtdvbm2tzx.1 |
| Gross and microscopic pathological photographs of the explanted lungs at time of lung transplant (day 379 of phage therapy). | This paper | DOI: 10.17632/jtdvbm2tzx.1 |
| Raw data from Figures 1A, 1F, 4A, 4B, 4C, 4D, 6 and Supplemental Table 1. https://data.mendeley.com/datasets/jtdvbm2tzx/draft?a=b138c41d-bc1b-458c-8d2a-98267555428d |
This paper | DOI: 10.17632/jtdvbm2tzx.1 |
| Oligonucleotides | ||
| MAG forward: 5’- CAC GGG GTG GAC AGG ATT TA -3’ MAG reverse: 5’- TAA GGA GCA CCA TTT CCC AG -3’ Probe: 5’- /56-FAM/TCA CCA AGT AGA TAY CCA CTA CAG A/36-TAMSp/ -3’ |
Rocchetti et al., 2017 Integrated DNA Technologies (IDT) |
N/A |
| ACTB-Fwd: 5’- CACCATTGGCAATGAGCGGTTC -3’ ACTB-Rev: 5’- AGGTCTTTGCGGATGTCCACGT -3’ oTM179: 5’- GATTCTCACTCTACCGGACTAGTC -3’ oTM180: 5’- CTTGCTGCGATGACACAAGTAAAC -3’ ClusterG-Fwd: 5’- GGCCGTGGGCAGAGGAAACC -3’ ClusterG-Rev: 5’- AGAACCTCAACACCGGCGCG -3’ |
Integrated DNA Technologies (IDT) | N/A |
| Software and algorithms | ||
| OriginLab 2021b version 9.8.5.212 | https://www.originlab.com/ | |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| MEGA-CC v7.0.26 | Kumar et al., 2016 | https://www.megasoftware.net/web_help_10/MEGA-CC.htm |
| Biorender | Biorender.com | N/A |
| BEAST v1.10.4 | Suchard et al., 2018 | https://beast.community/ |
| Tracer v1.7.1 | Rambaut et al., 2018 | https://github.com/beast-dev/tracer |
| ggtree (R package) | Yu et al., 2017 | https://bioconductor.org/packages/release/bioc/html/ggtree.html |
| Unicycler | Wick et al., 2017 | https://github.com/rrwick/Unicycler |
| Panaroo v1.2.6 | Tonkin-Hill et al., 2020 | https://github.com/gtonkinhill/panaroo |
| Other | ||
| Gen5 Microplate Reader and Imager Software | BioTek | TS Installation Version 2.06.10 |