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Information
Name
Host range of the 96 coliphages from the Antonina Guelin collection on the 403 natural isolates of Escherichia from the Bertrand
Life Domain
bacteria
Publication
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Description
The experiment was conducted by Inès Charachon, Juliette Bernier, and Nicolas Dib in Baptiste Gaborieau's lab (baptiste.gaborieau@inserm.fr) and Aude Bernheim's lab (aude.bernheim@pasteur.fr) using a spotting method. Phage-bacteria interactions were evaluated by depositing a 2 µL drop of phage solution onto a bacterial lawn incubated at 37°C. Each bacterial strain was spread onto agar plates from a fresh liquid culture that had reached the exponential growth phase (OD600nm 0.25, approximately 5 × 10⁷ CFU/mL). For each phage, three different concentrations (determined based on the phage isolation host) were tested: 5 × 10⁸ PFU/mL, 5 × 10⁷ PFU/mL, and 5 × 10⁶ PFU/mL. These corresponded to phage-to-bacteria ratio proxies of 10, 1, and 0.1, respectively. The interactions of 35,793 phage-bacteria pairs were assessed under these three ratio conditions, with each experiment performed in triplicate.

Result interpretation was standardized. After 16 hours of incubation, all plates were scanned at high resolution and manually reviewed. Each interaction was categorized based on bacterial lawn clearance, enabling the calculation of the minimum lytic concentration (MLC), defined as the lowest phage concentration at which bacterial lysis was observed. The scoring system was as follows: 0 (no lytic interaction), 1 (lysis observed at the highest phage concentration, 5 × 10⁸ PFU/mL), 2 (lysis at the intermediate concentration, 5 × 10⁷ PFU/mL), 3 (individual lysis plaques at the lowest concentration, 5 × 10⁶ PFU/mL), and 4 (complete bacterial lawn lysis at the lowest concentration). In cases of discrepancies between replicates, the most frequently observed score among the three replicates was retained.
Since the Viral Host Range Database only supports score values from 0 to 2, the data are here represented as follows: 0 (no lytic interaction), 1 (lysis observed at the highest phage concentration, 5 × 10⁸ PFU/mL), and 2 (lysis observed at intermediate and lowest concentrations, 5 × 10⁷ PFU/mL and 5 × 10⁶ PFU/mL). For the full version of the interaction matrix, refer to the manuscript ( DOI: 10.1038/s41564-024-01832-5) or visit https://github.com/mdmparis/coli_phage_interactions_2023.

The 96 phages from the Antonina Guelin collection were isolated by Jean-Damien Ricard and Laurent Debarbieux’s labs from urban sewage water in the Paris region (France). These phages were recovered using 34 Escherichia coli strains, which included clinical isolates from ventilator-associated pneumonia (n = 21), urinary tract infections (n = 2), and inflammatory bowel disease patients (n = 7), as well as an enteroaggregative E. coli strain (EAEC, n = 1), a commensal mouse strain (n = 1), and laboratory strains (K12 and E. coli B, n = 2).

The 403 bacterial strains of the Bertrand Picard collection were assembled into a collection reflecting the phylogenetic diversity of the Escherichia genus by Eric Denamur’s lab (PMID: 33112851), with the addition of the 34 strains used for phage isolation.

The two collections can be requested from the CRBIP of Institut Pasteur de Paris: https://catalogue-crbip.pasteur.fr/recherche_catalogue.xhtml.
Visibility
Public
Provided By
Baptiste GABORIEAU
Creation Date
Feb. 21, 2023, 6:57 p.m.
Last Edition Date
Feb. 4, 2025, 5:52 p.m.
Content
Viruses 96
Hosts 402
Responses 38435
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Response scheme used
Original response Response mapped
0.0 No infection
1.0 Intermediate
2.0 Infection
Viruses
536_P1, 536_P11, 536_P12, 536_P6, 536_P7, 536_P9, AL505_P2, AL505_P3, AN17_P1, AN17_P8, AN24_P2, AN24_P3, AN24_P4, BCH953_P1, BCH953_P2, BCH953_P3, BCH953_P4, BCH953_P5, BDX03_P1, BDX03_P2, BDX09_P1, CLB_P1, CLB_P2, DIJ06_P1, DIJ07_P1, DIJ07_P2, LF110_P1, LF110_P2, LF110_P3, LF110_P4, LF31_P1, LF31_P3, LF50_P3, LF7074_P1, LF7074_P2, LF7074_P3, LF73_P1, LF73_P3, LF73_P4, LF82_P1, LF82_P2, LF82_P3, LF82_P4, LF82_P5, LF82_P6, LF82_P8, LF82_P9, LI10_P1, LI10_P2, LI10_P3, LI10_P4, LI10_P5, LI10_P6, LM02_P1, LM07_P1, LM08_P1, LM08_P2, LM33_P1, LM40_P1, LM40_P2, LM40_P3, MT1B1_P3, NAN33_P1, NAN33_P2, NAN33_P4, NAN33_P5, NAN33_P6, NIC06_P2, NIC06_P3, NRG857C_P1, NRG857C_P2, NRG857C_P3, PDP110_P1, PDP110_P2, PDP21_P1, PDP21_P3, PDP21_P5, PDP21_P6, PDP21_P8, PDP351_P2, PDP351_P3, PDP351_P4, T145_P1, T145_P2, T145_P3, T145_P4, T145_P5, T147_P1, T147_P10, T147_P5, T147_P7, T147_P9, T205_P4, T205_P5, T4LD, T7LD
Hosts
001-023, 001-031-c1, 003-026, 013-008, 025-010, 034-008, 034-026-c1, 035-004, 370D, 381A, 536, 55989, 916A, 921A, AL505, AN03, AN17, AN24, Asp51g, ATCC35469T, B090, B1147, B12I13, B156, B1747, B1932, B253, B49, B691, B6A1, B992, BCH953, BDX03, BDX09, BE, Ben4d, BL21, C2-119, colF12g, DEC1a, DEC2a, DIJ06, DIJ07, E1426, E1492, E2052, E2348_69, E4962, E7519, E_albertiiCIP107988T, EC6230, ECOR-01, ECOR-02, ECOR-03, ECOR-04, ECOR-05, ECOR-06, ECOR-07, ECOR-08, ECOR-09, ECOR-10, ECOR-11, ECOR-12, ECOR-13, ECOR-14, ECOR-15, ECOR-16, ECOR-17, ECOR-18, ECOR-19, ECOR-20, ECOR-21, ECOR-22, ECOR-23, ECOR-24, ECOR-25, ECOR-26, ECOR-27, ECOR-28, ECOR-29, ECOR-30, ECOR-31, ECOR-32, ECOR-33, ECOR-34, ECOR-35, ECOR-36, ECOR-37, ECOR-38, ECOR-39, ECOR-40, ECOR-41, ECOR-42, ECOR-43_A, ECOR-44, ECOR-45, ECOR-46, ECOR-47, ECOR-48, ECOR-49, ECOR-50, ECOR-51, ECOR-52, ECOR-53, ECOR-54, ECOR-55, ECOR-56, ECOR-57, ECOR-58, ECOR-59, ECOR-60, ECOR-61, ECOR-62, ECOR-63, ECOR-64, ECOR-65, ECOR-66, ECOR-67, ECOR-69, ECOR-70, ECOR-71, ECOR-72, ED1a, EDL933, E_fergusonii-IVAN, FN116, FN126, FN89, FN-B4, FN-B7, FN-B9, H009, H1-001-0003-S-J, H1-001-0013-L-J, H1-001-0020-M-O, H1-001-0027-S-G, H1-001-0034-S-M, H1-001-0053-K-C, H1-001-0093-R-A, H1-001-0121-Q-J, H1-001-0125-B-M, H1-001-0131-C-A, H1-001-0154-T-K, H1-001-0155-M-I, H1-002-0007-M-M, H1-002-0011-M-G, H1-002-0060-C-T, H1-002-0064-E-M, H1-002-0069-V-G, H1-003-0010-G-J, H1-003-0019-B-M, H1-003-0035-D-E, H1-003-0054-P-P, H1-003-0071-C-J, H1-003-0079-G-R, H1-003-0088-B-J, H1-003-0090-V-J, H1-003-0105-C-R, H1-003-0115-L-R, H1-003-0116-V-R, H1-003-0120-P-R, H1-004-0007-O-M, H1-004-0017-B-M, H1-004-0021-W-I, H1-005-0012-L-M, H1-005-0058-M-A, H1-006-0003-S-L, H1-006-0022-L-R, H1-007-0015-D-G, H1-007-0037-H-D, H14, H384, H4, H442, H47, H48, H70, H95, IAI01, IAI02, IAI03, IAI04, IAI05, IAI06, IAI07, IAI08, IAI09, IAI10, IAI11, IAI12, IAI13, IAI14, IAI15, IAI16, IAI17, IAI18, IAI19, IAI20, IAI21, IAI22, IAI23, IAI24, IAI25, IAI26, IAI27, IAI28, IAI29, IAI30, IAI31, IAI32, IAI33, IAI34, IAI35, IAI36, IAI37, IAI38, IAI39, IAI40, IAI41, IAI42, IAI43, IAI44, IAI45, IAI46, IAI47, IAI48, IAI49, IAI50, IAI51, IAI53, IAI54, IAI55, IAI56, IAI57, IAI58, IAI59, IAI60, IAI61, IAI62, IAI63, IAI64, IAI65, IAI66, IAI67, IAI68, IAI69, IAI70, IAI71, IAI72, IAI73, IAI74, IAI75, IAI76, IAI77, IAI78, IAI79, IAI80, IAI81, IAI82, LF31, LF50, LF7074, LF73, LF82, LI10, LM02, LM07, LM08, LM33, LM40, LMR-3158, M863, MT1B1, NAN33, NIC06, NILS01, NILS02, NILS03, NILS04, NILS05, NILS06, NILS07, NILS08, NILS09, NILS10, NILS11, NILS12, NILS13, NILS14, NILS15, NILS16, NILS17, NILS18, NILS19, NILS20, NILS21, NILS22, NILS23, NILS24, NILS25, NILS26, NILS27, NILS28, NILS29, NILS30, NILS31, NILS32, NILS33, NILS34, NILS35, NILS36, NILS37, NILS38, NILS39, NILS40, NILS41, NILS42, NILS43, NILS44, NILS45, NILS46, NILS47, NILS48, NILS49, NILS50, NILS51, NILS52, NILS53, NILS54, NILS55, NILS56, NILS57, NILS58, NILS59, NILS60, NILS61, NILS62, NILS63, NILS64, NILS65, NILS66, NILS67, NILS68, NILS69, NILS70, NILS71, NILS72, NILS73, NILS74, NILS75, NILS76, NILS77, NILS78, NILS79, NILS80, NILS81, NILS82, NRG807C, PDP110, PDP21, PDP351, ROAR012, ROAR019, ROAR029, ROAR036, ROAR043, ROAR047, ROAR059, ROAR061, ROAR072, ROAR082, ROAR116, ROAR129, ROAR130, ROAR131, ROAR145, ROAR176, ROAR178, ROAR185, ROAR205, ROAR220, ROAR274, ROAR291, ROAR292, ROAR334, ROAR344, ROAR387, ROAR400, ROAR419, ROAR434, ROAR438, S1-109, S1-11, S1-76, S1-84, S1-91, S2-1, T145, T147, T205, TW10509, VDG427