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A new antibiotic selectively kills Gram-negative pathogens

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The current need for novel antibiotics is especially acute for drug-resistant Gram-negative pathogens1,2. These microorganisms have a highly restrictive permeability barrier, which limits the penetration of most compounds3,4. As a result, the last class of antibiotics acting against Gram-negative bacteria was developed in the 1960s2. We reason that useful compounds can be found in bacteria that share similar requirements for antibiotics with humans, and focus on Photorhabdus symbionts of entomopathogenic nematode microbiomes. Here we report a new antibiotic that we name darobactin, from a screen of Photorhabdus isolates. Darobactin is coded by a silent operon with little production under laboratory conditions, and is ribosomally synthesized. Darobactin has an unusual structure with two fused rings that form post-translationally. The compound is active against important Gram-negative pathogens both in vitro and in animal models of infection. Mutants resistant to darobactin map to BamA, an essential chaperone and translocator that folds outer membrane proteins. Our study suggests that bacterial symbionts of animals contain antibiotics that are particularly suitable for development into therapeutics.

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Author information

Correspondence to Kim Lewis.

Supplementary information

Supplementary Discussion

Extra comments on screen strategy, NMR stereochemistry assignment, and on transcriptomics and proteomics results in Extended Data Figures 7 and 8

Reporting Summary

Supplementary Figure 1

Raw image of the agarose gel confirming the dar operon knockout in Extended Data Figure 4c

Supplementary Data 1

ZIP file containing raw NMR Data for BamA-darobactin titration and BamA-scramble peptide experiments related to Extended Data Figure 5i,j

Supplementary Table 1 | Potency of darobactin against recent clinical isolates

Determination of darobactin and gentamicin MIC by broth microdilution was performed using broth microdilution by JMI laboratories (North Liberty, IA, USA)

Supplementary Table 2 | Thermal proteome profiling results

E. coli BW25113 living cells, with or without chloramphenicol pretreatment, or cell lysate, was treated with darobactin at five different concentrations. Aliquots of treated cells or lysates were then heated to ten different temperatures, and soluble proteins then analyzed by liquid chromatography coupled to tandem mass spectrometry (n=1 at each concentration for each experiment). Protein identification and quantification was performed using IsobarQuant and Mascot 2.4 (Matrix Science) against the E. coli Uniprot FASTA (Proteome ID: UP000000625). Data was analyzed with the TPP package for R followed by an FDR-controlled method for functional analysis of dose-response curves (see method reference). Supplementary Table 2 is related to Extended Data Figure 8

Supplementary Video 1 | Time-lapse microscopy of darobactin causing outer membrane disruption and lysis of E. coli

E. coli MG1655 cells cultured in MHIIB were placed on top of a MHIIB/darobactin agarose pad containing FM4-64 and Sytox Green dyes, and observed under the microscope. Acquisition recording DIC, FM4-64 (false-coloured in magenta) and Sytox Green (false-coloured in green) signals was performed every 30 minutes at 37 °C for 14 hours. Scale bar, 10 μm. This figure is representative of three biologically independent experiments performed with similar results

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Imai, Y., Meyer, K.J., Iinishi, A. et al. A new antibiotic selectively kills Gram-negative pathogens. Nature (2019) doi:10.1038/s41586-019-1791-1

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