Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus

Abstract

A 15-year-old patient with cystic fibrosis with a disseminated Mycobacterium abscessus infection was treated with a three-phage cocktail following bilateral lung transplantation. Effective lytic phage derivatives that efficiently kill the infectious M. abscessus strain were developed by genome engineering and forward genetics. Intravenous phage treatment was well tolerated and associated with objective clinical improvement, including sternal wound closure, improved liver function, and substantial resolution of infected skin nodules.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Patient status before and after phage treatment.
Fig. 2: A three-phage anti-M. abscessus GD01 cocktail.

References

  1. 1.

    Honda, J., Virdi, R. & Chan, E. D. Front. Microbiol. 9, 2029 (2018).

    Article  Google Scholar 

  2. 2.

    Bloom, B. R., et al. in Major Infectious Diseases (eds Holmes, K. K., Bertozzi, S., Bloom, B. R. & Jha, P.) Ch. 11 (The International Bank for Reconstruction and Development/The World Bank, Washington DC, 2017).

  3. 3.

    Martiniano, S. L., Davidson, R. M. & Nick, J. A. Pediatr. Pulmonol. 52, S29–S36 (2017).

    Article  Google Scholar 

  4. 4.

    Furukawa, B. S. & Flume, P. A. Semin. Respir. Crit. Care Med. 39, 383–391 (2018).

    Article  Google Scholar 

  5. 5.

    Griffith, D. E. F1000Prime Rep. 6, 107 (2014).

    Article  Google Scholar 

  6. 6.

    Osmani, M., Sotello, D., Alvarez, S., Odell, J. A. & Thomas, M. Transpl. Infect. Dis. 20, e12835 (2018).

    Article  Google Scholar 

  7. 7.

    Adler, F. R. et al. Proc. Am. Thorac. Soc. 6, 619–633 (2009).

    Article  Google Scholar 

  8. 8.

    Kakasis, A. & Panitsa, G. Int. J. Antimicrob. Agents 53, 16–21 (2019).

    CAS  Article  Google Scholar 

  9. 9.

    Sula, L., Sulova, J. & Stolcpartova, M. Czech Med. 4, 209–214 (1981).

    CAS  PubMed  Google Scholar 

  10. 10.

    Koz’min-Sokolov, B. N. & Vabilin Probl. Tuberk 4, 75–79 (1975).

    Google Scholar 

  11. 11.

    Trigo, G. et al. PLoS Negl. Trop. Dis. 7, e2183 (2013).

    Article  Google Scholar 

  12. 12.

    Schooley, R. T. et al. Antimicrob. Agents Chemother. 61, e00954–17 (2017).

    CAS  Article  Google Scholar 

  13. 13.

    Chan, B. K. et al. Evol. Med. Public Health 2018, 60–66 (2018).

    Article  Google Scholar 

  14. 14.

    Hatfull, G. F. J. Virol. 89, 8107–8110 (2015).

    CAS  Article  Google Scholar 

  15. 15.

    Jacobs-Sera, D. et al. Virology 434, 187–201 (2012).

    CAS  Article  Google Scholar 

  16. 16.

    Rybniker, J., Kramme, S. & Small, P. L. J. Med. Microbiol. 55, 37–42 (2006).

    CAS  Article  Google Scholar 

  17. 17.

    Marinelli, L. J. et al. PLoS ONE 3, e3957 (2008).

    Article  Google Scholar 

  18. 18.

    Dedrick, R. et al. Tuberculosis 115, 14–23 (2019).

    CAS  Article  Google Scholar 

  19. 19.

    Broussard, G. W. et al. Mol. Cell 49, 237–248 (2013).

    CAS  Article  Google Scholar 

  20. 20.

    Bankevich, A. et al. J. Comput. Biol. 19, 455–477 (2012).

    CAS  Article  Google Scholar 

  21. 21.

    Russell, D. A. Methods Mol. Biol.. 1681, 109–125 (2018).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank T. Sampson, L. Holst, and S. Pinches for the discovery of BPs, Muddy, and ZoeJ, respectively, and the students and faculty in the Mycobacterial Genetics Course at the University of KwaZulu Natal and in the SEA-PHAGES program for their contributions in isolating and characterizing the collection of phages used here. Further information about the phages, who isolated them and from where is available at https://phagesdb.org. We thank the Great Ormond Street Hospital staff in the Departments of Microbiology, Cell Therapy, and Pharmacy for excellent technical assistance, C. Murphy for assistance with strains and sera, J. Standing and B. Margetts for assistance with figures, D. Bain at the University of Pittsburgh for the ICP-MS analysis, and A. Betsko for electron microscopy. We greatly appreciate the advice of J. Hartley on regulatory aspects, and thank C. Hamilton for help with translation. We thank T. Mavrich for comments on the manuscript and we are grateful to S. Strathdee for general advice and comments on the manuscript. This work was funded by the National Institutes of Health (grant GM116884 to G.F.H.) and the Howard Hughes Medical Institute (grant 54308198 to G.F.H.).

Author information

Affiliations

Authors

Contributions

R.M.D., C.A.G.-B., R.A.G., D.A.R., D.J.S., K.H., and K.C.G. contributed to data collection, analysis, interpretation, and writing. K.F. contributed data collection, analysis, interpretation, writing, and regulatory approvals. J.S. contributed to literature search, data collection, analysis, interpretation, and writing. R.T.S., G.F.H., and H.S. contributed to the study design, data interpretation, and writing.

Corresponding authors

Correspondence to Graham F. Hatfull or Helen Spencer.

Ethics declarations

Competing interests

R.T.S. serves as an uncompensated member of the AmpliPhi Scientific Advisory Board. Other authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Timeline of drug administration.

Timeline showing administration of antibiotics, immunosuppressive drugs, and the phage cocktail. Levels of the immunosuppressive drug Tacrolimus are shown at the top, and the administration of drugs is as indicated.

Extended Data Fig. 2 Genome maps of phages Muddy, BPs, and ZoeJ.

Genes are shown as colored boxes above or below a genome track, reflecting rightwards and leftwards transcription, respectively. Pairwise nucleotide sequence similarity is indicated by spectrum-colored shading between genomes, with violet representing closest similarity.

Extended Data Fig. 3 In vitro selection of phage resistance.

a, Approximately 5 × 108 cells of M. abscessus GD01 in one ml were incubated with a cocktail of 109 pfu each of three phages for one week in liquid culture. Aliquots (100 µl) were plated onto solid media and incubated at 37 °C. In the absence of phage, a confluent lawn grew (left), and in the presence of phage (right), approximately 150 small colonies were observed. b, Six individual colonies were picked, grown and retested for phage susceptibilities. Top agar overlays with each strain were plated on solid media and 10-fold serial dilutions of phages (as indicated) were spotted onto each plate.

Extended Data Fig. 4 Detection of antisera recognizing phage proteins.

Phage preparations of Muddy, ZoeJΔ45, and BPs33ΔHTH-HRM10 (as shown) each containing approximately 2 × 1010 phage particles were separated by SDS-PAGE, together with protein markers (M) and a control sample of 10 µl of a 1:100 dilution of patient serum (serum) collected 72 days after initiation of phage treatment. The gel was stained with Coomassie Blue (left), transferred to a membrane for a Western blot which was probed with the same patient serum and an anti-human Horse Radish Peroxidase conjugated secondary antibody. These assays were repeated three times with similar results; a representative experiment is shown.

Extended Data Fig. 5 Phage susceptibilities of GD01 clinical isolates.

M. abscessus were recovered at 20-, 72-, 107, and 121-days after initiation of phage treatment, propagated, and tested for susceptibilities to each of the phages in the cocktail. Each phage was diluted serially 10-fold and spotted onto bacterial lawns. These assays were repeat at least twice with similar results; a representative experiment is shown.

Supplementary information

Supplementary Information

Supplementary Background and Results, Consent and other approvals, Data availability, Supplementary References, and Supplementary Tables 1–5

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Dedrick, R.M., Guerrero-Bustamante, C.A., Garlena, R.A. et al. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med 25, 730–733 (2019). https://doi.org/10.1038/s41591-019-0437-z

Download citation

Further reading