Genomic and transcriptomic profiling of phoenix colonies

Pseudomonas aeruginosa is a Gram-negative bacterium responsible for numerous human infections. Previously, novel antibiotic tolerant variants known as phoenix colonies as well as variants similar to viable but non-culturable (VBNC) colonies were identified in response to high concentrations of aminoglycosides. In this study, the mechanisms behind phoenix colony and VBNC-like colony emergence were further explored using both whole genome sequencing and RNA sequencing. Phoenix colonies were found to have a single nucleotide polymorphism (SNP) in the PA4673 gene, which is predicted to encode a GTP-binding protein. No SNPs were identified within VBNC-like colonies compared to the founder population. RNA sequencing did not detect change in expression of PA4673 but revealed multiple differentially expressed genes that may play a role in phoenix colony emergence. One of these differentially expressed genes, PA3626, encodes for a tRNA pseudouridine synthase which when knocked out led to a complete lack of phoenix colonies. Although not immediately clear whether the identified genes in this study may have interactions which have not yet been recognized, they may contribute to the understanding of how phoenix colonies are able to emerge and survive in the presence of antibiotic exposure.

10.1038/s41598-022-18059-1

2045-2322

Sindeldecker, Devin

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Dunn, Matthew

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Zimmer, Aubree

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Anderson, Matthew

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Alfonzo, Juan

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Stoodley, Paul

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12 August 2022

Sindeldecker, Devin

53899a0e-6c67-40e4-813d-ce3e907f3ee8

Dunn, Matthew

c47e5370-3f93-4371-9173-244294a54b17

Zimmer, Aubree

c1400c21-f255-4741-9454-366f71062eb7

Anderson, Matthew

a802e797-0d2d-4bc7-a2db-f063ef57b797

Alfonzo, Juan

1352e123-c784-4872-bee6-becb668b7f10

Stoodley, Paul

08614665-92a9-4466-806e-20c6daeb483f

Sindeldecker, Devin, Dunn, Matthew, Zimmer, Aubree, Anderson, Matthew, Alfonzo, Juan and Stoodley, Paul (2022) Genomic and transcriptomic profiling of phoenix colonies. Scientific Reports, 12 (1), [13726]. (doi:10.1038/s41598-022-18059-1).

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Accepted/In Press date: 4 August 2022

Published date: 12 August 2022

Additional Information: Funding Information: This work was supported in part by the Ohio State University College of Medicine and R01 NIH-GM124436 (PS), R01AI148788 (MZA), an NSF CAREER Award 2046863 (MZA), the American Heart Association Grant AHA 20PRE35200201 (MJD), NIH GM132254 (JDA), and NIH GM084065-11 (JDA). We would like to thank the Genomics Shared Resource of the Ohio State University Comprehensive Cancer Center for performing the RNA sequencing. We would also like to thank Robert Fillinger for technical assistance with the RNAseq data analysis. Additionally, we would like to thank the lab of Dr. Daniel Wozniak for providing strains from their stocks of Dr. Colin Manoil’s P. aeruginosa transposon library. Publisher Copyright: © 2022, The Author(s).