Rampant prophage movement among transient competitors drives adaptation during infection

Marshall et al 2021

Background

After 3-day to up to 4-week wound infection of Pseudomonas aeruginosa in pig, P. aeruginosa go through rapid genetic adapdation to better survive in the host. One of the variants is known as rugosa small colony variant (RSCV), which exhibits distinct color phenotype. The authors co-infect wounds in two pigs with 6 different strains (PA01 and PA14 models, and other four strains) of P. aeruginosa, and plated the isolates after 3, 14, and 28 days. After 3 days, the PA01 and PA14 strains became predominant. Based on the colony morphologies, up to 2% of the isolated belong to RSCVs. While in low abundance, the rise of RSCVs is indicative of chronic infection, hyperbiofilm activities, and worse clinic outcomes. The authors then sequenced both RSCVs and non-RSCVs.

Mutations in two genes wspF and retS account for the colony phenotype. SNP in wspF (T➔G, I68S), and RSCV-41 had a SNP in retS (A➔C, T443P) However, the majority of RSCVs show no point mutations or gene insertion/deletion. Therefore, alternative mechanisms could contribute to the different phenotype and hyperbiofilm in the RSCVs.

Close-up of prophage

The author reasons that there could be horizontal gene transfer which is masked by the reference-based mutation calling. Using a different method, the author mapped the homologous regions between the reference and the variant genome. They identified some evidence of mobile genetic elements (exogenous DNA), primarily prophage, swap from the later undetectable strains to near all PA01 strains.

Combine long reads with Illumina data

Identified not only mutation in retS but also prophage insertion at retS that inactivate the function of retS, leading to RSCV phenotype. Reintroducing wild type retS allele in trans restore the ancestral phenotype.

Acquisition of new prophages provides immunity to phage reinfection

Prophage-bearing RSCVs, all have aquired phages and inserted into key genes (retS, dipA), are immune to the phage infection whereas the non-RSCVs (some have aquired the prophages but not affect gene expression), are only immune to phage infection in a lysogeny-dependent fasion.