Comparative Genomic Analyses Reveal Core-Genome-Wide Genes Under Positive Selection and Major Regulatory Hubs in Outlier Strains of Pseudomonas aeruginosa.

Utkarsh Sood,Mallikarjun Shakarad,Princy Hira,Rup Lal,Roshan Kumar,Desiraju Lakshmi Narsimha Rao,Abhay Bajaj

doi:10.3389/fmicb.2019.00053

Utkarsh Sood, Mallikarjun Shakarad + Show 5 more

Open Access

https://doi.org/10.3389/fmicb.2019.00053

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Abstract

Genomic information for outlier strains of Pseudomonas aeruginosa is exiguous when compared with classical strains. We sequenced and constructed the complete genome of an environmental strain CR1 of P. aeruginosa and performed the comparative genomic analysis. It clustered with the outlier group, hence we scaled up the analyses to understand the differences in environmental and clinical outlier strains. We identified eight new regions of genomic plasticity and a plasmid pCR1 with a VirB/D4 complex followed by trimeric auto-transporter that can induce virulence phenotype in the genome of strain CR1. Virulence genotype analysis revealed that strain CR1 lacked hemolytic phospholipase C and D, three genes for LPS biosynthesis and had reduced antibiotic resistance genes when compared with clinical strains. Genes belonging to proteases, bacterial exporters and DNA stabilization were found to be under strong positive selection, thus facilitating pathogenicity and survival of the outliers. The outliers had the complete operon for the production of vibrioferrin, a siderophore present in plant growth promoting bacteria. The competence to acquire multidrug resistance and new virulence factors makes these strains a potential threat. However, we identified major regulatory hubs that can be used as drug targets against both the classical and outlier groups.

Highlights

Pseudomonas aeruginosa is one of the major opportunistic pathogens that has been isolated from a wide range of ecological niches including soil, water and clinical samples (Stover et al, 2000)
CR1 and PA7 had the complete set of 107 essential marker genes and all the draft genomes were more than 96–98% complete based on essential marker gene approach
The present results show that the genome size of strain CR1 is smallest among the outlier strains, primarily due to the lack of type I restrictionmodification system and mercury resistance cluster (RGP63 and RGP79)

Summary

INTRODUCTION

Pseudomonas aeruginosa is one of the major opportunistic pathogens that has been isolated from a wide range of ecological niches including soil, water and clinical samples (Stover et al, 2000). Strains lacking T3SS were thought to be less pathogenic due to the absence of injectosome machinery and its effector toxins (ExoS, ExoT, ExoU, and ExoY) that play a prominent role in acute as well as chronic infections (Hauser, 2009) These T3SS deficient strains are termed as outlier strains and they form a distinct phylogenetic clade represented by strain PA7 (Roy et al, 2010); and were shown to have diverged early from the classical strains of P. aeruginosa (Gomila et al, 2015). Core genome-wide genes under positive selection were determined for identifying the genes under strong positive selection that can provide advantageous variants to the outlier genomes The ability of these strains to gain virulence factors and acquired antibiotic resistance require new drug targets to be identified. Protein–protein interaction on the core genome of both the groups was used to identify major regulators that can be targeted as drug targets

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION