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

Frontiers in Microbiology
Utkarsh SoodMallikarjun Shakarad

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. Howeve...Continue Reading

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Citations

Jan 12, 2020·Nucleic Acids Research·Julian TrouillonSylvie Elsen
Jul 22, 2020·FEMS Microbiology Letters·Selene García-ReyesGloria Soberón Chávez
Jun 13, 2020·Frontiers in Microbiology·Romário Oliveira de SalesPatricia Severino
Jan 21, 2021·International Journal of Systematic and Evolutionary Microbiology·Priya SinghUtkarsh Sood
Jul 20, 2021·Current Microbiology·Zhenghong Zhang, Xuehong Zhang
Aug 7, 2021·Antibiotics·Viola Camilla ScoffoneSilvia Buroni

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Datasets Mentioned

BETA
FN645745.1
JQ418525.1
OGX61696.1
CP020560.1
CP020561.2

Methods Mentioned

BETA
environmental stress
PCA

Software Mentioned

Parsnp
PHYLIP
Harvest suite
PubMLST
MinPath
POTION
pyani
Genome to Genome Distance Calculator ( GGDC
MLST
Glimmer

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