Comparative Genomics of Pseudomonas aeruginosa Strains Isolated from Different Ecological Niches

The genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes...

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Published in:Antibiotics (Basel) 2023-05, Vol.12 (5), p.866
Main Authors: Gómez-Martínez, Jessica, Rocha-Gracia, Rosa Del Carmen, Bello-López, Elena, Cevallos, Miguel Angel, Castañeda-Lucio, Miguel, Sáenz, Yolanda, Jiménez-Flores, Guadalupe, Cortés-Cortés, Gerardo, López-García, Alma, Lozano-Zarain, Patricia
Format: Article
Language:English
Subjects:
Adaptation
Antibiotic resistance
Antibiotics
antimicrobial resistance
Carbapenems
Chromosomes
Clustering
comparative genomic
CRISPR
Cystic fibrosis
Drug resistance
Ecological niches
Genes
Genetic variability
Genomes
Genomics
Kinases
Niches
Nosocomial infections
Phylogeny
Plasmids
Proteins
Pseudomonas aeruginosa
Pseudomonas aeruginosa
Sputum
Urine
Urogenital system
Virulence
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Summary:The genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. (a variant of ) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that was most prevalent in the genomes of urinary samples and and in sputum samples. This study provides evidence regarding the genetic variability among isolated from different niches.
ISSN:2079-6382
2079-6382
DOI:10.3390/antibiotics12050866