An innovative approach to decoding genetic variability in Pseudomonas aeruginosa via amino acid repeats and gene structure profiles

• Published in: Scientific reports 2024-09, Vol.14 (1), p.22610-9, Article 22610
• Main Authors: Kim, Chaerin, Oh, Kwang-Kyo, Jothi, Ravi, Park, Dong Suk
• Format: Article
• Language: English
• Subjects: 631/208; 631/326; Amino acid sequence; Amino acids; Amino Acids - genetics; Bacterial Proteins - genetics; Cobalt; Comparative analysis; Comparative genome analysis; Gene mapping; Genes; Genetic analysis; Genetic diversity; Genetic markers; Genetic variability; Genetic Variation; Genomic analysis; Genotyping; Global health; Histidine; Humanities and Social Sciences; Humans; multidisciplinary; Multilocus Sequence Typing - methods; Nosocomial infection; Phylogeny; Pseudomonas aeruginosa; Pseudomonas aeruginosa - genetics; Public health; Science; Science (multidisciplinary); SHRs; Strains (organisms)
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-73031-5

Pseudomonas aeruginosa , a common pathogen in nosocomial infections, presents significant global health challenges due to its high prevalence and mortality rates. However, the origins and distribution of this bacterium remain unclear, partly due to the lack of effective gene typing methods. This situation necessitates the establishment of trustworthy and high-resolution protocol for differentiating closely related P. aeruginosa strains. In this context, the present study attempted to undertake a comparative genomic analysis of multiple P. aeruginosa strains available in the public database NCBI, with the goal of identifying potential genetic markers for measuring the genetic diversity. The preliminary comparative analysis of 816 P. aeruginosa strains revealed notable variations in two genes—specifically, the CDF family iron/cobalt efflux transporter AitP and the protease modulator HflC—across 44 strains. These variations were associated with single amino acid repeats (SHRs) that responsible for encoding histidine residue. Additionally, comparative gene map analysis revealed differential clustering patterns in the Rsx and TAXI genes among 16 strains. Interestingly, the gene structure pattern observed in TAXI groups displayed a strong correlation with the SHRs pattern in the CDF and HflC groups. In addition, the SHRs pattern of CDF and HflC were strongly correlated with MLST sequence type number. Overall, the study present a novel genetic markers based on SHRs and gene cluster patterns, offering a reliable method for genotyping of P. aeruginosa .