Genome-wide sRNA and mRNA transcriptomic profiling insights into carbapenem-resistant Acinetobacter baumannii

Front Cell Infect Microbiol. 2024 Jul 30:14:1419989. doi: 10.3389/fcimb.2024.1419989. eCollection 2024.

Abstract

Introduction: Acinetobacter baumannii (AB) is rising as a human pathogen of critical priority worldwide as it is the leading cause of opportunistic infections in healthcare settings and carbapenem-resistant AB is listed as a "super bacterium" or "priority pathogen for drug resistance" by the World Health Organization.

Methods: Clinical isolates of A. baumannii were collected and tested for antimicrobial susceptibility. Among them, carbapenem-resistant and carbapenem-sensitive A. baumannii were subjected to prokaryotic transcriptome sequencing. The change of sRNA and mRNA expression was analyzed by bioinformatics and validated by quantitative reverse transcription-PCR.

Results: A total of 687 clinical isolates were collected, of which 336 strains of A. baumannii were resistant to carbapenem. Five hundred and six differentially expressed genes and nineteen differentially expressed sRNA candidates were discovered through transcriptomic profile analysis between carbapenem-resistant isolates and carbapenem-sensitive isolates. Possible binding sites were predicted through software for sRNA21 and adeK, sRNA27 and pgaC, sRNA29 and adeB, sRNA36 and katG, indicating a possible targeting relationship. A negative correlation was shown between sRNA21 and adeK (r = -0.581, P = 0.007), sRNA27 and pgaC (r = -0.612, P = 0.004), sRNA29 and adeB (r = -0.516, P = 0.020).

Discussion: This study preliminarily screened differentially expressed mRNA and sRNA in carbapenem-resistant A. baumannii, and explored possible targeting relationships, which will help further reveal the resistance mechanism and provide a theoretical basis for the development of drugs targeting sRNA for the prevention and treatment of carbapenem-resistant A. baumannii infection.

Keywords: Acinetobacter baumannii; carbapenem resistance; small RNA (sRNA); target gene; transcriptomic profiling.

MeSH terms

  • Acinetobacter Infections* / microbiology
  • Acinetobacter baumannii* / drug effects
  • Acinetobacter baumannii* / genetics
  • Anti-Bacterial Agents* / pharmacology
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Carbapenems* / pharmacology
  • Computational Biology / methods
  • Gene Expression Profiling*
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial / genetics
  • Humans
  • Microbial Sensitivity Tests
  • RNA, Bacterial / genetics
  • RNA, Messenger* / genetics
  • RNA, Messenger* / metabolism
  • RNA, Small Untranslated / genetics
  • Transcriptome

Substances

  • Carbapenems
  • RNA, Messenger
  • Anti-Bacterial Agents
  • RNA, Bacterial
  • RNA, Small Untranslated
  • Bacterial Proteins

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the Science and Technology Project of Nanshan District (No. NS2022032), Science and Technology Planning Project of Shenzhen (No. JCYJ20230807115404009), and Major Science and Technology Project of Nanshan District (No. NSZD2024057).