Transcriptomic Insights into Differential Gene Expression in Acinetobacter baumannii Isolates from Colistin-Treated Patients Using Illumina Sequencing
Abstract
The rise of multidrug-resistant (MDR) Acinetobacter baumannii presents a critical threat to global health due to its remarkable antibiotic resistance. To explore its stress response mechanisms, RNA sequencing (RNA-seq) was conducted to compare the transcriptomes of A. baumannii ATCC19606 and a clinical isolate from a colistin-treated patient. Analysis identified 118 differentially expressed genes (DEGs) with thresholds of log2 fold change (Log2FC) > 1 or < −1 and FDR < 0.05.
Upregulated genes included those encoding twitching motility protein, p-aminobenzoate synthetase, pilin-like competence factor, and D-methionine-binding lipoprotein MetQ, with a 2-4 fold increase. Conversely, downregulated genes, such as ferredoxin, molecular chaperones GroES/GroL, and class C beta-lactamase ADC-158, suggested reduced metabolic activity.
These DEGs are implicated in stress response and metabolic transport pathways, providing critical insights into A. baumannii’s adaptive mechanisms and potential vulnerabilities for therapeutic targeting.
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Altschul, S et al (1990). Basic local alignment search tool". Journal of Molecular Biology 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2
Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome biology, 11(10), R106.
Andrade FF, Silva D, Rodrigues A, Pina-Vaz C. Colistin Update on Its Mechanism of Action and Resistance, Present and Future Challenges. Microorganisms. 2020 Nov 2;8(11):1716. doi: 10.3390/microorganisms8111716. PMID: 33147701; PMCID: PMC7692639.
Asokan GV, Ramadhan T, Ahmed E, Sanad H. WHO Global Priority Pathogens List: A Bibliometric Analysis of Medline-PubMed for Knowledge Mobilization to Infection Prevention and Control Practices in Bahrain. Oman Med J. 2019 May;34(3):184-193. doi: 10.5001/omj.2019.37. PMID: 31110624; PMCID: PMC6505350.
Bcl2Fastq:https://sapac.support.illumina.com/sequencing/sequencing_software/ bcl2fastq-conversion-software.html
Brady M.F., Jamal Z., Pervin N. StatPearls. StatPearls Publishing LLC.; Treasure Island, FL, USA: 2022. Acinetobacter
FastQC: Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data
Garrido-Mesa N., Zarzuelo A., Gálvez J. Minocycline: Far beyond an antibiotic. Br. J. Pharm. 2013;169:337–352. doi: 10.1111/bph.12139
Guo T., Sun X., Li M., Wang Y., Jiao H., Li G. The Involvement of the csy1 Gene in the Antimicrobial Resistance of Acinetobacter baumannii. Front. Med. 2022; 9:797104. doi: 10.3389/fmed.2022.797104
Hamidian M., Hall R.M. Acinetobacter baumannii ATCC 19606 Carries GIsul2 in a Genomic Island Located in the Chromosome. Antimicrob. Agents Chemother. 2017 ;61:e01991-16. doi: 10.1128/AAC.01991-16.
Howard A, O'Donoghue M, Feeney A, Sleator RD. Acinetobacter baumannii: an emerging opportunistic pathogen. Virulence. 2012 May 1;3(3):243-50. doi: 10.4161/viru.19700. Epub 2012 May 1. PMID: 22546906; PMCID: PMC3442836.
http://bowtie-bio.sourceforge.net/tutorial.shtml
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Hui Z., Liu S., Cui R., Zhou B., Hu C., Zhang M., Deng Q., Cheng S., Luo Y., Chen H., et al. A small molecule interacts with pMAC-derived hydroperoxide reductase and enhances the activity of aminoglycosides. J. Antibiot. 2021;74:324–329. doi: 10.1038/s41429-020-00401-2.
IGV browser Link:https://software.broadinstitute.org/software/igv/
Kümmerer K. Significance of antibiotics in the environment. J. Antimicrob. Chemother. 2003;52:5–7. doi: 10.1093/jac/dkg293.
Mancilla-Rojano J, Ochoa SA, Reyes-Grajeda JP, Flores V, Medina-Contreras O, Espinosa-Mazariego K, Parra-Ortega I, Rosa-Zamboni D, Castellanos-Cruz MDC, Arellano-Galindo J, Cevallos MA, Hernández-Castro R, Xicohtencatl-Cortes J, Cruz-Córdova A. Molecular Epidemiology of Acinetobacter calcoaceticus-Acinetobacter baumannii Complex Isolated From Children at the Hospital Infantil de México Federico Gómez. Front Microbiol. 2020 Oct 15;11:576673. doi: 10.3389/fmicb.2020.576673. PMID: 33178158; PMCID: PMC7593844.
Moriya, Yuki, et al(2007). "KAAS: an automatic genome annotation and pathway reconstruction server." Nucleic acids research 35.suppl_2: W182-W185.
Nocera FP, Attili AR, De Martino L. Acinetobacter baumannii: Its Clinical Significance in Human and Veterinary Medicine. Pathogens. 2021 Jan 27;10(2):127. doi: 10.3390/pathogens10020127. PMID: 33513701; PMCID: PMC7911418.
Pagdepanichkit, S., Tribuddharat, C., and Chuanchuen, R. (2016). Distribution and expression of the Ade multidrug efflux systems in Acinetobacter baumannii clinical isolates. Can. J. Microbiol. 62, 794–801. doi: 10.1139/cjm-2015-0730
Rfam database Link: https://rfam.xfam.org/
Shi J, Cheng J, Liu S, Zhu Y and Zhu M (2024) Acinetobacter baumannii: an evolving and cunning opponent. Front. Microbiol. 15:1332108. doi: 10.3389/fmicb.2024.1332108
Towner K.J. Acinetobacter: An old friend, but a new enemy. J. Hosp. Infect. 2009;73:355–363.
Yang H., Chen G., Hu L., Liu Y., Cheng J., Li H., Ye Y., Li J. In vivo activity of daptomycin/colistin combination therapy in a Galleria mellonella model of Acinetobacter baumannii infection. Int. J. Antimicrob. Agents. 2015; 45:188–191. doi: 10.1016/j.ijantimicag.2014.10.012.
Yang Liao, Gordon K. Smyth, Wei Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, Volume 30, Issue 7, 1 April 2014, Pages 923–930, https://doi.org/10.1093/bioinformatics/btt656
Zhu Y., Lu J., Zhao J., Zhang X., Yu H.H., Velkov T., Li J. Complete genome sequence and genome-scale metabolic modelling of Acinetobacter baumannii type strain ATCC 19606. Int. J. Med. Microbiol. 2020; 310:151412. doi: 10.1016/j.ijmm.2020.151412
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