WHOLE-GENOME ANALYSIS OF COLISTIN EXPOSED PSEUDOMONAS AERUGINOSA (ATCC 9027 Strain)

Colistin (polymyxin E) is the last-choice antibiotic to treat multidrug-resistant Gram-negative bacterial infections, such as Pseudomonas aeruginosa infection. However, the careless use of colistin caused the emergence of colistin-resistant Pseudomonas aeruginosa worldwide. By analyzing the genome alterations of colistin-exposed Pseudomonas aeruginosa, we could find the keys to contribute to the resistance. Whole-genome sequencing (WGS) data of Pseudomonas aeruginosa ATCC 9027 (original strain), Col-E1 (colistin-exposed strain for 14 days), and Col-E2 (Col-E1 cultured in colistin-free medium for 10 days) were analyzed. FASTQC (v0.11.9) was used to check the quality of the sequence reads. De novo assembly was performed using a program called Unicycler (v.0.5.0). The Bowtie2 (v2.4.5) and the Picard Tools (v.2.27.4) were used for alignment. The Bcftools (v.1.15) was used for variant calling. The SnpEff (v5.1) was used for variant annotation. Lastly, the Gene ontology (GO annotation) was used for further gene analysis. As a result, P. aeruginosa ATCC 9027 with a 6.03 Mb genome of 79 scaffolds with a scaffold N50 size of 277 Kb was obtained. The number of INDELs and SNPs from Col-E1 and Col-E2 were as follows: 204, 206 (INDELs); 135, 135 (SNPs), respectively. In the end, 9 genes that were identified share the possibility of participating in the colistin resistance mechanism (pstS, dnaE2, phzM, dppA_2, rpsJ, ccoP1, czcC_1, phzD2, betT1) which mainly involved the biofilm and pyocyanin formation and the efflux transmembrane transporter activity.