Genomic insights into colistin resistance evolution in Pseudomonas Aeruginosa

Abstract

Colistin (polymyxin E) is the last-resort antibiotic used to treat multidrug-resistant Gram-negative bacterial infections, including those caused by Pseudomonas aeruginosa. The global emergence of colistin-resistant Pseudomonas aeruginosa is a significant concern for healthcare professionals. Therefore, identifying key contributors to the development of colistin resistance is crucial for addressing this issue. In this study, P. aeruginosa ATCC 9027 was serially exposed to subminimal inhibitory concentrations (MICs) of colistin for 14 consecutive days to obtain the Col-E1 strain. The Col-E1 strain was then cultured for 10 days in antibiotic-free medium to acquire the Col-E2 strain. The whole-genome sequences of three strains, namely, P. aeruginosa ATCC 9027 (the original strain, PA-1), Col-E1 and Col-E2, were assembled, annotated and analyzed. The bioinformatics pipeline included FASTQC (v0.11.9) for quality control; Unicycler (v.0.5.0) for de novo assembly; Bowtie2 (v2.4.5) and Picard Tools (v.2.27.4) for alignment; SAMtools (v1.11) and BCFtools (v.1.15) for variant calling; and SnpEff (v5.1) for variant annotation. As a result, we obtained a draft genome of P. aeruginosa ATCC 9027 consisting of 6,314,207 bp with 146-fold coverage. After aligning Col-E1 and Col-E2 against the draft genome, the number of insertion-deletions (INDELs) and single nucleotide polymorphisms (SNPs) were found, with 486 INDELs and 162 SNPs for Col-E1 and 474 INDELs and 163 SNPs for Col-E2. A high overlap rate of variants, including 448 INDELs and 153 SNPs, was observed between Col-E1 and Col-E2, indicating that the number of variants was constant. The analysis revealed notable mutations in genes encoding ribosomal components (rpsL, rpsG, and rpsJ), genes involved in efflux transmembrane transporter activity (czcC_1), and genes encoding an outer membrane porin (oprD). The variants were found in upstream (36.5%), downstream (25.7%) or intergenic (19.1%) regions. These mutations may be involved in gene expression regulation, leading to the development of a colistin-resistant phenotype. In conclusion, this study provided a preliminary overview of how P. aeruginosa responds to colistin antibiotic stress at the genomic level. These mutations could be used as markers for colistin resistance and further investigated to clarify their role in the colistin resistance of Pseudomonas aeruginosa.