Ramanathan, B. and Jindal, H.M. and Le, C.F. and Gudimella, R. and Anwar, A. and Razali, R. and Poole-Johnson, J. and Manikam, R. and Sekaran, S.D. (2017) Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. PLoS ONE, 12 (8). e0182524. ISSN 1932-6203, DOI https://doi.org/10.1371/journal.pone.0182524.
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Abstract
Rapid progress in next generation sequencing and allied computational tools have aided in identification of single nucleotide variants in genomes of several organisms. In the present study, we have investigated single nucleotide polymorphism (SNP) in ten multi-antibiotic resistant Pseudomonas aeruginosa clinical isolates. All the draft genomes were submitted to Rapid Annotations using Subsystems Technology (RAST) web server and the predicted protein sequences were used for comparison. Non-synonymous single nucleotide polymorphism (nsSNP) found in the clinical isolates compared to the reference genome (PAO1), and the comparison of nsSNPs between antibiotic resistant and susceptible clinical isolates revealed insights into the genome variation. These nsSNPs identified in the multi-drug resistant clinical isolates were found to be altering a single amino acid in several antibiotic resistant genes. We found mutations in genes encoding efflux pump systems, cell wall, DNA replication and genes involved in repair mechanism. In addition, nucleotide deletions in the genome and mutations leading to generation of stop codons were also observed in the antibiotic resistant clinical isolates. Next generation sequencing is a powerful tool to compare the whole genomes and analyse the single base pair variations found within the antibiotic resistant genes. We identified specific mutations within antibiotic resistant genes compared to the susceptible strain of the same bacterial species and these findings may provide insights to understand the role of single nucleotide variants in antibiotic resistance.
| Item Type: | Article |
|---|---|
| Funders: | University of Malaya High Impact Research Grant (reference number: UM.C/HIR/MOHE/MED/40, account number: H-848 20001-E000079), University of Malaya Research Grant (UMRG Project no. RP020C-14AFR and RP001C-13ICT), Sunway University: research grant (INTS-2017-SST-RCBS-01) |
| Uncontrolled Keywords: | Anti-Bacterial Agents; Disk Diffusion Antimicrobial Tests; Drug Resistance, Bacterial; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Humans; Polymorphism, Single Nucleotide; Pseudomonas aeruginosa; Pseudomonas Infections; Sequence Analysis, DNA |
| Subjects: | Q Science > Q Science (General) R Medicine |
| Divisions: | Faculty of Medicine |
| Depositing User: | Ms. Juhaida Abd Rahim |
| Date Deposited: | 30 Aug 2018 09:01 |
| Last Modified: | 30 Aug 2018 09:01 |
| URI: | http://eprints.um.edu.my/id/eprint/19049 |
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