Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa

Babu Ramanathan, Hassan Mahmood Jindal, Cheng Foh Le, Ranganath Gudimella, Arif Anwar, Rozaimi Mohamad Razali, Johan Poole-Johnson, Rishya Manikam, Shamala Devi Sekaran

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Article numbere0182524
JournalPLoS One
Volume12
Issue number8
DOIs
Publication statusPublished - 1 Aug 2017
Externally publishedYes

Fingerprint

Pseudomonas aeruginosa
Genes
antibiotics
Genome
Anti-Bacterial Agents
genome
Nucleotides
nucleotides
mutation
genes
Mutation
single nucleotide polymorphism
Single Nucleotide Polymorphism
world wide web
Polymorphism
Terminator Codon
stop codon
DNA replication
Microbial Drug Resistance
DNA Replication

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. / Ramanathan, Babu; Jindal, Hassan Mahmood; Le, Cheng Foh; Gudimella, Ranganath; Anwar, Arif; Mohamad Razali, Rozaimi; Poole-Johnson, Johan; Manikam, Rishya; Sekaran, Shamala Devi.

In: PLoS One, Vol. 12, No. 8, e0182524, 01.08.2017.

Research output: Contribution to journalArticle

Ramanathan, B, Jindal, HM, Le, CF, Gudimella, R, Anwar, A, Mohamad Razali, R, Poole-Johnson, J, Manikam, R & Sekaran, SD 2017, 'Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa', PLoS One, vol. 12, no. 8, e0182524. https://doi.org/10.1371/journal.pone.0182524
Ramanathan, Babu ; Jindal, Hassan Mahmood ; Le, Cheng Foh ; Gudimella, Ranganath ; Anwar, Arif ; Mohamad Razali, Rozaimi ; Poole-Johnson, Johan ; Manikam, Rishya ; Sekaran, Shamala Devi. / Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. In: PLoS One. 2017 ; Vol. 12, No. 8.
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