Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa.
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 aerugi...
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Public Library of Science (PLoS)
2017-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0182524&type=printable |
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| author | Babu Ramanathan Hassan Mahmood Jindal Cheng Foh Le Ranganath Gudimella Arif Anwar Rozaimi Razali Johan Poole-Johnson Rishya Manikam Shamala Devi Sekaran |
| author_facet | Babu Ramanathan Hassan Mahmood Jindal Cheng Foh Le Ranganath Gudimella Arif Anwar Rozaimi Razali Johan Poole-Johnson Rishya Manikam Shamala Devi Sekaran |
| author_sort | Babu Ramanathan |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-d8e308a229194e2cb0baec608e7afced |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-d8e308a229194e2cb0baec608e7afced2025-08-20T03:04:38ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01128e018252410.1371/journal.pone.0182524Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa.Babu RamanathanHassan Mahmood JindalCheng Foh LeRanganath GudimellaArif AnwarRozaimi RazaliJohan Poole-JohnsonRishya ManikamShamala Devi SekaranRapid 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0182524&type=printable |
| spellingShingle | Babu Ramanathan Hassan Mahmood Jindal Cheng Foh Le Ranganath Gudimella Arif Anwar Rozaimi Razali Johan Poole-Johnson Rishya Manikam Shamala Devi Sekaran Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. PLoS ONE |
| title | Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. |
| title_full | Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. |
| title_fullStr | Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. |
| title_full_unstemmed | Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. |
| title_short | Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa. |
| title_sort | next generation sequencing reveals the antibiotic resistant variants in the genome of pseudomonas aeruginosa |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0182524&type=printable |
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