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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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Autores principales: Ramanathan, Babu, Jindal, Hassan Mahmood, Le, Cheng Foh, Gudimella, Ranganath, Anwar, Arif, Razali, Rozaimi, Poole-Johnson, Johan, Manikam, Rishya, Sekaran, Shamala Devi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557631/
https://www.ncbi.nlm.nih.gov/pubmed/28797043
http://dx.doi.org/10.1371/journal.pone.0182524
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author Ramanathan, Babu
Jindal, Hassan Mahmood
Le, Cheng Foh
Gudimella, Ranganath
Anwar, Arif
Razali, Rozaimi
Poole-Johnson, Johan
Manikam, Rishya
Sekaran, Shamala Devi
author_facet Ramanathan, Babu
Jindal, Hassan Mahmood
Le, Cheng Foh
Gudimella, Ranganath
Anwar, Arif
Razali, Rozaimi
Poole-Johnson, Johan
Manikam, Rishya
Sekaran, Shamala Devi
author_sort Ramanathan, Babu
collection PubMed
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.
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spelling pubmed-55576312017-08-25 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 Razali, Rozaimi Poole-Johnson, Johan Manikam, Rishya Sekaran, Shamala Devi PLoS One Research Article 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. Public Library of Science 2017-08-10 /pmc/articles/PMC5557631/ /pubmed/28797043 http://dx.doi.org/10.1371/journal.pone.0182524 Text en © 2017 Ramanathan et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Ramanathan, Babu
Jindal, Hassan Mahmood
Le, Cheng Foh
Gudimella, Ranganath
Anwar, Arif
Razali, Rozaimi
Poole-Johnson, Johan
Manikam, Rishya
Sekaran, Shamala Devi
Next generation sequencing reveals the antibiotic resistant variants in the genome of Pseudomonas aeruginosa
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
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557631/
https://www.ncbi.nlm.nih.gov/pubmed/28797043
http://dx.doi.org/10.1371/journal.pone.0182524
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