Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India

Malathi, Jambulingam; Murugan, Nandagopal; Vetrivel, Umashankar; Bagyalakshmi, R; Madhavan, H. N.

doi:10.1128/genomea.00425-13

Cited by 10 publications

(11 citation statements)

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“…By contrast, isolate 77 was related to several strains, including the multi-drug-resistant P. aeruginosa NCGM2.S1 [ 33 ] and the cytotoxic corneal isolate P. aeruginosa 6077 [ 34 ]. Finally, the 30-1, 42-1, 45, and 04 isolates presented a close relationship and were related to the multi-drug resistant P. aeruginosa VRFPA02 isolate from India [ 35 ].…”

Section: Resultsmentioning

confidence: 99%

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

et al. 2016

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Background: Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains. Results: The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15 % of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates. Conclusions: We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.

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Section: Resultsmentioning

confidence: 99%

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

et al. 2016

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“…We designed primers for the selected genes found to be most prevalent among clinical studies as well as our own observation from NGS based study and other reports [12–21]. Multiplex PCR Primer designed against drug resistance gene include Group‐1; (ESBL‐MBL) blaTem, blaOXA, blaCTX‐M‐15, blaVim) Group‐2, (blaGes, blaVeb and DIM and AmpC) Efflux pump genes‐ Group‐3 (MexA,B‐oprM); Group‐4 (MexC,D‐oprJ); Group‐5 (Mex X,Y‐oprN) Group‐6 (oprD, nfxB, MexR) primers were purchased from Eurofins Genomics India Pvt Ltd, Bangalore, India.…”

Section: Methodsmentioning

confidence: 99%

“…From our experience, emergence of culture negative intraocular specimens is steadily increasing, which leads to unwanted avoidable blindness. Hence, the current study designed to target most common betalactamase and efflux pump genes among P aeruginosa reported in literature and our own study experiences [3–5,12–17]. In addition, the current study will assess the coexistence of ESBL, MBL and efflux pump genes among P. aeruginosa isolates obtained from variety of clinical specimens (ocular tissues, blood, urine, pus and etc) using multiplex PCR and the same were compared with Phenotypic methods [18].…”

Section: Introductionmentioning

confidence: 99%

Application of six multiplex PCR's among 200 clinical isolates of Pseudomonas aeruginosa for the detection of 20 drug resistance encoding genes

Murugan

Malathi

Therese

et al. 2017

The Kaohsiung J of Med Scie

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Pseudomonas aeruginosa (P. aeruginosa) is a menacing opportunistic, nosocomial pathogen; become a growing concern as conventional antimicrobial therapy is now futile against it. Multi‐drug resistant P. aeruginosa (MDRPA) has distinctive resistance mechanisms such as production of β‐lactamases, repression of porin genes and over‐expression of efflux pumps. The focus of this study is to standardize and application of multiplex PCR (mPCR) to detect the presence of betalactamase genes encoding blaTem, blaOXA, blaCTX‐M‐15, blaVim, blaGes, blaVeb, blaDIM, AmpC and Efflux pump genes encoding Mex A,B‐oprM, Mex C,D‐oprJ, Mex X,Y‐oprN, oprD, nfxB, MexR. A total of 200 clinical isolates of P. aeruginosa were tested for the presence of the above mentioned genes genotypically through mPCR and characterized by phenotypic methods for ESBL and MBL production. Out of 200 isolates, 163 (81.5%) nfxB regulator gene, 102 (51%) MexA, 96 (48%) MexC, 93 (46.5%) MexB, 86 (43%) MexD, 81 (40.5%) OprM, 74 (37%) OprJ, 72 (36%) OprD and MexR, 53 (26.5%) Mex X and OprN, 49 (24.5%) MexY gene. Betalactamase genes 145 (72.5%) blaTem, 67 (33.5%) blaOXA, 35 (17.5%) blaVim, 25(12.50%), 23 (11.50%) blaVeb, 21 (11.5%) blaGes, 14 (7%) Ctx‐m and 10 (5%) AmpC and 5 (2.5%) blaDim‐1 gene were tested positive by mPCR. Phenotypically 38 (19%) and 29 (14.5%) out of 200 tested positive for ESBL and MBL production. Application of this mPCR on clinical specimens is fast, accurate, specific and low‐cost reliable tool for the screening, where culture negative Eubacterial PCR positive cases for an early molecular detection of drug resistance mechanism assisting the clinician to treat the disease with appropriate antibiotic selection.

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“…By contrast, isolate 77 was related to several strains, including the multi-drug-resistant Pseudomonas aeruginosa NCGM2.S1 [26] and the 305 cytotoxic corneal isolate Pseudomonas aeruginosa 6077 [27]. Finally, the 30-1, 42-1, 45, and 04 isolates presented a close relationship and were related to the multi-drug resistant Pseudomonas aeruginosa VRFPA02 isolate from India [28].…”

mentioning

confidence: 99%

Pangenome-wide and molecular evolution analyses of thePseudomonas aeruginosa species

Mosquera-Rendón

Rada

Cárdenas-Brito

et al. 2015

Preprint

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30Background. Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, 35 major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains. Results. The P. aeruginosa pangenome was estimated to contain almost 17,000 non-redundant genes, and approximately 15% of these constituted the core 40 genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with 45 the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates.Conclusions. We report the unprecedented pangenome characterization of P. aeruginosa 50 on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein

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Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India

Cited by 10 publications

References 4 publications

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species

Application of six multiplex PCR's among 200 clinical isolates of Pseudomonas aeruginosa for the detection of 20 drug resistance encoding genes

Pangenome-wide and molecular evolution analyses of thePseudomonas aeruginosa species

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