Resistome and pathogenomics of multidrug resistant (MDR) Pseudomonas aeruginosa VRFPA03, VRFPA05 recovered from alkaline chemical keratitis and post-operative endophthalmitis patient

Murugan, Nandagopal; Malathi, Jambulingam; Vetrivel, Umashankar; Hn, Madhavan

doi:10.1016/j.gene.2015.12.022

Cited by 15 publications

(18 citation statements)

References 30 publications

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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%

“…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]. Further, Multiplex PCR assay has higher sensitivity which could detect from the samples with lower bacterial load.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

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

Self Cite

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“…Finally, a search of NCBI for the L153R and S170N mutations in ParR revealed that these mutations are present in a cluster of P. aeruginosa belonging to ST-235 from East Asia. P. aeruginosa VRFP04 from this cluster has been analyzed in detail and it is colistin sensitive (14). Though additional experiments are underway to confirm these findings, the data strongly suggests that colistin non-susceptibility in P. aeruginosa MRSN 12280 is due to Mcr-5.…”

Section: Manuscriptmentioning

confidence: 99%

Chromosomally Encoded mcr-5 in Colistin Non-susceptible Pseudomonas aeruginosa

Snesrud

Maybank

Kwak

et al. 2018

Preprint

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15 Whole genome sequencing (WGS) of historical Pseudomonas aeruginosa clinical isolates 16 identified a chromosomal copy of mcr-5 within a Tn3-like transposon in P. aeruginosa MRSN 17 12280. The isolate was non-susceptible to colistin by broth microdilution and genome analysis 18 revealed no mutations known to confer colistin resistance. To the best of our knowledge this is 19 the first report of mcr in colistin non-susceptible P. aeruginosa. 20 89 This publication made use of the Pseudomonas aeruginosa MLST website (https://pubmlst.org/ 90 paeruginosa/) developed by Keith Jolley and sited at the University of Oxford (Jolley & Maiden 91 2010, BMC Bioinformatics, 11:595). The development of this site has been funded by the 92 Wellcome Trust.

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“…Moreover, clinical strains from keratitis prefer to carry exoU gene rather than exoS in their accessory genome [5,9], although the core genome, approximately 90% of the complete genome, contains most of the virulence genes [10]. Besides, the clinical strains carrying multiple antimicrobial drug resistance in the accessory genome are associated with poor clinical outcome in patients with keratitis [11]. Indeed, multiple drugresistant (MDR) strains carrying exoU protein may lead to poor clinical outcomes [11].…”

Section: Introductionmentioning

confidence: 99%

“…Besides, the clinical strains carrying multiple antimicrobial drug resistance in the accessory genome are associated with poor clinical outcome in patients with keratitis [11]. Indeed, multiple drugresistant (MDR) strains carrying exoU protein may lead to poor clinical outcomes [11].…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics of ocularPseudomonas aeruginosastrains from keratitis patients with different clinical outcomes

Kandasamy

Thirumalmuthu

Prajna

et al. 2020

Preprint

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Bacterial keratitis caused by Pseudomonas aeruginosa is a destructive disease of cornea.Pseudomonas keratitis progresses rapidly and leads to vision loss if untreated. Even with adequate treatment, many patients show poor visual outcomes. The virulence factors or multiple drug-resistant (MDR) mechanisms of the ocular strains responsible for poor clinical outcomes remain largely unknown. Here, we performed whole-genome sequencing of five P. aeruginosa strains cultured from corneal scrapings of the healed and corneal buttons of the poor outcome keratitis patients. We investigated the distribution of virulence factors, resistance genes and resistance-associated mutations, the efflux-pump system in all five genomes, and as groups between poor and good clinical outcome as well as MDR vs. non-MDR. We detected several resistance genes and mutations associated with drug resistance in MDR groups; however, a large number of virulence genes were detected in all our genomes. Among the virulence genes, exoU and exoS exotoxin of the Type III secretion system detected in MDR and non-MDR strains, respectively, considered as main virulence contributors of keratitis pathogenesis. Despite this fact, this study did not show an association between MDR with exoU and poor clinical outcomes. However, strain-specific resistance and virulence genes were observed in this study, suggesting their role in the clinical outcome. Mainly, the flagellar genes fliC and fliD, reported to altering the host immune response, might impact the clinical outcome.This comparative study may provide new insights into the genome of ocular strains and requires further functional studies.

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Resistome and pathogenomics of multidrug resistant (MDR) Pseudomonas aeruginosa VRFPA03, VRFPA05 recovered from alkaline chemical keratitis and post-operative endophthalmitis patient

Cited by 15 publications

References 30 publications

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

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

Chromosomally Encoded mcr-5 in Colistin Non-susceptible Pseudomonas aeruginosa

Comparative genomics of ocularPseudomonas aeruginosastrains from keratitis patients with different clinical outcomes

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