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Rise of Clinical Mi...
Rise of Clinical Microbial Proteogenomics : A Multiomics Approach to Nontuberculous Mycobacterium-The Case of Mycobacterium abscessus UC22
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- Advani, Jayshree (author)
- Inst Bioinformat, Int Technol Pk, Bangalore, Karnataka, India;Manipal Acad Higher Educ, Manipal, Karnataka, India
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- Verma, Renu (author)
- Inst Bioinformat, Int Technol Pk, Bangalore, Karnataka, India
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- Chatterjee, Oishi (author)
- Inst Bioinformat, Int Technol Pk, Bangalore, Karnataka, India;Yenepoya, Yenepoya Res Ctr, Ctr Syst Biol & Mol Med, Univ Rd, Mangalore 575018, India;Amrita Vishwa Vidyapeetham, Sch Biotechnol, Kollam, India
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- Balaya, Rex Devasahayam Arokia (author)
- Yenepoya, Yenepoya Res Ctr, Ctr Syst Biol & Mol Med, Univ Rd, Mangalore 575018, India
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- Najar, Mohd Altaf (author)
- Yenepoya, Yenepoya Res Ctr, Ctr Syst Biol & Mol Med, Univ Rd, Mangalore 575018, India
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- Ravishankara, Namitha (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,MS Ramaiah Inst Technol, Dept Biotechnol, Bangalore, Karnataka, India
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- Suresh, Sneha (author)
- MS Ramaiah Inst Technol, Dept Biotechnol, Bangalore, Karnataka, India;Univ Massachusetts Lowell, Dept Biol Sci, Lowell, MA USA
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- Pachori, Praveen Kumar (author)
- ICMR Natl JALMA Inst Leprosy & Other Mycobacteria, Dept Microbiol & Mol Biol, Agra, Uttar Pradesh, India
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- Gupta, Umesh D. (author)
- ICMR Natl JALMA Inst Leprosy & Other Mycobacteria, Dept Microbiol & Mol Biol, Agra, Uttar Pradesh, India
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- Pinto, Sneha M. (author)
- Yenepoya, Yenepoya Res Ctr, Ctr Syst Biol & Mol Med, Univ Rd, Mangalore 575018, India
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- Chauhan, Devendra S. (author)
- ICMR Natl JALMA Inst Leprosy & Other Mycobacteria, Dept Microbiol & Mol Biol, Agra, Uttar Pradesh, India
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- Tripathy, Srikanth Prasad (author)
- ICMR Natl JALMA Inst Leprosy & Other Mycobacteria, Dept Microbiol & Mol Biol, Agra, Uttar Pradesh, India;Natl Inst Res TB, Madras, Tamil Nadu, India
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- Gowda, Harsha (author)
- Inst Bioinformat, Int Technol Pk, Bangalore, Karnataka, India
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- Prasad, T. S. Keshava (author)
- Inst Bioinformat, Int Technol Pk, Bangalore, Karnataka, India;Yenepoya, Yenepoya Res Ctr, Ctr Syst Biol & Mol Med, Univ Rd, Mangalore 575018, India
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(creator_code:org_t)
- MARY ANN LIEBERT, INC, 2018
- 2018
- English.
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In: Omics. - : MARY ANN LIEBERT, INC. - 1536-2310 .- 1557-8100. ; 23:1, s. 1-16
- Related links:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
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- Nontuberculous mycobacterial (NTM) species present a major challenge for global health with serious clinical manifestations ranging from pulmonary to skin infections. Multiomics research and its applications toward clinical microbial proteogenomics offer veritable potentials in this context. For example, the Mycobacterium abscessus, a highly pathogenic NTM, causes bronchopulmonary infection and chronic pulmonary disease. The rough variant of the M. abscessus UC22 strain is extremely virulent and causes lung upper lobe fibrocavitary disease. Although several whole-genome next-generation sequencing studies have characterized the genes in the smooth variant of M. abscessus, a reference genome sequence for the rough variant was generated only recently and calls for further clinical applications. We carried out whole-genome sequencing and proteomic analysis for a clinical isolate of M. abscessus UC22 strain obtained from a pulmonary tuberculosis patient. We identified 5506 single-nucleotide variations (SNVs), 63 insertions, and 76 deletions compared with the reference genome. Using a high-resolution LC-MS/MS-based approach (liquid chromatography tandem mass spectrometry), we obtained protein coding evidence for 3601 proteins, representing 71% of the total predicted genes in this genome. Application of proteogenomic approach further revealed seven novel protein-coding genes and enabled refinement of six computationally derived gene models. We also identified 30 variant peptides corresponding to 16 SNVs known to be associated with drug resistance. These new observations offer promise for clinical applications of microbial proteogenomics and next-generation sequencing, and provide a resource for future global health applications for NTM species.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Infektionsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Infectious Medicine (hsv//eng)
Keyword
- acquired resistance
- next-generation sequencing
- global health
- proteogenomics
- multiomics
- nontuberculous mycobacterial species
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Advani, Jayshree
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Verma, Renu
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Chatterjee, Oish ...
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Balaya, Rex Deva ...
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Najar, Mohd Alta ...
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Ravishankara, Na ...
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Suresh, Sneha
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Pachori, Praveen ...
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Gupta, Umesh D.
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Pinto, Sneha M.
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Chauhan, Devendr ...
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Tripathy, Srikan ...
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Gowda, Harsha
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Prasad, T. S. Ke ...
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- MEDICAL AND HEALTH SCIENCES
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Omics
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Uppsala University