Oncotarget

Research Papers: Immunology:

Whole genome and transcriptome analysis reveal MALDI-TOF MS and SDS-PAGE have limited performance for the detection of the key outer membrane protein in carbapenem-resistant Klebsiella pneumoniae isolates

Naina Adren Pinto _, Roshan D’Souza, In Sik Hwang, Jongrak Choi, Yong Ha In, Hyung Soon Park, Choong-Min Ryu, Dongeun Yong and Kyungwon Lee

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Oncotarget. 2017; 8:84818-84826. https://doi.org/10.18632/oncotarget.19005

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Abstract

Naina Adren Pinto1,2, Roshan D’Souza1, In Sik Hwang1,2, Jongrak Choi1, Yong Ha In3, Hyung Soon Park3, Choong-Min Ryu4,5, Dongeun Yong1 and Kyungwon Lee1

1 Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea

2 Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea

3 ASTA Corporation, Suwon, Korea

4 Molecular Phytobacteriology Laboratory, KRIBB, Daejeon, Korea

5 Biosystems and Bioengineering Program, School of Science, University of Science and Technology, Daejeon, Korea

Correspondence to:

Dongeun Yong, email:

Keywords: MALDI-TOF MS, outer membrane protein, transcriptomic analysis, Klebsiella pneumoniae , whole-genome sequencing,  Immunology and Microbiology Section, Immune response, Immunity

Received: April 05, 2017 Accepted: June 20, 2017 Published: July 05, 2017

Abstract

To detect the outer membrane protein (OMP), which plays a key role in carbapenem resistance, whole-genome and transcriptome analysis of the clinical carbapenem-resistant Klebsiella pneumoniae was carried out. The index strain lacked both OmpK35 and OmpK36, whereas the other strains lacked only OmpK35. After SDS-PAGE, the putative OMP bands were excised and identified as OmpA and OmpK36. MALDI-TOF MS showed peaks at ~36 and ~38 kDa that corresponded to OmpA and OmpK36, respectively. In all the strains except YMC2014/03/P345, the ~38 kDa peaks were present. The K. pneumoniae ATCC 13883 isolate showed three bands on SDS-PAGE and three corresponding peaks on MALDI-TOF MS. The additional third peak at ~37 kDa corresponding to OmpK35 was observed. To verify OmpK35 peak detection in other K. pneumoniae isolates by MALDI-TOF MS, we analyzed six strains from our laboratory’s strain bank. Whole genome sequence indicated that only two isolates had intact OmpK35. Both MALDI-TOF MS and SDS-PAGE did not show a ~37 kDa peak or an OmpK35 band as observed in the K. pneumoniae ATCC 13883 isolate. Separation using SDS-PAGE showed a single peak representing OmpA. Therefore, both SDS-PAGE and MALDI-TOF MS were not completely reliable for OMP detection because they fail to detect OmpK35. To the best of our knowledge, this is the first report on the performance of SDS-PAGE and MALDI-TOF MS for the detection of OMP’s using whole-genome and RNA sequencing analyses.


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