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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

Authors
 Naina Adren Pinto  ;  Roshan D’Souza  ;  In Sik Hwang  ;  Jongrak Choi  ;  Yong Ha In  ;  Hyung Soon Park  ;  Choong-Min Ryu  ;  Dongeun Yong  ;  Kyungwon Lee 
Citation
 Oncotarget, Vol.8(49) : 84818-84826, 2017 
Journal Title
 Oncotarget 
Issue Date
2017
Keywords
Immune response ; Immunity ; Immunology and Microbiology Section ; Klebsiella pneumoniae ; MALDI-TOF MS ; outer membrane protein ; transcriptomic analysis ; whole-genome sequencing
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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DOI
10.18632/oncotarget.19005
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
용동은(Yong, Dong Eun) ORCID logo https://orcid.org/0000-0002-1225-8477
이경원(Lee, Kyungwon) ORCID logo https://orcid.org/0000-0003-3788-2134
최종락(Choi, Jong Rak) ORCID logo https://orcid.org/0000-0002-0608-2989
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URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/160652
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