Universal bacterial identification by mass spectrometry of 16S ribosomal RNA cleavage products

2007 ◽  
Vol 261 (2-3) ◽  
pp. 218-226 ◽  
Author(s):  
George W. Jackson ◽  
Roger J. McNichols ◽  
George E. Fox ◽  
Richard C. Willson
Keyword(s):  
Mass Spectrometry ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Rna Cleavage ◽  
Bacterial Identification

scholarly journals Rapid and accurate detection of aminoglycoside modifying enzymes and 16S ribosomal RNA methyltransferases by targeted LC-MS/MS

2021 ◽  
Author(s):  
Dimard E. Foudraine ◽  
Nikolaos Strepis ◽  
Corné H. W. Klaassen ◽  
Merel N. Raaphorst ◽  
Annelies Verbon ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Antimicrobial Resistance ◽  
Ribosomal Rna ◽  
Resistance Mechanism ◽  
Resistance Mechanisms ◽  
Diagnostic Methods ◽  
16S Ribosomal Rna ◽  
Aminoglycoside Resistance ◽  
E Coli ◽  
Liquid Chromatography Tandem Mass

New and rapid diagnostic methods are needed for the detection of antimicrobial resistance to aid in the curbing of drug-resistant infections. Targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a method that could serve this purpose, as it can detect specific peptides of antimicrobial resistance mechanisms with high accuracy. In the current study, we developed an accurate and rapid targeted LC-MS/MS assay based on parallel reaction monitoring for detection of the most prevalent aminoglycoside modifying enzymes and 16S ribosomal RNA methyltransferases in E. coli and K. pneumoniae that confer resistance to aminoglycosides. Specific tryptic peptides needed for detection were selected and validated for AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6’)-Ib, AAC(6’)-Ib-cr, ANT(2”)-I, APH(3’)-VI, ArmA, RmtB, RmtC and RmtF. In total, 205 isolates containing different aminoglycoside resistance mechanisms that consisted mostly of E. coli and K. pneumoniae were selected for assay development and evaluation. Mass spectrometry results were automatically analyzed and were compared to whole genome sequencing results. Of the 2460 isolate and resistance mechanism combinations tested, 2416 combinations matched. Discrepancies were further analyzed by repeating LC-MS/MS analysis and performing additional PCRs. Mass spectrometry results were also used to predict resistance and susceptibility to gentamicin, tobramycin and amikacin in only the E. coli and K. pneumoniae isolates (n=191). The category interpretations were correctly predicted for gentamicin in 97.4% of the isolates, for tobramycin in 97.4% of the isolates, and for amikacin in 82.7% of the isolates. Targeted LC-MS/MS can be applied for accurate and rapid detection of aminoglycoside resistance mechanisms.

scholarly journals Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3

2010 ◽  
Vol 17 (10) ◽  
pp. 1241-1246 ◽  
Author(s):  
C Leong Ng ◽  
Kathrin Lang ◽  
Nicola A G Meenan ◽  
Amit Sharma ◽  
Ann C Kelley ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Structural Basis ◽  
Rna Cleavage ◽  
Colicin E3

scholarly journals A functional pseudoknot in 16S ribosomal RNA.

1991 ◽  
Vol 10 (8) ◽  
pp. 2203-2214 ◽  
Author(s):  
T. Powers ◽  
H.F. Noller
Keyword(s):  
Ribosomal Rna ◽  
16S Ribosomal Rna

A Comparison Between Elastic Network Interpolation and MD Simulation of 16S Ribosomal RNA

2003 ◽  
Vol 21 (3) ◽  
pp. 395-405 ◽  
Author(s):  
Moon K. Kim ◽  
Wen Li ◽  
Bruce A. Shapiro ◽  
Gregory S. Chirikjian
Keyword(s):  
Ribosomal Rna ◽  
Md Simulation ◽  
16S Ribosomal Rna ◽  
Elastic Network

scholarly journals Detection of Alcaligenes chronic endophthalmitis mimicking noninfectious uveitis with 16S ribosomal RNA PCR

2021 ◽  
Author(s):  
Tina Felfeli ◽  
Felicia Tai ◽  
Peng Yan ◽  
Tony Mazzulli ◽  
Nupura K. Bakshi ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
16S Ribosomal Rna
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