Rapid phenotypic characterization of Salmonella enterica strains by pyrolysis metastable atom bombardment mass spectrometry with multivariate statistical and artificial neural network pattern recognition.
Pyrolysis mass spectrometry was investigated for rapid characterization of bacteria. Spectra of Salmonella were compared to their serovars, pulsed-field gel electrophoresis (PFGE) patterns, antibiotic resistance profiles, and MIC values. Pyrolysis mass spectra generated via metastable atom bombardment were analyzed by multivariate principal component-discriminant analysis and artificial neural networks (ANNs). Spectral patterns developed by discriminant analysis and tested with Leave-One-Out (LOO) cross-validation distinguished Salmonella strains by serovar (97% correct) and by PFGE groups (49%). An ANN model of the same PFGE groups was cross-validated, using the LOO rule, with 92% agreement. Using an ANN, thirty previously unseen spectra were correctly classified by serotype (97%) and at the PFGE level (67%). Attempts by ANN to model spectra grouped by resistance profile-but ignoring PFGE or serotype-failed (10% correct), but ANNs differentiating ten samples of the same serotype/PFGE class were more successful. To assess the information content of PyMS data serendipitously associated with or directly related to resistance character, the ten isolates were grouped into four, three, or two categories. The four categories corresponded to four resistance profiles. The four class and three class ANNs showed much improved but insufficient modeling power. The two-class ANN and a corresponding multivariate model maximized inferential power for a coarse antibiotic-resistance-related distinction. They each cross-validated by LOO at 90%. This is the first direct correlation of pyrolysis metastable atom bombardment mass spectrometry with immunological (e.g. serology) or molecular biology (e.g. PFGE) based techniques.
Wilkes
Jon G
JG
National Center for Toxicological Research, FDA, 3900 NCTR Drive, Jefferson, AR 72079, USA. jwilkes@nctr.fda.gov
Rushing
Larry
L
Nayak
Rajesh
R
Buzatu
Dan A
DA
Sutherland
John B
JB
D015373:Bacterial Typing Techniques; D001431:Bacteriological Techniques; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D024881:Drug Resistance, Bacterial; D016521:Electrophoresis, Gel, Pulsed-Field; D013058:Mass Spectrometry / Q000379:methods* / Q000706:statistics & numerical data; D015999:Multivariate Analysis; D016571:Neural Networks, Computer; D010363:Pattern Recognition, Automated; D010641:Phenotype; D025341:Principal Component Analysis; D019779:Salmonella enterica / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D012703:Serotyping
D004269:DNA, Bacterial