Furthermore, the PLS-DA and OPLS scores plots revealed a distinct separation of controls from pneumonia samples (Fig. S2).
RF analysis, utilizing the whole sample set of ions, showed distinct clustering of the two groups in positive mode; however, three of the pneumonia samples were misclassified as belonging in the control group.
A heatmap was additionally constructed based on the top fifty ranked metabolites of the positive mode data, revealing patterns of differential levels of urinary metabolites between controls and pneumonia samples (Fig. 2E).
To quantify further the differences in gene-expression pattern of the H1N1 influenza A and bacterial pneumonia samples on day 1 of admission to ICU, a Support Vector Machines (SVM) class predictor was built [ 20].
For MDR-RTI bacteria, methanol extract showed maximum inhibition (ZI 14 mm) against K. pneumoniae (Sample 38).
In case of MDR-UTI strain of E. coli (Sample 9) methanolic extract exhibited maximum inhibition (ZI 18 mm), whereas another strain of E. coli (Sample 5) and K. pneumoniae (Sample 26) showed maximum inhibition (ZI 15 mm and 16 mm respectively) with acetone extract.
Acetone extract of ex vitro plant exhibited maximum inhibition against MDR-RTI strain of Klebsiella pneumoniae (sample-38) [ZI 14 ± 0.22 mm, MIC 5.0 μg/mL, MBC 7.5 μg/mL].
According to the collection date of these K. pneumoniae samples, we divided them into two categories: S1, collected from 2002 to 2006, contains 110 strains; S2, collected from 2007 to 2008, includes 96 strains.
In our K. pneumoniae samples, we found a wide variety of antibiotic genes with exceptionally high copy numbers, including efflux pumps (e.g. tetracycline efflux pump, ABC transporter), and drug-inactivating enzymes (e.g. beta-lactamase, macrolide phosphotransferase, streptomycin adenylyltransferase, aminoglycoside acetyltransferase, aminoglycoside phosphotransferase).
In a retrospective study of S. pneumoniae samples (n = 20), the median (IQR; range) CSF S. pneumoniae bacterial load was 1.1 × 10 GE/μL (1.2 × 10; 1 to 6.1 × 10 DNA GE/μL).
