• Plasmid was extracted from carbapenem-resistant Klebsiella pneumoniae clinical isolate using plasmid extraction kit.
• The plasmid was transformed into the susceptible E. coli DH5a which gained carbapenem resistance after transformation.
• Plasmid was extracted from the transformant for PCR, OXA-48-like gene was detected by PCR and confirmed by Sanger sequencing of the amplicon.
• However, when the whole plasmid extract was sequenced (Whole plasmid sequencing), OXA-48-like gene was not found on the plasmid, and instead, NDM-1 gene was present (which was not detected by PCR initially, but was detected later when PCR was repeated)
• The question is:

1- Is there a logical explanation for the loss of OXA-48-like gene?

2- Why was NDM gene not detected initially by PCR if the same primers, master mix, and conditions were used both times?