PCR assay for rapid taxonomic differentiation of virulent Staphylococcus aureus and Klebsiella pneumoniae bacteriophages

Phage therapy is now seen as a promising way to overcome the current global crisis in the spread of multidrug-resistant bacteria. However, phages are highly strain specific and, in most cases, one will have to isolate a new phage, or search for a suitable for therapeutic application phage in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phage. Here, we proposed a simple PCR approach to differentiate between two families of virulent <em>Staphylococci</em> phages (<em>Herelleviridae</em> and <em>Rountreeviridae</em>) and eleven genera of virulent <em>Klebsiella</em> phages (<em>Przondovirus, Taipeivirus, Drulisvirus, Webervirus, Jiaodavirus, Sugarlandvirus, Slopekvirus, Jedunavirus, Marfavirus, Mydovirus</em>, and <em>Yonseivirus</em>). This assay included a thorough search for specific genes, that are highly conserved at the taxonomic group level, on a dataset comprising <em>S. aureus</em> (<em>n</em> = 269) and <em>K. pneumoniae</em> (<em>n</em> = 480) phage genomes available in the NCBI RefSeq/GenBank database. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which allows circumventing the DNA purification protocols. Our approach can be extended and applied to any group of phages, given the large number of available genomes in the databases.