PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> 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 phage suitable for a therapeutic application in existin...
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MDPI AG
2023-02-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/5/4483 |
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| author | Maria Kornienko Dmitry Bespiatykh Maja Malakhova Roman Gorodnichev Nikita Kuptsov Egor Shitikov |
| author_facet | Maria Kornienko Dmitry Bespiatykh Maja Malakhova Roman Gorodnichev Nikita Kuptsov Egor Shitikov |
| author_sort | Maria Kornienko |
| collection | DOAJ |
| description | 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 phage suitable for a therapeutic application in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phages. Here, we propose a simple PCR approach to differentiate between two families of virulent <i>Staphylococcus</i> phages (<i>Herelleviridae</i> and <i>Rountreeviridae</i>) and eleven genera of virulent <i>Klebsiella</i> phages (<i>Przondovirus</i>, <i>Taipeivirus</i>, <i>Drulisvirus</i>, <i>Webervirus</i>, <i>Jiaodavirus</i>, <i>Sugarlandvirus</i>, <i>Slopekvirus</i>, <i>Jedunavirus</i>, <i>Marfavirus</i>, <i>Mydovirus</i> and <i>Yonseivirus</i>). This assay includes a thorough search of a dataset comprising <i>S. aureus</i> (<i>n</i> = 269) and <i>K. pneumoniae</i> (<i>n</i> = 480) phage genomes available in the NCBI RefSeq/GenBank database for specific genes that are highly conserved at the taxonomic group level. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which permits circumventing 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. |
| first_indexed | 2024-03-11T07:23:14Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T07:23:14Z |
| publishDate | 2023-02-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-14c5bb7955d8421a9ed06ea0fde74dde2023-11-17T07:49:06ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-02-01245448310.3390/ijms24054483PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> BacteriophagesMaria Kornienko0Dmitry Bespiatykh1Maja Malakhova2Roman Gorodnichev3Nikita Kuptsov4Egor Shitikov5Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, RussiaDepartment of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, RussiaDepartment of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, RussiaDepartment of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, RussiaDepartment of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, RussiaDepartment of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, RussiaPhage 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 phage suitable for a therapeutic application in existing libraries. At an early stage of the isolation process, rapid screening techniques are needed to identify and type potential virulent phages. Here, we propose a simple PCR approach to differentiate between two families of virulent <i>Staphylococcus</i> phages (<i>Herelleviridae</i> and <i>Rountreeviridae</i>) and eleven genera of virulent <i>Klebsiella</i> phages (<i>Przondovirus</i>, <i>Taipeivirus</i>, <i>Drulisvirus</i>, <i>Webervirus</i>, <i>Jiaodavirus</i>, <i>Sugarlandvirus</i>, <i>Slopekvirus</i>, <i>Jedunavirus</i>, <i>Marfavirus</i>, <i>Mydovirus</i> and <i>Yonseivirus</i>). This assay includes a thorough search of a dataset comprising <i>S. aureus</i> (<i>n</i> = 269) and <i>K. pneumoniae</i> (<i>n</i> = 480) phage genomes available in the NCBI RefSeq/GenBank database for specific genes that are highly conserved at the taxonomic group level. The selected primers showed high sensitivity and specificity for both isolated DNA and crude phage lysates, which permits circumventing 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.https://www.mdpi.com/1422-0067/24/5/4483bacteriophagephagebacteriophage typingtherapy<i>Staphylococcus aureus</i><i>Klebsiella pneumoniae</i> |
| spellingShingle | Maria Kornienko Dmitry Bespiatykh Maja Malakhova Roman Gorodnichev Nikita Kuptsov Egor Shitikov PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> Bacteriophages International Journal of Molecular Sciences bacteriophage phage bacteriophage typing therapy <i>Staphylococcus aureus</i> <i>Klebsiella pneumoniae</i> |
| title | PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> Bacteriophages |
| title_full | PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> Bacteriophages |
| title_fullStr | PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> Bacteriophages |
| title_full_unstemmed | PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> Bacteriophages |
| title_short | PCR Assay for Rapid Taxonomic Differentiation of Virulent <i>Staphylococcus aureus</i> and <i>Klebsiella pneumoniae</i> Bacteriophages |
| title_sort | pcr assay for rapid taxonomic differentiation of virulent i staphylococcus aureus i and i klebsiella pneumoniae i bacteriophages |
| topic | bacteriophage phage bacteriophage typing therapy <i>Staphylococcus aureus</i> <i>Klebsiella pneumoniae</i> |
| url | https://www.mdpi.com/1422-0067/24/5/4483 |
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