Bacterial DNA was extracted by using the DNA Express set (LyTeh, Moscow, Russia). Multilocus sequence typing (MLST) of K. pneumoniae strains was performed by determining the nucleotide sequences of seven housekeeping genes as described previously [64 (link)]. The capsular type was determined by wzi gene sequencing [65 (link)]. Hypervirulence-associated genes rmpA, rmpA2, peg-344, fimH, iutA, and iroB were amplified using previously published sets of primers [28 (link),66 (link)] (Supplementary Table S2 ).
Extraction of the phage genomic DNA was performed using a standard phenol–chloroform extraction protocol [67 ]. Phage genome was sequenced using a high-throughput Illumina HiSeq system. SPAdes v3.14.0 software was used for genome assembly [68 (link)]. Phage terminal repeats were predicted with the PhageTerm tool v3.0.1 [69 (link)] and determined by direct Sanger sequencing using primers reported inSupplementary Table S2 . GeneMarkS v4.32 was used for identification of open reading frames (ORFs) within the genome [70 (link)]. The tRNA genes were searched using tRNAScan-SE v2.0 [71 (link)] and ARAGORN v1.2.41 [72 (link)]. The Clinker tool was used in comparative genomic analysis [73 (link)].
Annotation of predicted genes was conducted manually using BLASTp v2.13.0, HHPred, PHROG v4, and InterPro v5.59-91.0. The absence of potentially toxic genes and antibiotic resistance determinants was confirmed by comparison with the databases Virulence Factors of Pathogenic Bacteria [74 (link)] and Antibiotic Resistance Genes Databases [75 (link)]. The annotated genome sequence of the vB_KpnP_Klyazma phage was deposited in the NCBI GenBank database under accession number OP125547.1.
Extraction of the phage genomic DNA was performed using a standard phenol–chloroform extraction protocol [67 ]. Phage genome was sequenced using a high-throughput Illumina HiSeq system. SPAdes v3.14.0 software was used for genome assembly [68 (link)]. Phage terminal repeats were predicted with the PhageTerm tool v3.0.1 [69 (link)] and determined by direct Sanger sequencing using primers reported in
Annotation of predicted genes was conducted manually using BLASTp v2.13.0, HHPred, PHROG v4, and InterPro v5.59-91.0. The absence of potentially toxic genes and antibiotic resistance determinants was confirmed by comparison with the databases Virulence Factors of Pathogenic Bacteria [74 (link)] and Antibiotic Resistance Genes Databases [75 (link)]. The annotated genome sequence of the vB_KpnP_Klyazma phage was deposited in the NCBI GenBank database under accession number OP125547.1.
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