Comprehensive genomic analysis of Klebsiella pneumoniae and its temperate N-15-like phage: From isolation to functional annotation

Abstract A temperate N-15-like phage and an extensively drug-resistant (XDR) Klebsiella pneumoniae strain were studied in this research. The former was found in hospital wastewater, while the latter was retrieved from the sputum of an intensive care unit patient. The bacteria showed strong resistance to several antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). Yersiniabactin, enterobactin, and E. coli common pilus (ECP) genes were also present in the genome; these genes are essential for the acquisition of iron, adhesion, and immune evasion, among other virulence factors. kappa testing categorized the strain as K64 and O2a types. The presence of colicin genes, IncHI1B_1_pNDM-MAR and IncFIB replicons, and other plasmids in this strain demonstrate its ability to spread antibiotic resistance and facilitate horizontal gene transfer. Adding to its genetic variety and adaptability, the genome included CRISPR-Cas systems and eleven prophage regions. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8 percent of ORFs), DNA replication and repair enzymes (9.3 percent of ORFs), and a toxin-antitoxin system (0.4 percent of ORFs) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Lysogeny and horizontal gene transfer are two mechanisms by which phages may influence bacterial evolution. Learning about the phage’s role in bacterial evolution, host-phage relationships, and horizontal gene transfer is a great benefit. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research. Author Summary Antibiotic-resistant bacteria represent a significant global health threat, and comprehending their interactions with bacteriophages is essential for formulating novel antimicrobial tactics and elucidating the molecular development of bacteria. This work examined an extensively drug-resistant (XDR) strain of Klebsiella pneumoniae isolated from an ICU patient and a temperate N-15-like phage identified in hospital effluent. The bacterial strain exhibited resistance to multiple antibiotics owing to an array of resistance genes, plasmids, porin mutations, and virulence characteristics that facilitated its survival and pathogenicity. The genomic investigation of the phage elucidated its structural organization, replication mechanisms, and possible contribution to bacterial development through lysogeny and horizontal gene transfer. Our findings underscore the intricate host-phage interactions that affect antibiotic resistance and pathogenicity in K. pneumoniae, offering significant insights into microbial evolution and the prospective relevance of phages in therapeutic approaches.