Characterization of vB_Kpn_F48, a Newly Discovered Lytic Bacteriophage for Klebsiella pneumoniae of Sequence Type 101

Abstract

Resistance to carbapenems in Enterobacteriaceae, including Klebsiella pneumoniae, represents a major clinical problem given the lack of effective alternative antibiotics. Bacteriophages could provide a valuable tool to control the dissemination of antibiotic resistant isolates, for the decolonization of colonized individuals and for treatment purposes. In this work, we have characterized a lytic bacteriophage, named vB_Kpn_F48, specific for K. pneumoniae isolates belonging to clonal group 101. Phage vB_Kpn_F48 was classified as a member of Myoviridae, order Caudovirales, on the basis of transmission electron microscopy analysis. Physiological characterization demonstrated that vB_Kpn_F48 showed a narrow host range, a short latent period, a low burst size and it is highly stable to both temperature and pH variations. High throughput sequencing and bioinformatics analysis revealed that the phage is characterized by a 171 Kb dsDNA genome that lacks genes undesirable for a therapeutic perspective such integrases, antibiotic resistance genes and toxin encoding genes. Phylogenetic analysis suggests that vB_Kpn_F48 is a T4-like bacteriophage which belongs to a novel genus within the Tevenvirinae subfamily, which we tentatively named “F48virus”. Considering the narrow host range, the genomic features and overall physiological parameters phage vB_Kpn_F48 could be a promising candidate to be used alone or in cocktails for phage therapy applications.

Isolation and Characterization of Novel Lytic Bacteriophages Infecting Epidemic Carbapenem-Resistant Klebsiella pneumoniae Strains

“…However, both vB_Kpn_F48 and AmPh_EK29 appear to be narrow host-range phages. Phage vB_Kpn_F48 had a lytic activity specific to K. pneumoniae strains belonging to ST101 (K17) and its closely related strains ( Ciacci et al, 2018 ). Similarly, AmPh_EK29 was specifically active against K. pneumoniae ST258 clade 1 strains (KL106).…”

“…Although some novel β-lactam/β-lactamase inhibitor combinations, e.g., cefatazidime/avibactam, meropenem/vaborbactam, and imipenem/relebactam, were approved for the treatment of CRKP infections, they were not effective against all carbapenemase producers. Consequently, antibiotic therapeutic choices against CRKP remain limited, while other measures, such as phage therapy, have been considered as alternative measures to prevent and control CRKP infections ( Ciacci et al, 2018 ; Anand et al, 2019 ).…”

Strategy for Mass Production of Lytic Staphylococcus Aureus Bacteriophage pSa-3: Contribution of Multiplicity of Infection

“…One approach to slowly lyse the "factory," the host bacteria, is to lower the inoculum of phages. In this study, we focused on the fact that bacteria are gradually eradicated or partially suppressed at a low MOI, as described in the in vitro phage therapy studies [11,33,34,35,36]. We hypothesized that a lower bacteriophage inoculum results in a higher nal yield.…”

K. pneumoniaeST258 genomic variability and bacteriophage susceptibility

“…Lytic bacteriophages against problematic bacterial species can be readily isolated, but medical applicability is hindered by limited understanding of key issues such as optimal clinical protocols, penetration, and resistance, as well as disappointing clinical trials using phage that have been associated with inconsistent protocols and poor targeting (10-12). Bacteriophages capable of lysing K. pneumoniae , including MDR strains have been described (13-15), with complete genomes for more than 80 full double-stranded (ds) DNA phages available in NCBI databases to date. However, no effective therapeutic product has yet reached the bedside.…”