Weberviruses are gut-associated phages that infect Klebsiella spp

Abstract

Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life, and associated depolymerases. In this study, we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome, and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n = 258 from isolates, n = 65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n = 330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%), and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.

Keywords: Klebsiella pneumoniae; comparative genomics; environment; metagenome-assembled genomes; microbiota.

Figure 1.

ViPTree-generated phylogenetic analysis of the family Drexlerviridae. The genus Webervirus is represented by 330 genomes. The names of our seven newly identified weberviruses are shown in white bold text. A potentially novel genus (Defiantjazzvirus) was identified during the curation of our dataset. The colours covering the virus names represent taxa within the family Drexlerviridae; the outgroup has been collapsed to aid visualization. The tree (ViPTree bionj) was rooted at the midpoint.

Figure 2.

Further analyses of Drexlerviridae sequence data. (A) Phylogenetic relationships (maximum-likelihood tree) of members of the family Drexlerviridae based on analysis of large-subunit terminase (terL) nucleotide sequences encoded in phage genomes. Bootstrap values are expressed as a percentage of 100 replications; scale bar, mean number of nucleotide substitutions per position; the tree is rooted at the midpoint. (B) Gene-network-based analysis of proteomic data for members of the genus Webervirus and their nearest relatives. Full network shown in Supplementary Fig. C. (A and B) The legend shown applies to both figures, with isolate and MAG proteomes differentiated in (B). Names of our seven newly identified weberviruses are shown in bold white text.

Figure 3.

Distribution of weberviruses (A) Stacked bar graph showing the sources of the 330 webervirus genomes (n = 265 isolated phages; n = 65 MAGs). (B) Geographical distribution of 329 of the webervirus genomes included in this study (the location information was not available for one isolated phage, namely Klebsiella phage 5899STDY8049225).

Figure 4.

Phylogenetic analysis of depolymerases predicted to be encoded by weberviruses. The tree (maximum likelihood) is rooted at the midpoint. Bootstrap values are presented as a percentage of 100 replicates. Names of experimentally validated (i.e. functional) depolymerases are shown in bold black text; depolymerases predicted to be encoded by MAGs are shown in white text. Scale bar, mean number of amino acid substitutions per position.