Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Due to the prevalence of encapsulated bacteria, the capsule is the first barrier encountered by many phages. This layer, usually made of polysaccharides, can block phage access to their cell wall receptors. To overcome this, some phages encode specific depolymerase (Dpos) domains in their receptor-binding proteins. Here, we have quantified the predictability of phage-bacteria interactions based on the capsular locus type of host (CLT) and Dpos. For this, we used Klebsiella pneumoniae as a model due to its high capsular diversity and importance in global health. First, we established a collection of 138 clinical strains of K.pneumoniae representative of the genomic diversity of the species. These were challenged with 46 different environmental phages comprising 13 phylogenetic groups. Spot tests revealed that most of the phages (42 out of the 46) showed capsular specificity, with their infection pattern accurately predicted (92%) by the host CLT. Consequently, phage-encoded Dpos, which have often undergone horizontal gene transfer across large taxonomic scales, were key determinants of host tropism. The identity tolerance of phage Dpos was high, as shown by the predicted capsular tropism of RefSeq prophages for 13 important CLTs. Even though capsules and Dpos predicted the first steps of virion recognition and adsorption, their accuracy dropped for productive infections (53%). Apart from capsule-specialist phages, we found that the phages of groups S8/S9 had a broader host-range resulting from both capsule-dependent and independent tropism. Capsular tropism of S8/S9 phages was not mediated by depolymerases, instead these phages encoded long tail proteins with multiple carbohydrate-binding domains. Importantly, >90% of bacterial strains presented capsular phenotypic heterogeneity, with the co-existence of both encapsulated and non-encapsulated clones. This heterogeneity affected phage tropism, as broad-range phages preferentially infected bacteria with a higher number of acapsular bacteria, contrary to capsular-specialist phages. We found that acapsular mutants gained resistance in 286 of the 406 combinations tested (70%). Neither phage capsular specificity nor infection of acapsular bacteria was correlated with the phylogenetic classification of phages. Remarkably, 43% of the phages showed an obligate or facultative capsule attachment behavior depending on the bacterial strain and its mechanism of capsule inactivation, which in turn led to different trade-offs in resistance. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.
2023-07-21
