Genetic determinants of host tropism in Klebsiella phages
Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we used 46 newly-isolated phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. We tested all phage-bacterium pairs by spot-testing and confirmed positive results by bactericidal, progeny production, capsule depolymerization, and adsorption assays. Using full-length phage and host genome sequences, we applied computational methods to test how different bacteria and phage traits predict infection.
Steps to reproduce
To calculate the TPR of bacteria: % Rscript calculate_TPR_bacteria_df.r -i Beamud_et_al_infection_matrix_CLT_all.tsv -p TPR_PHAGE_ALL -m Beamud_et_al_phage_metadata_rbds_BACKT_final.csv To calculate the TPR of phages: % Rscript calculate_TPR_phage_df.r -i Beamud_et_al_Spotting_Matrix_binary_noIHosts_1021.tsv -p TPR_BACT_ALL -m Beamud_et_al_Kpn_collection_metadata_v4_short.csv