Isolation of Lytic Bacteriophages Against Carbapenem-Resistant Klebsiella pneumoniae of Capsular Type KL64 From Water Collected at Multiple Sites Across China.

Abstract

Carbapenem-resistant Klebsiella pneumoniae causes difficult-to-treat infections. Lytic phages able to infect and lyse bacterial hosts have gained prominence as a potential countermeasure. Given the predominance of sequence type 11 and capsular type KL64 (ST11-KL64) lineage in China, we sought to develop a dedicated phage bank against this high-priority target. We obtained 52 water samples collected at multiple sites from 18 provincial regions across China. Phages against ST11-KL64 carbapenem-resistant K pneumoniae clinical strains were isolated with a double-layer agar method. All phages were subjected to whole genome sequencing with Illumina HiSeq × 10. Phages were classified in accordance with the overall DNA similarity thresholds established by the International Committee on Taxonomy of Viruses. The 3-dimensional structure of phage tail fibers was predicted with AlphaFold. We isolated 22 lytic phages, which belonged to the family Autotranscriptaviridae (n = 21) or Ackermannviridae (n = 1). All Autotranscriptaviridae phages but one were of the genus Przondovirus, and the remaining one belonged to Benllochvirus. All Przondovirus and Benllochvirus phages here displayed a KL64-specific host range and encoded a single tail fiber protein containing a tail spike domain and 4 previously identified key residues, R405, Y526, W550, and F669, for governing the host range. The repeated recovery of Przondovirus phages from various sites illustrates a limited biogeographic diversity and restrained mutual phage-bacterium adaption. This suggests that for a common type of encapsulated bacterial pathogen, the attempt to recover phages from more sources may not be efficient and, conversely, phages recovered in one place have the potential to be used in another.