Klebsiella pneumoniae subsp. pneumoniae–bacteriophage combination from the caecal effluent of a healthy woman

A recent study characterizing bacteriophage populations within human caecal effluent demonstrated the presence of numerous Podoviridae, Siphoviridae and Myoviridae within this material (Hoyles et al., 2014, Res Microbiol 165, 803–812). Further to this work, anaerobic bacteria were isolated on fastidious anaerobe agar from the caecal effluent of a healthy 31-year-old woman. Ten colonies were selected at random, streaked to purity and screened against the remaining caecal effluent (filter-sterilized, 0.45 μm pore size) in an attempt to isolate lytic bacteriophages. Bacteriophages within the effluent [2×105 ± 2.65×103 (n=3) pfu/ml] were active against five of the isolates, all identified by 16S rRNA gene sequence analysis as Klebsiella pneumoniae. One of the five isolates, L4-FAA5, was characterized further and found to be K. pneumoniae subsp. pneumoniae capsule type K2 rmpA+, and was used to propagate a bacteriophage (which we named KLPN1) to purity. Bacteriophage KLPN1 was a member of the Siphoviridae with a rosette-like tail tip and exhibited depolymerase activity, demonstrated by the formation of plaque-surrounding haloes that increased in size over the course of incubation. When screened against a panel of 21 clinical strains representing unknown K. pneumoniae subsp. pneumoniae capsule types and types K1, K2, K5, K20, K54 and K57, KLPN1 infected only K2 strains, but did not exhibit depolymerase activity against these. Whole-genome sequence analysis of KLPN1 showed the bacteriophage to have a genome of 49,037 bp (50.53 GC mol%) comprising 73 predicted ORFs, of which 22 encoded genes associated with structure, host recognition, packaging, DNA replication and cell lysis. The host recognition-associated gene was a potential depolymerase. This is the first report of the isolation of a bacterium–bacteriophage combination from the human caecum, and only the third member of the Siphoviridae known to infect K. pneumoniae subsp. pneumoniae