Abstract
The emergence of multidrug-resistant bacteria is a major global health concern. The search for new therapies has brought bacteriophages into the spotlight, and new phages are being described as possible therapeutic agents. Among the bacteria that are most extensively resistant to current antibiotics is Klebsiella pneumoniae, whose hypervariable extracellular capsule makes treatment particularly difficult. Here, we describe two new K. pneumoniae phages, πVLC5 and πVLC6, isolated from environmental samples. These phages belong to the genus Drulisvirus within the family Podoviridae. Both phages encode a similar tail spike protein with putative depolymerase activity, which is shared among other related phages and probably determines their ability to specifically infect K. pneumoniae capsular types K22 and K37. In addition, we found that phage πVLC6 also infects capsular type K13 and is capable of striping the capsules of K. pneumoniae KL2 and KL3, although the phage was not infectious in these two strains. Genome sequence analysis suggested that the extended tropism of phage πVLC6 is conferred by a second, divergent depolymerase. Phage πVLC5 encodes yet another putative depolymerase, but we found no activity of this phage against capsular types other than K22 and K37, after testing a panel of 77 reference strains. Overall, our results confirm that most phages productively infected one or few Klebsiella capsular types. This constitutes an important challenge for clinical applications.
Highlights
Klebsiella pneumoniae is an encapsulated Gram-negative bacterium that can be found as a free-living organism, in natural environments
Phage πVLC5 was obtained from a water sample in an irrigation ditch near a wastewater treatment plant, whereas phage πVLC6 was isolated from a river, near its outflow to the sea, in an area where waste discharged by nearby villages accumulates
Our initial screening was carried out using a multidrug-resistant clinical isolate of K. pneumoniae as host, which belongs to capsular type K22
Summary
Klebsiella pneumoniae is an encapsulated Gram-negative bacterium that can be found as a free-living organism, in natural environments. Disruption or capsule loss makes bacteria susceptible to phage infection or antibiotic treatment, suggesting a therapeutic potential for phage depolymerases [5,11,12,13,14]. A limited number of enzymes in active particular capsular types have been described [16] In addition to their potential therapeutic applications, phage-borne depolymerases have been suggested for capsular typing [17]. Our group has isolated and characterized four new phages of K. pneumoniae (πVLC1 to πVLC4) from environmental samples in Valencia, Spain [18] All of these were closely related phylogenetically, belonged to the genus Drulisvirus, encoded only one depolymerase, and showed a very narrow capsular type range. As opposed to our previously described phages, these new isolates were capable of infecting several reference capsular types of Klebsiella spp. Whole genome analysis revealed that πVLC5 and πVLC6 encoded divergent depolymerases, potentially explaining their host tropisms
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