GeneBites

As bacteria evolve to become more resistant to antibiotics, scientists are revisiting “phage therapy” (using natural viruses that destroy bacteria) as an avenue for treating infections. A new community-driven resource called KlebPhaCol is a major effort to document traits of some of these viruses, giving researchers a toolset to fight back against some of the deadly bacteria that can no longer be killed using common treatments.

When faced with disease-causing bacterial infections, doctors often prescribe antibiotics to kill the pathogens. However, bacteria can evolve ways to avoid being killed by these drugs, as they develop antimicrobial resistance (AMR). AMR is a major threat, with many bacteria strains no longer being susceptible to our most common antibiotics, and some becoming resistant to even some last-resort antibiotics, such as carbapenems. One bacteria species that exhibits resistance to these antibiotics is Klebsiella pneumoniae, which is associated with conditions including pneumonia and sepsis. 

However, antibiotics aren’t the only things that can kill bacteria; there are viruses called phages that can infect and destroy them as well. As early as 1919, scientists began to use phages to treat disease, and phage therapies are still used in some eastern European countries, although their use declined in Western medicine after WWII. But with the rise of AMR, there is renewed interest in further developing and expanding phage therapy.

A recent project by Rothschild-Rodriguez et al. set out to consolidate and deeply characterize a wide set of Klebsiella bacteria strains and phages that infect them; the resulting information is available in an online resource called KlebPhaCol, and scientists can request samples of the KlebPhaCol strains for their own work. The KlebPhaCol researchers obtained the phages from wastewater sewage samples from the Netherlands and the United Kingdom (the Netherlands phages had been isolated and described for a previous study). In total, they studied 52 different phages from multiple different phage families and 74 Klebsiella bacteria strains. 

Based on genomic analysis, the Klebsiella bacteria strains had genes to potentially resist an average of 8 ± 4 antibiotics per strain, with possible resistance being found to 22 different antibiotics across the collection. When experimentally tested, not all the antibiotic resistance predictions were fully accurate; however, the carbapenem resistance predictions were accurate. Nevertheless, almost half of the Klebsiella bacteria strains could be infected by at least 1 of the tested phages, and one phage (Roth16), was able to infect almost a quarter of the Klebsiella bacteria strains, including different sub-types.

Phages infect bacteria by binding to specific proteins on the cell surface, called receptors. Previous studies had suggested that most already-described Klebsiella-infecting phages bind to a receptor called the capsule; however, many of the phages in KlebPhaCol do not require the capsule, and can use different receptors to get into the cells.The researchers also found that the ability of phages to infect bacteria depends on the media used to grow them. This finding aligns with a previous study demonstrating that media composition can influence whether the capsule receptor is inactivated. Additionally, although a few Klebsiella bacteria strains with notably low infectability have a lot of anti-phage defense systems, a strain’s infection susceptibility does not appear to correlate with its number of defense systems broadly, at least within the KlebPhaCol strains. This means that we can’t assume how well a bacteria strain can evade phage infection just based on the number of defense genes it has.

Since some types of Klebsiella bacteria are enriched in the guts of patients with Inflammatory Bowel Disease, the researchers next tested whether KlebPhaCol phages could infect gut-associated bacteria strains. They found that 4 KlebPhaCol phages could infect 2 of the tested bacteria strains (albeit these strains were not isolated from patient samples), and these phages maintained at least partial infectivity in low-oxygen conditions, which is a property of the gut environment.

Among all the different phages that were characterized for KlebPhaCol, the researchers found that phage RothD didn’t fit into any known phage families. They proposed creating new classification categories for this and any similar viruses. Using genomic data, the scientists found evidence of potential phages that could fit into this new classification within the Enterobacteriaceae bacteria family. Since many Enterobacteriaceae bacteria live in animal intestines, the researchers looked for genomic evidence of related phages in the Gut Phage Database, and found evidence of these phages in gut microbiomes around the world. 

The findings from just the initial creation and characterization of KlebPhaCol revealed the existence of a previously unclassified phage type that can infect clinically-relevant bacteria species. And now, since the resource is openly available, microbiologists across the globe have a consolidated place to go for data that can help them develop and build upon their own Klebsiella-infecting phage research projects. And while the collection doesn’t include every type of known Klebsiella-infecting phage, the team is open to contributions from other scientists who can help expand the resource further. Additionally, scientists can request samples of all of the phages and many of the bacteria strains for their own use in research. In a world where “superbugs” are becoming harder to treat with standard Western medicine, open tools like KlebPhaCol allow researchers to work together as they seek out new life-saving solutions.

Edited by Daniel Olivares-Cordero and Jayati Sharma