What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

Abstract

Phage therapy, a practice widespread in Eastern Europe, has untapped potential in the combat against antibiotic-resistant bacterial infections. However, technology transfer to Western medicine is proving challenging. Bioinformatics analysis could help to facilitate this endeavor. In the present study, the Intesti phage cocktail, a key commercial product of the Eliava Institute, Georgia, has been tested on a selection of bacterial strains, sequenced as a metagenomic sample, de novo assembled and analyzed by bioinformatics methods. Furthermore, eight bacterial host strains were infected with the cocktail and the resulting lysates sequenced and compared to the unamplified cocktail. The analysis identified 23 major phage clusters in different abundances in the cocktail, among those clusters related to the ICTV genera T4likevirus, T5likevirus, T7likevirus, Chilikevirus and Twortlikevirus, as well as a cluster that was quite distant to the database sequences and a novel Proteus phage cluster. Examination of the depth of coverage showed the clusters to have different abundances within the cocktail. The cocktail was found to be composed primarily of Myoviridae (35%) and Siphoviridae (32%), with Podoviridae being a minority (15%). No undesirable genes were found.

Metagenome analysis of Russian and Georgian Pyophage cocktails and a placebo‐controlled safety trial of single phage versus phage cocktail in healthy Staphylococcus aureus carriers

“…If multiple phages are amplified in a batch culture, it is possible that a ‘winner’ phage is amplified more efficiently and predominates the lysate, with less efficiently replicating phages representing low coverage phages. Previous investigations into the Eliava Intestiphage cocktails revealed that sequences detected with a low coverage were nevertheless biologically active and easily detected by infection assays (Zschach et al ., ; McCallin et al . ).…”

“…If multiple phages are amplified in a batch culture, it is possible that a 'winner' phage is amplified more efficiently and predominates the lysate, with less efficiently replicating phages representing low coverage phages. Previous investigations into the Eliava Intestiphage cocktails revealed that sequences detected with a low coverage were nevertheless biologically active and easily detected by infection assays (Zschach et al, 2015;McCallin et al 2013). Without metagenome sequencing or indicator strains for the detection of each specific ingredient phage, it will be difficult to maintain a constant ratio of ingredient phages in the cocktail -a likely regulatory requirement for medicinal products in the West.…”

HostPhinder: A Phage Host Prediction Tool

“…The Eliava Institute in Tbilisi, Georgia has in particular been dominant in this regard and produce cocktails containing a mixture of phages for a range of bacterial infections. One of the steps towards adopting phage therapy in the West, is likely to be a full characterization of the content of these cocktails, which due to the way they are manufactured is not known [ 38 ]. Further, the current approach to exploration of many ecological niches is done by untargeted sequencing of samples isolated directly from the environment, so called metagenomics.…”

Bacteriophage Therapy: Developments and Directions

“…Phage products such as Pyophage and Intestiphage are examples of modifiable cocktails that are still in use today in Georgia and Russia. Metagenomic analysis of these products indicates they are complex mixtures of phages [38][39][40]. This complexity combined with the periodic changes in composition means these products are not directly suited to a traditional regulatory drug development pathway such as the US FDA has established.…”