Understanding the complete reservoir of bacteriophage depolymerases against A. baumannii capsules

Abstract

A. baumannii is an important nosocomial and drug-resistant pathogen. The capsule is a major virulence factor that helps bacteria to avoid host immunity and viral predation. Acinetobacter phages can bind and degrade host capsules through capsular depolymerases with proven anti-virulence activity (1-3). Understanding the full reservoir of phage depolymerases against A. baumannii capsules, as well as relevant capsular types in clinical isolates, is crucial for developing depolymerase-based treatments. In this work, we 1) characterized 94 carbapenem-resistant A. baumannii Portuguese isolates; 2) isolated phages for relevant capsular types and characterized their depolymerases and 3) developed bioinformatic tools to collect the diversity of phage depolymerases. We show clonal shifts of A. baumannii KL2, KL7, KL9 and KL120 serotypes over time, with different virulence assessed in G. mellonella. Acinetobacter phages specific for particular k-types were isolated and several depolymerases (for KL1, KL2/KL19, KL9, KL30/KL45, KL32, KL38, KL44, KL67 types) characterized. We also demonstrate that most Acinetobacter phages encode capsular depolymerases (from 134 deposited in 2021, 73 contain capsular depolymerases), exclusively located in small viruses (<90 kb). To disclose the full genetic diversity, we developed PhageDPO (available in Galaxy uminho.pt server), a machine learning tool that identifies depolymerases in phages and bacteria genomes (prophages). We also present PhageKDB, a database that compiles available information of capsular depolymerases, retrieved through both manually and text-mining approaches, serving as an open portal to phage community. Overall, we present novel insights into A. baumannii isolates and phage depolymerase diversity and a collaborative tool to advance research in the field.