Characterization of Novel Mycobacteriophages of Subcluster A3: Evolutionary Plasticity of the Lysogeny Module and Lytic Potential

The increasing prevalence of drug-resistant Mycobacteriumtuberculosis (Mtb) and nontuberculous mycobacteria (NTM) underscores the need for novel strategies. Mycobacteriophages are attracting growing interest for therapeutic and diagnostic applications. Here, we describe four new subcluster A3 phages (Cat, Goose1D, Goose1X, and Shep) and investigate their genomic diversity and lytic activity. The phages share >98% nucleotide identity with known A3 members but carry distinct deletions within the lysogeny module: Cat and Goose1X have different repressor-loss variants, and Goose1D lacks the integrase gene, whereas Shep retains an intact module. All phages lysed M. tuberculosis H37Rv, with efficiencies of plating (EOPs) of 10−2–10−1, but showed limited activity against NTM. Cat was the most effective against drug-resistant Mtb isolates (EOPs of 10−1–1), remained stable across a broad pH and temperature range, but had a low burst size (8 PFU (plaque-forming units/cell). In lysogeny assays, 6% of Cat-exposed M. smegmatis colonies exhibited a lysogen-like phenotype, but no phage DNA was detected, suggesting spontaneous resistance. Sequencing of one strain revealed an H535Q substitution in the pyruvate carboxylase MSMEG_2412. These findings highlight lysogeny module plasticity in closely related phages and position Cat, with its naturally occurring repressor deletion and potent lytic activity, as a promising candidate against drug-resistant tuberculosis.