Genomic characterization of Pseudomonas aeruginosa clonal lineage ST162 isolated from bovine-milk in South Africa

Pseudomonas aeruginosa is an opportunistic pathogen that can colonize a wide range of habitats. This pathogen is associated with bovine mastitis; however, its genomic characteristics in a veterinary context remain poorly defined. We present the first comprehensive genomic analysis of P. aeruginosa isolates obtained from bovine milk in the Dr Kenneth Kaunda District, North West Province, South Africa. Bovine milk-derived isolates (n = 10) were analysed using whole-genome sequencing, resistome profiling and pangenome analysis. The 10 South African isolates shared a highly conserved resistome, harbouring antimicrobial resistance genes (ARGs) associated with β-lactams (blaOXA−396, blaPAO), aminoglycosides (aph (3’) -IIb₁, aadA6₁), tetracyclines (tet (G) ), and sulfonamides (sul1₅). The ppkA gene, a regulator of T6SS and biofilm dynamics, was absent in the sequenced genomes 4RF, 8RF, and 13RF13LH. The pchH gene, involved in pyochelin transport, was detected only in strains 11RH10LH and 1RF, indicating variability in specific virulence regulators and iron acquisition genes. Based on pangenomics analysis using hierarchical clustering, all 10 South African isolates belonged to sequence type ST162 and formed a tight monophyletic clade, clustering closely with human-derived ST162 strains from the United States and Australia. All genomes containing plasmid AF876 were associated with the presence of the crpP gene encoding a ciprofloxacin-modifying enzyme. PHAGEJBD25, PHAGEF10, PHAGE_ phi297, and PHAGE_ Pf1 were consistently identified as common, intact prophages, indicating a conserved prophage repertoire shared among the isolates. These findings highlight the importance of genomic surveillance in veterinary pathogens and offer valuable insights into the evolution and dissemination of P. aeruginosa within dairy environments. The detection of ST162 in both animal and human-associated strains suggests potential zoonotic transmission routes and raises concerns regarding the persistence, dissemination, and evolution of this lineage within livestock production environments.