Genome Mining Reveals a Sactipeptide Biosynthetic Cluster in Staphylococcus pseudintermedius

Abstract

Staphylococcus pseudintermedius, an opportunistic pathogen of veterinary and zoonotic concern, harbors diverse biosynthetic gene clusters (BGCs) that may contribute to its ecological fitness and virulence. In this study, we performed a comparative genomic analysis of 6815 S. pseudintermedius isolates. Using Roary, we identified core and accessory genomes, revealing the subtilosin A gene (sboA) as part of the accessory genome, present in a subset of S. pseudintermedius isolates from clinical (n = 657), environmental (n = 1031), and unclassified sources (n = 487). AntiSMASH v8.0.0 analysis confirmed the presence of subtilosin A BGCs annotated as a sactipeptide with low similarity confidence to Bacillus subtilis subsp. spizizenii ATCC 6633 subtilosin A cluster. Further characterization using BAGEL4 identified multiple genes homologous to the Bacillus subtilis subtilosin A biosynthetic machinery (sbo-albABCDEFG), although albB, albG, and sboX were not annotated, raising questions about cluster completeness and functionality. BLAST v2.12.0 analysis of the full BGC identified by BAGEL4, revealing high conservation (99.6-100% pairwise identity) of gene content and order in 395 clinical, 593 environmental, and 417 unclassified S. pseudintermedius isolates. Incomplete clusters were identified in 763 clinical, 942 environmental, and 201 unclassified S. pseudintermedius isolates. The discrepancy between the number of isolates containing sboA and those harboring the full cluster may reflect evolutionary divergence or could be attributed to limitations in assembly quality. The functional implications of the identified cluster in S. pseudintermedius remain to be elucidated; however, its potential role in conferring competitive fitness by inhibiting closely related species is supported by previous findings in other staphylococci.

Keywords: Staphylococcus pseudintermedius; antibiotics resistance; bacteriocin; subtilosin A.

Figure 1

Distribution of the subtilosin A core gene (sboA) among Staphylococcus pseudintermedius isolates. The sboA gene was detected in 657 of 1724 clinical isolates, 1031 of 3176 environmental isolates, and 487 of 1915 unclassified isolates. Bar segments represent the number of isolates present (blue) or absent (orange) for the sboA gene in each source category.

Figure 2

Biosynthetic gene clusters identified in Staphylococcus pseudintermedius 081661 using antiSMASHV8.0.0.

Figure 3

Comparison of the subtilosin A biosynthetic gene cluster (BGC) identified in Staphylococcus pseudintermedius 081661 with reference BGCs from the MIBiG database using antiSMASHV8.0.0 analysis. The top panel shows a visual representation of the query region from S. pseudintermedius (bottom track) aligned with the best-matching reference cluster, subtilosin A from Bacillus subtilis subsp. spizizenii ATCC 6633 (top track). Genes are represented as arrows, with lines connecting orthologous genes based on the best 1:1 BLAST matches. The lower panel shows the genetic similarity analysis of the identified subtilosin A BGC from S. pseudintermedius 081661. The highlighted row (black border) indicates the currently selected match, subtilosin A (BGC0000615), which shares 60% similarity with the query cluster and is classified as a ribosomal sactipeptide cluster. Red: core biosynthetic genes; Orange: additional biosynthetic genes; Blue: transport-related genes; Green: regulatory genes; Gray: other or uncharacterized genes.

Figure 4

Genetic organization of the subtilosin A biosynthetic gene cluster identified by BAGEL4 in Staphylococcus pseudintermedius 081661. The cluster was visualized with predicted functions color-coded according to gene classification. The core peptide (green), the protein involved in the modification process (blue), and transport (red).

Figure 5

The distribution of Staphylococcus pseudintermedius isolates containing subtilosin A genes across three sources: clinical, environmental, and unclassified. Each pie chart displays the proportion of isolates with complete, incomplete, or absent subtilosin A gene clusters. Complete: Isolates with full subtilosin A gene cluster; Incomplete: Isolates with partial/subset of subtilosin A genes; Absent: No detectable subtilosin A gene components. Colors: greenish = #66c2a5, orange = #fc8d62, blueish = #8da0cb.