Genome-Based Characterization of a Plasmid-Associated Micrococcin P1 Biosynthetic Gene Cluster and Virulence Factors in Mammaliicoccus sciuri IMDO-S72

Abstract

Analysis of the de novo assembled genome of Mammaliicoccus sciuri IMDO-S72 revealed the genetically encoded machinery behind its earlier reported antibacterial phenotype and gave further insight into the repertoire of putative virulence factors of this recently reclassified species. A plasmid-encoded biosynthetic gene cluster was held responsible for the antimicrobial activity of M. sciuri IMDO-S72, comprising genes involved in thiopeptide production. The compound encoded by this gene cluster was structurally identified as micrococcin P1. Further examination of its genome highlighted the ubiquitous presence of innate virulence factors mainly involved in surface colonization. Determinants contributing to aggressive virulence were generally absent, with exception of a plasmid-associated ica cluster. The native antibiotic resistance genes sal (A) and mecA were detected within the genome, amongst others, but were not consistently linked with a resistant phenotype. While mobile genetic elements were identified within the genome, such as an untypeable SCC element, they proved to be generally free of virulence- and antibiotic-related genes. These results further suggest a commensal lifestyle of M. sciuri and indicate the association of antibiotic resistance determinants with mobile genetic elements, as an important factor in conferring antibiotic resistance, in addition to their unilateral annotation. Importance Mammaliicoccus sciuri has been put forward as an important carrier of virulence and antibiotic resistance genes, which can be transmitted to clinically important staphylococcal species such as Staphylococcus aureus . As a common inhabitant of mammal skin, this species is believed to have a predominant commensal lifestyle although it has been reported as an opportunistic pathogen in some cases. This study provides an extensive genome-wide description of its putative virulence potential taking into consideration the genomic context in which these genes appear, an aspect that is often overlooked during virulence analysis. Additional genome and biochemical analysis linked M. sciuri with the production of micrococcin P1, gaining further insight to which extent these biosynthetic gene cluster are distributed amongst different related species. The frequent plasmid-associated character hints that these traits can be horizontally transferred and might confer a competitive advantage to its recipient within its ecological niche.

Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies

“…Concurrently, sequencing depth plays a pivotal role in determining the contiguity of the assembled sequences. Thus, sequencing depth and read quality are crucial for achieving highly contiguous and accurate genome assemblies which is the strength of hybrid assembly [ 47 49 ].…”

Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness

“…A number of studies have identified MP1 BGCs in a variety of staphylococcal species, including S. aureus ( 34 ), S. epidermidis ( 35 ), Staphylococcus equorum ( 36 ), Staphylococcus pseudintermedius ( 37 ), Staphylococcus agnetis , and S. hominis ( 20 ). Also, an isolate from Mammaliicoccus sciuri (formerly Staphylococcus sciuri ) ( 38 ) has been shown to produce MP1. Moreover, the NCBI database includes various homologous sequences in S. aureus genomes as well as many coagulase-negative staphylococci.…”

Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness

“…A number of studies have identified MP1-BGCs in a variety of staphylococcal species, including S. aureus (32), S. epidermidis (33), Staphylococcus equorum (34), Staphylococcus pseudintermediu s (35), Staphylococcus agnetis , and S. hominis (19). Also, an isolate from Mammaliicoccus sciuri (former Staphylococcus sciuri ) (36) has been shown to produce MP1. Moreover, the NCBI database includes various homologous sequences in S. aureus genomes as well as many coagulase-negative staphylococci.…”