Pharmaceutical Biotechnology

Statement of the Problem: Antibiotic resistance is one of the biggest threats to global health, food security, and development today. Staphylococci are common member of our skin and mucosa but they are also a common cause of severe infections and resistance to first line antimicrobial to treat their infections is widespread. Here, a multidrug- and methicillin-resistant Staphylococcus sciuri strain C2865 (canine nasal sample, Nigeria) showed thrimethoprim resistance for which all staphylococcal dfr genes were negative. This strain was subjected to whole-genome-sequencing (WGS) for resistome and mobilome profiling and to comparative genomics with all NCBI-deposited S. sciuri species group genomes for diversity analysis.

Methodology & Theoretical Orientation: Illumina Miseq was used for C2865 WGS and in-house pipelines (SPAdes, Prodigal, tRNAscan-SE, RNAmmer, NCBI NR, COG, TIGRfam, RAST, ISsaga2) were followed for data processing and analysis. Plasmid contigs identification and plasmids reconstruction were achieved by contig coverage, sequence similarity and composition. PCR plus sequencing was done for scaffolding regions of interest. Average Nucleotide Identity (ANI) between all 22 available S. sciuri group strains and comparative and pangenome analysis of S. sciuri group strains was calculated using JSpecies. progressiveMauve, ClonalFrame and Roary, respectively.

Findings: S. sciuri C2865 revealed 2,937,715 bp in size, a GC content of 32.7%, and 3316 CDSs, with 1887 genes categorized into COG functional groups. Two small resistance plasmids and two novel mobilizable plasmids were reconstructed. p2865-3, a multidrug resistance plasmid, revealed a trimethoprim resistance gene described for the first time in marine Exiguobacterium (order Bacillales). p2865-4 carried the intercellular adhesion gene cluster involved in biofilm formation. A novel staphylococcal cassette chromosome (SCCmec) was identified. Additional chromosomal resistance genes (antibiotic, metal, biocide) and mobile genetic elements (MGEs) were detected.

C2865 shared highest ID with S. sciuri Z8 and SNUDS-18 (99-98%), comprising a different branch within the species. WG alignment among all S. sciuri genomes revealed a core genome of 1.7 Mb (60.7%). Synteny was preserved among these genomes while there were several genomic islands with distinct gene content.

Conclusion & Significance: 1) Several novel MGEs are detected revealing, among others, a novel dfr gene conferring thrimethoprim resistance not only in S. sciuri but also in an environmental species. 2) WGS reveals a trustful tool to identify and characterize novel and already known resistance & virulence determinants and MGEs. 3) Comparative genomics shows high S. sciuri intraspecies diversity and high genome plasticity. 4) Commensal staphylococci represent a reservoir for mobilizable AMR & virulence determinants.