Whole Genome Sequencing of Methicillin-Resistant Staphylococcus epidermidis Clinical Isolates Reveals Variable Composite SCCmec ACME among Different STs in a Tertiary Care Hospital in Oman

Staphylococcus epidermidis has been recently recognized as an emerging nosocomial pathogen. There are concerns over the increasing virulence potential of this commensal due to the capabilities of transferring mobile genetic elements to Staphylococcus aureus through staphylococcal chromosomal cassette (SCCmec) and the closely related arginine catabolic mobile element (ACME) and the copper and mercury resistance island (COMER). The potential pathogenicity of S. epidermidis, particularly from blood stream infections, has been poorly investigated. In this study, 24 S. epidermidis isolated from blood stream infections from Oman were investigated using whole genome sequence analysis. Core genome phylogenetic trees revealed one third of the isolates belong to the multidrug resistance ST-2. Genomic analysis unraveled a common occurrence of SCCmec type IV and ACME element predominantly type I arranged in a composite island. The genetic composition of ACME was highly variable among isolates of same or different STs. The COMER-like island was absent in all of our isolates. Reduced copper susceptibility was observed among isolates of ST-2 and ACME type I, followed by ACME type V. In conclusion, in this work, we identify a prevalent occurrence of highly variable ACME elements in different hospital STs of S. epidermidis in Oman, thus strongly suggesting the hypothesis that ACME types evolved from closely related STs

The Genus <i>Xanthagaricus</i>: An Updated Global Species Distribution and Phylogeny with the Description of Two New Species from Oman

Xanthagaricus is a saprotrophic mushroom genus with small-sized basidiomata in the family Agaricaceae (Agaricales). Prior to this study, 26 species belonging to this genus have been described and published. In this study, we reported Xanthagaricus for the first time from Oman with the description of two new species. Basidiomata of the new species Xanthagaricus appendiculatus and X. omanicus were collected during the monsoon rains of summer in 2018 in the southern coastal region of Oman. Species descriptions are based on morphological and molecular characterization. Phylogenetic analyses based on internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS) of the nuclear ribosomal DNA clustered the new species in the Xanthagaricus clade with strong statistical support. The new species Xanthagaricusappendiculatus can be distinguished from other species by its purplish pileus with umbonate disc and X. omanicus with the largest pileus (70–90 mm diameter) among the known species of the genus. A detailed description, photographs, line drawings, and a phylogenetic tree showing the position of both new species are provided. A dichotomous key to the known taxa of Xanthagaricus is proposed. Morphological comparisons of new species with known Xanthagaricus taxa are provided. Our observations highlight the diversity of Xanthagaricus and other lepiotaceous mushrooms in southern Oman and further document the need for additional systematic focus on the region’s fungi