Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

Abstract

Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources, stone fragments and sandy soil in James Ross Island, Antarctica. Here we describe properties of novel species of the genus Staphylococcus that has near identical 16S rRNA gene sequence to Staphylococcus saprophyticus. However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at whole genome level, average nucleotide identity S. saprophyticus phylogenetic clade confirmed by multilocus sequence analysis of six housekeeping genes rpoB, hsp60, tuf, dnaJ, gap, and sod. MALDI-TOF MS and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbours. In contrast to S. saprophyticus subsp. saprophyticus, strains were pyrrolidonyl arylamidase- and β-glucuronidase-positive, β -galactosidase-negative, nitrate was reduced and acid produced aerobically from d-mannose. Whole genome sequencing of 2.75 Mb large chromosome revealed the presence of a number of mobile genetic elements including the 27-kb-long pseudo staphylococcus cassette chromosome mec (ψSCCmec_P5085) harboring mecC gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environment, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidin, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactams producers, which are common in a polar environment. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus edaphicus sp. nov. The type strain is P5085^T (=CCM 8730^T = DSM 104441^T).