Sequencing a CC239-MRSA-III with a novel composite SCCmec element from Kuwait

In Kuwait, microarray-based surveillance identified from 2019 to 2022 a series of isolates of a hitherto unknown variant of the ancient hospital-acquired MRSA strain CC239-MRSA-III that carried a second set of recombinase genes, ccrA/B-2. To elucidate the structure of this variants SCCmec element, two isolates were subjected to nanopore sequencing. For comparison, an older isolate of a presumed precursor strain was also sequenced.This revealed in addition to ccrA/B-2 in the new variant also a presence of hsdS (type I restriction-modification system site-specificity determinate), speG (spermidine N acetyltransferase), a couple of genes encoding putative proteins, cch (cassette chromosome helicase), transposase genes and a large E-domain containing protein (dubbed as edcP-SCC). This gene contained three regions consisting of multiple repeating units. In terms of sequence and structure it was similar but not identical to the biofilm-related aap gene known from S. epidermidis.All three isolates carried a prophage with the adhesion factor sasX/sesI and aminoglycoside resistance genes which is in accordance to an affiliation to the South-East Asian Clade of CC239.