Diversity of SCCmec Elements in Staphylococcus aureus as Observed in South-Eastern Germany

Abstract

SCCmec elements are very important mobile genetic elements in Staphylococci that carry beta-lactam resistance genes mecA/mecC, recombinase genes and a variety of accessory genes. Twelve main types and a couple of variants have yet been described. In addition, there are also other SCC elements harbouring other markers. In order to subtype strains of methicillin-resistant S. aureus (MRSA) based on variations within their SCCmec elements, 86 markers were selected from published SCC sequences for an assay based on multiplexed primer extension reactions followed by hybridisation to the specific probes. These included mecA/mecC, fusC, regulatory genes, recombinase genes, genes from ACME and heavy metal resistance loci as well as several genes of unknown function. Hybridisation patterns for published genome or SCC sequences were theoretically predicted. For validation of the microarray based assay and for stringent hybridisation protocol optimization, real hybridization experiments with fully sequenced reference strains were performed modifying protocols until yielded the results were in concordance to the theoretical predictions. Subsequently, 226 clinical isolates from two hospitals in the city of Dresden, Germany, were characterised in detail. Beside previously described types and subtypes, a wide variety of additional SCC types or subtypes and pseudoSCC elements were observed as well as numerous composite elements. Within the study collection, 61 different such elements have been identified. Since hybridisation cannot recognise the localisation of target genes, gene duplications or inversions, this is a rather conservative estimate. Interestingly, some widespread epidemic strains engulf distinct variants with different SCCmec subtypes. Notable examples are ST239-MRSA-III, CC5-, CC22-, CC30-, and CC45-MRSA-IV or CC398-MRSA-V. Conversely, identical SCC elements were observed in different strains with SCCmec IVa being spread among the highest number of Clonal Complexes. The proposed microarray can help to distinguish isolates that appear similar or identical by other typing methods and it can be used as high-throughput screening tool for the detection of putative new SCC types or variants that warrant further investigation and sequencing. The high degree of diversity of SCC elements even within so-called strains could be helpful for epidemiological typing. It also raises the question on scale and speed of the evolution of SCC elements.

Diversity of Staphylococcus aureus Isolates in European Wildlife

“…CC22 MRSA are extremely common in Western Europe, but the rook isolates were not identical to the ubiquitous Barnim/UK-EMRSA-15 epidemic strain differing in SCC mec subtype (IVc rather than IVh; [77]) and presence of PVL genes. They were identical to a strain observed in several Middle Eastern countries and people with Middle Eastern travel history [109,127,128,129,130]. …”

“…They did not carry relevant resistance or toxin genes. The two Austrian isolates carried an isolated recombinase homologue ccrAA and reacted with new experimental probes ( opp3B ; ACSQ01000050.1 [4287:4313] and opp3C -C427 ACSQ01000050.1 [5150:5174]; [129]) indicating the presence of a type 3 ACME element.…”

“…Among the German samples, this strain was detected once each in a hedgehog, a red fox and a fallow deer as well as in two hares [104]. The isolates harbored mecC , the SCC mec XI-associated beta-lactamase gene and an arsenic resistance operon ( arsB ; FR823292.1, [29339:29366:r] and arsC ; FR823292.1, [28080:28103:r]; [129]); they lacked lukF-P83/lukM but carried edinB and etD2 [39]. …”

Molecular Epidemiology of Staphylococcus aureus Lineages in Wild Animals in Europe: A Review

“…The J regions are cassette components that may contain determinants for additional antimicrobial resistance; thus, within the SCCmec we can also find resistance genes to other non-β-lactam antibiotics such as erythromycin, clindamycin, tetracycline, aminoglycosides, clindamycin, among others [81]. Furthermore, there are also determinants of virulence and resistance to heavy metals within the SCCmec [82]. Currently, there are many strains that carry non-typed SCCmec elements or even with two types of ccr and or mec complex, and so there is still much to discover about the SCCmec system.…”

Staphylococcus aureus related to bovine mastitis in Switzerland: Clonal diversity, virulence gene profiles, and antimicrobial resistance of isolates collected throughout 2017

“…In addition, strain NK_18 (CC20, ST389, t2094) was classified as resistant to oxacillin, although neither mecA/ mecC nor other staphylococcal cassette chromosomeassociated genes were detected by DNA microarray. It has recently been shown that the commonly known 12 SCCmec types and their variants are only a fraction of the true diversity of SCCmec elements (Monecke et al, 2016(Monecke et al, , 2018. Therefore, a modification of the respective genomic elements or a variant not covered by the microarray used may be present in NK_18.…”