Diversity of SCC<i>mec</i> Elements in <i>Staphylococcus aureus</i> as Observed in South-Eastern Germany

<div><p>SCC<i>mec</i> elements are very important mobile genetic elements in Staphylococci that carry beta-lactam resistance genes <i>mecA/mecC</i>, 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 <i>S</i>. <i>aureus</i> (MRSA) based on variations within their SCC<i>mec</i> 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 <i>mecA/mecC</i>, <i>fusC</i>, 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 SCC<i>mec</i> 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 SCC<i>mec</i> 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.</p></div

Clonal complexes, strains and SCC elements as identified by array hybridisation.

<p>Prevalence data (percentages and absolute numbers) refer to routine MRSA typing from the Dresden University Hospital, 2000—April 2016 (n = 1277).</p

SCC-associated markers used for this study, sorted alphabetically, references and estimated abundances in MRSA from Dresden (2000–2016; based on prevalence data from Table 1 and [10]).

<p>SCC-associated markers used for this study, sorted alphabetically, references and estimated abundances in MRSA from Dresden (2000–2016; based on prevalence data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162654#pone.0162654.t001" target="_blank">Table 1</a> and [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162654#pone.0162654.ref010" target="_blank">10</a>]).</p

SCC elements as identified by array hybridisation in this study, reference sequences, their gene contents, distributions across clonal complexes and their estimated abundances in MRSA from Dresden (2000–2016; based on prevalence data from Table 1 and [10]).

<p>SCC elements as identified by array hybridisation in this study, reference sequences, their gene contents, distributions across clonal complexes and their estimated abundances in MRSA from Dresden (2000–2016; based on prevalence data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162654#pone.0162654.t001" target="_blank">Table 1</a> and [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162654#pone.0162654.ref010" target="_blank">10</a>]).</p

Prevalence of resistance genes in 124 <i>S</i>. <i>aureus</i> isolates from wildlife.

<p>Prevalence of resistance genes in 124 <i>S</i>. <i>aureus</i> isolates from wildlife.</p

Detection of <i>S</i>. <i>aureus</i> by country and host species.

<p>Detection of <i>S</i>. <i>aureus</i> by country and host species.</p

CC/ST characteristics of <i>S</i>. <i>aureus</i> isolates investigated.

<p>CC/ST characteristics of <i>S</i>. <i>aureus</i> isolates investigated.</p

Table_1_Molecular Typing of ST239-MRSA-III From Diverse Geographic Locations and the Evolution of the SCCmec III Element During Its Intercontinental Spread.PDF

<p>ST239-MRSA-III is probably the oldest truly pandemic MRSA strain, circulating in many countries since the 1970s. It is still frequently isolated in some parts of the world although it has been replaced by other MRSA strains in, e.g., most of Europe. Previous genotyping work (Harris et al., 2010; Castillo-Ramírez et al., 2012) suggested a split in geographically defined clades. In the present study, a collection of 184 ST239-MRSA-III isolates, mainly from countries not covered by the previous studies were characterized using two DNA microarrays (i) targeting an extensive range of typing markers, virulence and resistance genes and (ii) a SCCmec subtyping array. Thirty additional isolates underwent whole-genome sequencing (WGS) and, together with published WGS data for 215 ST239-MRSA-III isolates, were analyzed using in-silico analysis for comparison with the microarray data and with special regard to variation within SCCmec elements. This permitted the assignment of isolates and sequences to 39 different SCCmec III subtypes, and to three major and several minor clades. One clade, characterized by the integration of a transposon into nsaB and by the loss of fnbB and splE was detected among isolates from Turkey, Romania and other Eastern European countries, Russia, Pakistan, and (mainly Northern) China. Another clade, harboring sasX/sesI is widespread in South-East Asia including China/Hong Kong, and surprisingly also in Trinidad & Tobago. A third, related, but sasX/sesI-negative clade occurs not only in Latin America but also in Russia and in the Middle East from where it apparently originated and from where it also was transferred to Ireland. Minor clades exist or existed in Western Europe and Greece, in Portugal, in Australia and New Zealand as well as in the Middle East. Isolates from countries where this strain is not epidemic (such as Germany) frequently are associated with foreign travel and/or hospitalization abroad. The wide dissemination of this strain and the fact that it was able to cause a hospital-borne pandemic that lasted nearly 50 years emphasizes the need for stringent infection prevention and control and admission screening.</p