s. aureus isolates can be divided into independently evolving clonal complex ( cc ) lineages .
each cc lineage has a unique and stable combination of surface protein variants and a unique restriction - modification ( rm ) system combination that controls horizontal gene transfer ( hgt ) between lineages .
while there are ten major human s. aureus lineages , only some lineages have acquired meca which is carried on variants of the relatively stable staphylococcal cassette chromosome ( scc ) .
the most successful hospital - associated ( ha)-mrsa clones include cc22 sccmeciv , cc30 sccmecii , st239 sccmeciii , cc5 sccmecii , and cc45 sccmeciv . these mrsa clones have evolved during the last two to three decades and in some cases have spread worldwide . in more recent years , independently evolving clones have caused infections predominately in the community [ cc8 sccmeciv ( usa300 ) , cc1 sccmeciv and cc59 sccmeciv ] and in pigs and persons with livestock contact ( cc398 sccmeciv ) .
mobile genetic elements ( mges ) account for approximately 1520% of the s. aureus genome .
they include scc elements , bacteriophage , s. aureus pathogenicity islands ( sapis ) , plasmids and transposons .
a range of resistance , virulence , toxin , immune evasion and host specificity factors can be encoded on these mges .
indeed , the emerging mrsa clones in the community and livestock have acquired stable and distinct mges that are responsible for their ability to adapt to new niches and hosts . in addition , over 80 whole genome sequencing projects are currently in the public domain , and these already show an enormous variety of mges in different isolates . however , relatively little is known about mge stability , movement and selection during evolution of s. aureus populations .
we investigated the evolution of mrsa in a single acute - care teaching hospital in london , uk over a ten - year period .
we saw mrsa cc22 sccmeciv become the dominant clone concurrent with acquisition of resistance to a range of antibiotics including aminoglycosides , chloramphenicol , clindamycin , fusidic acid , mupirocin , tetracyclines and trimethoprim ( fig .  1 ) .
instead , the antibiograms of isolates from both cc22 sccmeciv and cc30 sccmecii mrsa over time were highly variable , and could only have arisen due to frequent exchange of resistances , as well as frequent loss .
circle size corresponds to the proportion of total mrsa in each year and color represents the number of phenotypic resistances contained within the antibiogram .
cc22 became the dominant lineage by 2006 corresponding with an expanded resistance profile . over time
instead the frequent shuffling of resistance determinants is seen ; new antibiograms appear each year and resistances do not accumulate .
as mrsa cc22 sccmeciv became dominant in our hospital , it displaced mrsa cc30 sccmecii and mrsa st239 sccmeciii .
mrsa cc30 was also able to shuffle resistance genes , but mrsa st239 was not ( fig .  1 ) .
this suggests that both fitness and shuffling may provide an advantage for successful ha - mrsa clones .
in order to investigate mge variation , we characterized mrsa cc22 sccmeciv isolates ( n = 40 ) found in our hospital during summer 2009 in more detail .
we compared their genomes by using a recently constructed 62-strain s. aureus microarray ( sam-62 ) that contains 60-mer probes to all the predicted genes in the first 62 whole genome sequencing projects and 153 plasmids .
the range of mge variation among the 40 isolates was enormous , despite all isolates being found in the same hospital at the same time , and all belonging to the same mrsa clonal type .
figure  2 illustrates variation in known antibiotic , heavy metal and biocide resistance genes .
mccarthy et al . shows additional substantial variation in other mges , including 4/8 known bacteriophage families , 4/5 known sapi families , 9/18 known plasmid rep families , and 1/4 known transposon families detected in at least one of the isolates .
clustering of ha - mrsa cc22-sccmeciv isolates and distribution of mge - carried antibiotic , heavy metal and resistance genes by microarray .
isolates have been clustered using data from 60-mers that represent all genes on mobile genetic elements ( mges ) .
horizontal lines represent different 60-mer oligo probes specific to 43 different antibiotic , heavy metal and biocide resistance genes .
the color in the main figure is an indicator of test over reference signal ratio .
thus ; ( 1 ) yellow indicates presence in both test and reference ( mrsa252 ) isolates , ( 2 ) red indicated presence in the test but not the reference isolate , ( 3 ) blue indicates absence in the test but not the reference isolate , and ( 4 ) black indicates absence in both test and reference isolates .
color intensity is an indicator of signal intensity and may vary due to copy number or due to differences in probe homology .
this amount of mge variation has potential to be used as a typing tool to discriminate between isolates of clonal mrsa . to test this , we followed up patients from whom we had previously isolated nasal mrsa at hospital admission and subsequently developed mrsa infection . in 6/8 cases ,
the admission isolate was identical to the infecting isolate , and in one case the two isolates differed by one mge .
this shows that the majority of patients colonised with mrsa at admission , that subsequently develop an infection , became infected with their own endogenous strain rather than circulating hospital strains .
this raises important issues for our understanding of how mrsa and s. aureus spread between patients and how we can best combat infection .
we identified two small clusters of related isolates in our hospital that had very similar mge profiles . upon returning to the patient s notes
, we were able to uncover a link between the patients suggesting previously unrecognized transmission of mrsa in the hospital .
at least 1.8% of patients admitted to hospital are positive on nasal screen for mrsa .
colonisation is the greatest risk factor for subsequent infection , and this is because the colonising isolate is usually the same as the infecting isolate .
if mrsa can spread from infected patient to infected patient , then patients must also be at risk of becoming colonised with mrsa in hospital .
the proportion of colonised patients in hospital or at discharge are unknown , but more than half of admitted patients have previous hospital exposure , generating a cycle of mrsa isolates transmitted , discharged and re - admitted to hospital
. the diversity of mge seen in the cc22 population could indicate this substantial reintroduction of cc22 variants to the hospital by newly admitted patients .
our study showed that mge profiles have the potential to develop into rapid and inexpensive typing methods for tracking hospital spread and outbreaks in the healthcare setting .
current typing methods for mrsa concentrate on the cc lineage ( such as multi - locus sequencing typing ( mlst ) or restriction - modification ( rm ) typing ) and sccmec type .
however , these patterns are relatively stable and do not include the fine detail necessary for a typing method to discriminate between isolates to measure transmission and spread and to identify outbreaks .
spa - typing allows some variants of clonal types to be distinguished , but is ineffective for many clones such as mrsa cc22 sccmeciv .
variation in mge carriage could be developed into a rapid and inexpensive method using pcr or microarray / hybridization platforms .
alternatively , once bench - top genomic sequencing is widespread , data interpretation based on mge content may provide the clearest and most reliable interpretive data .
these studies also raise very interesting questions about the stability of mges in s. aureus and mrsa populations .
while we saw substantial diversity in mge profiles among mrsa of the same clonal group , the mges were stable enough to use as a typing method to identify isolates from the same patient or reservoir .
this suggests the mges are relatively stable , but our data also showed evidence of low level transfer and loss of a wide range of mge . during the time scale of a hospital stay , there can be some variation in mge carriage in clonal isolates from the same patient , but within a hospital the variation is large , possibly due to the accumulation of differences over longer time scales .
if we look back through the literature , we can now put this into context .
based on epidemiology , early typing methods such as pulse field gel electrophoresis ( pfge ) grouped isolates as the  same  if they had four or less band pattern differences . as a band shift is usually due to acquisition or loss of an mge , this argues that mge movement in isolates spreading in the hospital setting is frequent in epidemiologically linked isolates .
more recently , the acquisition and loss of bacteriophage from s. aureus during cystic fibrosis infection in individual patients has been well described .
the mechanism of hgt in mrsa is likely to be transduction , as transformation has not been demonstrated in s. aureus , and conjugative plasmids and transposons are found in only a small proportion of isolates .
transduction is dependent on bacteriophage ; it occurs when dna is packaged into a bacteriophage and then transferred from a donor cell to a recipient cell .
all clinical mrsa have prophage integrated into their chromosome and these bacteriophage can be induced to replicate and lyse the host cell by stresses such as uv light , mitogens and antibiotics .
some bacteriophage heads are able to package bacterial or plasmid dna , efficiently delivering their payload to s. aureus of the same lineage .
mges and resistances did not systematically accumulate suggesting the loss of mge is very important .
they may have a fitness cost on the host , or there may be mechanisms to limit the total size of the genome or number of variants of particular mge types . in the laboratory ,
most mges are stable , and the mechanisms for mge loss are unknown . at this stage
it is difficult to definitively prove that shuffling of mges is responsible for the success of ha - mrsa clones .
we are continuing to investigate a genetic explanation for how mrsa cc22 sccmeciv became more amenable to mge acquisition over time .
perhaps mrsa clones that can easily acquire or lose mges may adapt more quickly to new environmental conditions such as antibiotic prescribing or transfer between patients .
this may give them an advantage over other commensals that do not adapt so readily , leading to successful colonisation of patients , and ultimately to infection .
 methicillin - resistant staphylococcus aureus ( mrsa ) cc22 sccmeciv is a successful hospital - associated ( ha- ) mrsa , widespread throughout the world , and now the dominant clone in uk hospitals . 
 we have recently shown that mrsa cc22 is a particularly fit clone , and it rose to dominance in a uk hospital at the same time as it began acquiring an increased range of antibiotic resistances . 
 these resistances were not accumulated by individual cc22 isolates , but appear to shuffle frequently between isolates of the mrsa cc22 population . 
 resistances are often encoded on mobile genetic elements ( mges ) that include plasmids , transposons , bacteriophage and s. aureus pathogenicity islands ( sapis ) . 
 using multi - strain whole genome microarrays , we show that there is enormous diversity of mge carried within a mrsa cc22 sccmeciv population , even among isolates from the same hospital and time period . 
 mge profiles were so variable that they could be used to track the spread of variant isolates within the hospital . 
 we exploited this to show that the majority of patients colonised with mrsa at hospital admission that subsequently became infected were infected with their own colonising isolate . 
 our studies reveal mge spread , stability , selection and clonal adaptation to the healthcare setting may be key to the success of ha - mrsa clones , presumably by allowing rapid adaptation to antibiotic exposure and new hosts . 
HA-MRSA Clones
MGEs
Evolution of HA-MRSA in Hospital
MGE Variation
MGE Stability