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Antimicrobial Agents and Chemotherapy, December 2003, p. 3926-3934, Vol. 47, No. 12
0066-4804/03/$08.00+0 DOI: 10.1128/AAC.47.12.3926-3934.2003
Copyright © 2003, American
Society for
Microbiology. All Rights Reserved.
Evolutionary Models of the Emergence of Methicillin-Resistant Staphylococcus aureus
D. Ashley Robinson and Mark C. Enright*
Department
of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United
Kingdom
Received 23 May 2003/
Returned for modification 1 August 2003/
Accepted 8 September 2003

ABSTRACT
Five
major lineages of methicillin-resistant
Staphylococcus aureus
(MRSA) have evolved since the introduction of methicillin
for the
treatment of infections caused by penicillin-resistant
S.
aureus in 1959. The clones of these lineages are responsible
for
the vast majority of hospital-acquired MRSA disease globally.
We have
constructed high-resolution evolutionary models for
each lineage using
a parsimony approach with 15 partial gene
sequences from 147
geographically diverse isolates. On the basis
of these models, we infer
that MRSA has emerged at least 20
times upon acquisition of the
methicillin resistance determinant,
which is carried on a mobile
genetic element called the staphylococcal
cassette chromosome
mec (SCC
mec). The acquisition of SCC
mec by
sensitive clones was four times more common than the replacement
of one
SCC
mec with another. Notably, SCC
mec type IV was
found
in twice as many clones as any other SCC
mec type, and it
is
this SCC
mec type which is commonly found in clones from
patients
with community-acquired MRSA disease. Our findings suggest
that
most clones of MRSA arise by the acquisition of SCC
mec
type
IV by methicillin-sensitive
isolates.

INTRODUCTION
Staphylococcus aureus has a proven ability to adapt to the
selective
pressure of antibiotics. The emergence of strains with
resistance
to penicillin and methicillin was reported in 1948 and 1961,
respectively
(
2,
17). In both cases,
resistance developed within a few years
of the introduction of the
antibiotics into clinical medicine.
At present, methicillin-resistant
S. aureus (MRSA) strains with
resistance to vancomycin are
emerging (
4,
13). This trend is
a
cause of great public health concern, as vancomycin is the
antibiotic
of last resort for the treatment of MRSA infections.
There are
indications that the epidemiology of MRSA may also
be expanding, from
being a major cause of hospital-acquired
infections to becoming a cause
of community-acquired infections
(
3,
14).
Consequently, there
has been keen interest in understanding
how natural populations of MRSA
have evolved over the past half
century.
Our understanding of the
evolution of MRSA has benefited from the development of molecular tools
that allow characterization of both the strain phylogeny and the
methicillin resistance determinant. Strain phylogeny can be resolved by
multilocus sequence typing, which identifies a strain
unambiguously on the basis of its sequence at seven
housekeeping genes (8).
The product of the mecA gene confers methicillin resistance
and is carried on a mobile genetic element called the staphylococcal
cassette chromosome mec (SCCmec).Four main types of SCCmec, which differ in size and
composition, have been described for S. aureus
(16,
22). The application of
multilocus sequence typing and SCCmec typing to international
collections of MRSA and methicillin-susceptible S. aureus
(MSSA) isolates has revealed that (i) methicillin resistance has
emerged in five phylogenetically distinct lineages, (ii) methicillin
resistance has emerged on multiple occasions within a given
phylogenetic lineage, and (iii) most MRSA disease is caused by a
relatively small number of pandemic clones
(9).
The frequency
with which SCCmec is acquired in nature is unknown. Are new
clones of MRSA sporadically emerging by a frequent acquisition of
SCCmec, perhaps on a daily basis in the hospital setting, or
is SCCmec a relatively stable locus that has been acquired on
rare historical occasions? To address this question, we developed a
high-resolution multilocus typing method that could detect
SCCmec acquisitions among closely related isolates of S.
aureus. The data allowed us to construct detailed evolutionary
models upon which inferences regarding the acquisition of
SCCmec could be
based.

MATERIALS AND
METHODS
Bacterial isolates.
A previous study of 912 MRSA and MSSA
isolates found that methicillin
resistance had emerged in five
phylogenetically distinct lineages
of
S. aureus
(
9). We selected 136 of
these isolates, which represented
all hospital-acquired MRSA clones
with an international distribution,
plus related MRSA and MSSA
isolates. We also included four MSSA
isolates from Cuba and seven
historically early MSSA isolates
(
5).
Multiple isolates of
the same clone were selected to be geographically
diverse. A total of
147 isolates from 18 countries were included
in this study, of which 92
were MRSA and 55 were MSSA. All isolates
were stored at
-80°C and grown overnight on blood agar plates
at
37°C.
Sequence typing.
We selected seven S. aureus
surface protein (sas) genes that encode the LPXTG cell wall
attachment motif. The genes chosen were among the least
well-characterized sas genes and have been named
sasA, sasB, sasD, sasE,
sasF, sasH, and sasI by Mazmanian et al.
(24). sasB has
homology with fmtB, a gene required for methicillin resistance
(20). sasE has
also been named sai-1, which encodes a 29-kDa surface protein
(GenBank accession number
AB042826),
and isdA, an iron-responsive surface determinant
(25). sasH has
homology with a gene that encodes a 5' nucleotidase. On the
basis of the COL genome sequence
(http://www.tigr.org),
sasA and sasF were located
11 kb from each
other, and all other sas loci were >50 kb from each
other.
Polymorphic regions of the sas genes were
identified by using the publicly available S. aureus genomic
sequences, and primers were designed to amplify
450-bp
fragments (Table
1). The primers of Enright et al.
(8) were used for
multilocus sequencing of the seven housekeeping genes, arcC,
aroE, glpF, gmk, pta, tpi,
and yqiL. Primers were also designed to amplify the short
sequence repeats of the spa gene (Table
1). Chromosomal DNA was
isolated with a DNeasy kit (Qiagen). The PCR conditions were identical
to those of Enright et al.
(8), with a few
modifications. The PCR mixtures used 10 pmol of the sas- and
housekeeping gene-specific primers per µl and 100 pmol of the
spa-specific primers per µl. PCR annealing
temperatures were 45°C for the sas genes and
55°C for the housekeeping and spa genes. Sequencing of
the DNA of both strands was performed as described by Enright et al.
(8) with an ABI 3700
automated sequencer (PE Applied Biosystems).
For the
sas
and housekeeping genes, unique sequences defined
alleles, and the
unique series of alleles at each locus defined
a sequence type (ST).
For the
sas genes, a database of alleles
was compiled and is
available upon request. For the housekeeping
genes, the alleles were
identified by using the MLST database,
available at
http://www.mlst.net.
The
spa repeats were characterized
as described by Shopsin et
al. (
31). The resolution
obtained
by different typing methods was compared by using
Simpson's
index of diversity (
D) and was calculated as 1
- {[1/
N(
N -
1)]
ni(
ni
-
1)}, where
n is the number of isolates
belonging to the
ith
ST and
N is the total number of
isolates in the sample
(
12,
15).
SCCmec
typing.
SCCmec
types were assigned by PCR analysis of the ccr and
mec genes, as described by Okuma et al.
(27). The primers of Ito
et al. (16) were used for
PCR of the ccr genes, and new primers (Table
1) were used for PCR of
the mec genes. Structural variants of SCCmec were
detected by the multiplex PCR analysis of Oliveira and de Lencastre
(28).
Nomenclature.
This study used a newly proposed
nomenclature for MRSA clones that was based on a combination of the STs
at seven housekeeping genes and the SCCmec type
(9). For example, an MRSA
clone of ST250 and SCCmec type I is referred to as
ST250-MRSA-I, and an MSSA clone of ST8 is referred to as
ST8-MSSA.
Phylogenetic
analyses.
The alleles of
the sas and the housekeeping genes were aligned by using the
CLUSTALW program (33)
with default parameters, followed by manual inspection. Insertion and
deletion polymorphisms were ignored during phylogenetic analyses. MEGA
software (version 2.0)
(21) was used to
calculate ds/dn ratios by the
modified Nei and Gojobori method.
ds/dn is the ratio of the
number of synonymous or silent nucleotide changes
(ds) to the number of nonsynonymous or amino
acid-replacing nucleotide changes (dn). The
PAUP* program (version 4.0b10)
(32) was used to
construct neighbor-joining (NJ) and maximum-parsimony (MP) trees. NJ
trees were constructed by using the absolute number of nucleotide
differences between STs. MP trees of all STs were constructed with a
heuristic search and random addition of taxa. MP trees of specific
lineages were constructed with a branch-and-bound search to ensure that
all most parsimonious trees were found. Bootstrapping was performed
with 1,000 replicates.
Nucleotide
sequence accession numbers.
The sas gene sequences
reported in this study have been deposited in GenBank under accession
numbers
AY175407
to
AY175464.

RESULTS
Development
of a high-resolution multilocus typing method.
To develop a multilocus typing method
that could detect SCC
mec acquisitions
among closely related isolates, we sequenced fragments
of seven
S.
aureus surface protein (
sas) genes, which we expected
would
accumulate variations more rapidly than the seven housekeeping
genes.
We sequenced a similar number of nucleotides (
P
= 0.710, Mann-Whitney
U test) and observed a similar number of
alleles (
P = 0.165)
for the
sas and
housekeeping genes (Table
2). However, the
sas genes provided significantly more
polymorphic sites (
P = 0.011)
and
parsimony-informative sites (
P = 0.026)
than the housekeeping
genes (Table
2). The variation found in
sasD appeared to be
similar to that found in the housekeeping
genes.
sasD and
sasF both presented alleles with
insertion or deletion polymorphisms.
There is reason
to suspect that variations in genes encoding
surface proteins may be
influenced by the selective pressure
of the host immune system, but we
found no evidence of diversifying
selection in the fragments sequenced.
When all alleles were
considered, the proportion of synonymous
nucleotide changes
was greater than the proportion of nonsynonymous
nucleotide
changes (see the
ds/
dn ratios in Table
2). There were no
differences
in the
ds/
dn ratios
for the
sas and housekeeping genes (
P =
0.530).
The short sequence repeats of the spa gene,
which encodes immunoglobulin G-binding protein A, provides a highly
discriminatory sequence-based method for the typing of S.
aureus (31). We
compared the resolutions of the different typing methods using
Simpson's index of diversity, which takes into account the
observed numbers of STs and their frequencies of occurrence
(12,
15). The diversity
resolved by the spa repeats was significantly greater than the
diversity resolved by either multilocus method (i.e., the 95%
confidence intervals did not overlap), and the diversities resolved by
the multilocus methods were similar to each other (Table
3). However, the multilocus methods in combination provided a
significantly greater resolution than either multilocus method by
itself and a resolution similar to that obtained with the spa
repeats (Table
3).
Construction
of evolutionary models.
To
compare the phylogenetic signals of the
sas and housekeeping
genes,
we constructed NJ and MP trees based on the 3,185 nucleotides
of
the
sas genes and the 3,198 nucleotides of the housekeeping
genes.
Previously, it was found that MRSA had emerged in five
phylogenetically
distinct lineages called clonal complexes (CCs)
(
9). The
sas and
housekeeping genes classified all but one isolate of ST36
into the same
CCs on both NJ and MP trees with high bootstrap
support (Fig.
1). The bootstrap support for the CCs was generally
higher for the trees
based on the
sas genes, presumably because
these genes
provided the most polymorphisms (Table
2).
The branching
order between the CCs significantly differed between
the
sas
and housekeeping genes, as witnessed by the high bootstrap
support for
conflicting arrangements of CCs (Fig.
1). Thus,
no inferences
regarding the relationships between CCs are made
with these data. Of
note, the housekeeping genes grouped the
pandemic clones of ST8, ST250,
and ST239 and their variants
into a single lineage, called CC8 (Fig.
1). The
sas genes
grouped
ST8 and ST250 into the same lineage but clearly showed that
ST239
was a diverged branch of CC8. Moreover, the
sas genes
were identical
for ST235 and some isolates of ST8, but these clones
differed
at five of seven housekeeping genes (Fig.
1).
To investigate
the branching order within CCs, we combined the nucleotide sequences of
the 14 sas and housekeeping genes into a single data set with
6,383 nucleotides. This total evidence approach is justified, given
that the data classified the isolates into the same CCs, with the two
exceptions noted above. MP trees were constructed for each CC by using
the combined data set. CC5, CC8 (consisting of separate trees for
ST8-ST250 and ST239), and CC45 yielded single MP trees with perfect
consistency. CC22 yielded two MP trees that differed in the placement
of a single ST. CC30 yielded 17 MP trees. Evolutionary models for each
CC were constructed by expanding the MP trees to include
SCCmec type and spa type and assuming the fewest
additional changes to the trees (Fig.
2).
Of the 59 steps depicted in our evolutionary models (Fig.
2),
the housekeeping genes
and SCC
mec type resolved 21 steps, the
spa repeats
and
sas genes resolved 24 steps, and a combination
of these
two categories of typing methods resolved 14 steps.
While the
spa repeats and
sas genes provided a modest but
significant
increase in typing resolution of 6.1% (98.8%
diversity - 92.7%
diversity) over that of the
housekeeping genes (Table
3), these
markers provided
a large increase in phylogenetic resolution
of 40.7% (24/59
steps, respectively) over that provided by the
housekeeping genes and
SCC
mec type.
Evolution within CC5
and CC8.
CC5 and CC8
represented the most diversified lineages of MRSA and contained the
most pandemic clones (Fig.
2, left panel). The
putative ancestors of these lineages were the STs that had the largest
number of single-step variants (i.e., single-locus variants and
single-nucleotide variants) and were represented by historically early
MSSA isolates (5). Within
CC5, we propose that all four SCCmec types
were acquired once by ST5-MSSA ancestors (Fig.
2, left panel). Within
CC8, we propose that three SCCmec types were acquired on
multiple occasions (Fig.
2, left panel).
Of
note, we propose that ST254-MRSA-I, represented by two isolates from
the United Kingdom from 1962 and 1965, respectively, arose
independently of the archaic clone
(30) in the early days of
MRSA emergence. It is simpler to assume that ST254-MRSA-I evolved from
ST8-MSSA by acquiring SCCmec type I and point mutations in
aroE and sasF rather than to assume that ST254-MRSA-I
evolved from ST250-MRSA-I, which would require a back-mutation at
yqiL and the point mutations in aroE and
sasF. To our knowledge, there are no known isolates of
ST254-MSSA, but this possibility is indicated by dashed lines in Fig.
2 (left panel).
The
integration of pUB110 into the SCCmec locus
(28) gave rise to the
variant SCCmec types IA and IVA (Fig.
2, left panel). The
lineage leading to the Irish-1 clone is marked by several
uncharacterized modifications in the SCCmec locus. ST8-MRSA-IV
from Australia and Ireland have the ccr and mec genes
characteristic of SCCmec type IV
(27) but amplify only
mecA in a multiplex PCR
(28). Likewise,
ST8-MRSA-II from the United Kingdom and Ireland, the Irish-1 clone,
have the ccr and mec genes characteristic of
SCCmec type II but either lack the kdp gene
characteristic of SCCmec type II or have a multiplex PCR
pattern identical to that of SCCmec type IV. Thus, the
evolutionary pathways of this lineage remain unclear, as indicated by
the dashed lines in Fig. 2
(left panel).
A hypothesis for the origin
of ST239.
It was noted that
ST239 represents a distinct branch within CC8 (Fig.
1). This lineage includes
numerous clones such as the epidemic methicillin-resistant S.
aureus type 1 (EMRSA-1); EMRSA-4; EMRSA-7; EMRSA-9;
EMRSA-11; and the Brazilian, Portuguese, and Vienna clones
(7,
19,
23,
34). The proposed path
leading from ST8 to ST239 involved the acquisition of SCCmec
type III and alleles at arcC, sasA, sasD,
sasF, sasH, and spa (Fig.
2A). Surprisingly, with
the exception of sasD4, the derived alleles were exclusive to
ST239 and ST30 and their descendants; sasD4 also occurred in
two isolates from CC22. These data suggest either that parallel
evolution of multiple genes had occurred in unrelated lineages of
S. aureus or that recombination had occurred. We favor the
latter hypothesis for two reasons. First, the sasD4 allele had
two characteristic deletions of 18 and 42 nucleotides, respectively,
which are unlikely to arise independently in different lineages.
Second, the genes arcC, sasF, sasA,
sasH, spa, and sasD are contiguous on the
COL genome sequence and are centered around the origin of replication.
We propose that ST239 arose from a single recombination event that
involved the exchange of >200 kb of contiguous DNA between ST30
and ST8. The donor of SCCmectype III remains unknown; the only clone to carry this element besides
the clones in the ST239 branch was a single isolate from ST5 (Fig.
2, left
panel).
Evolution within CC22, CC30, and
CC45.
CC22, CC30, and CC45
represent less diversified lineages of MRSA strains mostly isolated
from Europe (Fig. 2, right
panel). The putative ancestors for CC22 and CC45 were the STs that had
the largest number of single-step variants. No historically early MSSA
isolates were available for these lineages. The putative ancestor for
CC30 was more difficult to assign. ST30 had one less single-step
variant than ST36 but was represented by an historically early MSSA
isolate (5) and shared
sas alleles with ST39, presumably an old clone within CC30
that has also evolved several single-step variants
(10). Thus, our
evolutionary model for CC30 is based on the assumption that ST30 should
be considered ancestral.
Within CC22, we propose that
SCCmec type IV was acquired once (Fig.
2, right panel). Within
CC30, we propose that both SCCmec types II and IV were
acquired once (Fig. 2,
right panel). To our knowledge, there are no known isolates of
ST36-MSSA, but this possibility is indicated by dashed lines in Fig.
2 (right panel). Within
CC45, we propose that SCCmec type IV was acquired four times
and that SCCmec type II was acquired once (Fig.
2, right panel).
Alternative evolutionary hypotheses within CC45 are indicated by dashed
lines in Fig. 2 (right
panel).
Patterns of acquisition and
variation of SCCmec.
Our evolutionary models indicate that a
minimum of 20 acquisitions of SCCmec have occurred in S.
aureus. There were 16 acquisitions of SCCmec by an MSSA
clone and 4 putative reacquisitions of SCCmec by an MRSA clone
(Table
4). There were 10 acquisitions of SCCmec type IV and 10
acquisitions of the other SCCmec types (Table
4). Nearly half (9 of 20)
of all acquisitions involved an MSSA clone that acquired
SCCmec type IV.
SCC
mec variants IA and IVA have
been characterized by others
(
28)
and were included in
our evolutionary models. We note that there
were two conflicts in the
classification of SCC
mec types based
on
the
ccr and
mec gene
(
16,
27) and multiplex PCR
(
28) analyses.
These
cases involved isolates of SCC
mec types II and IV and
types II
and III, which differed in the
ccr and
mec analyses
but
which had identical multiplex patterns (data not shown). We
observed
a total of 17 variants of SCC
mec (Table
4). The largest
SCC
mec types, types II and III, presented the most STs. As
further
work is necessary to characterize the new variants, we have
not
included them in our evolutionary
models.

DISCUSSION
For a decade it has
been recognized that methicillin resistance
has emerged multiple times
within
S. aureus
(
11,
26), but the
frequency of
resistance acquisition and any underlying historical
patterns have
remained unknown. Our previous work
(
9) has shown
that MRSA
has arisen on multiple occasions within successful
MSSA lineages, but
we were unable to resolve the full evolutionary
history of MRSA since
multiple acquisitions of the same SCC
mec type by a single ST
could not be discerned. In this work, we
augmented the standard
multilocus sequence typing scheme with
an additional set of highly
variable
sas genes which allowed
us to resolve a more complete
evolutionary history of MRSA.
We propose several novel hypotheses
for the emergence of MRSA. First, we propose that two MRSA clones
(ST247, ST257) emerged from the first MRSA clone (ST250) by stepwise
evolution and that one MRSA clone (ST254) emerged independently within
4 to 5 years of the first reported isolation of MRSA. These data make a
case for multiple emergences of MRSA early in its history. Second, we
propose that ST239 was created by the exchange of >200 kb of
contiguous DNA between ST30 and ST8. This hypothesis is supported by
partial sequencing of an additional 26 genes (D. A. Robinson
and M. C. Enright, submitted for publication).
ST239 and its descendants represent a phylogenetically distinct and
clinically important branch within CC8. de Lencastre and colleagues
(29) have reported that
clones of ST239 are among the most prevalent in Portuguese hospitals
and were recently found to be highly prevalent in hospitals in China
and Taiwan (6). Third, we
propose that CC22, CC30, and CC45 represent major lineages of MRSA that
account for 8 of 20 SCCmec acquisitions. CC45, in particular,
has not been widely recognized as a major lineage of MRSA, but we found
that isolates of CC45 were geographically distributed in both the
Eastern and the Western Hemispheres and that the lineage has acquired
SCCmec four or five times.
We provide the first
estimate of the number of times that SCCmec has been acquired
by S. aureus in nature. In most cases, SCCmec is
retained as the lineages evolve. Our data suggest that the spontaneous
excision of SCCmec does not occur frequently from an
evolutionary perspective. We propose that on four occasions
SCCmec was reacquired by an MRSA clone. The proposed
evolutionary events leading to the Irish-1 clone within CC8 are
unclear. However, the proposed evolutionary events leading to the
Hannover clone within CC8 and the EMRSA-16 clone within CC30 are
clearer, and there are no known MSSA intermediates to support an
alternative evolutionary path. The proposed acquisition of
SCCmec type II by an SCCmec type IV clone within CC45
can be interpreted differently and requires testing. A mechanism for
reacquisition of SCCmec could involve the loss of one
SCCmec type followed by acquisition of another SCCmec
type within a short time period. Although experiments have shown that
the recombinase genes encoded by SCCmec, ccrA, and
ccrB are sufficient to transfer the element from a multicopy
plasmid into the chromosome in a site-specific and orientation-specific
manner (18), the precise
mechanism by which SCCmec is transferred in nature is not
known. We note that our estimate provides a lower bound of the actual
number of acquisitions that have occurred in nature. The estimate will
undoubtedly increase as more isolates from patients with
community-acquired disease and more isolates from a wider geographic
area are studied.
The observation that the largest
SCCmec elements, types II and III, had the most structural
variants, as detected by PCR, might be explained by the fact that these
elements carry more copies of transposable elements, such as
IS431 and Tn554
(16). The activities of
these transposable elements might play a role in remodeling the
structure of SCCmec and, thus, lead to a greater number of
structural variants. The observation that the smallest SCCmec
element, type IV, had been acquired most often might be explained by a
size dependence on the efficiency of DNA transfer. Smaller
SCCmec elements may simply transfer more efficiently than
larger SCCmec elements.
Alternatively, SCCmec
type IV may have been acquired and subsequently retained in S.
aureus most often because it has been the selectively favored
element of methicillin resistance. Hiramatsu and colleagues
(22,
27) suggest that
SCCmec type IV may have a lower cost on fitness because it
carries only the structural and regulatory genes for methicillin
resistance and the recombinase genes for movement of the element. In
contrast, SCCmec types I to III can carry additional genes,
such as those encoding resistance to non-ß-lactam antibiotics
and heavy metals (16).
The combination of smaller size and lower cost on fitness may make
SCCmec type IV the selectively favored element for transfer
among all S. aureus isolates.
SCCmec type IV
was first discovered in recent studies that examined isolates of
community-acquired MRSA
(1,
22). Several new clones
that carry SCCmec type IV have also been identified from
samples from patients with community-acquired MRSA
(27). Our results, based
on inferences from evolutionary models, show that SCCmec type
IV is also the most frequently acquired element within the five major
lineages responsible for most hospital-acquired MRSA infections. While
the prevalence of disease caused by clones that carry SCCmec
types I to III at present may be higher than that caused by clones that
carry SCCmec type IV, the more frequent acquisition of
SCCmec type IV has markedly increased the genetic diversity of
MRSA and suggests that the prevalence of disease caused by clones that
carry this element will increase.

ACKNOWLEDGMENTS
We thank Brian Spratt and
Ed Feil for comments on the manuscript
and Paul Wilkinson for technical
assistance.
M.C.E. is a Royal Society University Research Fellow.
This work was supported by the Wellcome
Trust.

FOOTNOTES
* Corresponding
author. Mailing address: Department of Biology and Biochemistry,
University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.
Phone: 44-1225-386871. Fax: 44-1225-386779. E-mail:
m.c.enright{at}bath.ac.uk.


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