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MRSA is one
of the multi-drug resistant pathogenic bacteria responsible for both hospital
and community acquired infections. MRSA has been constituting a serious public
health since 1960s, because of its high power of acquiring resistance to
multiple antibiotics classes. MSSA changes to MRSA upon the acquisition of SCCmec, a unique mobile genetic element,
which carries the methicillin-resistant gene, mecA with its site specific cassette
chromosome recombinase (ccr) genes
and its regulatory proteins. In this cassette the presence of mecA gene represents that the particular
strain is methicillin resistant or sensitive. mecA gene encodes an additional penicillin-binding protein PBP2a,
which has low affinity for most of the semi-synthetic penicillin like
methicillin. This enables transpeptidase activity in the presence of
beta-lactams, preventing them from inhibiting cell wall synthesis (4). mecA gene is regulated by two regulator
proteins; mecR1 (encoding the signal
transducer protein MecR1) and mecI (encoding
the repressor protein MecI). Many types, subtypes and varients of SCCmec elements and SCCmec element lacking mecA
have been reported (IWS-SCC).

SCCmec are classified into 11 types based on the combination of two
essential components, the mec gene complex and the ccr gene complex. There are five classes of mec gene complex.

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classA consists of IS431mec-mecA-mecR1-mecI
gene linkage. While class B consists of a truncated mecR1 gene; IS431mec-mecA-DELTAmecR1-mecI gene
linkage. C1 is another class with the same mec gene complex, where the two IS elements
oriented in the same direction. While C2 class in which two IS elements are in
opposite direction. Recently mecC, a
homologue of mecA was identified with
gene linkage bla-mecC-mecR1 homologue and mecI homologue was designated as classE. The ccr gene complex is
the gene linkage composed of eight ORFs and ccr genes. There are three ccr
genes, ccrA, ccrB, ccrC has been
identified in staphylococcal species. These genes are distinguished based on
the nucleotide sequence identity with less than 50 percentages. SCCmec elements are highly diverse in their
structural organization and genetic content. Based on the ccr genes we can done
the typing of Staphylococcus strains.

         Here in
our study we are trying to identify the emergence and evolution of SCCmec elements among Staphylococcus aureus. First we had collected complete set of proteins
of 152 S. aureus strains available in
NCBI-Genome database. We had blasted each other and took the best blast hit to
cluster the homologues proteins using power-needle. We had end up with 4566
clusters. For finding the SCCmec
elements homologues in our 152 strains, we had collected 104 SCCmec elements, which includes both mec and
ccr gene complex protein sequences from reference strains. For collecting the
SCCmec elements, we had followed the International Working Group
on the Classification of Staphylococcal Cassette Chromosome
Elements (IWG-SCC). The structures of 11 types SCCmec are described in the below table with its representative
strains.

 

SCCmec type

ccr gene
complex

Representative strains

NCBI accession

mec gene
complex

I

1
(A1B1)

NCTC10442

AB033763

B

II

2
(A2B2)

N315

D86934

A

III

3
(A3B3)

85/2082

AB037671

A

IV

2
(A2B2)

CA05
ZH47

AB063172
AM292304

B

V

5
(C)

WIS
TSGH17
PM1

AB121219
AB512767
AB462393

C2

VI

4
(A4B4)

HDE288

AF411935

B

VII

5
(C)

JCSC6082

AB373032

C1

VIII

4
(A4B4)

C10682

FJ390057

A

IX

(A1B1)

JCSC6943

AB505628

1C2

X
 

(A1B6)

JCSC6945

AB505630

7C1

XI
 

(A1B3)

LGA251

FR821779.1

8E

Table: Structures of 11 types SCCmec

 

The
structures of 11 types of

SCC

mec

 are illustrated based on the nucleotide
sequences deposited in the DDBJ/

EMBL/GenBank
databases  as  follows:

The protein sequences of these
elements are taken from the above mentioned strains. We had found that, 47
clusters show homologue to 104 SCCmec elements
using the criteria greater than or equal to 30 percent identity and greater
than or equal to 70 query coverage and we only took the top most hit clusters.

By plotting the distribution of these 47 SCCmec homologues within 152 aureus strains,
we found that 111 strains are having mecA gene in their genome. That means
these strains can be classified as MRSAs (Methicillin
Resistant Staphylococcus aureus) and the rest 41 are MSSAs (Methicillin Sensitive Staphylococcus aureus).

In 152 strains only one strain, Staphylococcus
aureus LGA251 shows mecC gene. While
we are considering the presence regulatory genes like mecR1 and mecI it is
present in approximately 96 and 111 strains respectively. Another fact we found
is the metal coding genes like ars
and cop are universally distributed
in 152 strains. Again when we had typed 152 strains based on their presence of
ccr allotypes. We got total 8 types of SCCmec, in that 10 strains belongs to
Type I, 16 were in Type II, 13 were in Type III, 96 were in Type IV, 9 were in
type V, 2 were in Type VIII and IX, 1 were in Type XI and 3 Un-typed strains.

The next phase of our study was focused on how these
SCCmec elements distributed in all Bacterial
kingdom other than Staphylococcus aureus.

For that we had downloaded complete set of proteins of 7353 bacterial strains
available in NCBI and blasted the 47 cluster homologues of SCCmec to 7353 strains. We had programmatically
filtered the blast output using the threshold, sequence identity greater than
or equal to 30 percent and query coverage, greater than or equal to 70. We had analyzed
our data as 3 sessions. In the first session we had plotted the distribution of
47 clusters in 22 complete non- Staphylococcus
aureus species. In that mecA and mecI genes are present in 6 species.  They include Staphylococcus sciuri, Staphylococcus pseudintermedius,
Staphylococcus schleiferi, Staphylococcus epidermidis, staphylococcus argenteus and
Staphylococcus
haemolyticus. Except Staphylococcus
sciuri ccr genes and mecR1 genes are also widely distributed in
these non- Staphylococcus aureus species. In the next session, we had
checked, how these mec elements are distributed within firmicutes in order
level classification. We had plotted it in 10 orders, and found that mecA, mecI
and ccr genes except ccrA4, all are present in 3 orders. They are Clostridiales, Bacillales
and Lactobacillales. But for Lactobacillales mecR1 gene is absent. In the last
session we had checked SCCmec genes are present among non-firmicutes. For that
we had considered 36 classes of bacteria, none of them showing homologues to mecA gene. But notably, the other regulatory
genes and site-specific recombinase
genes are present in some classes especially, in Beta and Gamma proteobacteria.

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