Abstract:
Methicillin resistant S. aureus (MRSA) is a versatile and dangerous human’s
pathogen and is a common cause of nosocomial and community acquired infections.
S. aureus causes several types of infections such as bacteremia, folliculitis, sepsis,
mastitis, meningitis and toxic shock syndrome and staphylococcal pneumonia. S.
aureus has developed resistance to the antibiotic ‘methicillin’ and continued spread of
methicillin-resistant S. aureus (MRSA) strains poses a significant risk to patients and
contributes to a substantial financial burden on healthcare resources. HA-MRSA
isolates usually belong to six lineages (CC1, CC5, CC8, CC22, CC30 and CC45) out
of ten dominant clonal complexes (CCs) or lineages. Various methods have been
employed to identify and characterize S. aureus strains. Phenotypic techniques have
been replaced by more robust and accurate molecular techniques. The commonly
used molecular techniques are Pulse Field Gel Electrophoresis (PFGE), Multilocus
variable number of Tandem repeat analysis (MLVA), Restriction modification tests
(RM), multilocus sequence typing (MLST) and spa typing.
Present work focuses on genotyping of clinical MRSA isolates from three tertiary
care hospital located in “Rawalpindi/Islamabad”, in order to examine the types and
phylogenetic relationship of the isolates. In order to gain the understanding of the
distribution of MRSA clones in Pakistan, where unregulated antibiotic use is
widespread and distributions of MRSA is supposed to be high, an epidemiological
relationships between 123 methicillin resistant Staphylococcus aureus strains,
isolated between 2006 and 2008 from three tertiary care hospitals of Rawalpinidi and
Islamabad, were examined using MLVA scheme, combined with RM typing, PVL
sceening, STAR element analysis, spa typing and MLST to investigate the
phylogenetic relationships of the Pakistani MRSA isolates. Six loci (clfA, clfB, sdrC,
sdrD, spa and sspa) were used in a multilocus variable number tandem repeat
analysis (MLVA). A total of 63 MTs/haplotypes were obtained by MLVA. Analysis
of restriction modification (RM) genes detected, an RM3 type, associated with CC8,
in most strains and an RM1 type, associated with CC30, in only two strains. On
further typing of selected strains by Spa typing and MLST, it was found that the
RM3/CC8 isolates were ST113-t064, ST113-t451 or ST239, with one of four spa
types, whilst the RM1/CC30 isolates were ST30-t021. Analysis of STAR element of
these strains for three loci showed their close resemblance; only the strains belonging
to CC30 showed no STAR motif in gapR upstream region, confirming their genetic
homology to other CC30 strains. Furthermore, the ST30 strains were also found
positive for PVL gene.
The present genotypic study showed that in Pakistan, the isolates belonging to clonal
complex eight (CC8) are dominant in clinical settings. They belong to ST239, ST113
or ST8. The other clonal complex found was CC30 with presence of PVL gene and
isolates belong to ST30. The use of MLVA in resource poor laboratories as a rapid
and robust method for grouping noscomial MRSA isolates into clusters for
identification of localized outbreaks is quite fruitful and MLVA may also provide an
understanding of the evolutionary processes as changes in the number of repeats at
different loci, may be indicative of which loci are prone to natural selection resulting
in higher levels of variation, thus VNTRs serve as evolutionary clock for
investigating an outbreaks and transmission events. In this study, we observed more
variation in clfA and clfB than in sdrC, sdrD, spa and sspa. We also found that a
change in repeat number was not necessarily gradual but may have occurred as a
result of large jumps. Some isolates with significant differences in repeat numbers at
single locus but being identical numbers in all other loci. Further evidence is provided
by the spa typing results, i.e. with a loss of four repeats resulting in a shift from t987
to t030 and a two repeat difference changed t021 to t275. These large jumps might be
due to deletions or insertions mediated by recombination or as result of deletions due
to slip-strand impairing during DNA replication.
Thus MRSA infections have become a challenge across the globe. The MRSA
isolates which were once endemic to Europe and America, Africa has now been
reported from Asia and thus suggesting that the MRSA isolates which once was
endemic to a certain geographical area are no more confined to those boundaries.
More over the pandemic spread of one type of MRSA clone across the globe is the
result of antibiotic resistance. Therefore a joint global effort will be effective for the
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control of MRSA infection. Although this study was carried out on limited number of
isolated but it is quite useful to strengthen the MRSA data in Pakistan and to develop
the genetic profile of MRSA in Pakistan and then to link it globally. This study also
helped to under stand that, although there are only two lineages in these hospitals as
in most of other Asian countries but there is a diversity at subspecies level as some of
the isolates assumed a specific genetic profile as they evolved locally after they were
imported to this region.
The work presented in the thesis has been published in the following articles:
1-
2- Arfat Y1*, Johnson M2, Malik SA1, Morrissey J2 and Bayliss CD2 (2013).
Epidemiology of Methicillin Resistant Staphylococcus aureus (MRSA) Isolates
from Pakistan. African Journal of Microbiology Research; Vol.7 (7): 568-576.
H5 Index: 15.
2-
Joanne Purvees1*, Mathew Blades2, Yasrab Arfat3, Salman A Malik1,
Christopher D Bayliss1 and Julie Morrissey1 (2012). Variation in the genomic
locations and sequence conservation of STAR elements among Staphylococcus
aureus species provides insight into DNA repeat evolution. Genomics; 13: 515.
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