| Summary: | Published genomics data regarding CA-MRSA and HA-MRSA isolates from Malaysia
are scarce. Therefore, the aim of this study was to characterise the Malaysian CA-MRSA
and HA-MRSA isolates in depth using molecular typing, as well as whole-genome
sequencing. CA-S aureus isolates were obtained from the nasal swabs of undergraduate
students whereas HA-S aureus isolates were archived samples obtained from hospital
laboratories. Out of 168 S aureus nasal carriage isolates obtained, the occurrence of
MRSA was 8.3% and IS% among undergraduate students of the agriculture
biotechnology and health sciences programmes, respectively, with multidrug resistance
were observed in IS% (26/168) of the isolates. Among the 146 hospital archived samples
ofS aureus, 28% (41/146) were MRS A, out of which 63% (i.e. 26/41) were categorised
as multidrug-resistant (MDR; resistant to three or more classes of antimicrobial
compounds).
The most predominant SCCmec type among both CA- and HA-MRSA was SCCmec-II1,
with the highest occurrences observed among HA-MRSA (68%; 28/41) compared to
CA-MRSA (41%; 9/22) isolates. Other SCCmec types that were found in CA-MRSA
were SCCmec-IV (32%), SCCmec-I (23%), and SCCmec-II (4%), while in HA-MRSA
were SCCmec-IV (22%), SCCmec- V (7%), and SCCmec-I (2%). spa type t037 was the
most predominantly found among CA-MRSA (SO%) and HA-MRSA (61 %). Higher
occurrence of the pvl gene (which encodes the pore-forming Panton-Valentine
leucocidin) at 27% (11141) among HA-MRSA compared to CA-MRSA at 23% (S/22).
Another virulence factor, the staphylococcal surface protein gene (sasX) , was more
prevalent in HA-MRSA at 61 % (2S/41) compared with CA-MRSA (SO%; 11/22).
Nine S. aureus isolates representing HA-MRSA (SAZ_1 SAZ_lO, AZ_16, SAZ_31,
and KTIY21), hospital-associated methicillin-susceptible S. aureus (HA-MSSA,
M314250), and CA-MRSA (ZS_Z30, ZS_Z37 and ZS_Z46) were subjected to whole
genome sequence analysis. Genomic content of all isolates were diverse with the
presence of various mobile genetic elements (MGEs) such as insertional sequence (IS),
transposoos, plasmids, genomic islands (vSAa and vSA~), phages, Staphylococcal
pathogenicity islands (SaPIs: SaPIl, SaPI2, SaPI3, and SaPI5) as well as both virulence
and resistance determinants. In-silico, MLST and spa type of nine representative isolates
revealed five sequence types (ST)-spa types combinations, i.e. STl-t127 (M314250),
ST30-tl22 (SAZ_31), ST239-t037 (SAZ_IO, ZS_Z30, ZS_Z37, and ZS_Z46), ST239-
t421 (SAZ_I), and ST772-t657 (SAZ_16 and KTIY21). Interestingly, one of the HA
MRSA isolates, SAZ_10, harboured a novel 35 kb conjugative plasmid designated
pSAZI0A that carried multiple antimicrobial resistance (AMR) determinants (aadD,
ileS, and t aA) as well as complete conjugative transfer (tra) genes.
Genome analyses showed the presence of multidrug efflux pumps and AMR genes,
which were likely to contribute to the MDR phenotypes in these isolates. Moreover,
various virulence factors were revealed among both CA and HA-MRSA isolates, which
were likely to play es entia I roles in their pathogenesis. Pan-genome analysis of all
representative isolates and other 49 global reference strains revealed an open genome
with a large accessory genome aUowing acquisition of exogenous DNA and facilitating
successful adaptation to the selective hospital and community environment.
Thus, this analysis provided us an insight into the characteristics and adaptability related
to both virulence and resistance of MRS A and MSSA of Malaysian isolates, which will
assist in the surveillance, prevention and control of pathogenic S. aureus particularly in
community- and hospital-associated environment.
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