Staphylococcus aureus Programme 2007 (SAP 2007) Hospital Survey MRSA Epidemiology and Typing Report

AGAR The Australian Group on Antimicrobial Resistance http://antimicrobial-resistance.com Staphylococcus aureus Programme 2007 (SAP 2007) Hospital Survey MRSA Epidemiology and Typing Report PREPARED BY: Mr Geoffrey Coombs Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Royal Perth Hospital. Western Australia. Ms Julie Pearson Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Royal Perth Hospital. Western Australia. Dr Graeme Nimmo Division of Microbiology, Queensland Pathology Central Laboratory Brisbane, Queensland. Associate Professor Keryn Christiansen Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Royal Perth Hospital. Western Australia. On behalf of the Australian Group for Antimicrobial Resistance (AGAR) Funded by Commonwealth of Australia, Department of Health and Ageing June 2009 1

Epidemiology and Typing Report of Methicillin Resistant Staphylococcus aureus (MRSA) Isolates from the Australian Group on Antimicrobial Resistance (AGAR) 2007 Staphylococcus aureus Surveillance Programme (SAP 2007) Contents 1.0 Overview 2.0 Summary 2.1 Healthcare-Associated MRSA (HA-MRSA) Clones 2.2 Community-Associated MRSA (CA-MRSA) Clones 2.3 Panton-Valentine Leucocidin (PVL) Toxin 3.0 SAP 2007 Protocol 3.1 Commencement Date 3.2 Isolates 3.3 Participating Laboratories 3.4 Methicillin Susceptibility Testing 3.5 Epidemiological Typing 3.6 MRSA Nomenclature Multilocus Sequence Typing (MLST) Staphylococcal Cassette Chromosome mec (SCCmec) 3.7 Panton-Valentine Leucocidin (PVL) Toxin 4.0 Methods 4.1 Epidemiological Typing Methods Antibiogram Resistogram Urease Coagulase Gene PCR-RFLP Assay Contour-clamped Homogeneous Electric Field Electrophoresis Chromosomal DNA Preparation Multi Locus Sequence Typing (MLST) Staphylococcal Cassette Chromosome mec (SCCmec) 4.2 Identification of HA-MRSA Clones ST239-MRSA-III (Aus-2 and Aus-3 EMRSA) ST1282-MRSA-III (ST239slv) ST22-MRSA- (EMRSA-15) ST36-MRSA-II (EMRSA-16 or USA200) ST247-MRSA-I (EMRSA-17) ST5-MRSA-II (New York/Japan MRSA or USA100) ST8-MRSA-VI (Irish 2 EMRSA) ST228-MRSA-I (Southern German EMRSA) 4.3 Identification of CA-MRSA Clones ST30-MRSA- (Western Samoan Phage Pattern MRSA WSPP MRSA) ST93-MRSA- (Queensland MRSA) 2 3

ST8-MRSA- ( MRSA-12 or USA300) MRSA 4.4 Detection of Panton-Valentine Leucocidin (PVL) Toxin Genes 5.0 Results 5.1 AGAR Hospital SAP 2005-2007 Percentage of Staphylococcus aureus Identified as MRSA Regional Distribution of MRSA 5.2 SAP 2007 Epidemiological Typing of MRSA Typing Tests Performed Regional Distribution of HA-MRSA and CA-MRSA Clones SAP 2005 and SAP 2007 Regional Distribution of HA-MRSA and CA-MRSA Clones SAP2005 and SAP 2007 Regional Distribution of HA-MRSA and CA-MRSA Clones as a Proportion of Staphylococcus aureus SAP 2007: HA-MRSA Clones by AGAR Laboratory SAP 2007 CA-MRSA Clones by AGAR Laboratory 5.3 HA-MRSA Clones SAP 2007 HA-MRSA Clones SAP 2005 and 2007: Percentage of MRSA Identified as HA- MRSA Clones ST239-MRSA-III Phenotypic Characteristics Resistogram Aus-2 EMRSA Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST239-MRSA-III (Aus-2 EMRSA) SAP 2005 and SAP 2007 Regional Distribution of ST239-MRSA-III (Aus-2 EMRSA) Aus-3 EMRSA Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST239-MRSA-III (Aus-3 EMRSA) SAP 2005 and SAP 2007 Regional Distribution of ST239-MRSA-III (Aus-3 EMRSA) Aus-3 variant EMRSA (ST1282-MRSA-III) Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST1282-MRSA-III (Aus-3 variant EMRSA) SAP 2005 and SAP 2007 Regional Distribution of ST1282-MRSA-III (Aus-3 variant EMRSA) Aus-2 and Aus-3 (including variant) EMRSA (ST239/ ST1282-MRSA-III) Epidemiology 3 4

SAP 2005 and SAP 2007 Regional Distribution of ST239/1282-MRSA-III (Aus-2 and Aus-3 (including variant EMRSA) ST239/1282-MRSA-III (Aus-2 and Aus-3 (including variant EMRSA) ST22-MRSA- Phenotypic Characteristics Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST22- MRSA- (EMRSA-15) SAP 2005 and SAP 2007 Regional Distribution of ST22- MRSA- (EMRSA-15) ST36-MRSA-II (EMRSA-16) Phenotypic Characteristics Epidemiology ST247-MRSA-I (EMRSA-17) Phenotypic Characteristics Epidemiology ST8-MRSA-VI (Irish 2 EMRSA Phenotypic Characteristics Epidemiology ST5-MRSA-II (New York Japan MRSA) Phenotypic Characteristics Epidemiology ST228-MRSA-I (Southern German EMRSA) Phenotypic Characteristics Epidemiology Summary of HA-MRSA Isolated in SAP 2005 and 2007 5.4 CA-MRSA Clones SAP 2005 and SAP 2007: Percentage of MRSA Identified as CA- MRSA Clones Major CA-MRSA Clones SAP 2007 CA-MRSA ST1-MRSA- Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST1- MRSA- ( MRSA-1) SAP 2005 and SAP 2007 Regional Distribution of ST1- MRSA- ( MRSA-1) ST93-MRSA- Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST93- MRSA- (Qld CA-MRSA) SAP 2005 and SAP 2007 Regional Distribution of ST93- MRSA- (Qld CA-MRSA) ST5-MRSA- 4 5

Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST5- MRSA- ( MRSA-3) SAP 2005 and SAP 2007 Regional Distribution of ST5- MRSA- ( MRSA-3) ST30-MRSA- Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST30- MRSA- (SWP CA-MRSA) SAP 2005 and SAP 2007 Regional Distribution of ST30- MRSA- (SWP CA-MRSA) ST78-MRSA- Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST78- MRSA- ( MRSA-2) SAP 2005 and SAP 2007 Regional Distribution of ST78- MRSA- ( MRSA-2) ST45-MRSA- Epidemiology SAP 2005 and SAP 2007 Regional Distribution of ST45- MRSA- ( MRSA-23 or Victorian CA-MRSA) SAP 2005 and SAP 2007 Regional Distribution of ST45- MRSA- ( MRSA-23 or Victorian CA-MRSA) International CA-MRSA Clones SAP 2005 and SAP 2007 Regional Distribution of ST8-MRSA- (USA300) Minor CA-MRSA Clones 5.5 Panton-Valentine Leucocidin (PVL) Toxin HA-MRSA Clones CA-MRSA Clones Panton-Valentine Leucocidin (PVL) Toxin Regonal Distribution of CA-MRSA Clones 5.6 CA-MRSA Antibiogram 6.0 References 7.0 Acknowledgments 5 6

Staphylococcus aureus Programme 2007 (SAP 2007) Hospital Survey MRSA Epidemiology and Typing Report 1.0. Overview Of the 889 S. aureus classified as MRSA in the SAP 2007 Hospital Survey, molecular typing was performed on 874 (98.3%) isolates. The percentage of S. aureus characterized as Healthcare-Associated MRSA (HA-MRSA) clones was similar in this survey (24.6%) when compared to the 2005 survey (24.9%). Although seven HA-MRSA clones were characterized, 99.2% of HA-MRSA were classified as either ST239/1282-MRSA-III (Aus- 2/3 EMRSA) or ST22-MRSA- (EMRSA-15). Apart from in Western Australia, Aus-2/3 remains the prominent HA-MRSA clone in Australian hospitals. Over the two surveys EMRSA-15 increased significantly in several regions particularly in the Victorian/Tasmanian hospitals (5.8% of MRSA in 2005 to 19.8% in 2007). Community- Associated MRSA clones (CA-MRSA) accounted for 23.9% of MRSA and 7.7% of all S. aureus. In 2005 20.7% of S. aureus were characterized as CA-MRSA. As in the 2005 survey CA-MRSA were multiclonal (24 clones) however 85.2% of isolates could be characterized into six clones. Although ST1-MRSA- was the most frequently isolated CA-MRSA clone in most regions of Australia (33.0% of CA-MRSA), approximately 30% of CA-MRSA were characterized as either ST93-MRSA- (Queensland CA-MRSA) or ST30-MRSA- (SWP CA-MRSA). These two clones are Panton Valentine leucocidin (PVL) positive. Overall 31.6% of CA-MRSA were PVL positive, a 10% increase when compared to the 2005 survey. Although this increase in PVL-positive CA-MRSA was primarily due to the expansion of the ST93-MRSA- clone three international CA-MRSA clones including ST30-MRSA- (SWP MRSA), ST8-MRSA- (USA300) and ST1-MRSA- (possibly USA400) were characterised. The introduction of these clones into Australian hospitals is a major public health concern. 2.0. Summary The Australian Group for Antimicrobial Resistance (AGAR) biennial hospital Staphylococcus aureus surveillance programme commenced in 2005. In the 2007 programme (SAP 2007) up to 100 clinically significant consecutive isolates of S. aureus from different patients were collected by each of 31 institutions located across Australia. Isolates were collected from hospitalised patients (>48 hours at the time of collection). All methicillin-resistant S. aureus (MRSA) isolates were referred to the Western Australian () Gram-positive Bacteria Typing and Research Unit (GPBTRU) for clone characterization and Panton-Valentine leucocidin (PVL) toxin determination. The molecular characterization of the MRSA isolates is designed to provide a snapshot of MRSA clones circulating in Australian hospitals. Of the 889 (32.9%) S. aureus classified as MRSA in SAP 2007, 874 (98.3%) were referred to the GPBTRU. Overall 76.1% and 23.9% of MRSA were characterized as 6 7

healthcare-associated MRSA (HA-MRSA) strains and community-associated MRSA (CA-MRSA) strains respectively. Throughout Australia the percentage of S. aureus characterized as HA-MRSA was 24.6% ranging from 4.8% in to 34.7% in the ACT/NSW region. 40 35 30 25 20 15 10 5 0 ACT/NSW NT/Qld SA Tas/Vic Aust % S. aureus 2005 2007 Percentage of S. aureus characterised as HA-MRSA Overall 7.7% of S aureus were characterized as CA-MRSA ranging from 4.4% in the Tas/Vic region to 14.3% in. 20 % S. aureus 15 10 5 0 2005 2007 ACT/NSW NT/Qld SA Tas/Vic Aust Percentage of S. aureus characterised as CA-MRSA 7 8

2.1. HA-MRSA (Healthcare-Associated MRSA) Clones Seven HA-MRSA clones were identified in the Australian community; 74.9% were ST239-MRSA-III or ST1282-MRSA-III [a single locus variant of ST239] (Aus-2/3 EMRSA), 24.4% ST22-MRSA- (EMRSA-15), and single isolates of ST36-MRSA-II (EMRSA-16 or USA200), ST247-MRSA-I (EMRSA-17), ST8-MRSA-VI (Irish 2 EMRSA), ST5-MRSA-II (New York Japan EMRSA or USA100) and ST228-MRSA-I (Southern German EMRSA). ST239-MRSA MRSA-III/ST1282-MRSA-III (Aus-2/3 EMRSA) ST22-MRSA MRSA- (EMRSA 15 or Barnim EMRSA) ST5-MRSA MRSA-II (New York Japan EMRSA or USA 100) ST36-MRSA MRSA-II (EMRSA 16 or USA200) ST247-MRSA MRSA-I I (EMRSA 17) ST8-MRSA MRSA-VI (Irish 2 EMRSA) ST228-MRSA MRSA-I I (Southern German MRSA) 68% National: 76.1% of MRSA Northern Territory/Queensland: 143 isolates (3 clones) 25% 68% 86% Australian Capital Territory/ New South Wales 280 isolates ( 3 clones) Western Australia 15 isolates (4 clones) South Australia 48 isolates (2 clones) HA-MRSA Clones 86% Tasmania/Victoria: (179 isolates (3 clones) ST239-MRSA-III and ST1282-MRSA-III (Aus-2/3 EMRSA) was isolated in all regions, accounting for 66.2% and 63.3% of MRSA in the Tas/Vic and ACT/NSW regions respectively. ST1282-MRSA-III, an Aus-3 EMRSA variant, was confined to a single Queensland hospital. As a consequence of the state s MRSA prevention policy the percentage of MRSA identified as ST239-MRSA-III in remained low accounting for only 3.3% of MRSA. Overall 57.0% of MRSA were identified as Aus-2/3 EMRSA compared to 63.1% in SAP 2005. ST22-MRSA- (EMRSA-15), which was initially reported in Australia in 1997, accounted for 18.5% of all MRSA isolated in Australia (15.6% in SAP2005), ranging from 9.1% in the NT/Qld region to 26.8% in SA. The percentage of MRSA characterized as EMRSA-15 has increased in three Australian regions over the two surveys noticeably in the Tas/Vic region (5.8% to 19.8% of MRSA). 8 9

2.2. CA-MRSA (Community-Associated MRSA) Clones Twenty four community MRSA clones were identified by pulsed-field gel electrophoresis (corresponding to 18 MLST/SCCmec clones) of which 85.2% were: - ST1-MRSA- [ MRSA-1] (33.0%) - ST93-MRSA- [Queensland CA-MRSA] (19.1%) - ST5-MRSA- [ MRSA-3] (11.5%) - ST30-MRSA- [SWP MRSA] (9.6%) - ST78-MRSA- [ MRSA-2] (7.2%) - ST45-MRSA- [ MRSA-23 or Victorian CA-MRSA] (4.8%) Three USA300 (ST8-MRSA-) isolates were characterized one in ACT/NSW, NT/Qld and Tas/Vic regions. ST1-MRSA MRSA-* (-MRSA MRSA-1) ST93-MRSA MRSA-* (Qld CA-MRSA) ST5-MRSA MRSA- (-MRSA MRSA-3) ST30-MRSA MRSA-* (SWP CA-MRSA) ST78-MRSA MRSA- (-MRSA MRSA-2) ST45-MRSA MRSA- (Vic CA-MRSA) OTHER South Australia: 23 isolates (8 clones) National: 23.9% of MRSA 32% Northern Territory/Queensland: 66 isolates (13 clones) 75% Western Australia: 45 isolates (6 clones) 32% 14% Australian Capital Territory/New South Wales: 47 isolates (9 clones) CA-MRSA Clones *PVL positive clones 14% Tasmania/Victoria: 28 isolates (13 clones) 9 10

2.3. Panton Valentine Leucocidin (PVL) Toxin HA-MRSA Clones No PVL positive HA-MRSA were detected. CA-MRSA Clones 66 CA-MRSA (4 clones) were PVL positive: - ST93-MRSA- (Queensland CA-MRSA) 40 isolates (100% PVL positive) - ST30-MRSA- [WSPP MRSA] 19 isolates (95% PVL positive) - ST8-MRSA- [USA300] 2 isolates (67% PVL positive) - ST1-MRSA- [ MRSA-1] 5 isolates (7% PVL positive) It is possible that the five MRSA-1 isolates are USA400 strains however further molecular studies are required to confirm 100 % CA-MRSA 80 60 40 20 0 ACT/NSW NT/Qld SA Tas/Vic Aust Percentage of CA-MRSA PVL positive 2005 2007 Overall 32% of CA-MRSA were identified as PVL positive ranging from 7% in to 53% in the ACT/NSW region. In the previous hospital survey (SAP 2005) 22% of CA- MRSA were PVL positive ranging from 0% in to 46% in the ACT/NSW region. The percentage of CA-MRSA that were PVL positive increased in all regions except for NT/Qld. However in SAP 2005 isolates from NT were not characterised. 10 11

3.0. SAP 2007 Protocol 3.1. Commencement Date 1 st July 2007 3.2. Isolates Approximately 100 consecutive clinical isolates of Staphylococcus aureus from 100 different patients at each site were tested by 31 laboratories located across Australia (total number of isolates = 2,705). Isolates were collected from inpatients only (hospital stay >48 hours at the time of collection). 3.3. Participating Laboratories Australian Capital Territory (1) South Australia (3) The Canberra Hospital New South Wales (8) Flinders Medical Centre Institute of Medical Veterinary Science Women s and Children s Hospital Concord Hospital Nepean Hospital Tasmania (2) Royal North Shore Hospital South West Area Pathology Services Royal Hobart Hospital Westmead Hospital Launceston General Hospital Douglass Hanly Moir Pathology Royal Prince Alfred Hospital Victoria (6) John Hunter Hospital Alfred Hospital Queensland (6) Gribbles Pathology Royal Children s Hospital Princess Alexandra Hospital St Vincent s Hospital Royal Brisbane and Women s Hospital Austin Health Sullivan Nicolaides Pathology Monash Medical Centre Cairns Base Hospital Gold Coast Hospital Western Australia (4) Prince Charles Hospital PathWest- Fremantle Hospital Northern Territory (1) PathWest- Queen Elizabeth II PathWest- Royal Perth Hospital Royal Darwin Hospital Saint John of God Pathology 11 12

3.4. Methicillin Susceptibility Testing Vitek2 AST-P545 susceptibility card according to the manufacturer s guidelines. 3.5. Epidemiological Typing Performed by the Gram-positive Bacteria Typing and Research Unit Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine, Royal Perth Hospital, Perth Western Australia. Molecular Genetics Research Unit, School of Biomedical Sciences, Curtin University of Technology, Bentley, Western Australia. 3.6. MRSA Nomenclature The Gram-positive Bacteria Typing and Research Unit employs the international MRSA nomenclature system described by Enright et al. (1). This system provides a universally standardised MRSA nomenclature allowing MRSA clones to be readily compared between laboratories and countries. It is based upon the combination of the sequences of seven housekeeping genes combined to define a sequence type (ST) using multilocus sequence typing (MLST), and the SCCmec type. The MRSA genotype is therefore the sum of the SCCmec type and the type of its recipient chromosome. For example, a MRSA clone of ST22 and SCCmec type is referred to as ST22-MRSA- (previously known as EMRSA-15). Multilocus Sequence Typing (MLST) MLST is a highly discriminatory method of characterising MRSA. For each of the seven housekeeping gene fragments, different sequences are assigned as distinct alleles, and an isolate is defined by the alleles of each of the seven housekeeping loci (the allelic profile or ST). The ST can be compared with the STs of other strains using the program BURST which is located on the MLST website (www.saureus.mlst.net). As there are many alleles for each loci, isolates are highly unlikely to have identical ST by chance, and therefore isolates with the same ST or STs that differ at no more than two alleles are considered to belong to the same clonal complex (CC) and be members of the same clone. Staphylococcal Cassette Chromosome mec (SCCmec) The gene for methicillin resistance, meca, is contained within a mobile element known as the mec region or staphylococcal cassette chromosome mec (SCCmec). The SCCmecs differ depending on variations in the meca regulatory region (mec complex), the type of cassette chromosome recombinases (ccr genes), and the resistance determinants they have acquired due to the integration of plasmids and transposons. 12 13

Eight SCCmec types have been identified globally. Types I, II, III and VI are associated with healthcare-associated MRSA while Types, V, VII and VIII are normally associated with community-associated MRSA. In this report MRSA are classified as either healthcare-associated MRSA (HA-MRSA) clones or community-associated MRSA (CA-MRSA) clones and are assigned an MLST/SCCmec type. The previous nomenclature that was applied to HA-MRSA and CA-MRSA clones is also reported. HA-MRSA clones are also known as Epidemic MRSA (EMRSA) clones, however with the epidemic properties of several CA-MRSA clones, the term HA-MRSA is used in this report. 3.7. Panton-Valentine Leucocidin (PVL) Toxin CA-MRSA have been shown to acquire several virulence genes including the determinants for PVL (2). PVL is a necrotizing toxin that causes leucocyte destruction and tissue necrosis and is associated with abscesses and severe pneumonia. It is present in the majority of CA-MRSA studied in Europe and USA (3). In Australia, it was initially reported that CA-MRSA infrequently carry the genes encoding PVL (4). However, two CA-MRSA clones now frequently isolated in Australia are PVL positive; ST30-MRSA- and ST93-MRSA-. These clones were originally reported in Auckland, New Zealand and Queensland, Australia respectively. ST30-MRSA- was first noted in Australia in 1997 in the Polynesian population living in the eastern Australian states and the Australian Capital Territory (5). ST93-MRSA- was first identified as a cause of community-acquired infection in the Caucasian population in Ipswich, Queensland in 2000 (6). Both clones are now frequently isolated in several regions of Australia especially on the east coast (7). Several imported PVL-positive CA-MRSA clones have recently been identified in Australia including (8): 1. ST8-MRSA- (USA300) 2. ST80-MRSA- (European CA-MRSA) 3. ST59-MRSA-V T (Taiwan CA-MRSA) 4. ST1-MRSA- (USA400) PVL genes have been shown to be transmitted by a temperate phage indicating that the PVL determinants are transferable (9). Recently PVL-positive ST1-MRSA- strains have been isolated in Queensland (10) and New South Wales (11), Australian states that have reported an increasing incidence of ST30-MRSA- and ST93-MRSA- (6,12,13). This may suggest that the PVL determinants are being transferred and raises the prospect that more CA-MRSA in Australia may become PVL positive in the future. 13 14

4.0. Methods 4.1. Epidemiological Typing Methods Antibiogram Participating laboratories performed antimicrobial susceptibility tests using the Vitek2 AST-P545 card (BioMerieux, Durham, NC). Antimicrobials tested were benzylpenicillin, oxacillin, cefazolin, vancomycin, rifampicin, fusidic acid, gentamicin, erythromycin, clindamycin, tetracycline, trimethoprim/sulphamethoxazole (cotrimoxazole), ciprofloxacin, quinupristin/dalfopristin (Synercid ), teicoplanin, linezolid, imipenem, and nitrofurantoin. Penicillin susceptible strains were tested for β-lactamase production using nitrocefin. A cefoxitin disc diffusion test was used to confirm methicillin-resistance. Mupirocin and cefoxitin were tested by disc diffusion using the CLSI or CDS methods. The MIC of mupirocin resistant isolates was determined by Etest (AB Biodisk, Solna, Sweden). Resistogram Disk Diffusion (14, 15) Urease mercuric chloride (HgCl 2 ) (0.4μM) phenylmercuric acetate (PMA) (5 mm) Christensen s Urea broth incubated for 24hrs at 37 o C (16). Coagulase Gene PCR-Restriction Fragment Length Polymorphisms (RFLP) Assay Coagulase gene restriction fragment length polymorphism typing was performed as previously described (17). Contour-clamped Homogeneous Electric Field Electrophoresis (CHEF) Electrophoresis of chromosomal DNA was performed as previously described (18) using the CHEF DR III System (Bio-Rad Laboratories Pty Ltd). Chromosomal patterns were examined visually, scanned with a Quantity One and digitally analysed using FPQuest (Bio-Rad Laboratories). CHEF patterns were grouped according to the criteria of Tenover et al. (19) and using a dendogram similarity of 80% or greater to assign strain relatedness. S aureus NCTC 8325 was used as the size marker. 14 15

Chromosomal DNA Preparation Chromosomal DNA for MLST and SCCmec typing was prepared using the DNeasy Tissue kit (Qiagen Pty Ltd, Clifton Hill, Victoria, Australia 3068). Multi Locus Sequence Typing (MLST) MLST was performed on selected isolates as specified by Enright et al. (1). The sequences obtained were compared with the sequences at the MLST web site at http://www.mlst.net/, to assign a sequence type (ST). Using the MLST database, clones were subsequently grouped into clonal complexes. Staphylococcal Chromosomal Cassette mec (SCCmec) The SCCmec was typed by PCR using previously published primers that identified the class of mec complex and type of cassette chromosome recombinase (ccr) encoded on the element (20,21,22) 4.2. Identification of HA-MRSA Clones ST239-MRSA-III (Aus-2 and Aus-3 EMRSA) Antibiogram Resistogram CHEF (Multilocus Sequence Typing) (SCCmec PCR) ST1282-MRSA-III (ST239slv) Antibiogram Resistogram CHEF (Multilocus Sequence Typing) (SCCmec PCR) ST22-MRSA- (EMRSA-15) Antibiogram Urea Broth CHEF 15 16

ST36-MRSA-II (EMRSA-16 or USA200) Antibiogram Urea Broth Coagulase PCR-RFLP CHEF ST247-MRSA-I (EMRSA-17) Antibiogram Urea Broth Coagulase PCR-RFLP CHEF Antibiogram Resistogram Multilocus Sequence Typing SCCmec PCR ST5-MRSA-II (New York Japan MRSA or USA100 MRSA) Antibiogram Urea Broth Coagulase PCR-RFLP CHEF Multilocus Sequence Typing SCCmec PCR ST8-MRSA-VI (Irish 2 EMRSA) Antibiogram Urea Broth Coagulase PCR-RFLP CHEF ST228-MRSA-I (Southern German EMRSA) Antibiogram Urea Broth Coagulase PCR-RFLP CHEF Multilocus Sequence Typing SCCmec PCR 16 17

4.3. Identification of CA-MRSA Clones ST30-MRSA- (South Western Pacific MRSA - SWP MRSA) Antibiogram Urea Broth CHEF ST93-MRSA- (Queensland CA-MRSA) Antibiogram Urea Broth CHEF ST8-MRSA- ( MRSA-12 or USA300) MRSA Antibiogram Urea Broth Coagulase PCR-RFLP CHEF ST1-MRSA- (-1) ST78-MRSA- (-2) ST45-MRSA- (-23) Antibiogram Urea Broth CHEF ST5-MRSA- (-3) ST45-MRSA-V (-4) ST8-MRSA- (-5) ST75-MRSA- (-8) ST5-MRSA- (-21) ST5-MRSA-V (-35) ST883-MRSA- (-47) ST835-MRSA- (-48) ST5-MRSA- (-64) ST73-MRSA- (-65) ST6-MRSA- (-66) Antibiogram Urea Broth 17 18

Coagulase PCR-RFLP CHEF ST72-MRSA- (-44) ST7-MRSA-V (unique) ST1-MRSA-V (unique) ST8-MRSA- (unique) ST779-MRSA-V (unique) ST5-MRSA-V (unique) Antibiogram Urea Broth Coagulase PCR/RFLP CHEF Multilocus Sequence Typing SCCmec PCR 4.4. Detection of Panton-Valentine Leucocidin (PVL) Toxin Genes The presence of the PVL determinants was detected by PCR using previously published primers (23). 18 19

5.0. Results In SAP 2007, 889 (32.9%) Staphylococcus aureus were classified as MRSA. 5.1. AGAR Hospital SAP 2005 and 2007 Percentage of Staphylococcus aureus Identified as MRSA SAP Laboratories (n) S aureus (n) MRSA (n) MRSA (%) 2005 32 2,908 928 31.9% 2007 31 2,705 889 32.9% 50 40 % MRSA 30 20 10 0 2005 2007 Year of Survey Percentage figures relate to the total number of Staphylococcus aureus isolates 19 20

Regional Distribution of MRSA Region 2005 2007 ACT/NSW 358 (43.4%) 333 (41.3%) Qld/NT 177 (26.7%) 212 (31.0%) SA 84 (24.7%) 71 (27.2%) Tas/Vic 229 (31.6%) 213 (33.3%) 80 (22.5%) 60 (19.0%) TOTAL 928 (31.9%) 889 (32.9%) Percentage figures relate to the total number of Staphylococcus aureus isolates 60 50 % of MRSA 40 30 20 10 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region Percentage figures relate to the total number of Staphylococcus aureus isolates 20 21

5.2. SAP 2007 Epidemiological Typing of MRSA Of the 889 MRSA identified in SAP 2007, 874 were referred to the GPBTRU for epidemiological typing. Typing Tests Performed Test N Cefoxitin Susceptibility Testing 896 Coagulase Gene PCR-RFLP Assay 194 Resistogram 503 Contour-clamped Homogeneous Electric Field Electrophoresis (CHEF) 874 Urease Reaction 882 Multilocus Sequencing Typing (MLST) 19 SCCmec PCR 19 Panton-Valentine leucocidin PCR 880 Regional Distribution of HA-MRSA and CA-MRSA Clones Region HA-MRSA (%) CA-MRSA (%) Total MRSA ACT/NSW 280 (85.6) 47 (14.4) 327 Qld/NT 143 (68.4) 66 (31.6) 209 SA 48 (67.6) 23 (32.4) 71 Tas/Vic 179 (86.5) 28 (13.5) 207 15 (25.0) 45 (75.0) 60 TOTAL 665 (76.1) 209 (23.9) 874 Percentage figures in parenthesis relate to the total number of MRSA isolates 21 22

SAP 2005 and SAP 2007 Regional Distribution of HA-MRSA and CA- MRSA Clones In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures 2005 (n = 881) 2007 (n = 874) Region HA-MRSA (%) CA-MRSA (%) HA-MRSA (%) CA-MRSA (%) ACT/NSW 308 (88.3) 41 (11.7) 280 (85.6) 47 (14.4) NT/Qld 108 (74.5) 37 (25.5) 143 (68.4) 66 (31.6) SA 52 (62.7) 31 (37.3) 48 (67.6) 23 (32.4) Tas/Vic 200 (89.3) 24 (10.7) 179 (86.5) 28 (13.5) 31 (38.8) 49 (61.2) 15 (25.0) 45 (75.0) TOTAL 699 (79.3) 182 (20.7) 665 (76.1) 209 (23.9) Percentage figures relate to the total number of MRSA isolates SAP 2005 and SAP 2007: Regional Distribution of HA-MRSA and CA-MRSA Clones as a Proportion of Staphylococcus aureus 2005 2007 Region Total HA-MRSA (%) CA-MRSA (%) Total HA-MRSA (%) CA-MRSA (%) ACT/NSW 825 308 (37.3) 41 (5.0) 806 280 (34.7) 47 (5.8) NT/Qld 564 108 (19.1) 37 (6.6) 684 143 (20.9) 66 (9.6) SA 340 52 (15.3) 31 (9.1) 261 48 (18.4) 23 (8.8) Tas/Vic 724 200 (27.6) 24 (3.3) 639 179 (28.0) 28 (4.4) 355 31 (8.7) 49 (13.8) 315 15 (4.8) 45 (14.3) TOTAL 2,808 699 (24.9) 182 (6.5) 2,705 665 (24.6) 209 (7.7) 22 23

SAP 2007: HA-MRSA Clones by AGAR Laboratory LAB ST239 MRSA-III Aus 2 EMRSA ACT/NSW (280) ST239 MRSA-III Aus 3 EMRSA ST1282 MRSA-III Aus 3 EMRSA variant ST22 MRSA- EMRSA 15 ST36 MRSA-II EMRSA 16 ST2471 MRSA-1 EMRSA 17 ST8 MRSA-VI Irish2 EMRSA ST5-MRSA- I1 NY/Japan MRSA ST228 MRSA-I Southern German EMRSA 1 18 4 1 23 2 18 21 39 3 9 13 22 4 27 9 36 5 45 5 50 6 40 1 5 46 7 10 3 13 8 35 8 43 9 4 4 8 NT/Qld (143) SA (48) 10 11 6 1 18 11 12 1 5 18 12 10 1 2 13 13 8 1 5 1 15 28 13 2 3 18 29 14 3 17 30 17 2 25 44 14 2 4 12 18 15 4 19 7 30 16 0 TOTAL 23 24

LAB ST239 MRSA-III Aus 2 EMRSA Tas/Vic (179) (15) ST239 MRSA-III Aus 3 EMRSA ST1282 MRSA-III Aus 3 EMRSA variant ST22 MRSA- EMRSA 15 ST36 MRSA-II EMRSA 16 ST2471 MRSA-1 EMRSA 17 ST8 MRSA-VI Irish2 EMRSA ST5-MRSA- I1 NY/Japan MRSA ST228 MRSA-I Southern German EMRSA 18 1 1 2 19 1 33 5 39 20 1 14 15 21 2 2 22 2 11 3 16 23 8 24 6 38 31 4 24 2 1 31 32 5 7 24 36 24 2 3 1 6 25 7 7 26 1 1 27 1 1 TOTAL TOTAL 322 151 25 162 1 1 1 1 1 665 25

SAP 2007 CA-MRSA Clones by AGAR Laboratory LAB 93 30 1 78 5 45 45 8 75 5 5 V 72 883 835 5 73 6 45 8 7 V 1 V 8 779 V 5 V Total Qld SWP 1 2 3 23 Vic 4 5 8 NT 21 35 44 47 48 64 65 66 75 USA 300 ACT/NSW (47) 1 1 1 2 1 5 2 1 1 2 3 2 4 2 1 9 4 1 1 1 1 4 5 4 1 1 1 7 6 1 2 3 7 2 2 8 2 3 1 6 9 6 3 9 NT/Qld (66) 10 6 1 5 5 1 1 19 11 6 3 1 10 12 3 2 1 1 7 13 2 6 2 10 28 1 1 2 29 3 5 2 1 1 1 13 30 3 1 1 5 SA (23) 14 3 2 2 1 8 15 3 3 1 7 16 2 3 1 1 1 8 Tas/Vic (28) 18 1 1 19 1 1 20 0 21 4 1 1 6 22 1 1 1 1 4 23 1 5 6 31 1 4 1 2 8 32 2 2 26

LAB 93 30 1 78 5 45 45 8 75 5 5 V 72 883 835 5 73 6 45 8 7 V 1 V 8 779 V 5 V Total Qld SWP 1 2 3 23 Vic 4 5 8 NT 21 35 44 47 48 64 65 66 75 USA 300 (45) 24 1 10 3 2 16 25 1 5 4 1 11 26 1 9 5 1 16 27 1 1 2 Total 40 20 69 15 24 10 5 1 1 1 1 1 1 2 1 1 1 3 3 1 1 1 1 5 209 27

5.3. HA-MRSA Clones Certain strains of MRSA are known to spread easily between and within hospitals and are designated as healthcare associated MRSA (HA-MRSA) clones [previously known as Epidemic MRSA or EMRSA]. SAP 2007 HA-MRSA Clones In SAP 2007 seven international HA-MRSA clones (665 isolates) were identified CLONE ALTERNATE NAME n (%) ST239-MRSA-III ST1282-MRSA-III Aus -2 and Aus -3 EMRSA or EA MRSA Aus-3 EMRSA single locus variant (slv) 498 (74.9%) ST22-MRSA- EMRSA-15 162 (24.4%) ST36-MRSA-II EMRSA-16 or USA200 1 (0.2) ST247-MRSA-I EMRSA-17 1 (0.2) ST8-MRSA-VI Irish 2 EMRSA 1 (0.2) ST5-MRSA-II New York Japan MRSA or USA100 1 (0.2) ST228-MRSA-I Southern German EMRSA 1 (0.2) TOTAL 665 Percentage figures in parenthesis relate to HA-MRSA isolates 27 28

SAP 2005 and 2007: Percentage of MRSA Identified as HA-MRSA 100 80 % MRSA 60 40 20 0 2005 2007 Year of Survey 28 29

ST239-MRSA-III In Australia ST239-MRSA-III has been classified into two subclones: Aus-2 and Aus- 3 EMRSA. This classification is based on the mercuric acetate and phenylmercuric chloride resistogram and CHEF pattern. ST239-MRSA-III evolved from the Eastern Australian EMRSA clone described in the 1980s. ST239-MRSA-III has emerged as one of the most commonly encountered and internationally disseminated multidrugresistant HA-MRSA clones. It is also known as EMRSA-1, the Portuguese/Brazilian clone or the Vienna clone Phenotypic Characteristics Aus-2 EMRSA (n = 322) Aus-3 EMRSA (n = 151) Aus-3 variant ST1282 EMRSA (n = 25) Erythromycin R 100% 97% 100% Tetracycline R 99% 97% 0% Cotrimoxazole R 98% 98% 96% Gentamicin R 95% 97% 100% Ciprofloxacin R 95% 100% 100% Fusidic Acid R 1% <1% 0% Rifampicin R 2% 6% 100% Mupirocin R <1% <1% 0% Resistogram Aus-2 EMRSA (n = 322) Aus-3 EMRSA (n = 151) Aus-3 variant ST1282 EMRSA (n = 25) Mercuric 5% 81% 100% Acetate R Mercuric 5% 81% 100% Chloride R 29 30

Aus-2 EMRSA Epidemiology ST239-MRSA-III (Aus-2 EMRSA): n = 322 (36.8%) 85 (40.7%) 1-10% 10% 10-20% 20-30% 30-40% >40% 6 (8.5%) 2 (3.3%) 206 (63.0%) 23 (11.1%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST239-MRSA-III (Aus- 2 EMRSA) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 230 (65.9%) 206 (63.0%) Qld/NT 57 (39.3%) 85 (40.7%) SA 10 (12.0%) 6 (8.5%) Tas/Vic 32 (14.3%) 23 (11.1%) 4 (5.0%) 2 (3.3%) TOTAL 333 (37.8%) 322 (36.8%) Percentage figures in parenthesis relate to the total number of MRSA isolates 30 31

SAP 2005 and 2007: Regional Distribution of ST239-MRSA-III (Aus- 2 EMRSA) % of MRSA 70 60 50 40 30 20 10 0 2005 2007 ACT/NSW NT/Qld SA Tas/Vic Aust Region 31 32

Aus-3 EMRSA Epidemiology ST239-MRSA-III (Aus-3 EMRSA): n =151 (17.3%) 13 (6.2%) 1-10% 10% 10-20% 20-30% 30-40% >40% 23 (32.4%) 0 1(0.3%) 114 (55.1%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST239-MRSA-III (Aus- 3 EMRSA) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 14 (4.0%) 1 (0.3%) Qld/NT 31 (21.4%) 13 (6.2%) SA 23 (27.7%) 23 (32.4%) Tas/Vic 154 (68.8%) 114 (55.1%) 1 (1.3%) 0 TOTAL 223 (25.3%) 151 (17.3%) Percentage figures in parenthesis relate to the total number of MRSA isolates 32 33

SAP 2005 and 2007: Regional Distribution of ST239-MRSA-III (Aus- 3 EMRSA) % of MRSA 70 60 50 40 30 20 10 0 2005 2007 ACT/NSW NT/Qld SA Tas/Vic Aust Region 33 34

Aus-3 variant EMRSA (ST1282-MRSA-III) Epidemiology ST1282-MRSA-III (Aus-3variant EMRSA): n =25 (2.9%) 25 (12.0%) 1-10% 10% 10-20% 20-30% 30-40% >40% 0 0 0 0 Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST1282-MRSA-III (Aus-3 variant EMRSA) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 0 0 Qld/NT 0 25 (12.0%) SA 0 0 Tas/Vic 0 0 0 0 TOTAL 0 25 (2.9%) Percentage figures in parenthesis relate to the total number of MRSA isolates 34 35

SAP 2005 and 2007: Regional Distribution of ST1282-MRSA-III (Aus-3 variant EMRSA) % of MRSA 70 60 50 40 30 20 10 0 2005 2007 ACT/NSW NT/Qld SA Tas/Vic Aust Region 35 36

Aus-2 and Aus-3 (including variant) EMRSA (ST239 and ST1282- MRSA-III) Epidemiology ST239/1282-MRSA-III (Aus-2 and Aus-3 (including variant) EMRSA): n = 498 (57.0%) 123 (58.8%) 1-10% 10% 10-20% 20-30% 30-40% >40% 29 (40.8%) 2 (3.3%) 207 (63.3%) 137 (66.2%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST239/1282-MRSA-III (Aus-2 and Aus-3 (including variant) EMRSA) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 244 (69.9%) 207 (63.3%) Qld/NT 88 (60.7%) 123 (58.8%) SA 33 (39.8%) 29 (40.8%) Tas/Vic 186 (83.0%) 137 (66.2%) 5 (6.3%) 2 (3.3%) TOTAL 556 (63.1%) 498 (57.0%) Percentage figures in parenthesis relate to the total number of MRSA isolates 36 37

SAP 2005 and 2007: Regional Distribution of ST239/1282-MRSA-III (Aus-2 and Aus-3 (including variant) EMRSA) % of MRSA 90 80 70 60 50 40 30 20 10 0 2005 2007 ACT/NSW NT/Qld SA Tas/Vic Aust Region 37 38

ST22-MRSA- (EMRSA-15) Also known as EMRSA-15 or the German Barnim strain, ST22-MRSA- has become a major HA-MRSA clone in many parts of the world including Australia, United Kingdom (UK), New Zealand, several European countries and Singapore. First identified in the Midlands and South-East England in the early 1990s it accounts for over half of UK isolates sent to the Laboratory of Hospital Infection in Colindale for typing. It is typically resistant to ciprofloxacin and erythromycin only and is staphylococcal enterotoxin C, G and I positive. In New Zealand and Australia ST22- MRSA- is frequently isolated from patients in long term care facilities and is associated with pre-employment screening of health staff from the UK. Phenotypic Characteristics Antibiogram: Ciprofloxain R 99% Erythromycin R 69% Mupirocin R 3% Fusidic Acid R 2% Tetracycline R 2% Rifampicin R 1% Gentamicin R 1% Cotrimoxazole R 0% Urease: Negative Epidemiology ST22-MRSA- (EMRSA-15): n = 162 (18.5%) 19 (9.1%) 1-10% 10% 10-20% 20-30% 30-40% >40% 19 (26.8%) 11 (18.3%) 72 (22.0%) 41 (19.8%) Percentage figures in parenthesis relate to the total number of MRSA isolates 38 39

SAP 2005 and 2007: Regional Distribution of ST22-MRSA- (EMRSA-15) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 63 (18.1%) 72 (22.0%) Qld/NT 19 (13.1%) 19 (9.1%) SA 17 (20.5%) 19 (26.8%) Tas/Vic 13 (5.8%) 41 (19.8%) 25 (31.3%) 11 (18.3%) TOTAL 137 (15.6%) 162 (18.5%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST22-MRSA- (EMRSA-15) 50 % of MRSA 40 30 20 10 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region 39 40

ST36-MRSA-II (EMRSA-16) Also known as EMRSA-16 or USA200, ST36-MRSA-II was first identified in a single hospital outbreak in London in 1991-2. It now accounts for almost a quarter of UK isolates sent to the Laboratory of Hospital Infection in Colindale for typing. ST36-MRSA-II has been isolated in several European countries including Denmark, Finland, Sweden and Turkey, and in the USA. ST36-MRSA-II is resistant to ciprofloxacin, erythromycin and variably resistant to the aminoglycosides. It carries staphylococcal enterotoxin A, G and I and TSST-1. Phenotypic Characteristics Antibiogram: Urease: Ciprofloxain R Erythromycin R Tetracycline R Rifampicin R Gentamicin R Cotrimoxazole R Mupirocin R Fusidic Acid R Positive Epidemiology ST36-MRSA-II (EMRSA-16): n = 1 (0.1%) 1 (0.5%) 1-10% 10% 10-20% 20-30% 30-40% >40% Percentage figures in parenthesis relate to the total number of MRSA isolates 40 41

ST247-MRSA-I (EMRSA-17) Also known as EMRSA-17, ST247-MRSA-I was first reported in an extensive outbreak in a hospital on the south coast of England in 2000. Multiresistant, the strain was phenotypically similar to a strain seen in several hospitals in that region since 1996. The strain is urease positive and typically resistant to multiple antibiotics including methicillin, ciprofloxacin, erythromycin, fusidic acid, rifampicin, gentamicin, kanamycin, neomycin, streptomycin and tetracycline, with or without high- or low-level mupirocin resistance. Borderline resistance to teicoplanin has also been reported. The strain usually carries the toxin sea gene and may carry seg, sei and tst. Phenotypic Characteristics Antibiogram: Urease: Ciprofloxain R Erythromycin R Tetracycline R Rifampicin R Gentamicin R Cotrimoxazole S Mupirocin R Fusidic Acid R Positive Epidemiology ST247-MRSA-I (EMRSA-17): n = 1 (0.1%) 1-10% 10% 10-20% 20-30% 30-40% >40% 1 (0.3%) Percentage figures in parenthesis relate to total MRSA isolates 41 42

ST8-MRSA-VI (Irish 2 EMRSA) Also known as Irish 2 EMRSA, ST8-MRSA-VI is a major HA-MRSA of Ireland and forms part of clonal complex 8. Phenotypic Characteristics Antibiogram: Urease: Ciprofloxain R Erythromycin R Tetracycline S Rifampicin S Gentamicin S Cotrimoxazole R Mupirocin S Fusidic Acid S Negative Epidemiology ST8-MRSA-VI (Irish 2 EMRSA): n = 1 (0.1%) 1-10% 10% 10-20% 20-30% 30-40% >040% 1 (1.7%) Percentage figures in parenthesis relate to the total number of MRSA isolates 42 43

ST5-MRSA-II (New York Japan MRSA) Also known as New York Japan MRSA, ST5-MRSA-II is a major HA-MRSA of the USA and Japan and forms part of clonal complex 5. Phenotypic Characteristics Antibiogram: Urease: Ciprofloxain R Erythromycin R Tetracycline S Rifampicin S Gentamicin S Trimethoprim S Mupirocin R Fusidic Acid S Positive Epidemiology ST5-MRSA-II (New York Japan MRSA): n = 1 (0.1%) 1-10% 10% 10-20% 20-30% 30-40% >040% 1 (0.5%) Percentage figures in parenthesis relate to the total number of MRSA isolates 43 44

ST228-MRSA-I (Southern German EMRSA) Also known as Southern German EMRSA, ST228-MRSA-I is a major HA-MRSA in Europe and forms part of clonal complex 228. Phenotypic Characteristics Antibiogram: Urease: Ciprofloxain R Erythromycin R Tetracycline S Rifampicin S Gentamicin S Cotrimoxazole S Mupirocin S Fusidic Acid S Positive Epidemiology ST228-MRSA-I (Southern German EMRSA): n = 1 (0.1%) 1 (1.7%) 1-10% 10% 10-20% 20-30% 30-40% >040% Percentage figures in parenthesis relate to the total number of MRSA isolates 44 45

Summary of HA-MRSA Isolated in AGAR SAP 2005 and 2007 Clone Alternative Name SAP 2005 SAP 2007 ST239-MRSA-III Aus-2, -3 EMRSA 556 (63.1%) 498 (57.0%) ST22-MRSA- EMRSA-15 137 (15.6%) 162 (18.5%) ST36-MRSA-II EMRSA-16 2 a (0.2%) 1 b (0.1%) ST247-MRSA-I EMRSA 17 2 c (0.2%) 1 d (0.1%) ST8-MRSA-VI Irish-2 EMRSA 0 1 e (0.1%) ST5-MRSA-II New York Japan 2 f (0.2%) 1 g (0.1%) ST228-MRSA-I Southern German EMRSA 0 1 h (0.1%) Total 699 (79.35) 665 (76.1%) Percentage figures relate to the total number of MRSA a Isolated in SA (n=1) and Vic/Tas (n=1) b Isolated in Qld/NT c Isolated in (n=1) and NSW/ACT (n=1) d Isolated in NSW/ACT e Isolated in f Isolated in SA (n=1) and Qld/NT (n=1) g Isolated in Vic/Tas h Isolated in 45 46

5.4. CA-MRSA Clones CA-MRSA was first reported in Australia in the early 1980s in aboriginal communities living in the Kimberley region of Western Australia (). Known collectively as MRSA they were subsequently isolated in other remote communities in, South Australia and Northern Territory. These strains are usually susceptible to most non- -lactams antibiotics. MRSA has acquired the community associated SCCmec types and V, which usually lack transposons, integrated plasmids and other antibiotic resistance genes. Although they have been introduced into teaching hospitals outbreaks have rarely been reported. In the 1990s non-multiresistant MRSA were isolated on the eastern seaboard in suburban/regional areas of south east Queensland, Sydney and Canberra (5). They were frequently isolated in people of Pacific Island descent and were subsequently identified as South Western Pacific MRSA (SWP MRSA). SWP MRSA has previously been reported in New Zealand and several Pacific islands. In 2000 a non-multiresistrant MRSA was identified as a cause of community acquired infection in the Caucasian population living in Ipswich Queensland and was subsequently identified as Queensland MRSA (6). Although both strains initially caused skin infections they have now been associated with serious invasive disease and have been shown to be PVL positive. 46 47

SAP 2007 CA-MRSA Clones In SAP 2007 24 community MRSA clones (eighteen MLST/SCCmec clone types) were identified. Clone CC Alternative Name n (%) ST1-MRSA- 1 MRSA -1 69 (33.0%) ST93-MRSA- Singleton Queensland MRSA 40 (19.1%) ST5-MRSA- 5 MRSA 3 24 (11.5%) ST30-MRSA- 30 SWP MRSA 20 (9.6%) ST78-MRSA- 78 MRSA 2 15 (7.2%) ST45-MRSA- 45 MRSA 23 (Victorian CA-MRSA) 10 (4.8%) ST45-MRSA-V 45 MRSA 4 5 (2.4%) ST5-MRSA-V 5 5 (2.4%) ST8-MRSA- 8 USA300 3 (1.4%) ST45-MRSA- 45 MRSA-75 3 (1.4%) ST835-MRSA- 5 MRSA-48 2 (1.0%) ST883-MRSA- Singleton MRSA-47 1 (0.5%) ST779-MRSA-V UD 1 (0.5%) ST1-MRSA-V 1 1 (0.5%) ST5-MRSA- 5 MRSA-21 1 (0.5%) ST5-MRSA-V 5 MRSA-35 1 (0.5%) ST5-MRSA- 5 MRSA-64 1 (0.5%) ST73-MRSA- 5 MRSA-65 1 (0.5%) ST6-MRSA- 5 MRSA-66 1 (0.5%) ST7-MRSA-V 7 1 (0.5%) ST8-MRSA- 8 MRSA 5 1 (0.5%) ST8-MRSA- 8 1 (0.5%) ST72-MRSA- 72 MRSA-44 1 (0.5%) ST75-MRSA- 75 MRSA-8 (Northern Territory CA-MRSA) 1 (0.5%) Total 209 Percentage figures in parenthesis relate to community MRSA isolates 47 48

SAP 2005 and 2007: Percentage of MRSA Identified as CA-MRSA 100 80 % MRSA 60 40 20 0 2005 2007 Year of Survey 48 49

Major CA-MRSA Clones ST1-MRSA- Also known as MRSA-1, ST1-MRSA- forms part of clonal complex 1. Although normally PVL-negative, PVL-positive USA400 MRSA-like strains are isolated in Australia. Epidemiology ST1-MRSA- ( MRSA-1): n = 69 (7.9%) 21 (10.0%) 1-10% 10% 10-20% 20-30% 30-40% >40% 9 (12.7%) 25 (41.7%) 11 (3.4%) 3 (1.5%) Percentage figures in parenthesis relate to the total number of MRSA isolates 49 50

SAP 2005 and 2007: Regional Distribution of ST1-MRSA- (- MRSA-1) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 15 (4.3%) 11 (3.4%) Qld/NT 11 (7.6%) 21 (10.0%) SA 18 (21.7%) 9 (12.7%) Tas/Vic 8 (3.6%) 3 (1.5%) 24 (30.0%) 25 (41.7%) TOTAL 76 (8.6%) 69 (7.9%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST1-MRSA- (- MRSA-1) 50 % of MRSA 40 30 20 10 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region 50 51

ST93-MRSA- Also known as the Queensland MRSA clone, ST93-MRSA-is a singleton (ie does not form part of a clonal complex) and is PVL positive. Epidemiology ST93-MRSA- (QLD MRSA): n = 40 (4.6%) 12 (5.7%) 1-10% 10% 10-20% 20-30% 30-40% >40% 2 (2.8%) 2 (3.3%) 20 (6.1%) 4 (1.9%) Percentage figures in parenthesis relate to the total number of MRSA isolates 51 52

SAP 2005 and 2007: Regional Distribution of ST93-MRSA- (Qld CA-MRSA) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 15 (4.3%) 20 (6.1%) Qld/NT 7 (4.8%) 12 (5.7%) SA 3 (3.6%) 2 (2.8%) Tas/Vic 2 (0.9%) 4 (1.9%) 0 2 (3.3%) TOTAL 27 (3.1%) 40 (4.6%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST93-MRSA- (Qld CA-MRSA) 20 % of MRSA 15 10 5 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region 52 53

ST5-MRSA- Also known as MRSA-3, ST5-MRSA- forms part of clonal complex 5 and is PVL negative. Epidemiology ST5-MRSA- ( MRSA-3): n = 24 (2.8%) 13 (6.2%) 1-10% 10% 10-20% 20-30% 30-40% >40% 2 (2.8%) 4 (6.7%) 4 (1.2%) 1 (0.5%) Percentage figures in parenthesis relate to the total number of MRSA isolates 53 54

SAP 2005 and 2007: Regional Distribution of ST5-MRSA- (- MRSA-3) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures Region SAP 2005 SAP 2007 ACT/NSW 1 (0.3%) 4 (1.2%) Qld/NT 8 (5.5%) 13 (6.2%) SA 5 (6.0%) 2 (2.8%) Tas/Vic 2 (0.9%) 1 (0.5%) 5 (6.3%) 4 (6.7%) TOTAL 21 (2.4%) 24 (2.8%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST5-MRSA- (- MRSA-3) 20 % of MRSA 15 10 5 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region 54 55

ST30-MRSA- Also known as SWP MRSA, ST30-MRSA- was originally described in Polynesians living in New Zealand and the Pacific islands. This clone forms part of clonal complex 30 and is PVL positive. Epidemiology ST30-MRSA- (SWP MRSA): n = 20 (2.3%) 11 (5.3%) 1-10% 10% 10-20% 20-30% 30-40% >40% 3 (4.2%) 1 (1.7%) 4 (1.2%) 1 (0.5%) Percentage figures in parenthesis relate to total MRSA isolates 55 56

SAP 2005 and 2007: Regional Distribution of ST30-MRSA- (SWP CA-MRSA) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures. Region SAP 2005 SAP 2007 ACT/NSW 3 (0.9%) 4 (1.2%) Qld/NT 6 (4.1%) 11 (5.3%) SA 3 (3.6%) 3 (4.2%) Tas/Vic 0 1 (0.5%) 0 1 (1.7%) TOTAL 12 (1.4%) 20 (2.3%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST30-MRSA- (SWP CA-MRSA) 20 % of MRSA 15 10 5 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region 56 57

ST78-MRSA- Also known as MRSA-2, ST78-MRSA- forms part of clonal complex 78 and is PVL negative. Epidemiology ST78-MRSA- ( MRSA-2): n = 15 (1.7%) 0 1-10% 10% 10-20% 20-30% 30-40% >40% 1 (1.4%) 12 (20.0%) 2 (0.6%) 0 Percentage figures in parenthesis relate to the total number of MRSA isolates 57 58

SAP 2005 and 2007: Regional Distribution of ST78-MRSA- (- MRSA-2) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures. Region SAP 2005 SAP 2007 ACT/NSW 4 (1.1%) 2 (0.6%) Qld/NT 1 (0.7%) 0 SA 0 1 (1.4%) Tas/Vic 1 (0.4%) 0 14 (17.5%) 12 (20.0%) TOTAL 20 (2.3%) 15 (1.7%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST78-MRSA- (- MRSA-2) 25 % of MRSA 20 15 10 5 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region 58 59

ST45-MRSA- Also known as MRSA-23 or Victorian CA-MRSA, ST45-MRSA- forms part of clonal complex 45 and is PVL negative. Epidemiology ST45-MRSA- ( MRSA-23 or Victorian CA-MRSA): n = 10 (1.1%) 0 1-10% 10% 10-20% 20-30% 30-40% >40% 0 2 (2.8%) 2 (0.6%) 6 (2.9%) Percentage figures in parenthesis relate to the total number of MRSA isolates 59 60

SAP 2005 and 2007: Regional Distribution of ST45-MRSA- (- MRSA-23 or Victorian CA-MRSA) In SAP 2005 MRSA from NT were not characterized and are therefore not included in the 2005 NT/Qld figures. Region SAP 2005 SAP 2007 ACT/NSW 0 2 (0.6%) Qld/NT 0 0 SA 0 2 (2.8%) Tas/Vic 3 (1.3%) 6 (2.9%) 0 0 TOTAL 3 (0.3%) 10 (1.1%) Percentage figures in parenthesis relate to the total number of MRSA isolates SAP 2005 and 2007: Regional Distribution of ST45-MRSA- (- MRSA-23 or Victorian CA-MRSA) 10 % of MRSA 8 6 4 2 2005 2007 0 ACT/NSW NT/Qld SA Tas/Vic Aust Region 60 61

International CA-MRSA Clones In SAP 2007 the PVL positive international CA-MRSA clone USA300 was identified. CLONE ALTERNATE NAME n (%) ST8-MRSA- USA300 3 (0.34%) Percentage figures in parenthesis relate to the total number of MRSA isolates A single isolate of USA300 was isolated in the SAP 2005 survey SAP 2005 and 2007: Regional Distribution of ST8-MRSA- (USA300) CLONE SAP 2005 SAP 2007 ACT/NSW 0 1 NT/Qld 1 1 SA 0 0 Tas/Vic 0 1 0 0 Total 1 3 61 62

Minor CA-MRSA Clones Clone Clonal Complex PFGE 2005 (n = 25) 2007 (n = 38) ST883-MRSA- Singleton MRSA-47 0 1 Qld/NT ST1-MRSA-V 1 Novel 0 1 Qld/NT ST5-MRSA-V 5 MRSA-11 2 (1 ACT/NSW) (1 ) 0 ST526-MRSA- 5 MRSA-39 1 Qld 0 ST5-MRSA- 5 MRSA-21 1 ACT/NSW 1 Vic/Tas ST641-MRSA-V 5 Novel 1 Vic/Tas ST5-MRSA-V 5 MRSA-35 2 1 ACT/NSW 1 Vic/Tas 1 Qld/NT ST835-MRSA- 5 MRSA-48 0 2 Vic/Tas ST5-MRSA- 5 MRSA-64 0 1 ACT/NSW ST8-MRSA- 8 MRSA-5 4 1 Qld 2 Vic/Tas 1 1 Tas/Vic ST8-MRSA-V 8 Novel 1 SA 0 ST45-MRSA-V 45 MRSA-4 5 4 1 SA 5 2 ACT/NSW 4 SA 1 Vic/Tas 1 ST45-MRSA- 45 MRSA-23 (Vic CA- MRSA) 3 Vic/Tas 10 2 ACT/NSW 2 SA 6 Vic/Tas ST45-MRSA- 45 MRSA-75 0 3 2 ACT/NSW 4 SA ST59-MRSA- 59 MRSA-15 3 1 Qld 2 Vic/Tas 0 62 63

Clone Clonal Complex PFGE 2005 (n = 25) 2007 (n = 38) ST72-MRSA- 72 MRSA-44 0 1 Vic/Tas ST75-MRSA- 75 MRSA-8 0 1 Qld/NT (NT CA-MRSA) ST73-MRSA- 5 MRSA-65 0 1 Qld/NT ST6-MRSA- 5 MRSA-66 0 1 Qld/NT ST5-MRSA-novel 5 Novel 1 Vic/Tas 0 ST5-MRSA-V 5 Novel 1 Vic/Tas 0 ST7-MRSA-V 7 Novel 0 1 Vic/Tas ST8-MRSA- 8 Novel 0 1 Qld/NT ST779-MRSA-V UD Novel 0 1 Qld/NT ST5-MRSA-V 5 Novel 0 5 Vic/Tas UD = Undetermined 63 64

5.5. Panton Valentine Leucocidin (PVL) Toxin HA-MRSA Clones Clone Alternative Name Positive Negative Total ST239-MRSA-III Aus -2 and Aus -3 EMRSA or EA MRSA 0 473 473 ST1282-MRSA-III Aus-3 EMRSA single locus variant (slv) 0 25 25 ST22-MRSA- EMRSA-15 0 162 162 ST36-MRSA-II EMRSA-16 or USA200 0 1 1 ST247-MRSA-I EMRSA-17 0 1 1 ST8-MRSA-VI Irish 2 EMRSA 0 1 1 ST5-MRSA-II ST228-MRSA-1 New York Japan MRSA or USA100 Southern German EMRSA 0 1 1 0 1 1 Total 0 665 665 65 65

CA-MRSA Clones Clone Alternative Name Positive Negative Total ST1-MRSA- MRSA -1 5 64 69 ST93-MRSA- Queensland MRSA 40 0 40 ST5-MRSA- MRSA 3 0 24 24 ST30-MRSA- SWP MRSA 19 1 20 ST78-MRSA- MRSA 2 0 15 15 ST45-MRSA- MRSA 23 (Victorian CA-MRSA) 0 10 10 ST45-MRSA-V MRSA 4 0 5 5 ST5-MRSA-V 0 5 5 ST8-MRSA- USA300 2 1 3 ST45-MRSA- MRSA-75 0 3 3 ST835-MRSA- MRSA-48 0 2 2 ST883-MRSA- MRSA-47 0 1 1 ST779-MRSA-V 0 1 1 ST1-MRSA-V 0 1 1 ST5-MRSA- MRSA-21 0 1 1 ST5-MRSA-V MRSA-35 0 1 1 ST5-MRSA- MRSA-64 0 1 1 ST73-MRSA- MRSA-65 0 1 1 ST6-MRSA- MRSA-66 0 1 1 ST7-MRSA-V 0 1 1 ST8-MRSA- MRSA 5 0 1 1 ST8-MRSA- 0 1 1 ST72-MRSA- MRSA-44 0 1 1 ST75-MRSA- MRSA-8 (NT CA-MRSA) 0 1 1 Total 66 (31.6%) 143 (68.4%) 209 66 66