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Database Overview

44
Total Lineages
18
HA-MRSA Lineages
19
CA-MRSA Lineages
7
LA-MRSA Lineages
9
High Risk Lineages
5
PVL-Positive

Important Usage Notes

  • This reference database should be used for comparison and education only
  • Always verify lineage assignments with additional methods and recent literature
  • Lineage distributions and characteristics can vary geographically and change over time
  • Gene presence varies within lineages - not all strains carry all listed virulence factors
  • Refer to PubMLST for current distributions and additional sequence types
  • Note that not all references have been attached and verify any classifications from literature

Complete Lineage Database

CC1
USA400/Western Samoan Clone
🏘️ Community-associated MRSA Risk: HIGH
Sequence Types
1, 122, 124, 128, 129, 1229, 1247
Common spa Types
t127, t128, t136, t159, t174, t178, t227, t321, t384, t573
SCCmec Types
IV, IVa, V
Geographic Distribution
Early CA-MRSA clone with pediatric association
Regions: Global, USA, Australia, Europe, Asia
Virulence Profile
lukS-PVlukF-PVsekseqfnbAclfAscnchpaurspl
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Early CA-MRSA clone, causes skin infections, necrotizing pneumonia
Key References: PMID: 34223815, https://doi.org/10.1186/s40001-024-02076-z, https://doi.org/10.3389/fmicb.2019.00139
CC10
Community-associated Lineage
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
10, 11, 12
Common spa Types
t021, t045, t128
SCCmec Types
IV, V
Geographic Distribution
Distinct lineage, community-associated
Regions: Global, Eastern Asia, Europe
Virulence Profile
seasekfnbAclfAscnchp
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Community-associated lineage with global distribution
Key References: PMID: 19178545
CC101
CC101 (reported in animals and humans)
Occasional livestock-associated / human isolates Risk: LOW
Sequence Types
ST101 reported in some studies; other STs possible
Common spa Types
spa types reported but variable; see PubMLST for details
SCCmec Types
variable / not consistently reported
Geographic Distribution
Reported in animal surveillance studies; not a dominant LA-MRSA lineage (see refs).
Regions: Reported in livestock/food-animal studies (various countries)
Virulence Profile
variable / not consistently reportedvariable
Resistance Profile
Classes: variable; MRSA and MSSA reports exist
mecA may be present in MRSA isolates but not universal
Clinical Significance
Occasional livestock-associated isolates; low prevalence in surveys
Key References: PMID: 31920996, PMID: 19178545, PMID: 19178545
CC1153
Arabian Gulf/North African Clone
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
1153, 1526, 1527
Common spa Types
t657, t1081, t1869
SCCmec Types
V, chimeric
Geographic Distribution
PVL-positive with fusidic acid resistance (fusC)
Regions: Arabian Gulf, North Africa, Middle East
Virulence Profile
lukS-PVlukF-PVfusC positive
Resistance Profile
Classes: Methicillin, Fusidic Acid
mecAfusC
Clinical Significance
Emerging CA-MRSA clone in Arabian Gulf and North Africa
Key References: PMID: 30951513, PMID: 36671279
CC12
European MSSA/MRSA Clone
🏥 Healthcare-associated MRSA Risk: MEDIUM
Sequence Types
12, 13, 218, 1226
Common spa Types
t160, t189, t230, t344, t878
SCCmec Types
IV
Geographic Distribution
Common MSSA background that acquired SCCmec
Regions: Europe, UK, Global
Virulence Profile
seasekseqfnbAclfAsdrCscnchpsak
Resistance Profile
Classes: Methicillin, Erythromycin
mecAerm(C)
Clinical Significance
Healthcare-associated lineage from common MSSA background
Key References: PMID: 21521706, PMID: 17956927
CC121
European CA-MRSA
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
121, 954, 1125, 1529, 1530
Common spa Types
t159, t314, t342, t525, t645, t852
SCCmec Types
IV, V
Geographic Distribution
Emerging CA-MRSA clone
Regions: Europe, Global
Virulence Profile
lukS-PVlukF-PVfnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Emerging CA-MRSA clone
Key References: https://doi.org/10.4269/ajtmh.16-0746
CC130
mecC-MRSA/Livestock-associated
🐄 Livestock-associated MRSA Risk: LOW
Sequence Types
130, 425, 1945, 1947, 1948
Common spa Types
t843, t1736, t3256, t3570
SCCmec Types
XI
Geographic Distribution
mecC-positive MRSA, zoonotic transmission from livestock and wildlife
Regions: Europe, UK, Global
Virulence Profile
Limited virulence factorsLivestock adaptationmecC geneLower virulence in human models
Resistance Profile
Classes: Methicillin
mecC
Clinical Significance
mecC-positive MRSA with zoonotic transmission, lower human virulence
Key References: https://doi.org/10.3168/jds.2013-7378, PMID: 33841383, PMID: 27992523, https://doi.org/10.1007/s00248-019-01328-4
CC133
Ruminant-associated LA-MRSA
🐄 Livestock-associated MRSA Risk: MEDIUM
Sequence Types
133, 134, 135
Common spa Types
t1166, t1730, t2245
SCCmec Types
IV, V
Geographic Distribution
Associated with ruminants, zoonotic potential
Regions: Europe, Middle East, Global
Virulence Profile
Limited virulence factorsLivestock adaptation genesAnimal-specific factors
Resistance Profile
Classes: Methicillin, Tetracycline
mecAtet(K)tet(M)
Clinical Significance
Associated with ruminants, emerging zoonotic potential
Key References: PMID: 27992523, PMID: 25976751, PMID: 28916003, PMID: 19528163
CC14
Animal-associated/Community Lineage
🏘️ Animal-associated/Community MRSA Risk: LOW
Sequence Types
14, 15, 16
Common spa Types
t034, t108, t164
SCCmec Types
IV, V
Geographic Distribution
Associated with animals but also human infections
Regions: Global, Europe, Asia
Virulence Profile
seasekfnbAclfAAnimal adaptation genes
Resistance Profile
Classes: Methicillin, Tetracycline
mecAtet(K)
Clinical Significance
Animal-associated lineage with zoonotic potential, occasional human infections
Key References: PMID: 36689019, PMID: 39281059
CC15
European MRSA
🏥 Healthcare-associated Risk: MEDIUM
Sequence Types
15, 22, 508, 582, 583, 1047, 1136
Common spa Types
t084, t085, t163, t346, t586, t078
SCCmec Types
IV
Geographic Distribution
Healthcare-associated lineage
Regions: Global
Virulence Profile
VariablefnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Healthcare-associated lineage
Key References: PMID: 23675030, PMID: 35056595, PMID: 27992523
CC151
Emerging Livestock-associated
🐄 Livestock-associated MRSA Risk: LOW
Sequence Types
151, 152, 153
Common spa Types
t084, t085, t127
SCCmec Types
IV, V, XIII
Geographic Distribution
Emerging in livestock settings
Regions: Europe, Global
Virulence Profile
Limited virulenceAnimal adaptation
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Emerging in livestock settings
Key References: PMID: 39565128, PMID: 29567305, PMID: 18375551, PMID: 36074767
CC16
Pediatric Infections Clone
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
16, 17, 18
Common spa Types
t084, t085, t127
SCCmec Types
IV, V
Geographic Distribution
Specifically associated with pediatric populations
Regions: Global
Virulence Profile
sealukS-PVlukF-PVfnbAclfAscn
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Specifically associated with pediatric infections
Key References: PMID: 23055880, PMID: 27992523
CC17
Neonatal Infections Clone
🏥 Healthcare-associated MRSA Risk: MEDIUM
Sequence Types
17, 18, 19
Common spa Types
t701, t304, t843
SCCmec Types
IV, V
Geographic Distribution
Important in neonatal intensive care units
Regions: Global
Virulence Profile
seasekfnbAclfAscnchp
Resistance Profile
Classes: Methicillin, Gentamicin, Erythromycin
mecAaac(6')-aph(2'')erm(C)
Clinical Significance
Important in neonatal intensive care units, outbreaks in NICU settings
Key References: PMID: 27992523
CC18
EMRSA-18
🏥 Healthcare-associated MRSA Risk: MEDIUM
Sequence Types
18, 19, 20
Common spa Types
t032, t037, t045
SCCmec Types
II, IV
Geographic Distribution
Significant healthcare clone in Europe
Regions: Europe, UK
Virulence Profile
seasekseqfnbAclfAclfBscnchp
Resistance Profile
Classes: Methicillin, Erythromycin
mecAerm(C)
Clinical Significance
Significant healthcare clone in Europe, hospital-associated
Key References: PMID: 27992523
CC20
European Hospital Clone
🏥 Healthcare-associated MRSA Risk: MEDIUM
Sequence Types
20, 21, 22, 23, 24
Common spa Types
t164, t021, t032, t037
SCCmec Types
II, IV
Geographic Distribution
Hospital-associated with specific geographic distribution
Regions: Europe, Middle East, Global
Virulence Profile
seasekseqfnbAclfAsdrCaur
Resistance Profile
Classes: Methicillin, Aminoglycosides
mecAaac(6')-aph(2'')
Clinical Significance
Hospital-associated clone, often associated with device-related infections
Key References: PMID: 23675030, PMID: 27992523
CC22
EMRSA-15/Barnim Clone
🏥 Healthcare-associated MRSA Risk: HIGH
Sequence Types
22, 217, 221, 224, 228, 230, 233, 1057, 1137
Common spa Types
t022, t032, t223, t309, t852, t899
SCCmec Types
IV, IVh
Geographic Distribution
Major epidemic clone in UK and European hospitals
Regions: Global, UK, Europe, Middle East
Virulence Profile
etaetbtstfnbAclfAclfBscnchp
Resistance Profile
Classes: Methicillin, Erythromycin, Gentamicin, Mupirocin
mecAerm(C)aac(6')-aph(2'')mupA
Clinical Significance
Major epidemic clone in UK and Europe, causes nosocomial infections
Key References: PMID: 35056595, PMID: 11310446, PMID: 23675030, https://doi.org/10.1016/J.JIPH.2010.09.004, DOI:10.4084/MJHID.2021.050
CC22-PVL+
PVL-positive ST22 / CA-MRSA Variant
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
22
Common spa Types
Variable - associated with local epidemic strains
SCCmec Types
IV, V
Geographic Distribution
Emerging as a dominant CA-MRSA clone in specific regions, distinct from the classic healthcare-associated EMRSA-15. Reported to replace other local clones like ST398.
Regions: China (Beijing), Potentially wider dissemination in Asia
Virulence Profile
lukS-PVlukF-PVtst-1 (common)eta (rare)icaAicaD (biofilm formation)
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Emerging community clone associated with skin and soft tissue infections. Represents a virulent, community-adapted offshoot of the ST22 lineage.
Key References: PMID: 31616166, PMID: 35992657
CC239
Brazilian/Hungarian Clone
🏥 Healthcare-associated MRSA Risk: HIGH
Sequence Types
239, 241, 247
Common spa Types
t037, t030, t045
SCCmec Types
III
Geographic Distribution
Major epidemic clone, recombinant lineage (CC8/CC30 hybrid)
Regions: South America, Europe, Asia
Virulence Profile
tstseasecfnbAclfAscnchp
Resistance Profile
Classes: Methicillin, Aminoglycosides, Macrolides
mecAaac(6')-aph(2'')erm(A)
Clinical Significance
Major epidemic healthcare clone, recombinant lineage
Key References: https://doi.org/10.1128/jcm.43.10.5069-5073.2005, PMID: 38990431, PMID: 36504833, https://doi.org/10.1089/fpd.2013.171
CC25
European MRSA
🏥 Healthcare-associated Risk: MEDIUM
Sequence Types
25, 1172, 1173, 1131
Common spa Types
t078, t186, t280, t324
SCCmec Types
IV
Geographic Distribution
Healthcare-associated lineage
Regions: Europe
Virulence Profile
VariablefnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Healthcare-associated lineage
Key References: , PMID: 27605711, PMID: 27992523
CC27
Rare Documented Lineage
Rare Lineage Risk: LOW
Sequence Types
27, 28, 29
Common spa Types
Variable
SCCmec Types
Variable
Geographic Distribution
Rare but documented lineage
Regions: Global
Virulence Profile
VariableVariable
Resistance Profile
Classes: Variable
mecA if MRSA
Clinical Significance
Rare but documented lineage
Key References: PMID: 32110980
CC3
EMRSA-3/UK Hospital Clone
🏥 Healthcare-associated MRSA Risk: HIGH
Sequence Types
3, 254, 255, 256, 257, 258, 1094
Common spa Types
t037, t045, t091, t186, t242
SCCmec Types
I, II, III
Geographic Distribution
Early hospital clone in UK, major European healthcare clone
Regions: UK, Europe, Global
Virulence Profile
tstseasecselfnbAclfAclfBsdrCscnchpsakaurspl
Resistance Profile
Classes: Methicillin, Aminoglycosides, Macrolides, Tetracyclines
mecAaac(6')-aph(2'')erm(A)erm(C)tet(K)
Clinical Significance
Major European healthcare-associated clone, early hospital clone in UK, causes bacteremia, pneumonia, surgical site infections
Key References: PMID: 11310446, PMID: 23675030, PMID: 27992523
CC30
EMRSA-16/Southwest Pacific Clone
🏥 Healthcare-associated/Community-associated MRSA Risk: HIGH
Sequence Types
30, 34, 36, 37, 38, 39, 834, 1092
Common spa Types
t018, t019, t021, t024, t037, t138, t318, t937
SCCmec Types
II, IV
Geographic Distribution
Major healthcare clone with community transmission
Regions: Global, Europe, South America, Oceania
Virulence Profile
tstseasecsellukS-PVlukF-PVfnbAclfAscnsak
Resistance Profile
Classes: Methicillin, Erythromycin, Clindamycin, Aminoglycosides
mecAerm(A)erm(C)
Clinical Significance
Major healthcare clone, also community-associated in some regions
Key References: PMID: 22586109, PMID: 23284024, PMID: 27992523
CC31
Emerging Healthcare Clone
🏥 Healthcare-associated MRSA Risk: MEDIUM
Sequence Types
31, 32, 33
Common spa Types
t032, t037, t045
SCCmec Types
II, IV
Geographic Distribution
Emerging in some healthcare settings
Regions: Global, Europe, Asia
Virulence Profile
seasekfnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Emerging healthcare-associated clone
Key References: PMID: 27992523
CC34
Emerging Regional Clone
🏥 Healthcare-associated MRSA Risk: LOW
Sequence Types
34, 35, 36
Common spa Types
t032, t037, t045
SCCmec Types
II, IV
Geographic Distribution
Emerging in some regions
Regions: Specific regions, Emerging
Virulence Profile
seasekfnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Emerging in some regions
Key References: PMID: 22535928
CC398
LA-MRSA/Pig-associated
🐄 Livestock-associated MRSA Risk: MEDIUM
Sequence Types
398, 813, 929, 1232, 1234, 1580
Common spa Types
t011, t034, t108, t1250, t1451, t1456, t1457, t2383, t571, t899, t1939
SCCmec Types
IV, V, III
Geographic Distribution
Dominant livestock-associated clone, occupational risk for farmers/vets
Regions: Global, Europe, North America, Asia
Virulence Profile
Limited human virulence factorsLivestock adaptationOften lacks human immune evasion cluster
Resistance Profile
Classes: Methicillin, Tetracycline, Lincosamides
mecAtet(M)tet(K)lincosamide resistance
Clinical Significance
Dominant livestock-associated clone, occupational infections, can cause human infections
Key References: PMID: 19701815, PMID: 27605711, PMID: 27992523, PMID: 32822004, https://doi.org/10.1371/journal.pone.0010990
CC4
USA800/Pediatric Clone
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
4, 5, 6
Common spa Types
t008, t064, t121
SCCmec Types
IV, V
Geographic Distribution
Often associated with pediatric infections
Regions: USA, Global
Virulence Profile
lukS-PVlukF-PVseafnbAclfAscnsak
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Pediatric clone, community-associated, often associated with skin infections in children
Key References: PMID: 23055880, PMID: 27992523
CC40
Common MSSA Background
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
40, 41, 42
Common spa Types
t084, t085, t127
SCCmec Types
IV, V
Geographic Distribution
Common MSSA background lineage
Regions: Global
Virulence Profile
seasekseqfnbAclfAsdrCscnchpsak
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Common MSSA lineage that can acquire SCCmec to become MRSA
Key References: PMID: 36689019, PMID: 22535928, PMID: 37047168
CC425
mecC-MRSA/Wildlife Clone
🐄 Livestock-associated/Wildlife MRSA Risk: LOW
Sequence Types
425, 130, 1945, 1946
Common spa Types
t843, t2346, t3256, t3570
SCCmec Types
XI
Geographic Distribution
mecC-MRSA associated with wildlife, particularly hedgehogs
Regions: Europe, UK, Scandinavia
Virulence Profile
Limited virulence factorsWildlife adaptationmecC geneWildlife adaptation genes
Resistance Profile
Classes: Methicillin (mecC)
mecC
Clinical Significance
mecC-MRSA associated with wildlife, potential zoonotic transmission
Key References: PMID: 39650146, https://doi.org/10.1186/1751-0147-55-6, https://doi.org/10.1038/s41586-021-04265-w
CC45
USA600/Berlin Clone
🏥 Healthcare-associated MRSA Risk: MEDIUM
Sequence Types
45, 47, 49, 50, 51, 52, 508, 1093, 1134
Common spa Types
t015, t026, t038, t040, t067, t071, t186, t231, t269, t742
SCCmec Types
IV, V
Geographic Distribution
Healthcare-associated lineage with moderate spread
Regions: Global, Europe, North America
Virulence Profile
seasekseqfnbAclfAaurspl
Resistance Profile
Classes: Methicillin, Erythromycin, Tetracycline
mecAerm(C)tet(K)
Clinical Significance
Healthcare-associated lineage with moderate virulence
Key References: PMID: 27605711, PMID: 23887918, PMID: 32822004
CC5
New York/Japan Clone
🏥 Healthcare-associated MRSA Risk: HIGH
Sequence Types
5, 105, 125, 225, 228, 231, 235, 236, 240, 245, 685, 1034, 1057, 1089
Common spa Types
t002, t045, t067, t106, t242, t311, t548, t688
SCCmec Types
II, IV
Geographic Distribution
Dominant healthcare clone in many regions, SCCmec II predominant
Regions: Global, North America, Europe, Asia, South America
Virulence Profile
seasekseqtstfnbAfnbBclfAclfBscnchpsakaursplgeh
Resistance Profile
Classes: Methicillin, Erythromycin, Clindamycin, Aminoglycosides
mecAerm(A)erm(C)aac(6')-aph(2'')
Clinical Significance
Major healthcare-associated pandemic clone causing bacteremia, pneumonia, surgical site infections
Key References: PMID: 22527128, PMID: 22617140, PMID: 19680247, PMID: 27992523
CC51
Asian Healthcare MRSA
🏥 Healthcare-associated Risk: MEDIUM
Sequence Types
51, 149, 150
Common spa Types
t037, t045, t067
SCCmec Types
III
Geographic Distribution
Healthcare-associated lineage
Regions: Global
Virulence Profile
VariablefnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Healthcare-associated lineage
Key References: PMID: 19178545
CC59
Taiwan/Asian-Pacific Clone
🏘️ Community-associated MRSA Risk: HIGH
Sequence Types
59, 338, 339, 340, 341, 375, 954, 1123
Common spa Types
t437, t441, t454, t632, t1635
SCCmec Types
IV, V
Geographic Distribution
Major CA-MRSA clone in Asia with increasing global spread
Regions: Asia-Pacific, Taiwan, China, Korea, USA, Australia
Virulence Profile
lukS-PVlukF-PVetaetbfnbAclfAaur
Resistance Profile
Classes: Methicillin, Erythromycin, Clindamycin
mecAerm(B)erm(C)
Clinical Significance
Major CA-MRSA clone in Asia, causes skin infections, necrotizing fasciitis
Key References: PMID: 32544568, PMID: 20211891, PMID: 23966409, https://doi.org/10.1371/journal.pone.0070602, DOI https://doi.org/10.2147/IDR.S284781
CC6
UK/Irish Hospital Clone
🏥 Healthcare-associated MRSA Risk: MEDIUM
Sequence Types
6, 7, 258, 259, 1221
Common spa Types
t304, t701, t843, t955
SCCmec Types
IV
Geographic Distribution
Early hospital clone in UK and Ireland
Regions: UK, Ireland, Europe
Virulence Profile
seasekseqfnbAclfAclfBscnchp
Resistance Profile
Classes: Methicillin, Erythromycin
mecAerm(C)
Clinical Significance
Early hospital-associated clone in UK and Ireland
Key References: PMID: 22189119, PMID: 24395241, PMID: 27992523
CC7
Pediatric/Neonatal Clone
🏥 Healthcare-associated/Community-associated MRSA Risk: MEDIUM
Sequence Types
7, 6, 72, 254, 1223
Common spa Types
t091, t148, t657, t1234
SCCmec Types
IV, V
Geographic Distribution
Associated with pediatric and neonatal infections
Regions: North America, Europe, Global
Virulence Profile
lukS-PVlukF-PVseafnbAclfAscnsak
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Pediatric and neonatal infections, both community and healthcare-associated
Key References: PMID: 23055880, PMID: 23177801, PMID: 19178545
CC73
Common MSSA Lineage
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
73, 74, 75
Common spa Types
t084, t085, t091
SCCmec Types
IV, V
Geographic Distribution
Common MSSA lineage with MRSA potential
Regions: Global
Virulence Profile
seasekfnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Common MSSA lineage with potential to become MRSA
Key References: PMID: 26856837, PMID: 19713400, PMID: 22514264
CC772
Bengal Bay Clone
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
772, 2884
Common spa Types
t657, t1081
SCCmec Types
IV, V
Geographic Distribution
PVL-positive, often associated with travel
Regions: Indian Subcontinent, UK, Middle East
Virulence Profile
lukS-PVlukF-PVetaetb
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
CA-MRSA clone from Indian subcontinent with global travel-associated spread
Key References: PMID: 33122734, PMID: 29238933, https://doi.org/10.3389/fmicb.2019.02505
CC8
USA300/Pandemic CA-MRSA
🏥 Healthcare-associated/Community-associated MRSA Risk: HIGH
Sequence Types
8, 72, 241, 247, 250, 254, 260, 1139, 1223
Common spa Types
t008, t024, t064, t121, t334, t622
SCCmec Types
IV, IVa, V
Geographic Distribution
USA300 is major community clone with global spread
Regions: Global, North America, Europe
Virulence Profile
lukS-PVlukF-PVseasekseqfnbAclfAsdrCscnchpsakACMEPSM-mec
Resistance Profile
Classes: Methicillin, Fluoroquinolones, Erythromycin
mecAnorAerm(C)
Clinical Significance
Includes both HA-MRSA and CA-MRSA, USA300 is hypervirulent community clone
Key References: PMID: 26484389, PMID: 20610826, PMID: 27992523, PMID: 39431343
CC80
European CA-MRSA
🏘️ Community-associated MRSA Risk: HIGH
Sequence Types
80, 1154, 1239, 1250
Common spa Types
t044, t131, t376, t860
SCCmec Types
IV
Geographic Distribution
Major CA-MRSA clone in Europe and Middle East
Regions: Europe, Middle East, North Africa
Virulence Profile
lukS-PVlukF-PVetaetbfnbAclfAaur
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Major CA-MRSA clone in Europe and Middle East
Key References: PMID: 25078407, https://doi.org/10.1016/j.cmi.2017.06.022, https://doi.org/10.1128/jcm.01381-07
CC88
African/Mediterranean CA-MRSA
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
88, 78, 1002, 1187, 1249
Common spa Types
t786, t325, t861, t1324, t1869
SCCmec Types
IV, V
Geographic Distribution
Emerging CA-MRSA clone in specific regions
Regions: North Africa, Middle East, Southeast Asia, Mediterranean
Virulence Profile
lukS-PVlukF-PVfnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Emerging CA-MRSA clone in developing regions
Key References: PMID: 22745670, https://doi.org/10.3390/microorganisms12010017, PMID: 27992523
CC89
Major Community-associated Lineage
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
89, 90, 91
Common spa Types
t084, t085, t127
SCCmec Types
IV, V
Geographic Distribution
Major community-associated lineage
Regions: Global
Virulence Profile
sealukS-PVlukF-PVfnbAclfAscnsak
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Major community-associated lineage
Key References: PMID: 33463096, PMID: 21398072, PMID: 30694723, PMID: 20392913, PMID: 40667846
CC9
Asian LA-MRSA
🐄 Livestock-associated MRSA Risk: MEDIUM
Sequence Types
9, 834, 835, 1187, 1347
Common spa Types
t899, t1430, t1939, t337
SCCmec Types
III, IV, V
Geographic Distribution
Livestock-associated in Asia, emerging human infections
Regions: Asia, China, Korea, Increasing global
Virulence Profile
Limited virulence factorsLivestock adaptation
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Livestock-associated in Asia, emerging human infections
Key References: PMID: 36363707, https://doi.org/10.3389/fmicb.2012.00103
CC93
Queensland/Australian Clone
🏘️ Community-associated MRSA Risk: MEDIUM
Sequence Types
93, 1179, 1180
Common spa Types
t202, t334, t573, t1340
SCCmec Types
IV, V
Geographic Distribution
CA-MRSA clone primarily in Australia and New Zealand
Regions: Australia, New Zealand
Virulence Profile
lukS-PVlukF-PVfnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
CA-MRSA clone in Australia and New Zealand
Key References: DOI: 10.1111/apm.12181, https://doi.org/10.1111/apm.12181, https://doi.org/10.1016/j.cmi.2016.11.002
CC97
Bovine/Human Associated
Animal-associated/Human Risk: MEDIUM
Sequence Types
97, 71, 1265, 1303, 1394, 1715
Common spa Types
t173, t267, t359, t911, t1344, t1736, t2247
SCCmec Types
IV, V
Geographic Distribution
Originally bovine-associated, now human infections
Regions: Europe, Global
Virulence Profile
seasekseqfnbAclfA
Resistance Profile
Classes: Methicillin
mecA
Clinical Significance
Originally bovine-associated, now human infections
Key References: https://doi.org/10.1016/j.vetmic.2022.109374, https://doi.org/10.3390/foods9040439, PMID: 26590279, PMID: 27992523
CC98
Livestock-associated Lineage
🐄 Livestock-associated MRSA Risk: LOW
Sequence Types
98, 99, 100
Common spa Types
t267, t359, t1730
SCCmec Types
IV, V
Geographic Distribution
Livestock-associated lineage
Regions: Europe, Global
Virulence Profile
LimitedAnimal adaptation
Resistance Profile
Classes: Methicillin, Tetracycline
mecAtet(K)
Clinical Significance
Livestock-associated lineage with occasional human infections
Key References: PMID: 15252717, PMID: 27991847, PMID: 36830286

Specialized Lineage Profiles

Pvl Positive

CC8-USA300

ST: 8
SCCmec: IV
spa: t008
Clinical: Necrotizing pneumonia, skin infections, osteomyelitis
Risk: VERY HIGH
lukS-PVlukF-PVseasekseq

CC1-USA400

ST: 1
SCCmec: IV
spa: t128
Clinical: Necrotizing pneumonia, severe skin infections
Risk: HIGH
lukS-PVlukF-PVsekseq

CC80-European

ST: 80
SCCmec: IV
spa: t044
Clinical: Severe skin infections, necrotizing fasciitis
Risk: HIGH
lukS-PVlukF-PVetaetb

CC59-Taiwan

ST: 59
SCCmec: V
spa: t437
Clinical: Skin infections, necrotizing fasciitis
Risk: HIGH
lukS-PVlukF-PVetaetb

CC1153-Arabian

ST: 1153
SCCmec: V
spa: t657
Clinical: Skin and soft tissue infections
Risk: MEDIUM
lukS-PVlukF-PV

Tst Positive

CC30-EMRSA16

ST: 30
SCCmec: II
spa: t019
Clinical: Toxic shock syndrome, menstrual TSS
Risk: HIGH
tstseasec

CC5-USA100

ST: 5
SCCmec: II
spa: t002
Clinical: Toxic shock syndrome, healthcare-associated
Risk: HIGH
tstseasekseq

CC239-Brazilian

ST: 239
SCCmec: III
spa: t037
Clinical: Toxic shock syndrome, healthcare-associated
Risk: HIGH
tstseasec

Exfoliative Toxin

CC121-ETA

ST: 121
SCCmec: IV
spa: N/A
Clinical: Staphylococcal scalded skin syndrome
Risk: MEDIUM
eta

CC80-ETB

ST: 80
SCCmec: IV
spa: N/A
Clinical: Bullous impetigo, scalded skin syndrome
Risk: MEDIUM
etb

CC772-BengalBay

ST: 772
SCCmec: IV
spa: N/A
Clinical: Bullous impetigo, scalded skin syndrome
Risk: MEDIUM
etaetb

Fusidic Acid Resistant

CC1153-Arabian

ST: 1153
SCCmec: V
spa: t657
Clinical: Skin infections in Middle East/North Africa
Risk: MEDIUM
Resistance: fusC

CC80-European

ST: 80
SCCmec: IV
spa: t044
Clinical: Community skin infections in Europe
Risk: MEDIUM
Resistance: fusC

Mec C Positive

CC130-LA-MRSA

ST: 130
SCCmec: XI
spa: t843
Clinical: Zoonotic infections from livestock, often missed by routine tests
Risk: MEDIUM
mecC

CC425-Wildlife

ST: 425
SCCmec: XI
spa: t843
Clinical: Wildlife-associated, potential zoonotic transmission
Risk: LOW
mecC

Pediatric Associated

CC7-Pediatric

ST: 7
SCCmec: IV
spa: t091
Clinical: Neonatal and pediatric infections
Risk: MEDIUM
lukS-PVlukF-PV

CC1-USA400

ST: 1
SCCmec: IV
spa: t128
Clinical: Pediatric necrotizing pneumonia
Risk: HIGH
lukS-PVlukF-PV

Global Geographic Distribution

Region Lineage/Clone Clonal Complex Prevalence Setting
North America USA300 CC8 High Community/Hospital
North America USA100 CC5 High Hospital
North America USA400 CC1 Medium Community
North America USA500 CC8 Low Hospital
North America USA600 CC45 Low Hospital
North America USA800 CC8 Low Hospital
Europe EMRSA-15 CC22 High Hospital
Europe EMRSA-16 CC30 High Hospital
Europe Berlin CC45 Medium Hospital
Europe Irish-1 CC8 Medium Hospital
Europe European CA-MRSA CC80 Medium Community
Europe Barnim CC22 Medium Hospital
Asia Taiwan CC59 High Community
Asia Japanese CC5 High Hospital
Asia Korean CC5 Medium Hospital
Asia Chinese CC9 Medium Livestock/Human
Asia Bengal Bay CC772 Medium Community
Asia Vietnamese CC59 Medium Community
South America Chilean CC5 High Hospital
South America Brazilian CC239 High Hospital
South America Argentinian CC30 Medium Hospital
Africa African CA-MRSA CC88 Medium Community
Africa North African CC80 Medium Community
Africa Arabian Gulf CC1153 Emerging Community
Oceania Southwest Pacific CC30 High Hospital/Community
Oceania Queensland CC93 Medium Community
Oceania Western Australian CC1 Medium Community
Middle East Arabian Gulf CC1153 High Community
Middle East Middle Eastern CC80 Medium Community
Middle East Gaza CC22 Medium Hospital
Scandinavia mecC-MRSA CC130 Emerging Livestock/Wildlife
Scandinavia Baltic CA-MRSA CC80 Medium Community
Southeast Asia Taiwan Clone CC59 High Community
Southeast Asia Vietnamese CC59 Medium Community
Southeast Asia Malaysian CC88 Medium Community

About StaphScope Lineage Database

Database Information

Version: 2025

Last Updated: 20/10/2025

Total Lineages: 44

Coverage: Global S. aureus lineages including HA-MRSA, CA-MRSA, and LA-MRSA

Database Structure

  • Lineage Database: clonal complexes with detailed metadata
  • Specialized Profiles: categories of specialized lineages
  • Geographic Data: regions with lineage distributions

Technical Support & Inquiries

Author: Brown Beckley

GitHub: bbeckley-hub

Email: brownbeckley94@gmail.com

Affiliation: University of Ghana Medical School - Department of Medical Biochemistry

Note: This database is for reference and educational purposes. Always verify lineage assignments with current literature, Pubmlst and additional molecular methods.