Table S1: List of isolates used in this study and their related information: location, source of isolation (CLIN: clinical, VET: veterinary and ENV: environmental), specific source and date of isolation. Mating types, allele numbers for the seven MLST loci and the corresponding sequence type (ST) are also presented.

Other collection Source of Mating GPD LAC SOD URA WM number Specific location Specific source Isolation date CAP59 PLB1 IGS1 ST number isolation type 1 1 1 5 a Eucalyptus tereticornis, i l Australia, NSW, WM 1008 ENV association with frass of a 2000 α 2 6 4 2 15 2 10 7 a

r Blacktown t moth larva s Australia, NSW, u WM 437 New8; H 18 CLIN Skin 1994 α 2 6 4 2 15 2 10 7 Newcastle A VPB 571-015; Australia, NSW, WM 198 VET Cat 1990 α 2 6 4 2 15 2 10 7 McBride Sydney, Camden Australia, NSW, Cat (15 years old), lymph WM 08.245 571 270 VET 1996 α 2 6 4 2 15 2 10 7 Sydney node 49435; CBS 10082; Australia, NSW, **,¶ CLIN Lung 1991 α 1 17 16 14 19 7 16 21 WM 178 IFM 50894 Sydney Australia, NSW, ‡,¶ 571116; V20 VET Dog, abdominal mass 1995 α 2 6 4 2 15 2 10 7 WM 05.230 Sydney, Bradbury VPB 571-058; PR563; Australia, NSW, †,‡,¶ VET Cat (Birman cat), nasal 1991 α 2 6 4 2 15 2 10 7 WM 04.71 V4; CP 2500 / 91 Sydney, Chiswick Australia, NSW, †,‡,¶ C 194; V9 VET Cat (Pusska Shepherd) 1992 α 2 6 4 2 15 2 10 7 WM 08.284 Sydney, Coogee Australia, NSW, WM 08.267 571 327 VET Cat, nasal 2006 α 2 6 4 2 15 2 10 7 Sydney, Gladesville Australia, NSW, WM 2209 1607/96 VET Cat (3.5 years old), nasal 1996 α 2 6 4 2 15 2 10 7 Sydney, Rosemeadow Australia, NT, †,‡,¶ RDH06 CLIN CSF 1996 α 2 6 4 2 15 2 10 7 WM 04.70 Arnhemland Australia, NT, **,†,‡,¶ NT-08 CLIN Lung 1983 α 3 2 7 1 18 5 6 33 WM 06.1 Arnhemland Australia, NT, †,‡ H 16 CLIN Lung 1996 α 3 2 7 1 18 5 6 33 WM 2606 Arnhemland Australia, NT, †,‡,¶ NT-07 CLIN CSF 1989 α 3 2 7 1 18 5 6 33 WM 3030 Arnhemland Australia, NT, Eucalyptus tree (near ¶ ARN 001 ENV 21/06/1999 α 2 6 4 2 15 2 10 7 WM 03.456 Arnhemland, house) Australia, NT, **,†,‡,¶ NT-13 CLIN Lung 1985 α 2 6 4 2 15 2 10 7 WM 05.229 Arnhemland Australia, NT, ¶ RAM 002 ENV Eucalyptus tree 22/06/1999 α 2 6 4 2 15 2 10 7 WM 03.27 Arnhemland Australia, NT, ‡,¶ RAM 005 ENV E. tetrodonta 22/06/1999 α 2 6 4 2 15 2 10 7 WM 04.187 Arnhemland Australia, NT, E. miniata (100 m north of ‡,¶ RAM 015 ENV 22/06/1999 α 2 6 4 2 15 2 10 7 WM 04.69 Arnhemland oval) †,‡ WM 3032 NT-14 Australia, NT, CLIN CSF 1983 α 3 2 7 1 18 5 6 33 Katherine Region Australia, QLD, WM 09.4 37098-9217 CLIN Male (50 years old) 2008 α 2 6 4 2 15 2 10 7 Aurukun WM 08.141 571156 Australia, QLD, Maleny VET Cat, nasal 1996 α 2 6 4 2 15 2 10 7 PWQ 875, 5018; Q99; WM 08.306 Australia, WA VET Horse (name RIjInski ) 15/12/1999 α 2 6 4 2 15 2 10 7 86773K PWQ 606, 14-1419; Horse (name: Olivieri; 5 WM 08.308; WM 2971 S00 3895-U; MA Australia, WA, Perth VET 12/07/1995 α 2 6 4 2 15 2 10 7 years old), tracheal wash 21832 PWQ 320; 91/684; Horse (name: Grey all WM 09.85 Australia, WA VET 06/02/1991 α 2 6 4 2 15 2 10 7 91/183; noble), tracheal wash PWQ 321; 88/1337; Horse (cough after exercise, WM 09.86 Australia, WA VET 08/03/1988 α 2 6 4 2 15 2 10 7 88/460 lung lesion) Australia, WA, near WM 09.88 PWQ 494; 93/3258 VET Sheep L2 (horn lesion) 04/06/1993 α 2 6 4 2 15 2 10 7 Busselton Australia, WA. near WM 09.89 PWQ 496; 93/3257 VET Sheep L1 (eye lesion) 04/06/1993 α 2 6 4 2 15 2 10 7 Busselton PWQ 474; P93/133; Australia, WA, near WM 09.90; WM 08.307 VET Sheep 093-133, cid (tumor) 20/01/1993 α 2 6 4 2 15 2 10 7 93/355; 14-1408 Busselton Horse (name: Gavin "Kiwi WM 09.91 PWQ 628; 95/3662 Australia, WA VET 24/05/1995 α 2 6 4 2 15 2 10 7 Habit") tracheal wash PWQ 1781; WM 09.98 Australia, WA VET Dog, cid, nasal swab 16/12/2008 α 2 6 4 2 15 2 10 7 P08/2061902G PWQ 1009; Australia, WA, Dog, cid, cerebrospinal fluid WM 09.94 VET 21/12/2001 a 14 21 28 27 46 2 27 38 Q01/1067864N Geraldton area (3 years old) PWQ 730, 14-1431; Horse (name: Solidago), WM 08.309; WM 447 SOLIDAGO; M31557; Australia, WA VET 04/04/1997 α 27 6 4 1 43 7 4 48 lung M29004 PWQ 655, 14-1433; Horse (name: Malley Natasi WM 08.310 Australia, WA VET 29/11/1995 α 27 6 4 1 43 7 4 48 Malley; M25183 Aztec) PWQ 1675; Australia, WA, Cow # 1004 (tumor-like WM 09.97 VET 11/03/2008 α 2 6 4 2 15 2 10 7 P08/2030588F Busselton, Alton Park lesions through the lungs) Australia, WA, Eucalyptus log under Koala, WM 09.153 - Caversham Wildlife ENV 08/07/2009 α 2 6 4 2 15 2 10 7 new shed Park Australia, WA, WM 09.154 - Caversham Wildlife ENV Eucalyptus log, new shed 08/07/2009 α 2 6 4 2 15 2 10 7 Park Australia, WA, Eucalyptus tree trunk I, old WM 09.163 - Caversham Wildlife ENV 08/07/2009 α 2 6 4 2 15 2 10 7 shed Park Australia, WA, Vertical Eucalyptus log, old WM 09.164 - Caversham Wildlife ENV 08/07/2009 α 2 6 4 2 15 2 10 7 shed Park Australia, WA, Vertical Eucalyptus log WM 09.166 - Caversham Wildlife ENV 08/07/2009 α 2 6 4 2 15 2 10 7 (second), visitor area Park WM 09.155 - Australia, WA, VET Koala (name: Sarah), nasal 08/07/2009 α 2 6 4 2 15 2 10 7 Caversham Wildlife swab right nose●, new shed Park Australia, WA, Koala (name: J), nasal swab WM 09.156 - Caversham Wildlife VET 08/07/2009 α 2 6 4 2 15 2 10 7 ●●, Park right nose new shed Australia, WA, Koala (name: Amie), nasal WM 09.157 - Caversham Wildlife VET 08/07/2009 α 2 6 4 2 15 2 10 7 ●, Park swab right nose new shed Australia, WA, Koala (name: Amelie), nasal WM 09.158 - Caversham Wildlife VET 08/07/2009 α 2 6 4 2 15 2 10 7 ●, Park swab left nose new shed Australia, WA, Koala (adult male), nasal WM 09.160 - Caversham Wildlife VET swab left and right nose●, 08/07/2009 α 2 6 4 2 15 2 10 7 Park new shed Australia, WA, Koala (no name, female), WM 09.161 - Caversham Wildlife VET nasal swab left and right 08/07/2009 α 2 6 4 2 15 2 10 7 Park nose●, new shed Australia, WA, Eucalyptus tree trunk II, old WM 09.165 - Caversham Wildlife ENV 08/07/2009 a 14 21 28 27 46 2 27 38 shed Park Australia, WA, Eucalyptus log above WM 09.152 - Caversham Wildlife ENV 08/07/2009 α 27 6 4 1 43 7 4 48 Eucalyptus trunk, new shed Park Australia, WA, Male (54 years old) WM 09.83 PWQ 309 CLIN 17/12/1985 α 27 6 4 1 43 7 4 48 Mandurah cerebrospinal fluid Australia, WA, Female (24 years old) WM 09.95 PWQ 1040 CLIN 26/08/2002 α 27 6 4 1 43 7 4 48 Meekatharra Sputum Australia, WA, Middle Male (40 years old) WM 09.96 PWQ 1671 CLIN 29/01/2008 α 27 6 4 1 43 7 4 48 Swan cerebrospinal fluid PWQ 697, 14-1434; WM 08.311; WM Dog (Dalmatian), cranial Jackson; 6003508t; Australia, WA, Perth VET 10/04/1996 α 3 16 4 9 23 2 15 5 *,**,¶ mediastinal mass 08.131; WM 2517 571140; WA861 Australia, WA, Perth, Male (40 years old), WM 1382 PWQ 777 CLIN 18/03/1998 α 2 6 4 2 15 2 10 7 Willetton cerebrospinal fluid WM 04.72 PWQ 314; W12 Australia, WA, Perth CLIN Male (49 years old) 31/07/1990 α 3 2 7 1 18 5 6 33

a Canada, British c *,**,‡‡ 20 i CDC R265 Columbia, Vancouver CLIN Male, bronchial wash 2001 α 1 1 4 1 14 7 4 r WM 02.32 (=VGIIa) e Island, Duncan

m Canada, British WM 06.25; WM 7 A *,**,‡‡ CDC R272 Columbia, Vancouver CLIN Female, bronchial wash 2001 α 2 6 4 2 15 2 10 02.39 (=VGIIb) h Island, Ladysmith t r 6

o - B7432 USA, Oregon CLIN Blood 05/01/2009 - 4 6 4 1 15 2 15 (=VGIIc) N ATCC 32609. USA, Maryland, ¶,** CLIN Sputum 1975 α 1 1 4 1 14 7 4 20 WM 06.4 NIH 444. CBS 6956 Bethesda CBS 7750 ; USA, California, San E. camaldulensis (bark ¶,** ENV 1990 α 1 1 4 1 14 7 4 20 WM 06.13 451-SF13.2 Francisco debris) WM 02.35 CDC R268 Canada, British CLIN Female, cerebrospinal fluid 2001 α 1 1 4 1 14 7 4 20 Columbia, Lantzville CBS11511; Female (53 years old),

e WM 09.113 Switzerland CLIN 2006 α 1 1 4 1 14 7 4 20 RKI06/496 cerebrospinal fluid p

o CBS10485; Male (51 years old), lung

r WM 09.144 Denmark, Herning CLIN 2006 α 1 1 4 1 14 7 4 20 E758/2005 biopsy u

E WM 05.77** AV55 ; CBS 10090 Greece, Athens CLIN Female (26 years old) 1998 a 2 27 4 1 8 7 10 18 Republic of Korea, Male (57 years old), - K71 CLIN 2006 α 2 6 4 2 15 2 10 7 Asia Gyeonggi cerebrospinal fluid ¶,** WM 06.33 CBS 1930 ; RV 71421 Aruba VET Goat 1953 a 2 6 4 18 12 10 25 25 Male (18 years old),

a WM 05.452** LMM 417 ; LA 55 Brazil, Piaui CLIN 1995 a 2 27 4 1 8 7 15 16 cerebrospinal fluid c i r WM 05.470 LMM 547.18.13A3 Brazil, Piaui ENV Wood 1994 α 2 16 4 26 15 2 42 26 e LA 43 ; NUAM 176; Uruguay, Quebrada de Nest of wasp Polybia

m ¶,** WM 06.8 ENV 1996 α 7 6 21 25 2 2 32 3

A CBS 8684 los Cuervos occidentalis Brazil, Mato Grosso do Female (18 years old), h

t WM 05.533 LMM 892 CLIN 1997 α 10 6 30 16 20 2 16 11 Sul cerebrospinal fluid u

o LA 84 ; HEC 11102 ; WM 477 Brazil, Rio de Janeiro CLIN Male (47 years old), urine 1994 α 28 6 29 18 1 1 15 4 S LMM 21 Male (33 years old), WM 05.529 LMM 855 Brazil, Roraima CLIN 1997 α 2 32 30 1 13 7 25 27 cerebrospinal fluid Isolates used in other population genetic studies: † [25]; ‡ [17]; ‡‡ [27]; ¶ [16]; * [29]; ** [30]; ● Animals were colonized or had subclinical infections; ●● Koala with an infection of the right claw treated with Fluconazole daily and Amphotericin B 2x weekly.