A.
B.
Figure A1. Phylogenetic trees based on concatenated sequences of eight MLST loci. Phylogenetic trees were constructed based on concatenated sequences of eight housekeeping loci for 12 unique STs using Maximum-likelihood (A) and Neighbour-joining (B) methods. Individual strains and STs can be identified in the traditional rectangular branch style. Bootstrap support values of over 70% are shown.
A. ADK-4 ADK-3 ADK-1 ADK-2 ADK-4 ADK-3 ADK-1 ADK-2 VANTTGLFHLSTGDIFRTVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL VANTTGLFHLSTGDIFRSVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL VANTTGLFHLSTGDIFRSVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL VANTTGLFHLSTGDIFRSVMQEQGALSQTLAHYMNQGLYVPDELTNQTFWHFVTTHQNEL *****************:****************************************** ADK-4 KPPLKANQCDRCHATLQARNDDTEAVILKRLTLYEDT 157 ADK-3 KPPLKANQCDLCHATLQARNDDTEAVILKRLTLYEDT 157 ADK-1 KPPLKANQCDRCHATLQARNDDTEAVILKRLTLYEDT 157 ADK-2 KPPLKANQCDRCHAMLQARNDDTEAVILKRLTLYEDT 157 ********** *** ********************** B. ARCC-1 ARCC-2 ARCC-1 ARCC-2 ARCC-1 ARCC-2 PHQAVYFLTQTLVEASDPAFQNPNKPVGPFYNTEETARSANPNSTVVEDAGRGWRKVVAS PHQAVYFLTQTLVEASDPAFQNPNKPVGPFYNTEETARSANPNSTVVEDAGRGWRKVVAS PKPVDVLGIDAIKSSFNQGNLVIVGGGGGVPTIKTKSGYATVDGVIDKDLALSEIAIKVE PKPVDVLGIDAIKSSFNQGNLVIVGGGGGVPTIKTKSGYATVDGVIDKDLALSEIAIKVE ADLFVILTAVDFVYINYGQPNEQKLTCINTKEAKTLMAANQFAKGSMLPKVEACLNFVQS ADLFVILTAVDFVYINYGQPNEQKLTCINTKEAKTLMAANQFAKGSMLPKVEACLNFVQS ARCC-1 GTNKTAIIAQ 190 ARCC-2 GTNKTAIIAQ 190 ********** C. GLYA-1 GLYA-3 GLYA-2 GLYA-1 GLYA-3 GLYA-2 GLYA-1 GLYA-3 GLYA-2 ENYVSRDILEVTGSILTNKYAEGYPTRRFYEGCEVVDESESLAINTCKELFGAKWANVQP ENYVSRDILEVTGSILTNKYAEGYPTRRFYEGCEVVDESESLAINTCKELFGAKWANVQP ENYVSRDILEVTGSILTNKYAEGYPTRRFYEGCEVVDESESLAINTCKELFGAKWANVQP HSGSSANYAVYLALLKPGDAILGLDLNCGGHLTHGNKFNFSGKQYQPYSYTINPETEMLD HSGSSANYAVYLALLKPGDAILGLDLNCGGHLTHGNKFNFSGKQYQPYSYTINPETEMLD HSGSSANYAVYLALLKPGDAILGLDLNCGGHLTHGNKFNFSGKQYQPYSYTINPETEMLD YDEVLRVAREVKPKLIICGFSNYSRTVDFERFSAIAKEVGAYLLADIAHIAGLVAAGLHP YDEVLRVAREVKPKLIICGFSNYSRTVDFERFSAIAKEVGAYLLADIAHIAGLVAAGLHP YDEVLRVAREVKPKLIICGFSNYSRTVDFERFSAIAKEVGAYLLADIAHIAGLVAAGLHP GLYA-1 NPLPYTDVVTSTTHKTLRGPRGGLIMSNNEAIIRKLDSGVFPGC 224 GLYA-3 NPLPYTDVVTSTTHKTLRGPRGGLIMSNNEAIIRKLDSGVFPGC 224 GLYA-2 NPLPYADVVTSTTHKTLRGPRGGLIMSNNEAIIRKLDSGVFPGC 224 *****:**************************************
D. VTDSMKYTTVVCATASNPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL VTDSMKYTTVVCATASNPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL VTDSMKYTTVVCATASDPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL VTDSMKYTTVVCATASDPASMIYLTPFTGITIAEYWLKQGKDVLIVFDDLSKHAIAYRTL ****************:******************************************* SLLLRRPPGREAFPGDVFYLHSRLL 265 SLLLRRPPGREAFPGDVFYLHSRLL 265 SLLLRRPPGREAFPGDVFYLHSRLL 265 SLLLRRPPGREAFPGDVFYLHSRLL 265 ************************* E. GMK-1 GMK-2 GMK-1 GMK-2 SGVGKSSLVRCLIDHFKDKLRYSISATTRKMRNSETEGVDYFFKDKAEFEKLIAADAFVE SGVGKSSLVRCLIDHFKDKLRYSISATTRKMRNSETEGVDYFFKDKAEFEKLIAADAFVE WAMYNDNYYGTLKSQAEQIIHNGGNLVLEIEYQGALQVKQKYPNDVVLIFIKPPSMEELL WAMYNDNYYGTLKSQAEQIIHNGGNLVLEIEYQGALQVKQKYPNDVVLIFIKPPSMEELL GMK-1 VRLKKRNDEDA 131 GMK-2 VRLKKRNDEDA 131 *********** F. GYRB-1 GYRB-2 GYRB-1 GYRB-2 VPDFTVMEKSDYKQTVIASRLQQLAFLNKGIQIDFVDERRQNPQSFSWKYDGGLVQYIHH VPDFTVMEKSDYKQTVIASRLQQLAFLNKGIQIDFVDERRQNPQSFSWKYDGGLVQYIHH LNNEKEPLFEDIIFGEKTDTVKSVSRDESYTIKVEVAFQYNKTYNQSIFSFCNNINTTEG LNNEKEPLFEDIIFGEKTDTVKSVSRDESYTIKVEVAFQYNKTYNQSIFSFCNNINTTEG GYRB-1 GTHVEGFRNALVKIINRFAVEN 142 GYRB-2 GTHVEGFRNALVKIINRFAVEN 142 **********************
G. H. APCTMKSDLEAFMVFLKDYHNVIIGTLGGRYYGMDRDQRWDREEIAYNAILGNSKASFTD APCTMKSDLEAFMVFLKDYHNVIIGTLGGRYYGMDRDQRWDREEIAYNAILGNSKASFTD APCTMKSDLEAFMVFLKDYHNVIIGTLGGRYYGMDRDQRWDREEIAYNAILGNSKASFTD PVAYVQSAYDQKVTDEFLYPAVNGNVDKEQFALKDHDSVIFFNFRPDRARQMSHMLFQTD PVAYVQSAYDQKVTDEFLYPAVNGNVDKEQFALKDHDSVIFFNFRPDRARQMSHMLFQTD PVAYVQSAYDQKVTDEFLYPAVNGNVDKEQFALKDHDSVIFFNFRPDRARQMSHMLFQTD 120 120 120 YYDYTPKAGRKHNLFFVTMMNYEGIKPSAVVFPPETIPNTFGEVIAHNKLKQLRIAETEK YYDYTPKAGRKYNLFFVTMMNYEGIKPSAVVFPPETIPNTFGEVIAHNKLKQLRIAETEK YYDYTPKAGRKHNLFFVTMMNYEGIKPSAVVFPPETIPNTFGEVIAHNKLKQLRIAETEK ***********:************************************************ 180 180 180 YAHVTFFFDGGVEVDLPNETKCMVPSLKVATYDLAPEMACKGITDQLLNQINQFDLTVLN YAHVTFFFDGGVEVDLPNETKCMVPSLKVATYDLAPEMACKGITDQLLNQINQFDLTVLN YAHVTFFFDGGVEVDLPNETKCMVPSLKVATYDLAPEMACKGITDQLLNQINQFDLTVLN 240 240 240 FANPDMVGHTGNYAACVQGLEALDVQIQRIIDFCKANHITLFLTADHGNAEEMIDSNNNP FANPDMVGHTGNYAACVQGLEALDVQIQRIIDFCKANHITLFLTADHGNAEEMIDSNNNP FANPDMVGHTGNYAACVQGLEALDVQIQRIIDFCKANHITLFLTADHGNAEEMIDSNNNP 300 300 300 VTKHTVNKVPFVCTDTNIDLQQDSASLANIAPTILAYLGLKQPAEMTANSLLYKKV VTKHTVNKVPFVCTDTNIDLQQDSASLANIAPTILAYLGLKQPAEMTANSLLISKK VTKHTVNKVPFVCTDTNIDLQQDSASLANIAPTILAYLGLKQPAEMTANSLLISKK ****************************************************.* PPA-1 PPA-2 IFADQAFLPGVVVPTRIVGALEMVDDGELDTKLLGVIDCDPRYKEINSVNDLPKHRVDEI IFADQAFLPGVVVPTRIVGALEMVDDGELDTKLLGVIDCDPRYKEINSVNDLPKHRVDEI PPA-1 PPA-2 IGFLKTYKLLQKKEVIIKGVQSLEW IGFFKTYKLLQKKEVIIKGVQSLEW ***:********************* 356 356 356 85 85 Figure A2. Alignments of amino acid sequences of each allelic type at each of the eight MLST loci. Amino acid sequence alignments were generated for each of the eight loci based on nucleotide sequence of each allelic type. Synonomous changes in amino acid sequence are highlighted in yellow. * (asterix) indicates positions which have a single, fully conserved residue; : (colon) indicates conservation between groups of strongly similar properties - scoring > 0.5 in the Gonnet PAM 250 matrix;. (period) indicates conservation between groups of weakly similar properties - scoring < 0.5 in the Gonnet PAM 250 matrix.