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Volume 17, Number 11—November 2011


Comparative Genomics of Vibrio cholerae from Haiti, Asia, and Africa

Aleisha R. Reimer, Gary Van Domselaar, Steven Stroika, Matthew Walker, Heather Kent, Cheryl Tarr, Deborah Talkington, Lori Rowe, Melissa Olsen-Rasmussen, Michael Frace, Scott Sammons, Georges Anicet Dahourou, Jacques Boncy, Anthony M. Smith, Philip Mabon, Aaron Petkau, Morag Graham, Matthew W. Gilmour, Peter Gerner-SmidtComments to Author , and the V. cholerae Outbreak Genomics Task Force
Author affiliations: Author affiliations: Public Health Agency of Canada, Winnipeg, Manitoba, Canada (A.R. Reimer, G. Van Domselaar, M. Walker, H. Kent, P. Mabon, A. Petkau, M. Graham, M.W. Gilmour); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (S. Stroika, C. Tarr, D. Talkington, L. Rowe, M. Olsen-Rasmussen, M. Frace, S. Sammons, P. Gerner-Smidt); Centers for Disease Control and Prevention, Port-au-Prince, Haiti (G.A. Dahourou); Ministry of Public Health and Population, Port-au-Prince (J. Boncy); National Institute for Communicable Diseases, Johannesburg, South Africa (A.M. Smith)

Main Article

Table A1

Conserved open reading frames and hqSNPs used to refine evolutionary relationship between highly related outbreak Vibrio cholerae isolates and isolates 2009V-1085 (India), 2009V-1096 (India), and 2010EL-1749 (Cameroon)*

Locus ID† Product hqSNP, 5′→3′‡ Chromosome Chromosome location§ Reference allele¶ Major allele# Minor allele** Minor allele strains††
70 Transposase Tn3 family protein CAAAAACAAG[G/T]TCACTCATCA 1 93944 T T G 2011V-1021
307 K10937 accessory colonization factor AcfB CTTGTTTCTA[A/G]TCGACCATGA 1 379769 A A G 2010EL-2010N
307 K10937 accessory colonization factor AcfB TGTTTCTATT[C/G]GACCATGATA 1 379771 C C G 2010EL-2010N
612 Anthranilate synthase component II CGGGCTGCAT[A/G]CCAGAGCTGC 1 724118 G G A 2009V-1096
644 Conserved hypothetical protein TTATGCCAAT[C/T]CCTTATTCCT 1 763380 C C T 2010EL-1749
769 Conserved hypothetical protein TTGAGCTACT[C/T]GCGAGTGAAA 1 916351 C C T 2010EL-1749
771 GGDEF family protein CTCCGGAACT[C/T]ACCTTATTAC 1 919120 C C T 2009V-1096
1199 K00426 cytochrome bd-I oxidase subunit II GCGTTATCTT[C/T]ACCGCAGGTT 1 1453325 T T C 2009V-1085, 2009V-1096, 2010EL-1749
1221 K00656 formate C-acetyltransferase TTCATGGGTT[C/T]TGGCAACACA 1 1479808 C C T 2010EL-1749
1302 K08305 membrane-bound lytic murein transglycosylase B TTGTGGGGGG[G/T]TGAAAGTAAT 1 1581661 T T G 2010EL-1749
1580 Outer membrane protein OmpH GAAGTCGTTT[G/T]GCAAAAGATG 1 1876106 G G T 2009V-1085, 2009V-1096, 2010EL-1749
1641 Exodeoxyribonuclease V, 67-kDa subunit CTCAAATTGT[A/G]TTGCGATAAC 1 1936753 G G A 2009V-1085, 2009V-1096, 2010EL-1749
1923 Ribosomal protein S12 methylthiotransferase GGCTGCCTCG[A/G]CGCGTGAAGA 1 2259456 G G A 2009V-1096
2052 Alkaline serine exoprotease A precursor TTTTAAGCTT[A/G]CATTGTTTCG 1 2405353 A A G 2009V-1085, 2009V-1096, 2010EL-1749
2142 Shikimate-5-dehydrogenase TATTCATACG[A/C]TGTTTGCACG 1 2502464 C C A 2010EL-2010N
2247 K01414 oligopeptidase A AGAGCGCGGA[G/T]TGCCAAGCTT 1 2617657 T T G 2010EL-1749
2292 O-antigen ligase TGTAAGAAAA[A/T]TAAAATTTAA 1 2667285 T A T 2010EL-1798
2453 Conserved hypothetical protein ATCATGCAAC[A/G]AGCCAACTAT 1 2846497 A G A 2009V-1085
2475 Conserved hypothetical protein TTGGAAAAGG[G/T]GATTTCCGAT 1 2874265 T T G 2010EL-1961
2539 Erythrose 4-phosphate dehydrogenase TCGACAACAC[C/T]CATCTATGGC 1 2931479 T T C 2010EL-1749
143 Pyruvate:ferredoxin (flavodoxin) oxidoreductase TATTGGATCG[C/T]ACCAAAGAGC 2 168453 C C T 2011V-1021
167 GGDEF family protein AATTCCACCA[G/T]GCTTGAACTC 2 199181 G T G 2009V-1085
701 Transcriptional regulator CdgA TTAGAACGCC[A/C]CCGCCGCAGC 2 856230 C A C 2010EL-1786
740 K11891 type VI secretion system protein ImpL GCAGAGGCCG[A/G]CCAACCCATT 2 908788 G G A 2009V-1085
763 TagA-related protein TGGAGTCCGG[G/T]GGGGTGGGAT 2 938668 G G T 2010EL-1798

*hqSNP, high-quality single-nucleotide polymorphisms; ID, identification. SNPs in boldface are unique to this clade, i.e., they are not represented in the all strain core genome hqSNO set (Technical Appendix 1).
†From reference strain 2010EL-1786.
‡hqSNP and flanking sequences are reported in the coding direction for each locus.
§Chromosomal coordinate for the hqSNP is taken from the direct strand of reference strain 2010EL-1786.
¶Refers to allele harbored by reference strain 2010EL-1786.
#Refers to most abundant allele in strains being compared.
**Refers to least abundant allele in the strains being compared.
††Refers to strains harboring least abundant allele being compared.

Main Article

1Members of the V. cholerae Outbreak Genomics Task Force are Arunmozhi Balajee, Shanna Bolcen, Cheryl A. Bopp, John Besser, Ifeoma Ezeoke, Patricia Fields, Molly Freeman, Lori Gladney, Dhwani Govil, Michael S. Humphrys, Maria Sjölund-Karlsson, Karen H. Keddy, Elizabeth Neuhaus, Michele M. Parsons, Efrain Ribot, Maryann Turnsek, Shaun Tyler, Jean M. Whichard, Anne Whitney, and the authors.

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