Article Figures & Data
- FIG 1
Minimum spanning tree (MST) constructed from 45 hqSNPs. Intermediate hypothetical ancestors were inferred for some lineages and manually placed in the network. Nucleotide substitutions are indicated by dashes along the branches, and deletion events are indicated by arrows. ASP, antimicrobial susceptibility pattern. The ~10 kb deletion in the SXT is inferred twice in the model, and occurs between two transposase genes, VCH1786_I0078 and VCH1786_I0087. *, nonsynonymous transversion.
- FIG 2
BLAST atlas. Genes from each de novo assembly were compared against both chromosomes of the completed genome 2010EL-1786. Absence of color (white) indicates that a strain is missing genetic material that is present in the reference. Regions of interest are denoted by black rectangles on the circumference. Three genomes have a shorter Illumina read length (36 bp), which might have resulted in fewer gene predictions, which manifests as an artifact on the atlas in the superintegron region. The isolate names are listed from the outermost to the innermost tracks.
- FIG 3
Circos plot showing structural genome rearrangements. Each alternating white/gray band represents one of the nine strains sequenced on the PacBio RS platform, with an inner tenth track representing the published reference strain (7). Each band contains three tracks. The outermost, orange tiles represent contigs from de novo assemblies aligned back to the 2010EL-1786 reference. Inversions within contigs are highlighted in blue. Black line plots show local alignment quality over 1kb windows, in terms of Phred QV, for long read assembled contigs compared to the 2010EL-1786. Note the smallest dips in QV correspond to single SNPs. Green line plots show local coverage of Illumina short reads mapped to the reference over 500bp windows. The innermost band contains a purple track showing contigs from a separate long read de novo assembly of 2010EL-1786. The black QV track highlights differences between the long read and short assembly, indicating potential areas of misassembly in the original reference.
- TABLE 1
Haiti isolates are defective for transformation with C6706 gDNA with kan at lacZ
gDNA Recipient strain TFa Rangeb Fold reductionc C6706lacZ(kan) C6706 <1.3E-5 1.9E-5–7.8E-6 1 C6706lacZ(kan) 2010EL-1786 <3.8E-9 – >3,428 C6706lacZ(kan) 2010EL-1799 <2.5E-9 – >5,200 C6706lacZ(kan) 2010EL-2026 <1.9E-9 – >6,948 C6706lacZ(kan) 2011EL-1818 <1.6E-9 – >8,196 C6706lacZ(kan) 2011EL-1841 <1.5E-9 – >8,392 C6706lacZ(kan) 2011EL-2319 <5.4E-9 – >2,399 C6706lacZ(kan) 2011EL-2320 <1.3E-9 – >9,588 C6706lacZ(kan) 2011EL-2321 <1.4E-9 – >9,508 C6706lacZ(kan) 2011EL-2322 <3.6E-9 <DL–8.6E-9 >3,621 C6706lacZ(kan) 2011EL-2323 <1.8E-9 – >7,223 C6706lacZ(kan) 2012EL-1410 <7.3E-10 – >17,648 C6706lacZ(kan) 2011EL-1300 <9.5E-10 – >13,635 C6706lacZ(kan) C6706 ΔhapR <6.5E-9 – >2,001 - TABLE 2
Haiti isolates are defective for transformation with self-derived tn(kan) gDNAa
gDNA donor Test sample Control Fold reductionb Recipient strain TF Range Recipient strain TF Range 2010EL-1786 2010EL-1786 <5.1E-9 – C6706 5.3E-6 4.7E-6–5.7E-6 >1,046 2010EL-1799 2010EL-1799 <2.1E-9 – C6706 1.8E-5 1.1E-5–1.9E-5 >8,462 2010EL-2026 2010EL-2026 <1.7E-9 – C6706 6.0E-6 1.8E-6–1.0E-6 >3,484 2011EL-1818 2011EL-1818 <2.1E-9 <DL-2.5E-9 C6706 1.4E-5 8.8E-6–1.9E-5 >6,842 2011EL-1841 2011EL-1841 <8.1E-9 <DL-1.3E-8 C6706 1.9E-5 1.2E-5–2.5E-5 >2,314 2011EL-2319 2011EL-2319 <2.0E-9 – C6706 1.4E-5 5.6E-6–1.7E-5 >7,087 2011EL-2320 2011EL-2320 <1.9E-9 – C6706 1.7E-5 1.1E-5–1.8E-5 >8,826 2011EL-2321 2011EL-2321 <5.4E-9 <DL-9.9E-9 C6706 1.9E-5 9.3E-6–6.2E-5 >3,437 2011EL-2322 2011EL-2322 <5.7E-9 <DL-3.3E-9 C6706 1.0E-5 1.1E-6–2.3E-5 >1,789 2011EL-2323 2011EL-2323 <3.7E-9 <DL-1.9E-9 C6706 1.1E-5 4.7E-6–1.1E-5 >2,966 2012EL-1410 2012EL-1410 <4.2E-9 – C6706 4.8E-5 3.7E-6–5.6E-6 >1,161 2011EL-1300 2011EL-1300 <1.6E-9 – C6706 9.4E-6 5.7E-6–1.4E-5 >5,960 2011EL-1300 C6706 ΔhapRc <6.4E-9 – C6706 9.4E-6 5.7E-6–1.4E-5 >1,476
Supplemental Material
Figure S1
Map of Haiti showing the year of isolation and geographic locations from which the isolates subjected to whole-genome sequencing at the CDC were sampled. Isolates, including those from other studies, were sampled from the Haitian departments Artibonite (n = 22), Ouest (n = 28), Sud (n = 5), Sud-Est (n = 1), Nord Ouest (n = 2) and Centre (n = 16) and also included one from a travel-associated case from the Dominican Republic. The map was drawn using Google Maps and Nicolas Mollet’s Map Icons Collection. Download Figure S1, PDF file, 0.4 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S1
Source, serogroup, PFGE pattern combination, and antibiotic susceptibility pattern for Haiti isolates sequenced for this study. Table S1, DOCX file, 0.1 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S2
Previously published genome sequences used in the analysis and unpublished genomes from recent outbreaks. Table S2, DOCX file, 0.1 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S4
Maximum-likelihood phylogenies constructed from core hqSNPs. The robustness of the tree was ascertained with the Shimodaira-Hasegawa-like procedure (35), and the resulting P values were scaled 0 to 100. The circular phylogeny (A) consists of 108 genomes using 566 SNP positions and is rooted on the branch leading to the South American O1 isolate C6706 (branch lengths not shown). (B) Tree showing phylogenetic relationships among 60 Haiti and 3 Nepalese genomes constructed from 45 hqSNPs. Download Figure S4, PDF file, 0.1 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Table S3
Annotations and positions of the 45 high-quality SNPs (hqSNPs). Table S3, DOCX file, 0.1 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S5
Molecular clock. (A) Likelihood values for each demographic growth model as calculated by Bayes factors. ln(p) is given as ln(P(model|data)). SE, standard error. (B) The inferred phylogeny is overlaid with the date on which each isolate was collected. The credibility interval, derived from posterior probabilities, is shown in red near the root of the Haiti clade, with the median date indicated by a vertical line. Download Figure S5, PDF file, 0.1 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S6
Genetic organization of the O-antigen region. Gene content of the nonagglutinating isolate 2012V-1060 is shown in green in comparison to the reference strain 2010EL-1786 (in red). Individual gene annotations are shown across the top, and the biological functions of each gene cluster are indicated across the bottom. Download Figure S6, PDF file, 0.3 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S7
BLAST atlases. (a) Pangenome BLAST atlas for representative Haiti genomes and Nepal genomes (9). Chromosomes I and II of 2010EL-1786 are shown concatenated along with additional genes in the pangenome (shown in black on the inner ring). (b) Expanded view of the SXT region with representative deletion variants from the Haiti and Nepalese outbreaks. Red tracks represent Nepal genomes; blue represents Haiti genomes. Deletions in the genome are shown in white. Genetic organization of the region is shown across the bottom. Coordinates (kilobase pairs) are based on 2010EL-1786 chromosome I. Download Figure S7, PDF file, 0.8 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S2
Composite dendrogram based on the PFGE pattern combinations of Vibrio cholerae isolates after restriction with two enzymes (SfiI and NotI). The predominant pattern combination from the outbreak is KZGS12.0088/KZGN11.0092 with 30 PFGE pattern variants detected between October 2010 and June 2012. The straight vertical lines at the right indicate that isolates that are indistinguishable by PFGE. A single asterisk indicates isolates that were serotyped as O1 Inaba. Three closely related isolates from Nepal were included and are designated by double asterisks. Collection date, location, and PFGE pattern information were used to guide selection of strains for whole-genome sequencing. The isolates that were sequenced and the sequencing platform are indicated by blue squares (Illumina GAIIx) and yellow circles (PacBio RS platform). Download Figure S2, PDF file, 0.7 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Figure S3
Timeline of PFGE pattern variant detection. The month when each variant was detected is indicated across the bottom. The month of first detection for each of the three phenotypic variants investigated in this study is indicated with a yellow arrow. Download Figure S3, PDF file, 0.1 MB.
Copyright © 2013 Katz et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
Additional Files
Supplementary Data
Files in this Data Supplement:
- Figure sf01, PDF - Figure sf01, PDF
- Figure sf02, PDF - Figure sf02, PDF
- Figure sf03, PDF - Figure sf03, PDF
- Figure sf04, PDF - Figure sf04, PDF
- Figure sf05, PDF - Figure sf05, PDF
- Figure sf06, PDF - Figure sf06, PDF
- Figure sf07, PDF - Figure sf07, PDF
- Table st1, DOCX - Table st1, DOCX
- Table st2, DOCX - Table st2, DOCX
- Table st3, DOCX - Table st3, DOCX
