Limits...
A recalibrated molecular clock and independent origins for the cholera pandemic clones.

Feng L, Reeves PR, Lan R, Ren Y, Gao C, Zhou Z, Ren Y, Cheng J, Wang W, Wang J, Qian W, Li D, Wang L - PLoS ONE (2008)

Bottom Line: We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7(th) pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed.We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes.The approaches used open up new avenues for analysing the origin and history of other important pathogens.

View Article: PubMed Central - PubMed

Affiliation: TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China.

ABSTRACT
Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6(th) (1899-1923) and 7(th) (1961-present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7(th) pandemic clone, while the 6(th) pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6(th) pandemic isolate, and compared them with the published 7(th) pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7(th) pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed. We then used this to estimate the divergence date of the 6(th) and 7(th) pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000-50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.

Show MeSH

Related in: MedlinePlus

A.Comparison of the CTX phage regions in the 3 genomes M66-2, N16961 and O395. The 6 indels (B8–B13) in this region are also shown and discussed in Supporting Discussion Text S1. The CTX phage on the small chromosome in O395 is also shown for comparison. The genes are named for M66-2, and the genes of the CTX phage missing in M66-2 are named in N16961. The colour codes are; orange, rtx toxin region; black, the 17 bp attRS sites; red, core region of the CTX phage; dark green, the RS1 (rstC, rstB, rstA, rstR) region of the CTX phage of N16961; light green, the RS2 (rstB, rstA, rstR) region of the CTX phage of N16961; purple, the divergent rstR gene of RS2 of O365; light blue, genes not related to CTX; dark blue, the 5-gene toxin-linked cryptic (TLC) element–2–3 copies in each strain. The first and second copies of TLC differ between N16961 and O395 by 2 and 3 SNPs respectively. Only cri and tlcR are named and the others given locus tags as in N16961; yellow, IS3. B. Plot of base changes in the CTX phage genomes of O395 and N16961. The base changes in the homologous region of the CTX phage genome between O395 and N16961 were plotted using the same approach as in Figure 4. Except that red and green are specifically for presence and absence respectively in N16961 relative to O395. The differences in rstR are too numerous to be shown. The residual fragment of the rtxA gene upstream of the CTX phage in O395 differs by 1 base from the homologue in N16961.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2605724&req=5

pone-0004053-g006: A.Comparison of the CTX phage regions in the 3 genomes M66-2, N16961 and O395. The 6 indels (B8–B13) in this region are also shown and discussed in Supporting Discussion Text S1. The CTX phage on the small chromosome in O395 is also shown for comparison. The genes are named for M66-2, and the genes of the CTX phage missing in M66-2 are named in N16961. The colour codes are; orange, rtx toxin region; black, the 17 bp attRS sites; red, core region of the CTX phage; dark green, the RS1 (rstC, rstB, rstA, rstR) region of the CTX phage of N16961; light green, the RS2 (rstB, rstA, rstR) region of the CTX phage of N16961; purple, the divergent rstR gene of RS2 of O365; light blue, genes not related to CTX; dark blue, the 5-gene toxin-linked cryptic (TLC) element–2–3 copies in each strain. The first and second copies of TLC differ between N16961 and O395 by 2 and 3 SNPs respectively. Only cri and tlcR are named and the others given locus tags as in N16961; yellow, IS3. B. Plot of base changes in the CTX phage genomes of O395 and N16961. The base changes in the homologous region of the CTX phage genome between O395 and N16961 were plotted using the same approach as in Figure 4. Except that red and green are specifically for presence and absence respectively in N16961 relative to O395. The differences in rstR are too numerous to be shown. The residual fragment of the rtxA gene upstream of the CTX phage in O395 differs by 1 base from the homologue in N16961.

Mentions: There are 29 insertions and deletions involving at least one gene, which we refer to as large indels to distinguish them from mutations involving one or few base pairs. They are named B1 to B20, and S1 to S9 respectively in the large and small chromosomes (Table S5), and marked in Figure S1 or Figure 6. Three (B9, B16 and B20) can be identified as deletions and 2 (S2 and B17) as insertions in M66-2, as we have O395 as outgroup, and likewise for the 3 presumed insertions (B2, B3 and B5) in N16961. In addition B8 and S3 are thought to be a deletion and insertion respectively in O395 for reasons given in the Supporting Discussion Text S1. The remaining 19 indels are attributed to events during the O/NM divergence, with 15 present and 4 absent in O395.


A recalibrated molecular clock and independent origins for the cholera pandemic clones.

Feng L, Reeves PR, Lan R, Ren Y, Gao C, Zhou Z, Ren Y, Cheng J, Wang W, Wang J, Qian W, Li D, Wang L - PLoS ONE (2008)

A.Comparison of the CTX phage regions in the 3 genomes M66-2, N16961 and O395. The 6 indels (B8–B13) in this region are also shown and discussed in Supporting Discussion Text S1. The CTX phage on the small chromosome in O395 is also shown for comparison. The genes are named for M66-2, and the genes of the CTX phage missing in M66-2 are named in N16961. The colour codes are; orange, rtx toxin region; black, the 17 bp attRS sites; red, core region of the CTX phage; dark green, the RS1 (rstC, rstB, rstA, rstR) region of the CTX phage of N16961; light green, the RS2 (rstB, rstA, rstR) region of the CTX phage of N16961; purple, the divergent rstR gene of RS2 of O365; light blue, genes not related to CTX; dark blue, the 5-gene toxin-linked cryptic (TLC) element–2–3 copies in each strain. The first and second copies of TLC differ between N16961 and O395 by 2 and 3 SNPs respectively. Only cri and tlcR are named and the others given locus tags as in N16961; yellow, IS3. B. Plot of base changes in the CTX phage genomes of O395 and N16961. The base changes in the homologous region of the CTX phage genome between O395 and N16961 were plotted using the same approach as in Figure 4. Except that red and green are specifically for presence and absence respectively in N16961 relative to O395. The differences in rstR are too numerous to be shown. The residual fragment of the rtxA gene upstream of the CTX phage in O395 differs by 1 base from the homologue in N16961.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2605724&req=5

pone-0004053-g006: A.Comparison of the CTX phage regions in the 3 genomes M66-2, N16961 and O395. The 6 indels (B8–B13) in this region are also shown and discussed in Supporting Discussion Text S1. The CTX phage on the small chromosome in O395 is also shown for comparison. The genes are named for M66-2, and the genes of the CTX phage missing in M66-2 are named in N16961. The colour codes are; orange, rtx toxin region; black, the 17 bp attRS sites; red, core region of the CTX phage; dark green, the RS1 (rstC, rstB, rstA, rstR) region of the CTX phage of N16961; light green, the RS2 (rstB, rstA, rstR) region of the CTX phage of N16961; purple, the divergent rstR gene of RS2 of O365; light blue, genes not related to CTX; dark blue, the 5-gene toxin-linked cryptic (TLC) element–2–3 copies in each strain. The first and second copies of TLC differ between N16961 and O395 by 2 and 3 SNPs respectively. Only cri and tlcR are named and the others given locus tags as in N16961; yellow, IS3. B. Plot of base changes in the CTX phage genomes of O395 and N16961. The base changes in the homologous region of the CTX phage genome between O395 and N16961 were plotted using the same approach as in Figure 4. Except that red and green are specifically for presence and absence respectively in N16961 relative to O395. The differences in rstR are too numerous to be shown. The residual fragment of the rtxA gene upstream of the CTX phage in O395 differs by 1 base from the homologue in N16961.
Mentions: There are 29 insertions and deletions involving at least one gene, which we refer to as large indels to distinguish them from mutations involving one or few base pairs. They are named B1 to B20, and S1 to S9 respectively in the large and small chromosomes (Table S5), and marked in Figure S1 or Figure 6. Three (B9, B16 and B20) can be identified as deletions and 2 (S2 and B17) as insertions in M66-2, as we have O395 as outgroup, and likewise for the 3 presumed insertions (B2, B3 and B5) in N16961. In addition B8 and S3 are thought to be a deletion and insertion respectively in O395 for reasons given in the Supporting Discussion Text S1. The remaining 19 indels are attributed to events during the O/NM divergence, with 15 present and 4 absent in O395.

Bottom Line: We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7(th) pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed.We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes.The approaches used open up new avenues for analysing the origin and history of other important pathogens.

View Article: PubMed Central - PubMed

Affiliation: TEDA School of Biological Sciences and Biotechnology Nankai University, Tianjin, China.

ABSTRACT
Cholera, caused by Vibrio cholerae, erupted globally from South Asia in 7 pandemics, but there were also local outbreaks between the 6(th) (1899-1923) and 7(th) (1961-present) pandemics. All the above are serotype O1, whereas environmental or invertebrate isolates are antigenically diverse. The pre 7th pandemic isolates mentioned above, and other minor pathogenic clones, are related to the 7(th) pandemic clone, while the 6(th) pandemic clone is in the same lineage but more distantly related, and non-pathogenic isolates show no clonal structure. To understand the origins and relationships of the pandemic clones, we sequenced the genomes of a 1937 prepandemic strain and a 6(th) pandemic isolate, and compared them with the published 7(th) pandemic genome. We distinguished mutational and recombinational events, and allocated these and other events, to specific branches in the evolutionary tree. There were more mutational than recombinational events, but more genes, and 44 times more base pairs, changed by recombination. We used the mutational single-nucleotide polymorphisms and known isolation dates of the prepandemic and 7(th) pandemic isolates to estimate the mutation rate, and found it to be 100 fold higher than usually assumed. We then used this to estimate the divergence date of the 6(th) and 7(th) pandemic clones to be about 1880. While there is a large margin of error, this is far more realistic than the 10,000-50,000 years ago estimated using the usual assumptions. We conclude that the 2 pandemic clones gained pandemic potential independently, and overall there were 29 insertions or deletions of one or more genes. There were also substantial changes in the major integron, attributed to gain of individual cassettes including copying from within, or loss of blocks of cassettes. The approaches used open up new avenues for analysing the origin and history of other important pathogens.

Show MeSH
Related in: MedlinePlus