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Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid.

Holt KE, Phan MD, Baker S, Duy PT, Nga TV, Nair S, Turner AK, Walsh C, Fanning S, Farrell-Ward S, Dutta S, Kariuki S, Weill FX, Parkhill J, Dougan G, Wain J - PLoS Negl Trop Dis (2011)

Bottom Line: To investigate whether PST6 conferred a selective advantage compared to other IncHI1 plasmids, we used a phenotyping array to compare the impact of IncHI1 PST6 and PST1 plasmids in a common S.Typhi host.The PST6 plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom. kholt@unimelb.edu.au

ABSTRACT
Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains a serious global health concern. Since their emergence in the mid-1970s multi-drug resistant (MDR) S. Typhi now dominate drug sensitive equivalents in many regions. MDR in S. Typhi is almost exclusively conferred by self-transmissible IncHI1 plasmids carrying a suite of antimicrobial resistance genes. We identified over 300 single nucleotide polymorphisms (SNPs) within conserved regions of the IncHI1 plasmid, and genotyped both plasmid and chromosomal SNPs in over 450 S. Typhi dating back to 1958. Prior to 1995, a variety of IncHI1 plasmid types were detected in distinct S. Typhi haplotypes. Highly similar plasmids were detected in co-circulating S. Typhi haplotypes, indicative of plasmid transfer. In contrast, from 1995 onwards, 98% of MDR S. Typhi were plasmid sequence type 6 (PST6) and S. Typhi haplotype H58, indicating recent global spread of a dominant MDR clone. To investigate whether PST6 conferred a selective advantage compared to other IncHI1 plasmids, we used a phenotyping array to compare the impact of IncHI1 PST6 and PST1 plasmids in a common S. Typhi host. The PST6 plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU.

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Phylogenetic tree for IncHI1 plasmid sequences.Phylogenetic tree based on 347 SNPs identified among 8 publicly available IncHI1 plasmid sequences (Table 2), constructed using BEAST (with 20 million iterations, 4 replicate runs, exponential clock model). Terminal nodes are labelled with the organism of origin (STy  =  Salmonella enterica serovar Typhi, SCh  =  Salmonella enterica serovar Choleraesuis, STm  =  Salmonella enterica serovar Typhimurium, SPa  =  Salmonella enterica serovar Paratyphi A, Ec  =  E. coli O111:H-) and date of isolation. Isolation dates were input into the BEAST model in order to estimate divergence dates for internal nodes (open circles, labelled with divergence date estimates; brackets indicate 95% highest posterior density interval). Insertion sites (grey) are based on sequence data and verified (except for pO111_1 and pMAK1) by PCR. Precise insertion sites and PCR primers for verification are given in Tables 3 & 4. Four major plasmid groups, PST1, PST5, PST6, PST7, are coloured as labelled.
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pntd-0001245-g001: Phylogenetic tree for IncHI1 plasmid sequences.Phylogenetic tree based on 347 SNPs identified among 8 publicly available IncHI1 plasmid sequences (Table 2), constructed using BEAST (with 20 million iterations, 4 replicate runs, exponential clock model). Terminal nodes are labelled with the organism of origin (STy  =  Salmonella enterica serovar Typhi, SCh  =  Salmonella enterica serovar Choleraesuis, STm  =  Salmonella enterica serovar Typhimurium, SPa  =  Salmonella enterica serovar Paratyphi A, Ec  =  E. coli O111:H-) and date of isolation. Isolation dates were input into the BEAST model in order to estimate divergence dates for internal nodes (open circles, labelled with divergence date estimates; brackets indicate 95% highest posterior density interval). Insertion sites (grey) are based on sequence data and verified (except for pO111_1 and pMAK1) by PCR. Precise insertion sites and PCR primers for verification are given in Tables 3 & 4. Four major plasmid groups, PST1, PST5, PST6, PST7, are coloured as labelled.

Mentions: Plasmid sequences were downloaded from the European Nucleotide Archive (plasmid details and accessions in Table 2). SNPs between finished plasmid sequences were identified using the nucmer and show-snps algorithms within the MUMmer 3.1 package [43], via pairwise comparisons with pAKU_1. To identify SNPs in S. Typhi PST6 IncHI1 plasmids, 36 bp single-ended Illumina/Solexa sequencing reads from S. Typhi isolates E03-9804, ISP-03-07467 and ISP-04-06979 were aligned to the pAKU_1 sequence using Maq [44] and quality filters as described previously [45]. SNPs called in repetitive regions or inserted sequences were excluded from phylogenetic analysis, so that phylogenetic trees were based only on the conserved IncHI1 core regions. This resulted in a total of 347 SNPs, which were analyzed using BEAST [46] to simultaneously infer a phylogenetic tree and divergence dates (using the year of isolation of each plasmid as listed in Table 1, resulting tree in Figure 1). Parameters used were as follows: generalised time reversible model with a Gamma model of site heterogeneity (4 gamma categories); a relaxed molecular clock with uncorrelated exponential rates [46], a coalescent tree prior estimated using a Bayesian skyline model with 10 groups [47], default priors and 20 million iterations.


Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid.

Holt KE, Phan MD, Baker S, Duy PT, Nga TV, Nair S, Turner AK, Walsh C, Fanning S, Farrell-Ward S, Dutta S, Kariuki S, Weill FX, Parkhill J, Dougan G, Wain J - PLoS Negl Trop Dis (2011)

Phylogenetic tree for IncHI1 plasmid sequences.Phylogenetic tree based on 347 SNPs identified among 8 publicly available IncHI1 plasmid sequences (Table 2), constructed using BEAST (with 20 million iterations, 4 replicate runs, exponential clock model). Terminal nodes are labelled with the organism of origin (STy  =  Salmonella enterica serovar Typhi, SCh  =  Salmonella enterica serovar Choleraesuis, STm  =  Salmonella enterica serovar Typhimurium, SPa  =  Salmonella enterica serovar Paratyphi A, Ec  =  E. coli O111:H-) and date of isolation. Isolation dates were input into the BEAST model in order to estimate divergence dates for internal nodes (open circles, labelled with divergence date estimates; brackets indicate 95% highest posterior density interval). Insertion sites (grey) are based on sequence data and verified (except for pO111_1 and pMAK1) by PCR. Precise insertion sites and PCR primers for verification are given in Tables 3 & 4. Four major plasmid groups, PST1, PST5, PST6, PST7, are coloured as labelled.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3139670&req=5

pntd-0001245-g001: Phylogenetic tree for IncHI1 plasmid sequences.Phylogenetic tree based on 347 SNPs identified among 8 publicly available IncHI1 plasmid sequences (Table 2), constructed using BEAST (with 20 million iterations, 4 replicate runs, exponential clock model). Terminal nodes are labelled with the organism of origin (STy  =  Salmonella enterica serovar Typhi, SCh  =  Salmonella enterica serovar Choleraesuis, STm  =  Salmonella enterica serovar Typhimurium, SPa  =  Salmonella enterica serovar Paratyphi A, Ec  =  E. coli O111:H-) and date of isolation. Isolation dates were input into the BEAST model in order to estimate divergence dates for internal nodes (open circles, labelled with divergence date estimates; brackets indicate 95% highest posterior density interval). Insertion sites (grey) are based on sequence data and verified (except for pO111_1 and pMAK1) by PCR. Precise insertion sites and PCR primers for verification are given in Tables 3 & 4. Four major plasmid groups, PST1, PST5, PST6, PST7, are coloured as labelled.
Mentions: Plasmid sequences were downloaded from the European Nucleotide Archive (plasmid details and accessions in Table 2). SNPs between finished plasmid sequences were identified using the nucmer and show-snps algorithms within the MUMmer 3.1 package [43], via pairwise comparisons with pAKU_1. To identify SNPs in S. Typhi PST6 IncHI1 plasmids, 36 bp single-ended Illumina/Solexa sequencing reads from S. Typhi isolates E03-9804, ISP-03-07467 and ISP-04-06979 were aligned to the pAKU_1 sequence using Maq [44] and quality filters as described previously [45]. SNPs called in repetitive regions or inserted sequences were excluded from phylogenetic analysis, so that phylogenetic trees were based only on the conserved IncHI1 core regions. This resulted in a total of 347 SNPs, which were analyzed using BEAST [46] to simultaneously infer a phylogenetic tree and divergence dates (using the year of isolation of each plasmid as listed in Table 1, resulting tree in Figure 1). Parameters used were as follows: generalised time reversible model with a Gamma model of site heterogeneity (4 gamma categories); a relaxed molecular clock with uncorrelated exponential rates [46], a coalescent tree prior estimated using a Bayesian skyline model with 10 groups [47], default priors and 20 million iterations.

Bottom Line: To investigate whether PST6 conferred a selective advantage compared to other IncHI1 plasmids, we used a phenotyping array to compare the impact of IncHI1 PST6 and PST1 plasmids in a common S.Typhi host.The PST6 plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom. kholt@unimelb.edu.au

ABSTRACT
Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), remains a serious global health concern. Since their emergence in the mid-1970s multi-drug resistant (MDR) S. Typhi now dominate drug sensitive equivalents in many regions. MDR in S. Typhi is almost exclusively conferred by self-transmissible IncHI1 plasmids carrying a suite of antimicrobial resistance genes. We identified over 300 single nucleotide polymorphisms (SNPs) within conserved regions of the IncHI1 plasmid, and genotyped both plasmid and chromosomal SNPs in over 450 S. Typhi dating back to 1958. Prior to 1995, a variety of IncHI1 plasmid types were detected in distinct S. Typhi haplotypes. Highly similar plasmids were detected in co-circulating S. Typhi haplotypes, indicative of plasmid transfer. In contrast, from 1995 onwards, 98% of MDR S. Typhi were plasmid sequence type 6 (PST6) and S. Typhi haplotype H58, indicating recent global spread of a dominant MDR clone. To investigate whether PST6 conferred a selective advantage compared to other IncHI1 plasmids, we used a phenotyping array to compare the impact of IncHI1 PST6 and PST1 plasmids in a common S. Typhi host. The PST6 plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU.

Show MeSH
Related in: MedlinePlus