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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 trees of S. Typhi chromosome and IncHI1 plasmid.(A) Phylogenetic tree indicating chromosomal haplotypes of 454 S. Typhi isolates determined by SNP typing with the GoldenGate assay. Circles correspond to detected S. Typhi haplotypes; node sizes are scaled to the number of isolates detected with that haplotype and labelled with this number. Unfilled circle indicates tree root; reference isolates used to define the S. Typhi SNPs are labelled with the isolate name. S. Typhi haplotypes in which IncHI1 plasmids were detected (N = 201) are coloured; black circles indicate no IncHI1 plasmids were found among S. Typhi of that haplotype; other colours indicate the presence of specific IncHI1 plasmid haplotypes corresponding to the colours in (B). Note that most of the coloured nodes also contain S. Typhi isolates with no plasmid, and the colours do not represent the proportion of isolates harbouring the various plasmid types. (B) Phylogenetic tree of IncHI1 plasmids determined by SNP typing with the GoldenGate assay (coloured leaf nodes); grey leaf nodes indicate the position of non-S. Typhi plasmids, as determined from plasmid sequence data listed in Table 2.
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pntd-0001245-g003: Phylogenetic trees of S. Typhi chromosome and IncHI1 plasmid.(A) Phylogenetic tree indicating chromosomal haplotypes of 454 S. Typhi isolates determined by SNP typing with the GoldenGate assay. Circles correspond to detected S. Typhi haplotypes; node sizes are scaled to the number of isolates detected with that haplotype and labelled with this number. Unfilled circle indicates tree root; reference isolates used to define the S. Typhi SNPs are labelled with the isolate name. S. Typhi haplotypes in which IncHI1 plasmids were detected (N = 201) are coloured; black circles indicate no IncHI1 plasmids were found among S. Typhi of that haplotype; other colours indicate the presence of specific IncHI1 plasmid haplotypes corresponding to the colours in (B). Note that most of the coloured nodes also contain S. Typhi isolates with no plasmid, and the colours do not represent the proportion of isolates harbouring the various plasmid types. (B) Phylogenetic tree of IncHI1 plasmids determined by SNP typing with the GoldenGate assay (coloured leaf nodes); grey leaf nodes indicate the position of non-S. Typhi plasmids, as determined from plasmid sequence data listed in Table 2.

Mentions: The chromosomal haplotype of S. Typhi isolates was determined based on the SNPs present at 1,485 chromosomal loci identified previously from genome-wide surveys [41], [45] and listed in [22], [39]. IncHI1 plasmid haplotypes were determined using 231 SNPs located in the conserved IncHI1 backbone sequence, listed in Table S2 (note these do not include SNPs specific to pMAK1 or pO111_1 which were not available at the time of assay design, nor any SNPs falling within 10 bp of each other as these cannot be accurately targeted via GoldenGate assay; however additional SNPs identified via plasmid MLST [37] were included, see Table S2). Resistance gene sequences were interrogated using additional oligonucleotide probes, listed in [16]. All loci were interrogated using a GoldenGate (Illumina) custom assay according to the manufacturer's standard protocols, as described previously [16], [22], [39]. SNP calls were generated from raw fluorescence signal data by clustering with a modified version of Illuminus [48] as described previously [22]. The percentage of IncHI1 SNP loci yielding positive signals in the GoldenGate assay clearly divided isolates into two groups, indicating presence of an IncHI plasmid (signals for >90% of IncHI1 loci) or absence of such a plasmid (signals for <10% of IncHI1 loci), see Figure 2. SNP alleles were concatenated to generate two multiple alignments, one for chromosomal SNPs and one for IncHI1 plasmid SNPs. Maximum likelihood phylogenetic trees (Figure 3) were fit to each alignment using RAxML [49] with a GTR+Γ model and 1,000 bootstraps.


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 trees of S. Typhi chromosome and IncHI1 plasmid.(A) Phylogenetic tree indicating chromosomal haplotypes of 454 S. Typhi isolates determined by SNP typing with the GoldenGate assay. Circles correspond to detected S. Typhi haplotypes; node sizes are scaled to the number of isolates detected with that haplotype and labelled with this number. Unfilled circle indicates tree root; reference isolates used to define the S. Typhi SNPs are labelled with the isolate name. S. Typhi haplotypes in which IncHI1 plasmids were detected (N = 201) are coloured; black circles indicate no IncHI1 plasmids were found among S. Typhi of that haplotype; other colours indicate the presence of specific IncHI1 plasmid haplotypes corresponding to the colours in (B). Note that most of the coloured nodes also contain S. Typhi isolates with no plasmid, and the colours do not represent the proportion of isolates harbouring the various plasmid types. (B) Phylogenetic tree of IncHI1 plasmids determined by SNP typing with the GoldenGate assay (coloured leaf nodes); grey leaf nodes indicate the position of non-S. Typhi plasmids, as determined from plasmid sequence data listed in Table 2.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3139670&req=5

pntd-0001245-g003: Phylogenetic trees of S. Typhi chromosome and IncHI1 plasmid.(A) Phylogenetic tree indicating chromosomal haplotypes of 454 S. Typhi isolates determined by SNP typing with the GoldenGate assay. Circles correspond to detected S. Typhi haplotypes; node sizes are scaled to the number of isolates detected with that haplotype and labelled with this number. Unfilled circle indicates tree root; reference isolates used to define the S. Typhi SNPs are labelled with the isolate name. S. Typhi haplotypes in which IncHI1 plasmids were detected (N = 201) are coloured; black circles indicate no IncHI1 plasmids were found among S. Typhi of that haplotype; other colours indicate the presence of specific IncHI1 plasmid haplotypes corresponding to the colours in (B). Note that most of the coloured nodes also contain S. Typhi isolates with no plasmid, and the colours do not represent the proportion of isolates harbouring the various plasmid types. (B) Phylogenetic tree of IncHI1 plasmids determined by SNP typing with the GoldenGate assay (coloured leaf nodes); grey leaf nodes indicate the position of non-S. Typhi plasmids, as determined from plasmid sequence data listed in Table 2.
Mentions: The chromosomal haplotype of S. Typhi isolates was determined based on the SNPs present at 1,485 chromosomal loci identified previously from genome-wide surveys [41], [45] and listed in [22], [39]. IncHI1 plasmid haplotypes were determined using 231 SNPs located in the conserved IncHI1 backbone sequence, listed in Table S2 (note these do not include SNPs specific to pMAK1 or pO111_1 which were not available at the time of assay design, nor any SNPs falling within 10 bp of each other as these cannot be accurately targeted via GoldenGate assay; however additional SNPs identified via plasmid MLST [37] were included, see Table S2). Resistance gene sequences were interrogated using additional oligonucleotide probes, listed in [16]. All loci were interrogated using a GoldenGate (Illumina) custom assay according to the manufacturer's standard protocols, as described previously [16], [22], [39]. SNP calls were generated from raw fluorescence signal data by clustering with a modified version of Illuminus [48] as described previously [22]. The percentage of IncHI1 SNP loci yielding positive signals in the GoldenGate assay clearly divided isolates into two groups, indicating presence of an IncHI plasmid (signals for >90% of IncHI1 loci) or absence of such a plasmid (signals for <10% of IncHI1 loci), see Figure 2. SNP alleles were concatenated to generate two multiple alignments, one for chromosomal SNPs and one for IncHI1 plasmid SNPs. Maximum likelihood phylogenetic trees (Figure 3) were fit to each alignment using RAxML [49] with a GTR+Γ model and 1,000 bootstraps.

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