Chromosome Single Nucleotide Polymorphisms Research Articles

Single nucleotide polymorphisms associated with abnormal coronary microvascular function.

Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation. Although microvascular pathology is associated with cardiovascular events, genetic phenotypes causing microvascular disease remain largely unknown. This study identifies sex-specific SNPs associated with coronary microvascular dysfunction. Six hundred and forty-three patients without significant obstructive coronary heart disease were enrolled, referred for cardiac catheterization, and underwent invasive coronary microcirculatory assessment. Patient data were collected from 1529 autosomal SNPs and seven X chromosome SNPs, which were selected to represent the variability from 76 candidate genes with published associations with coronary vasoreactivity, angiogenesis, inflammation, vascular calcification, atherosclerosis risk factors, female hormones, blood coagulation, or coronary heart disease. Coronary flow reserve (CFR) was assessed by an intracoronary injection of adenosine. Patients were categorized according to a CFR above or below 2.5 and were stratified by sex.After adjusting for age, sex, and BMI, this study shows that SNPs within VEGFA and CDKN2B-AS1 are associated with abnormal CFR (P<0.005). SNPs within MYH15, VEGFA, and NT5E are associated with abnormal CFR in men. No SNPs were associated with abnormal CFR in women. Genetic variations within defined regions of VEGFA and CDKN2B-AS1 genes are associated with coronary microvascular dysfunction. Furthermore, sex-specific allelic variants within MYH15, VEGFA, and NT5E are associated with an increased risk of coronary microvascular dysfunction in men.

High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery.

BackgroundSingle nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 60-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains.ResultsA total of 1581 chromosomal SNPs precisely establish the phylogenetic relationships existing between the French strains. Phylogeography patterns within the three canSNP sub-lineages present in France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One of the more remarkable findings was the identification of a variety of genotypes within the A.Br.011/009 sub-group that are persisting in the different regions of France. The 560 SNPs defining the A.Br.011/009- affiliated French strains split the Trans-Eurasian sub-group into six distinct branches without any intermediate nodes. Distinct sub-branches, with some geographic clustering, were resolved. The 345 SNPs defining the major B.Br CNEVA sub-lineage clustered three main phylogeographic clades, the Alps, the Pyrenees, and the Massif Central, with a small Saône-et-Loire sub-cluster nested within the latter group. The French strains affiliated to the minor A.Br.001/002 group were characterized by 226 SNPs. All recent isolates collected from the Doubs department were closely related. Identification of SNPs from whole-genome sequences facilitates high-resolution strain tracking and provides the level of discrimination required for outbreak investigations. Eight diagnostic SNPs, representative of the main French-specific phylogeographic clusters, were therefore selected and developed into high-resolution melting SNP discriminative assays.ConclusionsThis work has established one of the most accurate phylogenetic reconstruction of B. anthracis population structure in a country. An extensive next-generation sequencing (NGS) dataset of 122 French strains have been created that allowed the identification of novel diagnostic SNPs useful to rapidly determine the geographic origin of any strain found in France.

Increased IVF pregnancy rates after microarray preimplantation genetic diagnosis due to parental translocations

We successfully performed preimplantation genetic diagnosis (PGD) and simultaneous preimplantation genetic screening (PGS) using single nucleotide polymorphism (SNP) microarrays for couples with balanced chromosome rearrangements in China. A total of 428 molecular karyotypes were diagnosed from 62 couples undergoing 68 in vitro fertilization (IVF) cycles. Of these, 48.1% of the embryos were chromosomally normal without translocation errors or aneuploidy. Of the 428 total embryos, 18.0% embryos were euploid, but were imbalanced due to the transmission of single translocation chromosome derivatives. A total of 6.5% of the embryos had chromosome abnormalities involving the parental chromosome aberration and other chromosomes aneuploidies. Significantly, 27.4% of the embryos were normal/balanced for the rearranged chromosomes, but were abnormal due to aneuploidy affecting other chromosomes. When evaluated on a per IVF cycle basis, 84% of the cycles had at least one chromosomally normal embryo available for uterine transfer. The clinical pregnancy rate per IVF cycle was 54%. Diagnosing genomically balanced embryos through 24 chromosome SNP microarray PGD/PGS, rather than minimally targeted fluorescence in situ hybridization (FISH), is a promising strategy to maximize the pregnancy potential of patients with known parental chromosomal translocations. Moreover, this is the first study to report the clinical application of SNP arrays to screen all 24 chromosome pairs of blastomeres and trophectoderm cells from patients carrying reciprocal translocations in China.

Retrieving Y chromosomal haplogroup trees using GWAS data

Phylogenetically informative Y chromosomal single-nucleotide polymorphisms (Y-SNPs) integrated in DNA chips have not been sufficiently explored in most genome-wide association studies (GWAS). Herein, we introduce a pipeline to retrieve Y-SNP data. We introduce the software YTool (http://mitotool.org/ytool/) to handle conversion, filtering, and annotation of the data. Genome-wide SNP data from populations in Myanmar are used to construct a haplogroup tree for 117 Y chromosomes based on 369 high-confidence Y-SNPs. Parallel genotyping and published resequencing data of Y chromosomes confirm the validity of our pipeline. We apply this strategy to the CEU HapMap data set and construct a haplogroup tree with 107 Y-SNPs from 39 individuals. The retrieved Y-SNPs can discern the parental genetic structure of populations. Given the massive quantity of data from GWAS, this method facilitates future investigations of Y chromosome diversity.

Analysis of Y chromosome haplogroups in Japanese population using short amplicons and its application in forensic analysis

We designed three mini multiplex PCR systems using single-base extension reactions to identify Japanese Y chromosome haplogroups. We selected a group of 22 Y chromosome single nucleotide polymorphisms (SNPs) from the haplogroups most commonly reported in East Asia. To make the systems more useful in analyzing degraded DNA samples, we designed primers to render amplicons of ≤ 150 bp. Applying these systems, we classified the Japanese population into major haplogroups and confirmed the applicability of these systems in forensic DNA analysis.

Male-Specific Region of the Y Chromosome and Cardiovascular Risk

Objective— Haplogroup I of male-specific region of the human Y chromosome is associated with 50% increased risk of coronary artery disease. It is not clear to what extent conventional cardiovascular risk factors and genes of the male-specific region may explain this association. Approach and Results— A total of 1988 biologically unrelated men from 4 white European populations were genotyped using 11 Y chromosome single nucleotide polymorphisms and classified into 13 most common European haplogroups. Approximately 75% to 93% of the haplotypic variation of the Y chromosome in all cohorts was attributable to I, R1a, and R1b1b2 lineages. None of traditional cardiovascular risk factors, including body mass index, blood pressures, lipids, glucose, C-reactive protein, creatinine, and insulin resistance, was associated with haplogroup I of the Y chromosome in the joint inverse variance meta-analysis. Fourteen of 15 ubiquitous single-copy genes of the male-specific region were expressed in human macrophages. When compared with men with other haplogroups, carriers of haplogroup I had ≈0.61- and 0.64-fold lower expression of ubiquitously transcribed tetratricopeptide repeat, Y-linked gene ( UTY ) and protein kinase, Y-linked, pseudogene ( PRKY ) in macrophages ( P =0.0001 and P =0.002, respectively). Conclusions— Coronary artery disease predisposing haplogroup I of the Y chromosome is associated with downregulation of UTY and PRKY genes in macrophages but not with conventional cardiovascular risk factors.

Genome‐wide androgenetic mosaicism

Individuals with mosaic paternal uniparental disomy (UPD) of apparently all chromosomes have recently been described. They show a 46,XX karyotype, but with a mixture of normal biparental cells and cells entirely of paternal isodisomic origin. We describe an infant who primarily showed signs of Beckwith-Wiedemann syndrome (BWS), but also had other severe and eventually lethal medical problems, notably refractory hypoglycemia. We performed methylation studies for BWS, but incidentally for Angelman syndrome (AS) on leukocytes and in a skin FFPE sample. We also performed chromosome microarray [CNV and single-nucleotide polymorphism (SNP) array] on leukocytes. We found that the patient had hypomethylation consistent with both BWS and AS. Remarkably, this was due to mosaic paternal UPD for chromosomes 11 and 15, respectively. The SNP microarray showed mosaic paternal UPD for all chromosomes. Patients with unusual phenotypes for a typical imprinting disorder should be studied further with assays for imprinted loci on other chromosomes. Chromosomal SNP microarrays are useful in identifying patients with multiple UPDs, sometimes of the whole genome.

Abstract 2562: Polymorphisms in microRNA (miRNA) pathways and survival in esophageal cancer (EC) patients.

Abstract Introduction: Polymorphisms within miRNA and in genes regulating miRNA biogenesis can regulate a variety of cancer pathways in EC patients. Comprehensive pathway analyses of miRNA-related genes were performed on EC outcomes. Methods: 324 EC patients from Princess Margaret Hospital (Toronto, Canada) were screened for 62 single nucleotide polymorphisms (SNPs) in 21 miRNA or miRNA biogenesis pathway genes. Multivariate Cox-proportional hazard models, adjusted for key prognostic factors evaluated the association of each SNP with overall survival (OS) and progression free survival (PFS). Significant SNPs were further analysed for joint effects, and also in subgroup and pathway analyses. All results were internally validated through bootstrapping. Results: Five polymorphisms belonging to the miRNA biogenesis pathway and one in a miRNA were nominally associated with OS or PFS, where adjusted hazard ratios (aHR) were between 1.23-1.41 for each comparison; p=0.003-0.04: AGO1 (rs595961; chromosome (chr) 1), GEMIN3 (rs197412; chr1) CD86 (rs17281995; chr 3) hs-miRNA-26a1 (rs7372209; chr 3), GEMIN4 (rs7813 and rs910924; chr 17). Joint effect analysis of SNPs in the same chromosome found additive effects of these risk alleles (RA) on outcome: chr 1 (2-4 vs 0-1: aHROS=1.82 [1.21-2.75], p=0.004), chr 3 (3-4 vs 0: aHROS=4.07 [1.91-8.67], p=0.003), chr 17 (4 vs 0: aHRPFS=2.21 [1.13-4.31], p=0.02). Pathway based analysis found each additional RA conferring a strong additive effect on OS (per 2 RA: aHR=1.50 [1.25-1.81], p=1.9x10E-5). Results on PFS were similar, with aHRPFS per 2RA of 1.51 [1.26-1.82], p=1.3x10E-5. Internal validation found consistent results for all analyses. Exploratory subgroup analysis identified two SNPs that had differential effects on OS based on histology: for adenocarcinomas, the aHR for KIAA0423 (rs1053667) was 0.51 [0.28-0.96], p=0.03, while for squamous cell carcinomas, the aHR was 7.36 [2.07-26.1], p=0.002. Similarly, for DICER (rs13078), aHRadenocarcinoma=0.96 [0.72-1.28], p=0.78 vs aHRsquamous=2.51[1.21-5.21], p=0.01). In subset analyses, hsa-mir-30a (rs1358379), hsa-mir-492 (rs2289030), hsa-mir-499 (rs3746444), and DGCR8 (rs1640299) were significantly associated with different outcomes by nodal status. Conclusion: We identified the miRNA biogenesis pathway as having an important role in the prognosis of EC patients, with a 50% increase in death or disease progression when carrying two additional miRNA risk alleles. Although some of the identified polymorphisms have been previously associated with risk or prognosis in other cancer disease sites, we report for the first time, their associations with esophageal cancer prognosis. Citation Format: Lawson Eng, Olusola O. Faluyi, Xin Qiu, Dangxiao Cheng, Daniel J. Renouf, Lorin Dodbiba, Sevtap Savas, Sharon Marsh, Jennifer J. Knox, Gail E. Darling, Rebecca KS Wong, Wei Xu, Geoffrey Liu, Abul K. Azad. Polymorphisms in microRNA (miRNA) pathways and survival in esophageal cancer (EC) patients. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2562. doi:10.1158/1538-7445.AM2013-2562 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

PVT1: A Cancer-associated Non-coding Gene Revisited

PVT1 was originally identified as a transcriptional unit from a human homologous sequence to Pvt1, which was cloned from murine plasmacytoma with t(6;15). Previous studies have revealed various genetic alterations in the PVT1 locus, including chromosome translocation, amplification, chromothripsis, and single nucleotide polymorphisms in human diseases, suggesting important roles of PVT1 in the pathogenesis. However, because this locus does not produce protein coding sequences, its functional properties have not been characterized and its biological significance remains unclear. Recent studies have shown that the PVT1 locus encodes lincRNAs and microRNAs. Therefore, current investigations are being performed focusing on the biological features of this long-standing puzzle gene as a non-coding gene.

The majority of women undergoing preimplantation genetic screeining (PGS) using 23 chromosome single nucleotide polymorphism (SNP) microarrays will have euploid embryos available for uterine transfer

The majority of women undergoing preimplantation genetic screeining (PGS) using 23 chromosome single nucleotide polymorphism (SNP) microarrays will have euploid embryos available for uterine transfer

Y-SNP miniplexes for East Asian Y-chromosomal haplogroup determination in degraded DNA

Four multiplex PCR systems followed by single base extension reactions were developed to score 22 single nucleotide polymorphisms (SNPs) and identify the most frequent East Asian Y chromosome haplogroups. Select Y chromosome SNPs allowed hierarchical testing for almost all of the major East Asian haplogroups along the revised Y chromosome tree. The first multiplex consists of six SNPs defining world-wide major haplogroups (M145, RPS4Y(711), M89, M9, M214, and M175). The second multiplex includes six SNPs of subhaplogroup O (M119, P31, M95, SRY(465), 47z, and M122). The third multiplex contains six SNPs that subdivide the subhaplogroup O3 (M324, P201, M159, M7, M134, and M133). The fourth multiplex comprises four SNPs of subhaplogroup C (M217, M48, M407, and P53.1). The sizes of the PCR amplicons ranged from 70 to 100bp to facilitate their application to degraded forensic and ancient samples. Validation experiments demonstrated that the multiplexes were optimized for analysis of low template DNA and highly degraded DNA. In a test using DNA samples from 300 Korean males, 16 different Y chromosome haplogroups were identified; haplogroup O2b* was the most frequently observed (29.3%), followed by haplogroups C3 (xC3c, C3d, C3e) (16.0%) and O3a3c1 (11.0%). These multiplex sets will be useful tools for Y-chromosomal haplogroup determination in anthropological and forensic studies of East Asian populations.

Y chromosome haplogroup diversity in a Mestizo population of Nicaragua

Y chromosome single nucleotide polymorphisms (Y-SNPs) are indispensable markers for haplogroup determination. Since Y chromosome haplogroups show a high specific geographical distribution, they play a major role in population genetics but can also benefit forensic investigations. Although haplogroup prediction methods based on Y chromosome short tandem repeats (Y-STRs) exist and are frequently used, precaution is required in this regard. In this study we determine the Y chromosome haplogroups of a Nicaraguan population using several Y-SNP multiplex reactions. Y chromosome haplogroups have been predicted before, but our results show that a confirmation with Y-SNP typings is necessary. These results have revealed a 4.8% of error in haplogroup prediction based on Y-STR haplotypes using Athey's Haplogroup Predictor. The Nicaraguan Mestizo population displays a majority of Eurasian lineages, mainly represented by haplogroup R-M207 (46.7%). Other Eurasian lineages have been observed, especially J-P209 (13.3%), followed by I-M170 (3.6%) and G-M201 (1.8%). Haplogroup E-P170 was also observed in 15.2% of the sample, particularly subhaplogroup E1b1b1-M35. Finally, the Native American haplogroup Q-M242 was found in 15.2% of the sample, with Q1a3a-M3 being the most frequent.

Genetic data from Y chromosome STR and SNP loci in Ukrainian population

We have tested a sample of 154 unrelated males from Lviv region (Ukraine) for 11 Y-chromosomal single nucleotide polymorphisms (SNPs) and 17 Y-chromosomal STR loci (DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1). Haplotype and haplogroup diversity values were calculated for the population under study. Genetic distances (R(ST)) to 9 other Slavic populations were calculated based on 12 Y-STR loci. Haplotype frequencies and MDS plots were constructed based on genetic distances. Haplogroup frequency patterns revealed in Ukraine are similar to those characteristic of other European populations. However, it also allowed for identification a specific genetic component in Ukrainian sample which seems to originate from areas dwelled by Western Slavs, i.e. subhaplogroup R1a1a7, at frequency of 13.65%. Analysis of R(ST) distances and AMOVA revealed high level of heterogeneity between Slavic populations inhabiting the south and north part of Europe, determined geographically rather than by linguistic factors. It has also been found a closer similarity (in the values of R(ST)) between Ukrainian and Slovak populations than between Ukrainians and other Slavic population samples.

A mega-analysis of genome-wide association studies for major depressive disorder

Prior genome-wide association studies (GWAS) of major depressive disorder (MDD) have met with limited success. We sought to increase statistical power to detect disease loci by conducting a GWAS mega-analysis for MDD. In the MDD discovery phase, we analyzed more than 1.2 million autosomal and X chromosome single-nucleotide polymorphisms (SNPs) in 18 759 independent and unrelated subjects of recent European ancestry (9240 MDD cases and 9519 controls). In the MDD replication phase, we evaluated 554 SNPs in independent samples (6783 MDD cases and 50 695 controls). We also conducted a cross-disorder meta-analysis using 819 autosomal SNPs with P<0.0001 for either MDD or the Psychiatric GWAS Consortium bipolar disorder (BIP) mega-analysis (9238 MDD cases/8039 controls and 6998 BIP cases/7775 controls). No SNPs achieved genome-wide significance in the MDD discovery phase, the MDD replication phase or in pre-planned secondary analyses (by sex, recurrent MDD, recurrent early-onset MDD, age of onset, pre-pubertal onset MDD or typical-like MDD from a latent class analyses of the MDD criteria). In the MDD-bipolar cross-disorder analysis, 15 SNPs exceeded genome-wide significance (P<5 × 10(-8)), and all were in a 248 kb interval of high LD on 3p21.1 (chr3:52 425 083-53 822 102, minimum P=5.9 × 10(-9) at rs2535629). Although this is the largest genome-wide analysis of MDD yet conducted, its high prevalence means that the sample is still underpowered to detect genetic effects typical for complex traits. Therefore, we were unable to identify robust and replicable findings. We discuss what this means for genetic research for MDD. The 3p21.1 MDD-BIP finding should be interpreted with caution as the most significant SNP did not replicate in MDD samples, and genotyping in independent samples will be needed to resolve its status.

Association of gender, ABCA1 gene polymorphisms and lipid profile in Greek young nurses

ObjectiveOne of the important proteins involved in lipid metabolism is the ATP-binding cassette transporter A1 (ABCA1) encoding by ABCA1 gene. In this study we evaluated the single nucleotide polymorphisms (SNPs) of ABCA1 gene. We analyzed SNPs in chromosome 9 such as rs2230806 (R219K) in the position 107620867, rs2230808 (R1587K) in the position 106602625 and rs4149313 (I883M) in the position 106626574 according to gender and lipid profile of Greek nurses.MethodsThe study population consisted of 447 (87 men) unrelated nurses who were genotyped for ABCA1 gene polymorphisms. Additionally, lipid profile [total cholesterol, triglycerides, high density lipoprotein cholesterol, low density lipoprotein cholesterol (LDL-C) and apolipoprotein A1] was evaluated.ResultsThe distribution of all three studied ABCA1 gene polymorphisms did not differ according to gender. However, only R219K genotype distribution bared borderline statistical significance (p = 0.08) between the two studied groups. Moreover, allele frequencies of R219K, R1587K and I88M polymorphisms did not differ according to gender. In general, blood lipid levels did not seem to vary according to ABCA1 gene polymorphisms, when testing all subjects or when testing only men or only women. However, a significant difference of LDL-C distribution was detected in all subjects according to R1587K genotype, indicating lower LDL-C levels with KK polymorphism (p = 0.0025). The above difference was solely detected on female population (p = 0.0053).ConclusionsThe ABCA1 gene polymorphisms frequency, distribution and lipid profile did not differ according to gender. However, in the female population the KK genotype of R1587K gene indicated lower LDL-C levels. Further studies, involving a higher number of individuals, are required to clarify genes and gender contribution.

Chromosomal duplications (≥200 KILOBASES (KB)) are more common than deletions ≥200 KB in developing human embryos as identified by 23 chromosome single nucleotide polymorphism (SNP) microarray

Chromosomal duplications (≥200 KILOBASES (KB)) are more common than deletions ≥200 KB in developing human embryos as identified by 23 chromosome single nucleotide polymorphism (SNP) microarray

Deletions and duplications identified by 23 chromosome single nucleotide polymorphism (SNP) microarray are associated with aneuploidy

Deletions and duplications identified by 23 chromosome single nucleotide polymorphism (SNP) microarray are associated with aneuploidy

23-chromosome single nucleotide polymorphism (SNP) microarray detects genomic aberrations that may be missed by comparative genomic hybridization (CGH) arrays in preimplantation genetic screening (PGS)

23-chromosome single nucleotide polymorphism (SNP) microarray detects genomic aberrations that may be missed by comparative genomic hybridization (CGH) arrays in preimplantation genetic screening (PGS)

23-chromosome single nucleotide polymorphism (SNP) microarray preimplantation genetic screening (PGS) on blastocysts, versus day-3 embryos, results in significantly higher clinical pregnancy rates

To determine the clinical pregnancy rate using SNP PGS in women primarily with recurrent pregnancy loss (RPL) undergoing in vitro fertilization (IVF) Retrospective. A retrospective review was conducted of all embryos that underwent PGS by 23 chromosome SNP microarrays from 1/1/2010 to 1/25/2011. Patients underwent standard in vitro fertilization (IVF) and PGS due to primarily a history of > 2 spontaneous miscarriages. Embryo biopsy was performed at either the cleavage or blastocyst stage. Sample DNA was amplified and analyzed using HumanCytoSNP-12 DNA beadchips and GenomeStudio and KaryoStudio software. Parental DNA was analyzed and compared to embryonic cells to determine the presence of benign copy number variations. Embryos derived from parents with known translocations or inversions were excluded from the study. Binomial confidence intervals for proportions were calculated by the modified Wald method. 2,976 embryos from 317 clinical IVF cycles were tested. 2,704 (90.8%) of these embryos, derived from 249 (78.5%) IVF cycles, were at Day-3 of development (D3 group) when biopsy was performed. Conversely, 272 (9.2%) of embryos, derived from 68 (21.5%) IVF cycles, were at the blastocyst stage (D5 group) when biopsy was performed. Aneuploidy was observed in 59% of the Day 3 embryos compared with only 41% of Day 5 embryos.The clinical pregnancy rates were significantly higher (86%, P<.05) in the D5 group compared to the D3 group (65%). The miscarriage rate in the D3 and D5 groups were 6% and 9% respectively. These miscarriage rates were not statistically different. PGS using 23-chromosome SNP microarrays is practical in improving clinical pregnancy rates in couples with RPL. In addition, PGS performed on blastocysts, versus Day-3 embryos, results in significantly higher clinical pregnancy rates in similar patient populations.

Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid

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.