Adjusted odds ratios (aOR) for clinical features, laboratory parameters (including malaria blood films), and DENV RDT results, versus reference diagnosis of DENV infection, or all cause admission to the critical care unit (see text for details of regression analyses and adjusting covariates).

<p>^a Clinical signs of probable dengue [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003424#pntd.0003424.ref022" target="_blank">22</a>];</p><p>^b clinical warning signs of dengue requiring inpatient management [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003424#pntd.0003424.ref022" target="_blank">22</a>]</p><p>Bold type indicates p<0.05 for an association between covariate and outcome variable association. See <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003424#pntd.0003424.s003" target="_blank">S3 Table</a> for unadjusted results.</p><p>Adjusted odds ratios (aOR) for clinical features, laboratory parameters (including malaria blood films), and DENV RDT results, versus reference diagnosis of DENV infection, or all cause admission to the critical care unit (see text for details of regression analyses and adjusting covariates).</p

Flowchart depicting enrollment, DENV reference assay results, and outcome of patients into this study of a DENV RDT from the main prospective study of cause of fever in the cohort [20].

<p>Flowchart depicting enrollment, DENV reference assay results, and outcome of patients into this study of a DENV RDT from the main prospective study of cause of fever in the cohort [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003424#pntd.0003424.ref020" target="_blank">20</a>].</p

Hospital based (inpatient) paediatric enteric fever surveillance.

<p>Hospital based (inpatient) paediatric enteric fever surveillance.</p

Conditional inference tree for the prediction of critical care unit admission using clinical diagnostics, laboratory parameters and DENV RDT results with an association with either the reference diagnosis of DENV infection, or all cause critical care admission.

<p>Conditional inference tree for the prediction of critical care unit admission using clinical diagnostics, laboratory parameters and DENV RDT results with an association with either the reference diagnosis of DENV infection, or all cause critical care admission.</p

Insertion sites of transposons observed in <i>S</i>. Typhi from Nepal.

<p>Genes and transposons are indicated according to the inset legend. TSD indicates target site duplication, and <i>Tn</i> indicates transposon.</p

Global population structure of Nepalese <i>S</i>. Typhi genotypes.

<p>(A) Global population structure of Non-H58 (4.3.1) Nepalese genotypes. (B) Global population structure of H58 (4.3.1). Inner ring shows patient status. Branch colours indicate country/region of origin, as do the second ring and third rings from the inside. Fourth ring from the inside indicates QRDR <i>gyrA</i> S83F mutation. Fifth ring from the inside indicates the number of additional <i>gyrA</i> and <i>parC</i> QRDR mutations. Outer ring describes the presence of MDR. All rings and branches are coloured as per the inset legend. Branch lengths are indicative of the estimated number of substitutions rate per variable site, and the tree was outgroup rooted with a <i>S</i>. Paratyphi A strain AKU_12601.</p

Conditional inference tree for the prediction of reference diagnosis of DENV infection using clinical diagnostics, laboratory parameters and DENV RDT results with an association (p<0.05) with reference diagnosis of DENV infection (DENV RDT, platelet levels, white cell levels, hepatomegaly).

<p>Conditional inference tree for the prediction of reference diagnosis of DENV infection using clinical diagnostics, laboratory parameters and DENV RDT results with an association (p<0.05) with reference diagnosis of DENV infection (DENV RDT, platelet levels, white cell levels, hepatomegaly).</p

Conditional inference tree for the prediction of reference diagnosis of DENV infection using clinical features and laboratory parameters with an association (p<0.05) with the reference diagnosis of DENV infection (platelet levels and white cell levels; note the model removes clinical features from the tree).

<p>Conditional inference tree for the prediction of reference diagnosis of DENV infection using clinical features and laboratory parameters with an association (p<0.05) with the reference diagnosis of DENV infection (platelet levels and white cell levels; note the model removes clinical features from the tree).</p

BEAST2 maximum-clade credibility phylogenetic tree of Nepalese genotype 4.3.1 (H58) <i>S</i>. Typhi.

<p>Tips colours indicate outpatient (red) vs. inpatient (blue) isolates. Acquisitions of molecular determinants of resistance are labelled.</p

Global population structure of <i>S</i>. Paratyphi A.

<p>Inner ring indicates patient status. Branch colours indicate country/region of origin, as do the second and third rings from the inside. Fourth ring from the inside indicates QRDR <i>gyrA</i> S83F mutation. Fifth ring from the inside indicates the number of additional <i>gyrA</i> and <i>parC</i> QRDR mutations. Outer ring describes the presence of MDR. All rings and branches are.</p