Admission features of 540 ofloxacin treated enteric fever patients recruited to clinical trials.

a<p>) continuous variables given as median (interquartile range), and proportions as number (%).</p>b<p>) Analysis of variance for proportions, Kruskall Wallis test for continuous variables.</p>c<p>) MDR – resistant to ampicillin, chloramphenicol and trimethoprim-sulfamethoxazole.</p>d<p>) NaR – resistant to nalidixic acid.</p

The distribution of <i>S.</i> Typhi MIC to ofloxacin in seven RCTs.

<p>Histogram showing the distribution of <i>S.</i> Typhi MICs (<0.06, 0.06, 0.125, 0.25, 0.5 and 1 µg/mL) to ofloxacin over seven individual randomised. The proportion of <i>S.</i> Typhi strains with the corresponding MIC are shaded accordingly, white; study TY1 (1992–1993) n = 19 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001163#pntd.0001163-Smith2" target="_blank">[25]</a>, very light grey; study CT1 (1993–1994) n = 102 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001163#pntd.0001163-Vinh1" target="_blank">[26]</a>, light grey; study TY2 (1993–1996) n = 103 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001163#pntd.0001163-Nguyen1" target="_blank">[24]</a>, mid grey; study DTC (1994–1995) n = 154 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001163#pntd.0001163-Vinh2" target="_blank">[28]</a>, dark grey; study DN (1995–1996) n = 55 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001163#pntd.0001163-Cao1" target="_blank">[29]</a>, very dark grey; study TY3 (1997–1998) n = 45 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001163#pntd.0001163-Chinh1" target="_blank">[23]</a> and black; study DTY2 (1998–2001) n = 62 <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001163#pntd.0001163-Parry3" target="_blank">[27]</a>.</p

The relationship between increasing <i>S.</i> Typhi MIC to ofloxacin and clinical failure.

<p>Histogram showing the proportion of enteric fever patients who failed treatment (white columns) or had persistent fever (black columns) (>38°C) for more than seven days after the commencement of treatment. Data was combined from seven randomised clinical trials and is comprised from 540 children and adults recruited with uncomplicated enteric fever. The patients are divided according to the MIC to ofloxacin of the infecting isolate.</p

The duration of febrile episodes in enteric fever patients infected with <i>S.</i> Typhi organisms with a range of MICs to ofloxacin.

<p>Kaplan Meir curve showing the proportion of patients remaining febrile (>38°C) after the start of treatment with ofloxacin. Data is composed from fever clearance times of 540 children and adults with uncomplicated enteric fever recruited to seven randomised clinical trial and treated with oral ofloxacin. The curves are divided according to the ofloxacin MIC of the infecting isolates and are highlighted on the diagram.</p

The validation of quantitative real-time PCR assays targeting <i>qnrA</i>, <i>qnrB</i> and <i>qnrS</i>.

<p>The inter-assay and intra-assay variability were checked on bacterial nucleic acid extracted from pure culture with and without internal control PhHV. No differences were observed between these two batches.</p><p>CV: Coefficient of variance.</p

Comparison of gene copy number for <i>qnrA</i>, <i>qnrB</i> and <i>qnrS</i> before and after three different alternative treatment regimes.

*<p><i>p</i><0.05. Statistical significance calculated by paired Wilcoxon rank-sum test.</p>a<p><i>p</i> value calculated by comparing <i>qnr</i> gene copy number between Day 0 and Day 7.</p>b<p><i>p</i> value calculated by comparing <i>qnr</i> gene copy number between Day 0 and Day 7 after adjusting for <i>Enterobacteriaceae</i> CFU ml⁻¹.</p

Baseline demographic characteristics of participants and the prevalence of <i>qnr</i> genes prior to antimicrobial therapy.

*<p>Districts within HCMC with population densities <10,000 (low), 10,000–30000 (medium) and >30,000 people/km² (high).</p

The median gene copy number of <i>qnrA</i>, <i>qnrB and qnrS</i> on enrolment and after antimicrobial therapy.

<p>Box plots showing the median and interquartile ranges of <i>qnrA</i>, <i>qnrB and qnrS</i> gene copy numbers in stool samples collected from children with ARIs on enrolment (Day 0) and after antimicrobial treatment (Day 7). Statistical significance between the <i>qnr</i> genes was calculated using the paired Wilcoxon rank-sum test; significant variation in gene copy number between the <i>qnr</i> genes is denoted at the head of the figure (*), all <i>p</i> values<0.001.</p

Comparison of <i>qnr</i> gene prevalence, <i>qnr</i> copy number and CFU ml⁻¹ of <i>Enterobacteriaceae</i> in stool samples on enrolment and seven days after enrolment.

<p>Evaluation of the prevalence of <i>qnr</i> genes, gene copy number, CFU ml⁻¹ and <i>qnr</i> gene copy number per CFU. Statistical significance was assessed by McNemar's test and paired Wilcoxon rank-sum test.</p>*<p>Statistically significant (<i>p</i><0.05).</p

Temporal Fluctuation of Multidrug Resistant <em>Salmonella</em> Typhi Haplotypes in the Mekong River Delta Region of Vietnam

<div><h3>Background</h3><p>Typhoid fever remains a public health problem in Vietnam, with a significant burden in the Mekong River delta region. Typhoid fever is caused by the bacterial pathogen <em>Salmonella enterica</em> serovar Typhi (<em>S</em>. Typhi), which is frequently multidrug resistant with reduced susceptibility to fluoroquinolone-based drugs, the first choice for the treatment of typhoid fever. We used a GoldenGate (Illumina) assay to type 1,500 single nucleotide polymorphisms (SNPs) and analyse the genetic variation of <em>S</em>. Typhi isolated from 267 typhoid fever patients in the Mekong delta region participating in a randomized trial conducted between 2004 and 2005.</p><h3>Principal Findings</h3><p>The population of <em>S</em>. Typhi circulating during the study was highly clonal, with 91% of isolates belonging to a single clonal complex of the <em>S</em>. Typhi H58 haplogroup. The patterns of disease were consistent with the presence of an endemic haplotype H58-C and a localised outbreak of <em>S</em>. Typhi haplotype H58-E2 in 2004. H58-E2-associated typhoid fever cases exhibited evidence of significant geo-spatial clustering along the Sông H u branch of the Mekong River. Multidrug resistance was common in the established clone H58-C but not in the outbreak clone H58-E2, however all H58 <em>S</em>. Typhi were nalidixic acid resistant and carried a Ser83Phe amino acid substitution in the <em>gyrA</em> gene.</p><h3>Significance</h3><p>The H58 haplogroup dominates <em>S</em>. Typhi populations in other endemic areas, but the population described here was more homogeneous than previously examined populations, and the dominant clonal complex (H58-C, -E1, -E2) observed in this study has not been detected outside Vietnam. IncHI1 plasmid-bearing <em>S</em>. Typhi H58-C was endemic during the study period whilst H58-E2, which rarely carried the plasmid, was only transient, suggesting a selective advantage for the plasmid. These data add insight into the outbreak dynamics and local molecular epidemiology of <em>S</em>. Typhi in southern Vietnam.</p></div