Bootstrapped ML trees, inferred with RAxML, for regions of the PA segment of avian H5N1 sequences.

<p>Tree A was inferred for the region defined by positions 1–1361 & 1939–2314. Tree B was inferred for the region defined by positions 1362–1938. The red sequence is the putative recombinant sequence. Blue and green sequences are major and minor parental sequences, respectively, as identified by 3SEQ. Trees are midpoint rooted. ML trees inferred with PAUP* have some non-critical differences the two subclades marked with open circles.</p

Summary of 18 datasets used in this study.

<p><b>Footnotes:</b> P-values are corrected with a Dunn-Sidak correction for the numbers of triplets tested in each dataset. P-values are shown as simple orders of magnitude when P<10⁻⁶.</p

Bootstrapped ML trees for the PA segment of avian H5N1 sequences.

<p>Tree A was inferred for the region defined by positions 1–139 & 2016–2314. Tree B was inferred for the region defined by positions 140–2015. ML trees inferred with PAUP* have some non-critical differences the two subclades marked with open circles. Phylogenetic relationships in these trees do not support a hypothesis of homologous recombination. Other features as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010434#pone-0010434-g001" target="_blank">Figure 1</a>.</p

False positives of 3SEQ algorithm on simulated clonal data sets of the same size and diversity as in this study.

<p><b>Footnote:</b> P-value in the column heading is the Dunn-Sidak corrected P-value.</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

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

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

Exposure to poultry for poultry workers in the 12 months prior to serum sample collection.

<p>*Missing data for 8 poultry workers.</p><p>#Missing data for 2 poultry workers.</p