Molecular detection of <i>M</i>. <i>ulcerans</i> in environment, Ivory Coast and number of environmental samples free of PCR inhibition and positive for the RT-PCR detection of <i>M</i>. <i>ulcerans</i> (CFU, colony-forming units, Ct cycle threshold).

<p>Molecular detection of <i>M</i>. <i>ulcerans</i> in environment, Ivory Coast and number of environmental samples free of PCR inhibition and positive for the RT-PCR detection of <i>M</i>. <i>ulcerans</i> (CFU, colony-forming units, Ct cycle threshold).</p

Map of Ivory Coast (Based on OCHA/ReliefWeb) showing the Buruli ulcer endemic areas based on World Health Organization data (2013) and location of studied environmental samples.

<p>Each circle figures the number of positive samples over collected samples. Blue teardrops, endemic areas; tan teardrops, non-endemic areas.</p

Detection of <i>Mycobacterium ulcerans</i> DNA in the Environment, Ivory Coast

<div><p>Background</p><p>Ivory Coast is a West African country with the highest reported cases of Buruli ulcer, a disabling subcutaneous infection due to <i>Mycobacterium ulcerans</i>. However, the prevalence of environmental <i>M</i>. <i>ulcerans</i> is poorly known in this country.</p><p>Methods</p><p>We collected 496 environmental specimens consisting of soil (n = 100), stagnant water (n = 200), plants (n = 100) and animal feces (n = 96) in Ivory Coast over five months in the dry and wet seasons in regions which are free of Buruli ulcer (control group A; 250 specimens) and in regions where the Buruli ulcer is endemic (group B; 246 specimens). After appropriate total DNA extraction incorporating an internal control, the <i>M</i>. <i>ulcerans</i> IS<i>2404</i> and KR-B gene were amplified by real-time PCR in samples. In parallel, a calibration curve was done for <i>M</i>. <i>ulcerans</i> Agy99 IS<i>2404</i> and KR-B gene.</p><p>Results</p><p>Of 460 samples free of PCR inhibition, a positive real-time PCR detection of insertion sequence IS<i>2404</i> and KR-B gene was observed in 1/230 specimens in control group A versus 9/230 specimens in group B (<i>P</i> = 0.02; Fisher exact test). Positive specimens comprised seven stagnant water specimens, two feces specimens confirmed to be of <i>Thryonomys swinderianus</i> (agouti) origin by real-time PCR of the <i>cyt</i>b gene; and one soil specimen. Extrapolation from the calibration curves indicated low inoculums ranging from 1 to 10² mycobacteria/mL.</p><p>Conclusion</p><p>This study confirms the presence of <i>M</i>. <i>ulcerans</i> in the watery environment surrounding patients with Buruli ulcer in Ivory Coast. It suggests that the agouti, which is in close contacts with populations, could play a role in the environmental cycle of <i>M</i>. <i>ulcerans</i>, as previously suggested for the closely related possums in Australia.</p></div

Comparison of different eukaryotic components extracted in 13 samples from HIV-infected patients using 4 methods of DNA extraction.

<p>Comparison of different eukaryotic components extracted in 13 samples from HIV-infected patients using 4 methods of DNA extraction.</p

The distribution of the major fungal OTUs obtained from the amplification of the ITS1 region in the fecal samples of HIV-infected patients and healthy subjects.

<p>The heatmap shows read counts for the 15 OTUs identified as contributing most to the variance (up to 86% across all samples) as determined by SIMPER analysis. The dendrogram shows the clustering of samples based on Bray-Curtis similarity distance.</p

The distribution of the major eukaryotic MOTUs detected in the fecal samples of HIV-infected patients and healthy subjects using cloning and sequencing methods.

<p>The heatmap shows read counts for the 33 MOTUs identified as contributing most to the variance (up to 86% across all samples) as determined by Similarity Percentage (SIMPER) analysis. The dendrogram shows the clustering of samples based on Bray-Curtis similarity distance.</p

Abundance and distribution of the fungal OTUs obtained from the amplification of the ITS2 region in fecal samples of HIV-infected patients and healthy subjects.

<p>Abundance and distribution of the fungal OTUs obtained from the amplification of the ITS2 region in fecal samples of HIV-infected patients and healthy subjects.</p

The distribution of the major fungal OTUs recovered from the amplification of the ITS2 region in the fecal samples of HIV-infected patients and healthy subjects.

<p>The heatmap shows read counts for the 13 OTUs identified as contributing most to the variance (up to 86% across all samples) as determined by SIMPER analysis. The dendrogram shows the clustering of samples based on Bray-Curtis similarity distance.</p