Species-level typing of mycobacterial isolates from camels.

<p>Ethidium bromide stained 2% agarose gel of PCR amplicons of the <i>hsp65</i> gene, following restriction enzyme analysis (REA) with <i>Pst</i>I. For each set, both undigested and digested products (second lane) are shown. A 100-bp Molecular size marker is shown in the first lane.</p

Histological analysis of camel samples collected from animals suffering from Johne's disease.

<p>A) A representative of lymph node thin section stained with H&E showing diffuse granulomatous response (arrows). B) A lymph node section stained with Zeil-Neelsen stain showing high level of acid-fast bacilli. C) A representative of intestinal section stained with H&E showing aggregates of lymphatic infiltration (arrows). D) An intestinal section stained with Zeil-Neelsen stain showing patches of acid-fast bacilli. Size bars are included in the bottom of each section.</p

List of genes with high number of SNPs in <i>M. ap</i> JQ5 compared to <i>M. ap</i> K-10.

<p>List of genes with high number of SNPs in <i>M. ap</i> JQ5 compared to <i>M. ap</i> K-10.</p

Primers used in this study.

<p>Primers used in this study.</p

IS<i>1311</i> polymorphisms in <i>M.av</i> and within <i>M.ap</i> strains.

<p>IS<i>1311</i> polymorphisms in <i>M.av</i> and within <i>M.ap</i> strains.</p

Summary of next generation sequencing results.

<p>Summary of next generation sequencing results.</p

Circular map of the newly identified SNPs and indels in camel isolate JQ5 relative to the <i>M. ap</i> K-10 strain [<b>51</b>].

<p>The outer circle shows the genomic scale. The second circle shows the location of the 4,395 ORFs in the <i>M. ap</i> K-10 genome. Genes (magenta) on the forward strand are shown outside of the baseline; genes (olivegreen) on the reverse strand are shown inside of the baseline. Inner circles show all indels (blue), synonymous SNPs (orange), and nonsynonymous SNPs (lime) identified in <i>M. ap</i> of camel origin. The figure was generated with GenVision software (DNAStar, Madison, WI).</p

Phylogenetic analysis of <i>M. ap</i> isolates form different hosts.

<p>A dendrogram displaying the relationship between several <i>M. ap</i> isolates based on the sequence of 3 genes (<i>gyrA, gyrB</i> and <i>recF</i>). Isolates with JQ designation were analyzed in this study either from camels (JQ5, JQ6) or sheep (JQS1, JQS2). <i>M. ap</i> S397 is the standard strain for <i>M. ap</i>-S <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031947#pone.0031947-Bannantine1" target="_blank">[25]</a>, <i>M. ap</i> K10 is the standard strain for <i>M. ap</i>–C <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031947#pone.0031947-Li1" target="_blank">[23]</a> while the rest of the isolates were genotyped before <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031947#pone.0031947-Castellanos1" target="_blank">[18]</a>. All of the known genotyped are included in the figure. The bootstrap values (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031947#pone-0031947-t002" target="_blank">Table 2</a> for the sequence accession numbers used here.</p

Genotyping of camel isolates.

<p>A) Ethidium bromide stained 3% agarose gel of PCR amplicons of the IS<i>1311</i> gene, following REA with <i>Hinf1</i>. For each set, both undigested and digested products (second lane) are shown. The PCR-REA analysis of IS<i>1311</i> shows <i>M. ap</i>-S (<i>M. ap</i> S397) and <i>M. ap</i>-C (<i>M. ap</i> K-10) strains in addition to camel isolates JQ5 and JQ6. A 100-bp Molecular size marker is included. B) DNA sequencing electropherogram showing the C/T nucleotide polymorphism surrounding base pair 223 in IS<i>1311</i>.</p

A list of accession numbers for organisms and genes used in this manuscript.

<p>A list of accession numbers for organisms and genes used in this manuscript.</p