Additional file 1: of Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Figure S1. (1) Colony morphology of (a) Bacillus endophyticus that is small circular, wet and non-mucoid and (b) B. anthracis appear circular, mucoid on nutrient agar supplemented with sodium bicarbonate at 5% CO2 after incubation at 37 °C.  Colony morphology of B. endophyticus and B. anthracis on sheep blood agar incubated at 37 °C. B. anthracis shows the characteristic shiny, rough with ground-glass appearance compared to the white slimy and smooth colonies of B. endophyticus. (TIFF 2652 kb

Additional file 4: of Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Table S1. Plasmid comparison of the four sequenced Bacillus endophyticus strains (3618_1C, 3631_9D, 3631_10C, 3617_2C) with B. endophyticus Hbe603 strain. (DOC 18 kb

Additional file 2: of Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Figure S2. Phenotypic electron microscopic examination of the morphology of B. endophyticus strains after 24 h incubation on nutrient agar containing 0.8% sodium bicarbonate stained using copper sulphate. (TIFF 4206 kb

NGS data and assembly metrics.

<p>NGS data and assembly metrics.</p

Concordance of molecular serotyping results of pneumococcal control strains.

<p>^armPCR: real-time Multiplex PCR.</p><p>N/A* = serotype not included in the rmPCR panel.</p><p>No ID ^b. = sequence identity of ≤98% with sequences in GenBank.</p><p>Neg^c = negative sequetyping PCR result.</p><p>^dThe Sequetyping assay mistyped serotype 18C as 18B.</p><p>Concordance of molecular serotyping results of pneumococcal control strains.</p

Similarity of 16F-like capsular polysaccharide (<i>cps</i>) gene loci.

<p>Sequences from pneumococci serotyped as 16F Quellung but sequetyped as 9V was compared to reference 9V (CR931648) and 16F (CR931668) <i>cps</i> sequences. Artemis Comparison Tool (ACT) was used to generate and view gene homology. The top lines represent the forward and reverse strand of a serotype 9v reference, the middle lines represent the queried 16F strain and the bottom lines shows the 16F reference. The portion of the <i>wzh</i> gene that is amplified by the sequetyping assay is shown by the blue rectangle. The clear blocks below the blue box shows regions were the genes that are not similar. BLASTN matches are shown as red bands between sequences, indicating the degree of similarity between the sequences.</p

Comparative genome analysis of pneumococcal serotypes 16F and 9V genetic background.

<p>When the sequence identities of all four genomes were compared using RAST(Rapid Annotation using Subsystem Technology), the genome backbone of all three 16F (103347 and 103385 from this study and a 16F control strain) were mostly identical but divergent from 9V. The colour codes represent how close or divergent the genomes are. Therefore, similar genome backgrounds will have similar colours.</p

Flow chart showing the pneumococcal isolates included in the study.

<p>*Of the 40 isolates that were tested by rmPCR, only 25 were included as part of the rmPCR targets.</p

Serotype distribution of nasopharyngeal pneumococcal isolates.

<p>The figure includes serotypes detected from the Drakenstein Child Health Study, determined by Quellung reaction, excluding duplicate serotypes from the same infant. Blue = serotypes included in PCV13; Red = serotypes not included in PCV13. Green = non-typable isolates.</p