Maximum likelihood phylogeny of <i>Mtb</i> isolated from patients with active pulmonary TB.

<p>Branches are coloured by lineage and tips are coloured by the sub-clades within the lineages. A star marks almost identical genomes (<3 SNVs difference) isolated from different patients. Adjacent data links strains to patient metadata: MDR and pre-XDR status, treatment status, HIV status, sex and recruitment site and date of sample reception.</p

Summary of the prevalence of MDR within the different clades among 63 patients.

<p>Summary of the prevalence of MDR within the different clades among 63 patients.</p

Summary of patient metadata for 63 patients included in the study.

<p>Summary of patient metadata for 63 patients included in the study.</p

Additional file 11: of Understanding pneumococcal serotype 1 biology through population genomic analysis

Distribution of genes associated with virulence and colonisation in the ST217 in serotype 1 isolates. Presence of the genes was screened in all the isolates using BLAST as described in the methods section. (PDF 1702 kb

Additional file 1: of An outbreak of pneumococcal meningitis among older children (≥5 years) and adults after the implementation of an infant vaccination programme with the 13-valent pneumococcal conjugate vaccine in Ghana

The weekly distribution of suspected meningitis cases in the hardest hit districts. (A) Jaman North District, (B) Tain District, (C) Techiman Municipal District and (D) Wenchi District. (JPG 609 kb

Additional file 13: of Understanding pneumococcal serotype 1 biology through population genomic analysis

Distribution of the accessory genes and antibiotic resistance conferring elements in the ST217 isolates. a) Maximum likelihood phylogeny of the isolates rooted using isolates from ST615 as an outgroup (not shown). b) Number of shared accessory open reading frames (ORFs) or genes between pairs of isolates in the phylogeny on the left side and at the top. c) Colour strips showing the continent and country of origin of the isolates and their SCs. d) A heatmap showing the number of shared accessory genes between each pair of isolates in the phylogeny (panel [a] and [e]). (PDF 4076 kb