Additional file 1: of Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients

A tabular list of all SNPs and indels per M. tuberculosis isolate, sputum and blood, created using nesoni nway program. Key: Highlighted = SNPs between concurrent sputum and blood M. tuberculosis isolates, p = patient. (XLS 15043 kb

Genotypic characterization directly applied to sputum improves the detection of <i>Mycobacterium africanum</i> West African 1, under-represented in positive cultures

<div><p>Background</p><p>This study aimed to compare the prevalence of <i>Mycobacterium tuberculosis</i> complex (MTBc) lineages between direct genotyping (on sputum) and indirect genotyping (on culture), to characterize potential culture bias against difficult growers.</p><p>Methodology/Principal findings</p><p>Smear-positive sputa from consecutive new tuberculosis patients diagnosed in Cotonou, (Benin) were included, before patients had started treatment. An aliquot of decontaminated sputum was used for direct spoligotyping, and another aliquot was cultured on Löwenstein Jensen (LJ) medium (90 days), for indirect spoligotyping. After DNA extraction, spoligotyping was done according to the standard method for all specimens, and patterns obtained from sputa were compared versus those from the derived culture isolates. From 199 patient’s sputa, 146 (73.4%) yielded a positive culture. In total, direct spoligotyping yielded a pattern in 98.5% (196/199) of the specimens, versus 73.4% (146/199) for indirect spoligotyping on cultures. There was good agreement between sputum- and isolate derived patterns: 94.4% (135/143) at spoligotype level and 96.5% (138/143) at (sub)lineage level. Two of the 8 pairs with discrepant pattern were suggestive of mixed infection in sputum. Ancestral lineages (Lineage 1, and <i>M</i>. <i>africanum</i> Lineages 5 and 6) were less likely to grow in culture (OR = 0.30, 95%CI (0.14 to 0.64), p = 0.0016); especially Lineage 5 (OR = 0.37 95%CI (0.17 to 0.79), p = 0.010). Among modern lineages, Lineage 4 was over-represented in positive-culture specimens (OR = 3.01, 95%CI (1.4 to 6.51), p = 0.005).</p><p>Conclusions/ Significance</p><p>Ancestral lineages, especially <i>M</i>. <i>africanum</i> West African 1 (Lineage 5), are less likely to grow in culture relative to modern lineages, especially <i>M</i>. <i>tuberculosis</i> Euro-American (Lineage 4). Direct spoligotyping on smear positive sputum is effective and efficient compared to indirect spoligotyping of cultures. It allows for a more accurate unbiased determination of the population structure of the <i>M</i>. <i>tuberculosis</i> complex.</p><p>Trial registration</p><p>ClinicalTrials.gov <a href="https://clinicaltrials.gov/ct2/show/NCT02744469" target="_blank">NCT02744469</a></p></div

Additional file 2: of Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients

SNPs and SNP functions identified by comparing concurrent sputum and blood M. tuberculosis strains from HIV-infected individuals. (DOC 30 kb

Discrepancies: Spoligotype profile, lineage and sub-lineage.

<p>Discrepancies: Spoligotype profile, lineage and sub-lineage.</p

Patients, specimens flow diagram and laboratory analyses.

<p>Patients, specimens flow diagram and laboratory analyses.</p

Time to culture positivity (on LJ medium) across lineages.

<p>Time to culture positivity (on LJ medium) across lineages.</p

Effect of prior culture on spoligotyping analysis for MTBc lineage detection.

<p>Effect of prior culture on spoligotyping analysis for MTBc lineage detection.</p

Availability of spoligotype patterns depending on the spoligotyping method used.

<p>Availability of spoligotype patterns depending on the spoligotyping method used.</p

Qualitative results per laboratory of the two rounds of clinical EQAP.

a<p>The total n° of suspensions analyzed varies per laboratory because some laboratories reported inconclusive results. ^b The number of concordant pairs divided by the total number of pairs. ^c Delay between the date of shipment of the panel and the reported date of analysis. NT: not tested; ER: enoyl reductase domain; KR: ketoreductase B domain.</p

Panel composition of the two rounds of clinical EQAP and concordant qualitative results per sample (inter-laboratory reproducibility).

a<p>No sample was inhibited. ^b The total number of respondent laboratories varies because inconclusive results were removed from the analysis as well as a missing suspension in one laboratory in round 1.</p