MOESM1 of G6PD deficiency alleles in a malaria-endemic region in the Western Brazilian Amazon

Additional file 1. Flow diagram of the study detailing exclusion criteria

Cycle threshold (Ct-value) versus grade of smear-positivity.

<p>Ct versus degree of smear positivity, coded as negative = 0, scanty = 1, 1+ = 2 etc (regression coefficient β = −5.02, 95%CI = −7.44 to −2.60). Ct for Xpert MTB/RIF Assay negatives was coded as 40.</p

Comparison of Xpert MTB/RIF Assay and other methods with reference standard for both HIV-positive and -negative participants.

a<p>all culture results include speciation test results (for confirmation of M<i>tb</i> or exclusion of M<i>tb</i> in case when NTM present).</p>b<p>reference standard for confirmed TB- diagnosis, defined as at least one positive culture (LJ or Mgit) confirmed as <i>Mtb</i> in speciation of per patient analysis; <i>Mtb-</i> negative defined as all cultures negative (LJ and Mgit) for <i>Mtb</i> in per patient analysis, speciation results included.</p><p>Smear = Sputum smear microscopy after ZN-staining; LJ = Loewenstein-Jensen culture on solid media; Mgit = BACTEC MGIT 960 liquid culture.</p

Cycle threshold (Ct-value) versus time to positivity in MGIT liquid culture.

<p>Ct versus days from inoculation into MGIT liquid culture to culture positivity as reported by the MGIT instrument (β = 1.19, 95%CI = 0.98 to 1.39). Ct for Xpert MTB/RIF Assay negatives was coded as 40.</p

Patient classification, HIV prevalence and Xpert MTB/RIF Assay results for each patient group.

a<p> = Xpert MTB/RIF Assay result per patient analysis.</p>b<p> = sensitivity in this group, 95%CI = 89.6% to 100.0%.</p>c<p> = sensitivity in this group, 95%CI = 35.7% to 82.7%.</p>d<p> = specificity in this group, 95%CI = 94.7% to 100.0%.</p><p>S+/C+ = sputum smear positive and culture positive; S−/C+ = sputum smear negative and culture positive; C− = culture negative.</p

Comparison of Xpert MTB/RIF Assay and other methods with reference standard in HIV-positives only.

a<p>all culture results include speciation test results (for confirmation of M<i>tb</i> or exclusion of M<i>tb</i> in case when NTM present).</p>b<p>reference standard for confirmed TB- diagnosis, defined as at least one positive culture (LJ or Mgit) confirmed as <i>Mtb</i> in speciation of per patient analysis; <i>Mtb-</i> negative defined as all cultures negative (LJ and Mgit) for <i>Mtb</i> in per patient analysis, speciation results included.</p><p>Smear = Sputum smear microscopy after ZN-staining; LJ = Loewenstein-Jensen culture on solid media; Mgit = BACTEC MGIT 960 liquid culture.</p

Additional file 2: of The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis

Protocol for gDNA extraction and dPCR quantification of materials. (PDF 394 kb