Table 1.
Study sample sets.
Fig 1.
Goodness of fit analysis for trial study.
ELISA and qPCR test results for the armadillo trial study as compared to the expected results based on known armadillo experimental infection statuses (infected n = 25, non-infected n = 20). Each assay type is compared to the expected using Chi-squared analyses. Assay types include the PGL1 ELISA (infected n = 11, non-infected n = 34, χ2 = 17.52, p<0.01), LID1 ELISA (infected n = 15, non-infected n = 30, χ2 = 8.92, p<0.01), 85B qPCR (infected n = 9, non-infected n = 36, χ2 = 22.90, p<0.01), rlep qPCR (infected n = 26, non-infected n = 19, χ2 = 0.12, p = 0.73), and combination of 85B and rlep qPCRs (85B+rlep, infected n = 18, non-infected n = 27, χ2 = 4.36, p = 0.04). Chi-squared analyses show all tests significantly differ from the expected (*p<0.01) except the qPCR tests performed using only the rlep target and the combination of 85B and rlep.
Fig 2.
Sensitivity, specificity, false positive rate, and false negative rate determined in trial study.
Analysis of the sensitivity (proportion of infected armadillos accurately identified as infected), specificity (proportion of non-infected armadillos identified as not infected), false positive rates (FPR, proportion of non-infected armadillos inaccurately identified as infected), and false negative rates (FNR, proportion of infected armadillos inaccurately identified as not infected) of ELISAs using blood samples and qPCRs using cheek swab samples. Assay types include the PGL1 ELISA (sensitivity = 0.44, specificity = 1.00, FPR = 0.00, FNR = 0.56), LID1 ELISA (sensitivity = 0.60, specificity = 1.00, FPR = 0.00, FNR = 0.40), 85B qPCR (sensitivity = 0.36, specificity = 1.00, FPR = 0.00, FNR = 0.60), rlep qPCR (sensitivity = 0.72, specificity = 0.60, FPR = 0.40, FNR = 0.28), and combination of 85B and rlep qPCRs (85B+rlep, sensitivity = 0.60, specificity = 0.85, FPR = 0.15, FNR = 0.40).
Fig 3.
Overall qPCR results for case study.
qPCR results for marmoset samples (n = 98). All marmosets were negative for the M. leprae-specific 85B and rlep genes and the MTBC-specific rpoB2 and IS6110 genes. However, 14 are positive for the mycobacterial rpoB1 gene. Approximately 0.001–0.137 mycobacterial genome copies per ng of DNA extracted were identified from these rpoB1-positive samples.
Fig 4.
Distribution of mycobacteria identified in case study.
Geographic and taxonomic distribution of rpoB1 positive marmoset samples. rpoB1 positive samples are found in Recife, Pernambuco (n = 4), the neighboring municipalities of Petrolina, Pernambuco and Juazeiro, Bahia (n = 1), and the neighboring cities of Silva Jardim and Rio Bonito, Rio de Janeiro (n = 9) and in C. jacchus (n = 3), hybrids (n = 10), and C. penicillata (n = 1).
Table 2.
Summary of sequencing results.
Table 3.
Summary of MEGAN results.