Fig 1.
qPCR assay for scabies diagnosis project flowchart.
qPCR assays were developed from targets sourced from next generation sequencing (NGS) data. Assay optimisation was subsequently carried out through a series of sensitivity and specificity testing. Sampling efficiency of swabbing was then evaluated with the assay using material collected from the pig model. The applicability of the assay was then tested in a clinic/hospital setting, prior to field evaluation.
Fig 2.
Sensitivity of probe-based qPCR assay detection on mite gDNA targeting SSR5, SSR6 and cox1.
Mean cycle quantification (Cq) values reported for the amplification of serial single mite dilutions with the SSR5 and SSR6 assays and the reference assay cox1. Each point represents the mean of triplicate reactions. No amplification was detected in the 1:1000 dilution of the genomic DNA extracted from a single mite.
Fig 3.
Comparative testing of FLOQ and Catch-All swabs.
Calculated DNA quantity (DNA copies per reaction) in samples collected by FLOQ and Catch-All swabs using the (A) SSR5 and (B) SSR6 assays. Standard curves constructed from assays dilution series were used to determine quantity of genomic DNA, represented as DNA copies per reaction. Each data point represents DNA recovery from one pig ear. The calculated quantity of target DNA recovered using FLOQ swabs was higher than using the Catch-All swabs in both assays. (All DNA copies reported are the mean values of triplicate reaction tested).
Fig 4.
Flowchart classification of patients from RDH and DD.
Patients were distributed in three groups: scabies group, which included patients clinically diagnosed with scabies who had not received treatment at the time of sampling; treated scabies group, which included patients clinically diagnosed with scabies who had received treatment before sampling; no scabies group, which included patients clinically diagnosed with non-specific conditions. RHD: Royal Darwin Hospital; DD: Darwin Dermatology clinic.
Table 1.
Demographics and disease history of patients from RDH and DD enrolled in this study.
Fig 5.
Comparison of qPCR results on samples collected by FLOQ swabs and skin scrapings from 7 untreated scabies patients.
Fig 6.
Comparison of qPCR results on samples collected by FLOQ swabs and skin scrapings from 5 treated patients.
Table 2.
Comparison of assay performance among patients with a positive qPCR result.