Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome

Lena Chng; Deborah C Holt; Matt Field; Joshua R Francis; Dev Tilakaratne; Milou H Dekkers; Greg Robinson; Kate Mounsey; Rebecca Pavlos; Asha C Bowen; Katja Fischer; Anthony T Papenfuss; Robin B Gasser; Pasi K Korhonen; Bart J Currie; James S McCarthy; Cielo Pasay

doi:10.1371/journal.pntd.0009149

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Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome

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Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome

Lena Chng, Deborah C Holt, Matt Field, Joshua R Francis, Dev Tilakaratne, Milou H Dekkers, Greg Robinson, Kate Mounsey, Rebecca Pavlos, Asha C Bowen, …

PLoS Neglected Tropical Diseases, Vol.15(2), pp.1-19

2021

DOI: https://doi.org/10.1371/journal.pntd.0009149

PMID: 33626043

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Abstract

Background: The suboptimal sensitivity and specificity of available diagnostic methods for scabies hampers clinical management, trials of new therapies and epidemiologic studies. Additionally, parasitologic diagnosis by microscopic examination of skin scrapings requires sample collection with a sharp scalpel blade, causing discomfort to patients and difficulty in children. Polymerase chain reaction (PCR)-based diagnostic assays, combined with non-invasive sampling methods, represent an attractive approach. In this study, we aimed to develop a real-time probe-based PCR test for scabies, test a non-invasive sampling method and evaluate its diagnostic performance in two clinical settings. Methodology/Principal findings: High copy-number repetitive DNA elements were identified in draft Sarcoptes scabiei genome sequences and used as assay targets for diagnostic PCR. Two suitable repetitive DNA sequences, a 375 base pair microsatellite (SSR5) and a 606 base pair long tandem repeat (SSR6), were identified. Diagnostic sensitivity and specificity were tested using relevant positive and negative control materials and compared to a published assay targeting the mitochondrial cox1 gene. Both assays were positive at a 1:100 dilution of DNA from a single mite; no amplification was observed in DNA from samples from 19 patients with other skin conditions nor from house dust, sheep or dog mites, head and body lice or from six common skin bacterial and fungal species. Moderate sensitivity of the assays was achieved in a pilot study, detecting 5/7 (71.4% [95% CI: 29.0% - 96.3%]) of clinically diagnosed untreated scabies patients). Greater sensitivity was observed in samples collected by FLOQ swabs compared to skin scrapings. Conclusions/Significance: This newly developed qPCR assay, combined with the use of an alternative non-invasive swab sampling technique offers the possibility of enhanced diagnosis of scabies. Further studies will be required to better define the diagnostic performance of these tests.

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Title: Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome
Authors: Lena Chng (Author) - QIMR Berghofer Medical Research Institute
Deborah C Holt (Author) - Charles Darwin University
Matt Field (Author) - James Cook University
Joshua R Francis (Author) - Charles Darwin University
Dev Tilakaratne (Author) - Royal Darwin Hospital
Milou H Dekkers (Author) - The University of Queensland
Greg Robinson (Author) - QIMR Berghofer Medical Research Institute
Kate Mounsey (Author) - University of the Sunshine Coast, Queensland, School of Health and Behavioural Sciences - Legacy
Rebecca Pavlos (Author) - The University of Western Australia
Asha C Bowen (Author) - Charles Darwin University
Katja Fischer (Author) - QIMR Berghofer Medical Research Institute
Anthony T Papenfuss (Author) - Walter and Eliza Hall Institute of Medical Research
Robin B Gasser (Author) - The University of Melbourne
Pasi K Korhonen (Author) - The University of Melbourne
Bart J Currie (Author) - Charles Darwin University
James S McCarthy (Author) - QIMR Berghofer Medical Research Institute
Cielo Pasay (Author) - QIMR Berghofer Medical Research Institute
Publication details: PLoS Neglected Tropical Diseases, Vol.15(2), pp.1-19
Publisher: Public Library of Science
Date published: 2021
DOI: 10.1371/journal.pntd.0009149
ISSN: 1935-2735
PMID: 33626043
Copyright note: © 2021 Chng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Organisation Unit: School of Health - Biomedicine; University of the Sunshine Coast, Queensland; School of Health and Behavioural Sciences - Legacy
Language: English
Record Identifier: 99510405702621
Output Type: Journal article

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Collaboration types: Domestic collaboration
Web Of Science research areas: Infectious Diseases; Parasitology; Tropical Medicine

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