6
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Development and evaluation of a droplet digital PCR assay for the diagnosis of paucibacillary leprosy in skin biopsy specimens

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background

          The reduced amounts of Mycobacterium leprae ( M. leprae) among paucibacillary (PB) patients reflect the need to further optimize methods for leprosy diagnosis. An increasing number of reports have shown that droplet digital polymerase chain reaction (ddPCR) is a promising tool for diagnosis of infectious disease among samples with low copy number. To date, no publications have investigated the utility of ddPCR in the detection of M. leprae. The aim of this study was to develop and evaluate a ddPCR assay for the diagnosis of PB leprosy.

          Methodology

          The two most sensitive DNA targets for detection of M. leprae were selected from electronic databases for assessment of sensitivity and specificity by quantitative polymerase chain reaction (qPCR) and ddPCR. Control patients (n = 59) suffering from other dermatological diseases were used to define the cut-off of the duplex ddPCR assay. For comparative evaluation, qPCR and ddPCR assays were performed in 44 PB patients and 68 multibacillary (MB) patients.

          Principal findings

          M. leprae-specific repetitive element ( RLEP) and groEL (encoding the 65 kDa molecular chaperone GroEL) were used to develop the ddPCR assay by systematically analyzing specificity and sensitivity. Based on the defined cut-off value, the ddPCR assay showed greater sensitivity in detecting M. leprae DNA in PB patients compared with qPCR (79.5% vs 36.4%), while both assays have a 100% sensitivity in MB patients.

          Conclusions/Significance

          We developed and evaluated a duplex ddPCR assay for leprosy diagnosis in skin biopsy samples from leprosy patients. While still costly, ddPCR might be a promising diagnostic tool for detection of PB leprosy.

          Author summary

          Leprosy, or Hansen’s disease, is a chronic bacterial disease caused by M. leprae. Although it is curable and early treatment averts most disabilities, it remains an important global health concern. This is mainly due to delayed diagnosis. In leprosy, a reliable and early diagnostic tool, is still needed. In recent decades years, the quantitative PCR (qPCR) based on nucleic acid detection has been employed for leprosy diagnosis, which exhibited high sensitivity. The performance of qPCR assays, however, greatly varied in different studies, especially in the diagnosis of PB patients. ddPCR is a new and sensitive method used in the examination of pathogenic microorganism, showing considerable reliability and efficiency in other infectious diseases. To our knowledge, no publication reported the ddPCR assay for leprosy diagnosis. Herein, we developed and evaluated a ddPCR assay for detecting M. leprae in skin biopsy samples. Our results suggest that ddPCR specially targeting RLEP and groEL genes could be a promising tool to the detection of M. leprae in PB leprosy with a higher sensitivity than qPCR. This research provides a new molecular biology methods for leprosy diagnosis.

          Related collections

          Most cited references27

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          The Missing Millions: A Threat to the Elimination of Leprosy

          Introduction Leprosy is a slow, chronic disease with a long incubation period caused by Mycobacterium leprae. The clinical presentation varies across a wide spectrum from tuberculoid to lepromatous leprosy. The condition is characterized by skin lesions and damage to peripheral nerves leading to physical disability and social problems. The past 50–60 years have witnessed remarkable progress in the fight against leprosy. The introduction of dapsone therapy in the late 1940s was the first effective treatment for leprosy, and this was followed by the move to short course multidrug therapy (MDT) in 1981. The World Health Assembly Resolution in 1991 [1] to “eliminate leprosy as a public health problem” by the year 2000 galvanised extraordinary international support resulting in the fall in the point prevalence of patients registered for treatment of leprosy by over 90% to less than 1 in 10,000 at the global level. The effort was led by the World Health Organization (WHO) and supported by national governments and their health service staff, the Nippon Foundation, Novartis, the International Federation of Anti-Leprosy Organizations (ILEP), local non-governmental organizations (NGOs), and by people affected by leprosy. Since 2000, the focus has moved from prevalence of leprosy to incidence as measured by reported new case detection to sustain the achievements and to reduce the burden of disease, particularly on reduction and prevention of disability associated with leprosy and rehabilitation of those facing the long-term consequences of the disease [2]. Understanding Transmission Despite this remarkable progress, understanding of the pathogenesis of leprosy has remained unclear. Basic knowledge of the transmission of M. leprae, portals of exit and entry, the role of the environment and animal reservoirs, the development of immune responses following infection, and the pathogenesis of M. leprae infection to the disease of leprosy are all limited. A recent expert group, hosted by effect: hope (The Leprosy Mission Canada) and the National School of Tropical Medicine at Baylor College of Medicine in Houston, Texas, United States, reviewed the evidence and recent research on transmission and how to block it. Novel methods in strain typing M. leprae and recent findings in both host genetics and immune responses open the potential for new solutions. However, the very long incubation period, the very low incidence rates in those exposed, and the insidious clinical presentation create real challenges to developing strategies to interrupt transmission [3]. Global Trends in Leprosy Global data on the trends in new case detection in leprosy are collated and published annually by WHO [4]. There are concerns about the quality and completeness of these data [5,6]. These data describe new case trends from detection through the completion of MDT at national, regional, and global levels. Fig 1 plots the number of new leprosy cases by year. The red continuous line represents the observed annual new case detection rate between 1985 and 2012, with extrapolation to 2020 based on the trend after 2005 (red dotted line). The blue continuous line is the predicted new case detection rate based on modeling with the SIMLEP model, applying an intermediate scenario in the presence of an infant BCG vaccination programme [7]. These trends in the last decade show a very striking feature (Fig 1, red line): a dramatic and sudden decline in new case detection of over 60% over a short period of time (2001–2005). Understanding the possible explanations for this dramatic fall is very important. One explanation is that this represents a true fall in the incidence of leprosy following reduction in transmission of M. leprae infection. Disease modeling work [7] has suggested that the long-term underlying trend in leprosy incidence in a good scenario including infant BCG immunization is a slow, gradual decline of around 4.4% per year. A large, sudden fall in transmission seems biologically implausible given the long and variable incubation period in leprosy and the evidence of continuing, significant rates of new cases in children [4]. A second explanation is that there was substantial overdiagnosis of leprosy prior to 2001, which has inflated the previous levels of new case detection. This may be a factor to explain the peak of new case detection between 1996 and 2001, a period of intensified case detection activities [8], such as Leprosy Elimination Campaigns (LEC) and Special Action Projects for the Elimination of Leprosy (SAPEL). However, the new case detection trends between 1985 and 1996 are remarkably stable and sustained overdiagnosis seems unlikely over this period. The third, and most probable, explanation is that the dramatic fall in new case detection is a result of a decline in leprosy activities following the declaration of elimination as a public health problem globally, and in individual countries. This decline includes reduced intensity and coverage of case detection activities, community awareness, and training in the diagnosis and treatment of leprosy often associated with the move from vertical leprosy control activities to integrated approaches. The recent rise in disability in new cases detected and the increasing delay in diagnosis reported by many countries supports this explanation [4]. WHO, along with the Nippon Foundation, called an International Leprosy Summit in 2013 to address what they called “stagnation” in the leprosy control. This resulted in the Bangkok Declaration [9], signed by the health ministers of the major leprosy endemic countries, calling for renewed political commitment to leprosy control. 10.1371/journal.pntd.0003658.g001 Fig 1 Number of new leprosy cases by year. The red continuous line represents the observed annual new case detection rate between 1985 and 2012, with extrapolation to 2020 based on the trend after 2005 (red dotted line). The blue continuous line is the predicted new case detection rate based on modeling with the SIMLEP model, applying an intermediate scenario in the presence of an infant BCG vaccination programme [7]. The Implications of the Decline in New Case Detection for the Elimination of Leprosy Fig 1 shows how the model prediction of the long-term trend in new leprosy case detection based on the observed figures before 2000 compares with the observed new case detection. The resulting difference between the expected and observed numbers of new cases of leprosy between 2000 and 2012 is approximately over 2.6 million. This number will increase to over 4 million by 2020. This analysis implies that there may be a large accumulation of people with leprosy in the community who remain undiagnosed and untreated. This assertion is supported by evidence from recent sample surveys in endemic areas detecting many as yet untreated cases in Bangladesh [10] and in India [11]. This large number of undetected cases represents a major threat to leprosy control and contributes to the increased burden of infection in the community and an increased pressure on transmission. This has major consequences for the road map for NTDs in the London Declaration [12–14], which targets “interruption of transmission” and “global elimination” of leprosy by 2020. Response to This Threat to Leprosy Elimination It is vital that all involved and concerned with leprosy control appreciate this situation and recognise that the London Declaration targets of “global elimination” of leprosy and “interruption of transmission” by 2020 are likely to be unobtainable and that revised targets are needed. Major commitments and resources need to be made available without delay. While local elimination (based on new cases detected in a defined locality) of leprosy through targeted leprosy control activities as recommended by WHO is necessary in the short-term, the complete interruption of transmission at a global level will require new tools based on game-changing discoveries. A significant investment in complementary research efforts, designed to better understand the basic elements of transmission, is necessary for achieving “interruption of transmission.” The development of collaboration with other NTD programmes represents a real opportunity to improve the coverage, quality, and cost-effectiveness of leprosy control with numerous cross-cutting opportunities in drug delivery, surveillance, training, disability prevention, and morbidity management. The commitment called for by health ministers in the Bangkok Declaration is also essential at all levels, internationally, nationally, and locally by national governments and by all agencies that support national programmes, including Governmental and non-governmental agencies, industry, and people affected by leprosy. The global introduction of post-exposure prophylaxis [15–17] is a real opportunity to re-energise leprosy control activities through increased community awareness, capacity building, and active management of contacts. The research opportunity recently launched by the Leprosy Research Initiative leads the way to develop further innovations for leprosy control, but much more support is needed for basic, as well as operational, research to develop strategies to interrupt transmission. For example, recent findings have revealed new insights into zoonotic relationships, genetic markers for host susceptibility and resistance, as well as environmental factors that continue to test our long-held notions of the ecology of M. leprae and leprosy. Understanding these relationships may provide the knowledge to move from management practices to strategies designed to stop transmission. The WHO priority to promote early detection and to monitor this through measuring disability in new case detection is a vital component to evaluate enhanced initiatives designed to reduce transmission. However, addressing the gap between the incidence and case detection of leprosy requires improved strategies for case detection, new tools for early diagnosis, and major efforts to improve community awareness and capacity of health staff to diagnose and manage leprosy and its complications. The challenge is to tackle the research gaps through novel collaborations, to improve operational collaborations with multiple players in all NTDs, and to incorporate new approaches in community engagement that would enhance public health at the community level. The leprosy world, including WHO, national governments, NGOs, the research community, and industry, together with people affected by leprosy, must respond to this situation that, if left unaddressed, could see all the past achievements in leprosy control reversed.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            Comparison of Droplet Digital PCR and Seminested Real-Time PCR for Quantification of Cell-Associated HIV-1 RNA

            Cell-associated (CA) HIV-1 RNA is considered a potential marker for assessment of viral reservoir dynamics and antiretroviral therapy (ART) response in HIV-infected patients. Recent studies employed sensitive seminested real-time quantitative (q)PCR to quantify CA HIV-1 RNA. Digital PCR has been recently described as an alternative PCR-based technique for absolute quantification with higher accuracy compared to qPCR. Here, a comparison was made between the droplet digital PCR (ddPCR) and the seminested qPCR for quantification of unspliced (us) and multiply spliced (ms) CA HIV-1 RNA. Synthetic RNA standards and CA HIV-1 RNA from infected patients on and off ART (N = 34) were quantified with both methods. Correlations were observed between the methods both for serially diluted synthetic standards (usRNA: R2 = 0.97, msRNA: R2 = 0.92) and patient-derived samples (usRNA: R2 = 0.51, msRNA: R2 = 0.87). Seminested qPCR showed better quantitative linearity, accuracy and sensitivity in the quantification of synthetic standards than ddPCR, especially in the lower quantification ranges. Both methods demonstrated equally high detection rate of usRNA in patient samples on and off ART (91%), whereas ddPCR detected msRNA in larger proportion of samples from ART-treated patients (p = 0.13). We observed an average agreement between the methods for usRNA quantification in patient samples, albeit with a large standard deviation (bias = 0.05±0.75 log10). However, a bias of 0.94±0.36 log10 was observed for msRNA. No-template controls were consistently negative in the seminested qPCR, but yielded a positive ddPCR signal for some wells. Therefore, the false positive signals may have affected the detection power of ddPCR in this study. Digital PCR is promising for HIV nucleic acid quantification, but the false positive signals need further attention. Quantitative assays for CA HIV RNA have the potential to improve monitoring of patients on ART and to be used in clinical studies aimed at HIV eradication, but should be cross-validated by multiple laboratories prior to wider use.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Comparison of next-generation droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of Cryptosporidium oocysts in faecal samples.

              Clinical microbiology laboratories rely on quantitative PCR for its speed, sensitivity, specificity and ease-of-use. However, quantitative PCR quantitation requires the use of a standard curve or normalisation to reference genes. Droplet digital PCR provides absolute quantitation without the need for calibration curves. A comparison between droplet digital PCR and quantitative PCR-based analyses was conducted for the enteric parasite Cryptosporidium, which is an important cause of gastritis in both humans and animals. Two loci were analysed (18S rRNA and actin) using a range of Cryptosporidium DNA templates, including recombinant plasmids, purified haemocytometer-counted oocysts, commercial flow cytometry-counted oocysts and faecal DNA samples from sheep, cattle and humans. Each method was evaluated for linearity, precision, limit of detection and cost. Across the same range of detection, both methods showed a high degree of linearity and positive correlation for standards (R(2)⩾0.999) and faecal samples (R(2)⩾0.9750). The precision of droplet digital PCR, as measured by mean Relative Standard Deviation (RSD;%), was consistently better compared with quantitative PCR, particularly for the 18S rRNA locus, but was poorer as DNA concentration decreased. The quantitative detection of quantitative PCR was unaffected by DNA concentration, but droplet digital PCR quantitative PCR was less affected by the presence of inhibitors, compared with quantitative PCR. For most templates analysed including Cryptosporidium-positive faecal DNA, the template copy numbers, as determined by droplet digital PCR, were consistently lower than by quantitative PCR. However, the quantitations obtained by quantitative PCR are dependent on the accuracy of the standard curve and when the quantitative PCR data were corrected for pipetting and DNA losses (as determined by droplet digital PCR), then the sensitivity of both methods was comparable. A cost analysis based on 96 samples revealed that the overall cost (consumables and labour) of droplet digital PCR was two times higher than quantitative PCR. Using droplet digital PCR to precisely quantify standard dilutions used for high-throughput and cost-effective amplifications by quantitative PCR would be one way to combine the advantages of the two technologies.
                Bookmark

                Author and article information

                Contributors
                Role: Formal analysisRole: MethodologyRole: Writing – original draft
                Role: Funding acquisitionRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: Methodology
                Role: MethodologyRole: Writing – review & editing
                Role: Methodology
                Role: Formal analysisRole: Methodology
                Role: Formal analysisRole: Methodology
                Role: Methodology
                Role: Methodology
                Role: Methodology
                Role: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Negl Trop Dis
                PLoS Negl Trop Dis
                plos
                plosntds
                PLoS Neglected Tropical Diseases
                Public Library of Science (San Francisco, CA USA )
                1935-2727
                1935-2735
                18 March 2019
                March 2019
                : 13
                : 3
                : e0007284
                Affiliations
                [1 ] Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, Shandong, China
                [2 ] Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, Shandong, China
                [3 ] National Clinical Key Project of Dermatology and Venereology, Jinan, Shandong, China
                [4 ] Shandong Provincial Hospital for Skin Diseases, Shandong University, Jinan, Shandong, China
                [5 ] School of Medicine and Life Science, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong, China
                Faculty of Science, Ain Shams University (ASU), EGYPT
                Author notes

                The authors have declared that no competing interests exist.

                ‡ HL and FZ also contributed equally to this work.

                Author information
                http://orcid.org/0000-0002-3383-1973
                Article
                PNTD-D-18-01629
                10.1371/journal.pntd.0007284
                6438576
                30883558
                e244e36f-97d6-475c-929d-d78332668ae8
                © 2019 Cheng 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.

                History
                : 23 October 2018
                : 7 March 2019
                Page count
                Figures: 1, Tables: 2, Pages: 11
                Funding
                Funded by: National Key Research and Development Program of China
                Award ID: 2016YFE0201500
                Award Recipient :
                Funded by: Innovation Project of Shandong Academy of Medical Science
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81601387
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100007129, Natural Science Foundation of Shandong Province;
                Award ID: JQ201616
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81822038
                Award Recipient :
                FZ is financially supported by the National Key Research and Development Program of China (2016YFE0201500), and the Innovation Project of Shandong Academy of Medical Science. LS is financially supported through a grant from the National Natural Science Foundation of China (81601387) ( https://isisn.nsfc.gov.cn/egrantweb/). HL is financially supported through a grant from the Natural Science Foundation of Shandong Province (JQ201616) ( http://jihlx.sdstc.gov.cn/STDPMS/JQ/Default.aspx) and the National Natural Science Foundation of China (81822038) ( https://isisn.nsfc.gov.cn/egrantweb/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
                Categories
                Research Article
                Medicine and Health Sciences
                Infectious Diseases
                Bacterial Diseases
                Leprosy
                Medicine and Health Sciences
                Tropical Diseases
                Neglected Tropical Diseases
                Leprosy
                Biology and Life Sciences
                Organisms
                Bacteria
                Actinobacteria
                Mycobacterium Leprae
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Medicine and Health Sciences
                Surgical and Invasive Medical Procedures
                Biopsy
                Medicine and Health Sciences
                Diagnostic Medicine
                Biology and Life Sciences
                Genetics
                DNA
                Biology and Life Sciences
                Biochemistry
                Nucleic Acids
                DNA
                Research and analysis methods
                Extraction techniques
                DNA extraction
                Medicine and Health Sciences
                Infectious Diseases
                Custom metadata
                vor-update-to-uncorrected-proof
                2019-03-28
                All relevant data are within the manuscript and its Supporting Information files.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

                Comments

                Comment on this article