Real-Time PCR Applications for Diagnosis of Leishmaniasis Luca Galluzzi* , Marcello Ceccarelli, Aurora Diotallevi, Michele Menotta and Mauro Magnani

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Real-Time PCR Applications for Diagnosis of Leishmaniasis Luca Galluzzi* , Marcello Ceccarelli, Aurora Diotallevi, Michele Menotta and Mauro Magnani Galluzzi et al. Parasites & Vectors (2018) 11:273 https://doi.org/10.1186/s13071-018-2859-8 REVIEW Open Access Real-time PCR applications for diagnosis of leishmaniasis Luca Galluzzi* , Marcello Ceccarelli, Aurora Diotallevi, Michele Menotta and Mauro Magnani Abstract Leishmaniasis is a vector-borne disease caused by many Leishmania species, which can infect both humans and other mammals. Leishmaniasis is a complex disease, with heterogeneous clinical manifestations ranging from asymptomatic infections to lesions at cutaneous sites (cutaneous leishmaniasis), mucosal sites (mucocutaneous leishmaniasis) or in visceral organs (visceral leishmaniasis), depending on the species and host characteristics. Often, symptoms are inconclusive and leishmaniasis can be confused with other co-endemic diseases. Moreover, co-infections (mainly with HIV in humans) can produce atypical clinical presentations. A correct diagnosis is crucial to apply the appropriate treatment and the use of molecular techniques in diagnosis of leishmaniasis has become increasingly relevant due to their remarkable sensitivity, specificity and possible application to a variety of clinical samples. Among them, real-time PCR (qPCR)-based approaches have become increasingly popular in the last years not only for detection and quantification of Leishmania species but also for species identification. However, despite qPCR-based methods having proven to be very effective in the diagnosis of leishmaniasis, a standardized method does not exist. This review summarizes the qPCR-based methods in the diagnosis of leishmaniasis focusing on the recent developments and applications in this field. Keywords: HRM, Leishmania, Leishmaniasis, Melting curve analysis, Molecular diagnosis, qPCR, Real-time PCR Background patients or animals is lacking [3], impairing accurate epi- Leishmaniasis is caused by protozoan parasites of the demiological data collection and thus limiting the disease genus Leishmania. This genus includes three subgenera: control. Moreover, false-negative results could delay treat- Leishmania, Viannia and Sauroleishmania. Each subgenus ment, thus contributing to reservoirs maintenance. Several presents different complexes and each complex includes immunological and molecular diagnostic tools for diagno- several species [1]. Depending on the Leishmania species sis of leishmaniasis have been developed recently [4]. In and host characteristics, the infection can be asymptomatic particular, the use of molecular techniques has become or it can lead to a spectrum of diseases, notably cutaneous increasingly relevant due to their high sensitivity, specifi- leishmaniasis (CL), visceral leishmaniasis (VL) or mucocu- city and possible application to a variety of clinical sam- taneous leishmaniasis (MCL). About 12 million people are ples. Among them, the real-time PCR, also named affected by the disease; moreover, 0.2–0.4 million cases per quantitative PCR (qPCR), has become increasingly popu- year and 0.7–1.2 million cases per year have been esti- lar recently since it is fast, has broad dynamic range, and matedforVLandforCL,respectively[2]. Infections are cross-contamination is drastically reduced because there widespread both in the Americas (New World) and in is no need to open reaction tubes for post-PCR analyses. Europe, Africa, Asia (Old World), therefore constituting an The qPCR relies on analysis of fluorescent signal pro- important global health problem. duced during amplification. Fluorescence can be gener- The diagnosis of leishmaniasis relies on clinical manifes- ated by using intercalating fluorescent dyes (e.g. SYBR tations, epidemiological and laboratory data. Concerning Green) or fluorescent probes (e.g. TaqMan®). The assays the laboratory methods, a gold-standard for human based on intercalating dyes are characterized by high sen- sitivity, as long as primers are highly specific to the target * Correspondence: [email protected] sequence to avoid generation of non-specific products that Department of Biomolecular Sciences, University of Urbino Carlo Bo, via Saffi would lead to overestimated or false positive results. A 2, 61029 Urbino, PU, Italy © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Galluzzi et al. Parasites & Vectors (2018) 11:273 Page 2 of 13 melting curve analysis can be performed post-PCR to (approximately 23 Kb each) linked in a concatenated ensure the presence of a single specific amplicon. For network. genotyping purposes, high resolution melt (HRM) analysis can be used to differentiate amplicons based on sequence Non-protein-coding regions variations [5]. The use of probes is typically more expen- The kDNA minicircles account for approximately 95% sive. However, using probes allows multiplexing (partially of kDNA and encode small guide RNAs (gRNAs), reducing the cost per assay) and furnish additional specifi- needed for RNA-editing of the transcripts encoded by city to the assay. Therefore, this approach is less subject to maxicircles [12]. Since minicircles are present in thou- false positives than the intercalating dye method. sands of copies per cell, they are ideal targets for highly A search in PubMed in February 2018 with the wildcard sensitive detection of Leishmania [13, 14]. Each minicir- term “Leishmania*” in conjunction with the search terms cle is composed of a conserved region containing the “real-time PCR or qPCR”, found over 540 published man- origin of replication, and a variable region encoding usu- uscripts from 2001 to February 2018. A further combin- ally a single gRNA [15]. The minicircle network is com- ation with the wildcard terms “quantif*” or “detect*” or posed of different minicircle classes. Their number can “diagnos*” and a manual sift of the papers identified nearly be variable and dependent from strain; in a recent work, 180 manuscripts focusing on the topic of this review. the presence of over 100 minicircles classes has been Nevertheless, many of these publications apply similar demonstrated in a strain of L. tarentolae using NGS assays. technology [16]. The pioneering works of Bretagne et al. [6] and The minicircle conserved region contains 3 conserved Nicolas et al. [7] described two qPCR-based methods to sequence blocks (CSB-1, CSB-2 and CSB-3) that could detect and quantify Leishmania parasites using the DNA be effective targets for PCR amplification of all minicir- polymerase gene and the minicircles kinetoplast DNA cle classes. However, polymorphisms have been shown (kDNA) as a target, respectively. Since then, a variety of in CSB-1 region of L. infantum [14] and, using primers qPCR-based assays have been developed on different amplifying a subpopulation of minicircles, also in CSB-2 molecular targets, not only for detection and quantifica- region of New World species [17]. In general, the assays tion of Leishmania species but also for genotyping and designed on minicircles conserved regions identify Leish- species identification. Regarding the detection chemistry, mania parasites only at the genus or subgenus level. In SYBR Green and TaqMan® probes were most widely fact, qPCR assays intended for a single species designed employed, followed by other probes, such as FRET on minicircles can potentially amplify more than one Leish- probes [8, 9] or MGB probes [10]. The sensitivity and mania species, as shown by several authors [14, 18–22]. specificity reported for published qPCR assays is vari- Among targets on chromosomal DNA, different able. For instance, qPCR assays developed for VL diag- regions of ribosomal RNA (rRNA) genes, termed riboso- nosis in humans showed a specificity variation between mal DNA (rDNA), have been used. Tens or hundreds of 29.6–100% and sensitivity between 91.3–100%, indicat- copies of rDNA unit can be present per Leishmania cell, ing the usefulness of the qPCR when a sensitive tool is allowing sufficient sensitivity for analyzing clinical sam- pivotal [4]. ple DNA [23, 24]. Each rDNA repeat unit consists of In this review, recent developments and applications several genes and spacers: the SSU rRNA gene (18S) is of qPCR-based methods in the diagnosis of leishmaniasis followed by 5.8S and LSU genes; two internal transcribed are summarized, highlighting advances and limits of this spacer regions -ITS1 and ITS2 - are located between the powerful technique. 18S and 5.8S genes and between 5.8S and LSUα genes, respectively [25]. The 18S rDNA region, due to its highly Molecular targets conserved nature, is commonly utilized to design Many qPCR-based approaches for the diagnosis of primers and/or probes for the diagnosis of Leishmania leishmaniasis have been published based on coding spp. [26]. On the other hand, the ITS regions, which and/or non-coding regions in the Leishmania genome. have more variable sequences, can be used for typing at Leishmania spp. have 34–36 chromosomes and a the species level [24, 27, 28]. unique genomic organization in which protein-coding In principle, qPCR assays designed on minicircles genes are
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