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      Leishmania enriettii (Muniz & Medina, 1948): A highly diverse parasite is here to stay

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          Abstract

          Leishmaniases are a spectrum of diseases caused by protozoans from the genus Leishmania (Kinetoplastida: Trypanosomatidae) and are divided into 2 main clinical forms: tegumentary leishmaniasis (TL) and visceral leishmaniasis (VL). Transmission occurs after the bite of sandfly vectors (Diptera: Phlebotominae) when females take a blood meal from the vertebrate host [1]. In the New World, several species of Leishmania (~20) cause disease to man, the symptoms and epidemiology of which vary depending on species. However, there are species that are nonpathogenic to humans, such as L. enriettii. In 1946, Medina observed ear lesions in 2 farm-reared guinea pigs (Cavia porcellus [Rodentia: Cavida]) from the neighboring state of São Paulo. After lesion analysis, Leishmania was confirmed as the pathogen. The complete L. enriettii description was published by Muniz and Medina in 1948 at the Federal University of Paraná, Brazil [2]. Although this species has been used as a model for cutaneous leishmaniasis (CL), many aspects of its biology remain unknown. In the past 6 years, an increased interest has emerged after the finding of a similar isolate in the red kangaroo (Macrofus rufus) in Australia [3]. This article aims to summarize some of the most important publications on this unique pathogen. It demonstrates a high phenotypic plasticity, being able to infect different vertebrate hosts and vectors. It also discusses recent human and veterinary infections due to other L. enriettii complex members. L. enriettii: Vertebrate hosts After L. enriettii discovery in C. porcellus in the 1940s [4], the authors failed to infect monkeys, dogs, and wild guinea pigs (C. aperea). They succeeded in infecting only 1 hamster out of 8 animals, and its lesion was poorly infected [2]. This is very likely to occur with wild reservoirs of Leishmania, such as opossums and armadillos, which, in nature, harbor low parasite densities without visible infection. At that time, no molecular approaches were available, opening the possibility of detecting L. enriettii in wild reservoirs other than C. aperea (Fig 1). 10.1371/journal.ppat.1006303.g001 Fig 1 Cavia porcellus infected with Leishmania enriettii in the nose. (A) Four to 7 weeks of infection and (B) healed lesion after 8–10 weeks of infection. In spite of that, L. enriettii epidemiological studies involving hosts in Brazil are scarce, and new information on this parasite did not emerge until almost 50 years later. Two infected guinea pigs from the city of Capão Bonito (São Paulo state) and 3 from Campina Grande do Sul (Paraná state) were found. Species status was confirmed by isoenzyme analysis, with the description of a zymodeme polymorphism in the strains from Paraná [5]. Those data suggest that L. enriettii seems located in the Southern parts of Brazil, but its presence in other states should be prospected. A recent interesting study on Leishmania detection in road-killed wild animals in São Paulo found 1 C. aperea (1/4) infected with Leishmania. Although this study did not type the species, it provided some evidence that sylvatic C. aperea could harbor Leishmania [6]. Although the above-mentioned rodents have been considered the most common reservoirs for L. enriettii in Brazil, the finding of a putative similar isolate in captive red kangaroos (M. rufus), northern wallaroos (Macropus robustus woodwardii), black wallaroos (M. bernardus), and agile wallabies (M. agilis) was a landmark in the leishmaniasis epidemiology in Australia. The complete identification at species level only came in 2011 [3], classifying this isolate as a member of the L. enriettii complex [7]. L. enriettii: Possible invertebrate vectors Only 20 years after the description of L. enriettii (1967), evidence appeared regarding its invertebrate host [8]. A survey of phlebotomine fauna in Paraná state identified Lutzomyia monticola and Lutzomyia correalimai in the vicinities where the guinea pigs were infected. Experimental sandfly infections on those guinea pigs were performed where 60% (6/10) of L. monticula exhibited a very high infection in their midguts. For this reason, L. enriettii was considered a suprapylarian species and included in the subgenus Leishmania. The authors recovered those parasites from sandflies and inoculated naive guinea pigs. However, no development of infection was observed, and transmission through L. monticola bite has yet to be determined. Since no L. monticola laboratory colony is available, transmission experiments are difficult to perform. For this reason, it is a challenge to ascertain its current status as a L. enriettii vector. This vector is widely spread from southern to northern Brazilian states. Although L. monticola has no human medical importance, it is very anthropophilic and is often captured together with vectors of CL and VL. More importantly, its distribution overlaps with domestic C. porcellus and wild C. aperea, reinforcing further studies with this vector. In spite of having many sandfly species in Australia, the first evidence that midges from the subgenus Forcipomyia (Lasiohelea) (Diptera: Ceratopogonidae) could be an alternative vector of Leishmania has emerged. Although this vector fell into most of the Killick-Kendrick criteria, transmission still needs to be demonstrated after its colonization [3]. It is important to mention that this work triggered a recent increase in studying L. enriettii by many groups. Recently, 2 other ceratopogonids (Culicoides nubeculosus and Culicoides sonorensis) and Lutzomyia longipalpis were tested for L. enriettii infection using 2 strains (Brazilian and Australian) [9]. Only C. sonorensis was able to sustain infection, whereas L. longipalpis (permissive vector) developed moderate infections. Those data remarkably demonstrated L. enriettii’s ability to sustain and develop infection in different invertebrate hosts. Also, those studies stimulate further epidemiological investigations to identify other potential/alternative non–sandfly vectors. The L. enriettii complex members in human and veterinary infections A detailed and historical review on Leishmania and sandflies was recently reported. However, a universal consensus regarding Leishmania classification is yet to be achieved [1], especially for the “L. enrietti complex.” In addition to L. enriettii, it may include Leishmania martiniquensis [10], “Leishmania siamensis” [11], and the Australian isolate [12]. In spite of the molecular techniques in establishing phylogenetic relationships among Leishmania species, a few studies have included L. enriettii complex members. The L. martiniquensis (strain MAR1) was isolated in Martinique Island, French Antilles, in 1995, causing diffuse CL in an HIV-infected patient [13]. A similar human isolate of L. martiniquensis causing VL was also reported from Thailand [14,15]. Finally, “L. siamensis” was first reported in Thailand as causing VL [16] and disseminated CL/VL in a patient with HIV. The isolate from this patient was named Trang strain and had 100% identity with L. enrietti after molecular analysis [11]. More recently, some isolates of L. enriettii complex members, probably “L. siamensis” and L. martiniquensis, were isolated from CL lesions in Ghana [15]. Detection of this species was also reported from a low number of cases in horses from Florida (2) [17] and Central Europe (6) [18] and in 1 cow from Switzerland [19]. However, as mentioned by Kwakye-Nuako et al. [15], although it appeared in the literature several times, the species “L. siamensis” was not formally described, and its name should be used in quotation marks. The above-mentioned data suggest that members of L. enriettii complex are able to infect a wide range of different hosts, from rodents to humans, and to cause many clinical manifestations. In Table 1, we summarized some of the main isolates and reference strains of the L. enriettii complex members. Therefore, an international consortium for whole genome sequencing could be useful to ascertain the taxonomic status of this complex using those strains. This is of importance since the real status of “L. siamensis” and L. martiniquensis are still the subject of debate. 10.1371/journal.ppat.1006303.t001 Table 1 Available isolates and strains of the Leishmania enriettii complex. Species World Health Organization code Reference L. enriettii MCAV/BR/1945/L88MCAV/BR/95/CUR3MCAV/BR/1985/COBAIA_SPMCAV/BR/45/LV90AM-2004 [20–23][22][23][9][12] “L. siamensis” TrangMHOM/GH/2012/GH5; LV757MHOM/GH/2012/GH10; LV758MHOM/GH/2012/GH11; LV759 [11][15][15][15] L. martiniquensis MHOM/MQ/92/MAR 1MHOM/MQ/92/MAR 2MHOM/TH/2012/LSCM1 [10, 13, 24][10][14] Concluding remarks Since its discovery in the 1940s, L. enriettii studies have been occurring in pulses. In the 1950s and 1960s, most of the studies were focused on its biology, transmission, and epidemiology. Later on, in the 1970s, some immunopathological and immunological studies appeared. In the 1990s, its use as a model for molecular biology was successfully employed. More recently, the findings of other putative L. enriettii complex members such as L. martiniquensis and “L. siamensis” have generated great interest in understanding the taxonomical relationships among those different isolates. Whole genome sequencing would be a very important tool to investigate such relationships and help to establish their real species status. The species of this complex exhibit a high phenotypic plasticity in being able to infect a wide range of vertebrate hosts, including humans and other vectors. They may also cause different symptoms, ranging from CL to VL. However, many aspects of their epidemiology are still unknown in the geographic areas where those parasites were isolated. Although there is strong evidence of some suspected vectors, another important gap yet to be demonstrated is vectorial transmission by either ceratopogonids or L. monticula. In this context, almost 70 years after L. enriettii discovery, many questions and uncertainties about its biology, epidemiology, classification, and immunology remain unanswered. The finding of members of this complex on different continents and its veterinary and human medical importance, especially in patients with HIV, reinforces the need for more studies. Several groups in the world are now investigating those parasites, and an increase in the published papers in the past years has demonstrated that this parasite is here to stay.

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          A Historical Overview of the Classification, Evolution, and Dispersion of Leishmania Parasites and Sandflies

          Background The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale. Methodology and Principal Findings Leishmania and sandfly classification has always been a controversial matter, and the increasing number of species currently described further complicates this issue. Despite several hypotheses on the origin, evolution, and distribution of Leishmania and sandflies in the Old and New World, no consistent agreement exists regarding dissemination of the actors that play roles in leishmaniasis. For this purpose, we present here three centuries of research on sandflies and Leishmania descriptions, as well as a complete description of Leishmania and sandfly fossils and the emergence date of each Leishmania and sandfly group during different geographical periods, from 550 million years ago until now. We discuss critically the different approaches that were used for Leishmana and sandfly classification and their synonymies, proposing an updated classification for each species of Leishmania and sandfly. We update information on the current distribution and dispersion of different species of Leishmania (53), sandflies (more than 800 at genus or subgenus level), and animal reservoirs in each of the following geographical ecozones: Palearctic, Nearctic, Neotropic, Afrotropical, Oriental, Malagasy, and Australian. We propose an updated list of the potential and proven sandfly vectors for each Leishmania species in the Old and New World. Finally, we address a classical question about digenetic Leishmania evolution: which was the first host, a vertebrate or an invertebrate? Conclusions and Significance We propose an updated view of events that have played important roles in the geographical dispersion of sandflies, in relation to both the Leishmania species they transmit and the animal reservoirs of the parasites.
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            Evidence incriminating midges (Diptera: Ceratopogonidae) as potential vectors of Leishmania in Australia.

            The first autochthonous Leishmania infection in Australia was reported by Rose et al. (2004) and the parasite was characterised as a unique species. The host was the red kangaroo (Macropus rufus) but the transmitting vector was unknown. To incriminate the biological vector, insect trapping by a variety of methods was undertaken at two field sites of known Leishmania transmission. Collected sand flies were identified to species level and were screened for Leishmania DNA using a semi-quantitative real-time PCR. Collections revealed four species of sand fly, with a predominance of the reptile biter Sergentomyia queenslandi (Hill). However, no Leishmania-positive flies were detected. Therefore, alternative vectors were investigated for infection, giving startling results. Screening revealed that an undescribed species of day-feeding midge, subgenus Forcipomyia (Lasiohelea) Kieffer, had a prevalence of up to 15% for Leishmania DNA, with high parasitemia in some individuals. Manual gut dissections confirmed the presence of promastigotes and in some midges material similar to promastigote secretory gel, including parasites with metacyclic-like morphology. Parasites were cultured from infected midges and sequence analysis of the Leishmania RNA polymerase subunit II gene confirmed infections were identical to the original isolated Leishmania sp. Phylogenetic analysis revealed the closest known species to be Leishmania enriettii, with this and the Australian species confirmed as members of Leishmania sensu stricto. Collectively the results strongly suggest that the day-feeding midge (F. (Lasiohelea) sp. 1) is a potential biological vector of Leishmania in northern Australia, which is to our knowledge the first evidence of a vector other than a phlebotomine sand fly anywhere in the world. These findings have considerable implications in the understanding of the Leishmania life cycle worldwide. Copyright © 2011 Australian Society for Parasitology Inc. All rights reserved.
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              First Isolation of Leishmania from Northern Thailand: Case Report, Identification as Leishmania martiniquensis and Phylogenetic Position within the Leishmania enriettii Complex

              Introduction The leishmaniases are a group of human parasitic diseases caused by several species of the genus Leishmania and transmitted by the bites of female phlebotomine sand flies [1], [2]. Their clinical presentation is highly variable but ranges from relatively benign localised cutaneous leishmaniasis, through a number of more destructive cutaneous forms including mucocutaneous leishmaniasis, to systemic visceral leishmaniasis, which can be fatal if left untreated [1]. Each species of Leishmania tends to cause one, but occasionally more, type of clinical disease. Leishmaniasis occurs in many tropical and subtropical regions of the world, but until relatively recently, excluding imported cases, had not been reported from South-East Asia [2]. The first known autochthonous case was discovered in Thailand in 1996, the patient presenting with visceral leishmaniasis (VL), and with no known immunodeficiency or other underlying disease, however, the species was not identified [3]. Since then, in total 13 cases of leishmaniasis have been reported from Thailand [3]–[10], the majority of these presenting as VL with no known accompanying immunodeficiency, but also some cases of HIV co-infection with broader symptomology, and in some cases cutaneous lesions, have been described [7], [9], [10]. Although the number of cases is still relatively small this certainly underestimates the true incidence, but the clinical picture that is emerging is broadly consistent with VL as found in other endemic regions of the world. Identification of the parasites responsible for leishmaniasis in Thailand has been performed on five occasions using molecular methods [5]–[7], [9], [10]. In one instance the parasite was identified as L. infantum [6], a known agent of VL, albeit in a new location that requires further confirmation. However, in three of the other reports [5], [7], [10] the parasites had very similar but non-identical rRNA ITS-1 sequences that differed from other known Leishmania species, and the fourth [9] reported an 18S rRNA sequence identical to that of one of the earlier reports [5]. These four reports have been taken by some to indicate that one new species is responsible for leishmaniasis in Thailand, and this has been referred to in the literature as “Leishmania siamensis”, the first recorded usage of this name appearing in Muller et al. 2009 [11]. However, to date the species has not been formally named and described, and so here is referred to as “L. siamensis”, nor has its relationship to other species of human-infective or non-pathogenic species been established. Also the view that these reports refer to one species only, the proposed “L. siamensis”, needs to be treated with caution as the only common sequence analysed is the rRNA ITS-1, and it is doubtful that this sequence alone is sufficiently taxonomically reliable or informative to reach such a conclusion. Interestingly, on the basis of ITS-1 sequences reports of parasites apparently similar to “L. siamensis” from Europe [11], [12] and the USA [13] in horses and cows have been made, but unfortunately none of these have been isolated into culture yet to enable more detailed characterisation. Nevertheless, these reports do indicate that “L. siamensis” or related species are emerging pathogens that have a potentially wide geographical range. In this report we describe the isolation for the first time of Leishmania from a person living in northern Thailand, and which we refer to as Leishmania strain Chiang Mai 1 (LSCM1). Moreover, based on large subunit of RNA polymerase II gene sequencing we show that LSCM1 appears to be identical to a parasite previously reported from the Caribbean island of Martinique, and recently named L. martiniquensis [14], [15]. We explore the relationship of LSCM1 to “L. siamensis” and other Leishmania species and show that both belong to the recently proposed L. enriettii complex [16], which appears to represent a new subgenus of Leishmania containing human pathogens. Methods Ethics Statement The patient who was the source of the parasites described in this study was admitted to Maharaj Nakorn Chiang Mai hospital due to ill health with an undiagnosed condition. All the biopsy samples and other clinical investigations performed were part of routine clinical investigative procedures to determine the nature of the illness. No samples or procedures were undertaken for research purposes only. This report does not contain any identifiable information that could be used to compromise patient confidentiality. Isolation of DNA from bone marrow Bone marrow aspiration was performed on the sternum with local anaesthesia, using a sternal puncture needle and 5 ml syringe. DNA extraction was performed using a QIAamp DNA Mini Kit (Qiagen), following the manufacturer's instructions. PCR and DNA sequencing PCR amplification of the rRNA ITS-1 sequence was performed with LeF/LeR primers as previously described [17]. Controls were L. donovani (MHOM/ET/67/HU3; LV9), L. infantum (MCAN/ES/98/LEM-935; JPC; M5), L. tropica (MHOM/IR/60/LV357), L. major (MHOM/IL/80/Friedlin; FV1) and “L. siamensis” (MHOM/TH/2010/PCM2; Trang). New sequences were generated for L. enriettii (MCAV/BR/45/LV90) and L. martiniquensis (MHOM/MQ/92/MAR1; LEM2494). Amplification of the large subunit of RNA Polymerase II was performed with several primer pairs: RPOF1/RPOR1 [16]; PolIIN5/PolIIN6 (GCACTTCATGTTGGACGACT/GTACTTGGTGCGGATCTCCT); PolIIN7/PolIIN8 (AGGAGTACAGGCTGAACGAC/TGTCGTCCACTTGCCGGA); PolIIS1/S2 (GCTACCTACAGCGCAAACTC/TCCTTCAGCAAGTACTCGAAC); and PolIIS3/PolIIS4 (TGCTGAAGGAGTACAAGCTGA/CGTCGCTCTCCATATTCGC), on DNA of LSCM1, L. martiniquensis (MHOM/MQ/92/MAR1; LEM2494), “L. siamensis” (MHOM/TH/2010/PCM2; Trang) and L. colombiensis (IHAR/CO/96/CL500; LEM2334). Amplification was performed with proof-reading DNA polymerase (Qiagen HotStar HiFidelity Polymerase) and products directly sequenced or cloned into pCR2.1-TOPO (Invitrogen) and sequenced using commercial services. Results were checked for quality using Chromas Lite 2.1.1 (http://technelysium.com.au/). Promastigote culture and cryopreservation Promastigote cultures were initiated and maintained at 26°C in 25 cm2 tissue culture flasks using 5–10 ml volumes of Schneider's Drosophila medium supplemented with 20% (v/v) fetal bovine serum, later they were also cultured in Medium 199 supplemented with 10% (v/v) fetal bovine serum and BME vitamins. Promastigotes were cryopreserved in 7.5% (v/v) glycerol in culture medium and stored at −80°C and liquid nitrogen. Phylogenetic analysis Initial alignments and analyses were performed using Clustal W2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/). For phylogenetic analysis, alignment and tree building programmes in MEGA version 6 were used [18]. Accession numbers of sequences used are given in S1 Table. For ITS-1 sequences the Kimura 2-parameter model gave the best fitting model of sequence evolution and was used for tree construction using the maximum likelihood (ML) and neighbour joining (NJ) methods. For the large subunit of RNA polymerase II the Tamura-Nei model gave the best fitting model and was used for tree construction using the ML and NJ methods. Bootstrapping was performed on all trees with 1000 replicates. Results Case report In July 2012, a 52-year-old Thai male farmer without any known underlying diseases was admitted to Maharaj Nakorn Chiang Mai hospital, a tertiary care, university hospital in Northern Thailand, following a 2-week history of low-grade fever, fatigue and 2-kg weight loss. The patient had a history of chronic smoking but had quit for 6 months prior to admission and was previously in good health. He lived in Ban Thi district, Lamphun province, which is located 30 km to the south-east of Chiang Mai and he had never been out of this area. Physical examination revealed body temperature of 37.8°C, heart rate of 72 beats/min, blood pressure of 120/70 mmHg, and respiratory rate of 16/min. The patient had moderate pallor without jaundice. The abdomen showed huge splenomegaly, extending 12 cm below the left costal margin, with a smooth surface, firm consistency and no tenderness. There was no hepatomegaly and no palpable lymph nodes. Laboratory investigations revealed a haemoglobin level of 7.5 g/dL, a white blood cell count of 2,560 cells/mm3 (neutrophils 46%, lymphocytes 34%, eosinophils 4%, basophils 1% and monocytes 15%) and platelet count of 89,000 cells/mm3. Peripheral blood smears showed normochromic and normocytic red blood cells, no rouleaux formation, and decreased white blood cell count with normal maturation. Blood urea nitrogen and creatinine were 18 and 1.4 mg/dL, respectively. Hypoalbuminemia (1.9 g/dL) and hypergammaglobulinemia (8.1 g/dL) were noted. HIV serology was negative. Bone marrow (BM) aspiration showed numerous amastigotes within macrophages (Fig. 1), recognised by their size and presence of nucleus and kinetoplast. Therefore, the patient was diagnosed with visceral leishmaniasis. The BM sample was sent to the Department of Parasitology, Faculty of Medicine, Chiang Mai University for Leishmania species identification. Amphotericin B deoxycholate (1 mg/kg/day) was administered for 21 days, and BM samples taken on the 2nd day and 14th day of treatment showed decreased numbers of amastigotes. The serum creatinine became elevated to a maximum level of 3.1 mg/dL while receiving treatment. However, at 2 weeks after discharge from the hospital the patient was doing well and his serum creatinine had returned to baseline levels. DNA was extracted from BM and used as a template for PCR using the LeF/LeR primers for Leishmania rRNA ITS-1 [17]. A correctly sized PCR product was amplified from initial BM samples, disappearing upon treatment (Fig. 2), confirming the clinical and parasitological diagnosis. 10.1371/journal.pntd.0003339.g001 Figure 1 Light micrograph of Leishmania amastigotes in bone marrow aspirate. Two infected macrophages are stained (large arrows), each with a nucleus (N) and numerous amastigotes (examples with small arrows) within the cytoplasm. The specimen was stained using Wright's stain. The bar represents 20 µm. 10.1371/journal.pntd.0003339.g002 Figure 2 Diagnosis of leishmaniasis by PCR. Agarose gel electrophoresis showing PCR products using the LeF/LeR primers for Leishmania rRNA ITS-1 [17] from patient bone marrow aspirate samples compared to five Leishmania species, 1% gel, stained with ethidium bromide. Lane 1, negative control – no DNA; lane 2, L. donovani; lane 3, L. infantum; lane 4, L. tropica; lane 5, L. major; lane 6, “L. siamensis”PCM2 Trang; lane 7, BM1 is bone marrow collected 2 days after commencement of treatment; lane 8, BM2 is bone marrow collected 14 days after commencement of treatment. Size markers (MW), 100 bp ladder, are as shown. Parasite characterization The Leishmania parasites from the BM specimens were cultured in Schneider's insect medium supplemented with 20% foetal bovine serum (FBS) at 25°C. Promastigote forms were first observed on day 3. Their morphology was generally similar to that described for other Leishmania species (Fig. 3). A range of promastigote morphologies was observed, including some similar to procyclic promastigotes, leptomonad promastigotes and nectomonad promastigotes (Fig. 3A–F) [19]. Although free swimming individual promastigotes were readily observed, rosettes and large aggregates of promastigotes were prevalent in culture (Fig. 3G, H). The strain was sub-cultured until neither red blood cells nor white blood cells were observed and then the promastigotes were cryopreserved in liquid nitrogen. These promastigotes have been continuously maintained in this medium for over one year, and have also been successfully transferred and grown in Medium 199 supplemented with 10% FBS. The WHO code for this strain is MHOM/TH/2012/LSCM1. 10.1371/journal.pntd.0003339.g003 Figure 3 Giemsa-stained promastigote forms from culture. A–H, examples showing morphological variation of forms observed, all at the same magnification, bar in F represents 5 µm. Procyclic-like promastigotes can be observed in A (arrows);, leptomonad-like promastigotes in B and C (arrows); nectomonad-like promastigotes in D, E and F; and rosettes and aggregates in G and H. Identification and phylogenetic analysis An initial molecular identification of LSCM1 was performed by cloning and sequencing the PCR product of the LeF/LeR primers. This was performed on DNA extracted from both an initial BM sample taken on the first day of admission to hospital (before treatment) and on the subsequent culture derived from the BM aspirate. The resulting ITS-1 DNA sequences were identical to each other, and also were identical or very similar to several of the nucleotide sequences previously reported for “L. siamensis” (Figure S1A), but differed from another “L. siamensis”, the PCM2 Trang strain (Figure S1B). However, the LSCM1 ITS-1 sequence was also identical to that of L. martiniquensis (Fig. 4A, 4B). These results indicate that LSCM1 is L. martiniquensis, and further suggest that several other so-called “L. siamensis” isolates may in fact be L. martiniquensis. The other member of the L. enriettii complex shown in Fig. 4 is the parasite described by Dougall et al. [16], a Leishmania species from Australia infecting kangaroos that also has not yet been formally named (AM-2004). 10.1371/journal.pntd.0003339.g004 Figure 4 Phylogenetic analysis of Leishmania strain CM1 using ITS-1 sequences. A: ML tree including LSCM1 (accession number JX898938) with various “L. siamensis” from Thailand and elsewhere: GQ281278 is from a horse, Germany [11]; GQ281282 is from a cow, Switzerland [12]; JX195637 is of human origin from Stun, Thailand [29]; JQ617283 is from a horse, USA [13]; JQ001751, JQ001752 are human isolates from Trang and Songkhla, Thailand [10]; GQ226034 is of human origin from Chantaburi, Thailand [7]; EF200012 is of human origin from Phang-nga, Thailand [5]; JX195640 is the human PCM2 isolate from Trang, Thailand [9]. Also included are sequences from L. enriettii, L. infantum, L. martiniquensis and Leishmania from Australia (AM-2004). B: NJ tree on the same dataset. Numbers at nodes indicate bootstrap values on 1000 replicates and L. infantum was used as an outgroup. These observations required further investigation, since the ITS-1 sequence is known to be polymorphic [20] and does not contain enough informative sites to be reliable for phylogenetic analysis of Leishmania species. Therefore, a different target was used for this analysis, the large subunit RNA Polymerase II (Pol II) gene (L. major chromosome 31) that has been previously used for Leishmania phylogenetic analyses [14], [16], [21], [22]. LSCM1 DNA was extracted from culture and amplified with RPOF1/RPOR1 and various newly designed primer pairs (see Methods) to generate sequences of the RNA Pol II gene. Additional sequences were also generated for L. martiniquensis, “L. siamensis” (PCM2 Trang strain, [9]) and for L. colombiensis. Analysis was performed on the 25 available Leishmania RNA Pol II sequences (21 existing +4 new sequences from this study), Endotrypanum monterogeii and using Trypanosoma brucei as an outgroup. The resulting Maximum Likelihood (ML) tree is shown in Fig. 5. A topologically identical Neighbour Joining (NJ) tree was also generated (Figure S2). Bootstrapping provided strong support for almost all of the nodes, the only two exceptions were 54% bootstrap support for the clade including subgenera Leishmania/Sauroleishmania/Viannia in the ML tree (Fig. 5), however, this node received 94% support in the NJ tree; and 66% support for the clade including all species except paraleishmania II in the NJ tree (Figure S2), however, this node received 85% support in the ML tree. We also tested alternate outgroups, such as Crithidia fasciculata, Leptomonas costaricensis and L. seymouri, and the topologies of the resulting ML trees were similar to Fig. 5. For example, with C. fasciculata as an outgroup the main difference was that the paraleishmania appear as a monophyletic clade, and consequently the rooting of tree is slightly different (Figure S3). 10.1371/journal.pntd.0003339.g005 Figure 5 Phylogenetic analysis by ML method of Leishmania strain CM1 using RNA Pol II sequences. Tree with 25 species of Leishmania and Endotrypanum monterogeii using Trypanosoma brucei as an outgroup, based on alignment of 1191-1206 homologous nucleotide sequences. AM-2004 is Leishmania from Australia, PCM2 is the “L. siamensis” PCM2 Trang isolate. Bootstrap values from 1000 replicates are given at the nodes. The first point to note from the RNA Pol II analysis is that LSCM1 grouped within the L. enriettii complex and was identical in sequence to the RNA Pol II sequence derived for L. martiniquensis, in agreement with the results of ITS-1 analysis. “L. siamensis” PCM2 Trang also grouped within the L. enriettii complex, but as suggested by the ITS-1 analysis, this was clearly distinct from LSCM1/L. martiniquensis, being most closely related to L. enriettii itself. The Leishmania from Australia (AM-2004) occupied an intermediate position. The existence of a monophyletic clade for the L. enriettii complex was strongly supported by bootstrapping in both ML (Fig. 5) and NJ trees (Figure S2), and when using alternate outgroups (Figure S3), as were the positions of the individual members of the complex within the clade. Each of the subgenera Leishmania, Sauroleishmania and Viannia were well supported and the paraleishmania segregated into group I, with tree porcupines as primary mammalian hosts, and group II, with sloths as primary mammalian hosts. Discussion The clinical features of leishmaniasis can be broadly classified into cutaneous, mucocutaneous and visceral disease. The patient described in this report had subacute fever, weight loss, pancytopenia and massive splenomegaly, all of which are common clinical features of VL [23], [24]. Although the recorded history of illness was only 2 weeks, it was apparent that the patient had endured a longer period of illness because he looked chronically ill and had hypoalbuminemia (1.9 g/dL). The incubation period of VL typically varies from 2 months to longer than a year, so the infection can be asymptomatic for a long period [1], [23]. The current first line treatments for VL consist of amphotericin B, or pentavalent antimony in areas where Leishmania isolates remain susceptible. Amphotericin B is available as a liposomal formulation (Ambisome), which has the advantage of lower toxicity, but amphotericin B deoxycholate can also be used if administered carefully [23], [25]. The patient was treated with amphotericin B deoxycholate at 1 mg/kg/day for 21 days. BM samples taken on the 2nd and the 14th day of treatment showed decreasing numbers of amastigotes by microscopy, and was clear evidence for a response to therapy. The final cure rate at 6 months of VL treated with amphotericin B deoxycholate 1 mg/kg daily for 20 days was 97% (95% CI, 95–98%) [26]. The identification and phylogenetic analysis of LSCM1 indicates that the epidemiology of leishmaniasis in Thailand is more complex than previously thought, and the limited amount of available data means that further work is clearly required to resolve questions around so-called “L. siamensis”. However, we can draw several conclusions from the current study. LSCM1 clearly belongs to the L. enriettii complex, which includes species both pathogenic (L. martiniquensis, “L. siamensis”) and non-pathogenic (L. enriettii, Leishmania from Australia) to humans, and itself appears to be an isolate of L. martiniquensis. Leishmania enriettii was discovered 70 years ago in 1944 in domestic guinea pigs from Paraná state, Brazil [27], and has only ever been isolated from these hosts in southern Brazil, mainly around Curitiba. As a species apparently non-pathogenic to human beings it has not received as much attention as other species of Leishmania, but has been used as a model system for chemotherapeutic and immunological studies. Its position within the genus Leishmania has varied with time, typically being regarded as a member of the subgenus Leishmania (Leishmania) [28]. However, more recent evidence [14], [16], and the results presented here, show that L. enriettii occupies a more basal position within the genus, and outside the established subgenera. The results presented here also indicate that “L. siamensis” contains more than one taxon. This has been suggested by data in some previous work, namely the analyses of Leelayoova et al. [29] and Van der Auwera et al. [30]. In both of these the PCM2 Trang isolate of “L. siamensis” from Bualert et al. [9] appears separated from other “L. siamensis” isolates, a similar result to that presented here, and in Leelayoova et al. [20] PCM2 Trang was attributed to a separate lineage of “L. siamensis”, the TR lineage, whereas the other “L. siamensis” isolates were attributed to the PG lineage. However, unlike these previous analyses, here we have included three members of the L. enriettii complex that are distinct species, and in our analysis these are interpolated between “L. siamensis” PCM2 Trang and LSCM1 in both ITS-1 and RNAPolII trees, indicating the occurrence of two taxa within “L. siamensis”. Further, the sequence identity between LSCM1 and the recently named L. martiniquensis [15] indicates that the majority of what have been previously called “L. siamensis” in Thailand (excluding PCM2 Trang) may actually be L. martiniquensis, and, if true, this name should take precedence and be used for these isolates, as “L. siamensis” has not been formally named. Although it may seem surprising that parasites from the island of Martinique and from northern Thailand belong to the same species, L. martiniquensis, when the wide geographical distribution of other known putative L. martiniquensis is also considered (southern Thailand, Germany, Switzerland, USA) this becomes more understandable. Thus, L. martiniquensis appears to be a globally distributed parasite causing visceral leishmaniasis in humans but probably at low frequency. This leaves open the possibility of naming PCM2 Trang as “L. siamensis”, subject to formal description, with perhaps a more restricted geographical distribution. There are insufficient data currently available to fully resolve these questions, further sequencing and other characterisation needs to be done on the various isolates included within “L. siamensis”. Testing of different potential outgroups produced some variations in tree topology regarding the position of the paraleishmania, whether these are a monophyletic group or not, and consequently the exact position of the root of the resulting trees. More work is clearly needed to resolve the evolutionary relationships between these groups. However, irrespective of these variations, the L. enriettii complex always appeared as a strongly supported monophyletic clade, with a consistent branching pattern within the clade, and was always the most basal of the clades containing human parasites. In conclusion, this is the first report of autochthonous visceral leishmaniasis in Northern Thailand and the aetiological agent is identified as L. martiniquensis. Although Thailand has traditionally not been regarded as a country endemic for leishmaniasis, visceral leishmaniasis should be considered in patients presenting with subacute or prolonged fever, huge splenomegaly, and pancytopenia. Epidemiological studies are needed for prevention and control of the disease transmission in Thailand, and further work to clarify the identity and relationships of “L. siamensis” to other species of Leishmania. Supporting Information Figure S1 Multiple sequence alignment of ITS-1 sequences. A: alignment of various “L. siamensis” from Thailand and elsewhere with LSCM1 (accession number JX898938). GQ281278 is from a horse, Germany [11]; GQ281282 is from a cow, Switzerland [12]; JX195637 is of human origin from Stun, Thailand [29]; JQ617283 is from a horse, USA [13]; JQ001751, JQ001752 are human isolates from Trang and Songkhla, Thailand [10]; GQ226034 is of human origin from Chantaburi, Thailand [7]; and EF200012 is of human origin from Phang-nga, Thailand [5]. B: alignment as in A but with the addition of JX195640, the human PCM2 isolate from Trang, Thailand [9]. Conserved sites are indicated by asterisks. (PDF) Click here for additional data file. Figure S2 Phylogenetic analysis by NJ method of Leishmania strain CM1 using RNA Pol II sequences. Tree with 25 species of Leishmania and Endotrypanum monterogeii using Trypanosoma brucei as an outgroup, based on alignment of 1191–1206 homologous nucleotide sequences. AM-2004 is Leishmania from Australia, PCM2 is the “L. siamensis” PCM2 Trang isolate. Bootstrap values from 1000 replicates are given at the nodes. (PDF) Click here for additional data file. Figure S3 Phylogenetic analysis by ML method of Leishmania strain CM1 using RNA Pol II sequences and Crithidia fasciculata as an outgroup. Tree with 25 species of Leishmania and Endotrypanum monterogeii using Crithidia fasciculata as an outgroup, based on alignment of 1191–1206 homologous nucleotide sequences. AM-2004 is Leishmania from Australia, PCM2 is the “L. siamensis” PCM2 Trang isolate. Bootstrap values from 1000 replicates are given at the nodes. (PDF) Click here for additional data file. Table S1 Accession numbers of sequences used for phylogenetic analysis. *Those that have been generated as part of this study are indicated. †TriTrypDB identifier (http://tritrypdb.org/tritrypdb/), Stephen M. Beverley and The Genome Institute, Washington University School of Medicine. (PDF) Click here for additional data file.
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                Contributors
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                25 May 2017
                May 2017
                : 13
                : 5
                : e1006303
                Affiliations
                [1 ]Departamento de Parasitologia, Universidade Federal Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
                [2 ]Departamento de Patologia, Universidade Federal Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
                [3 ]Universidade Federal de São Paulo (UNIFESP), Diadema, São Paulo, Brazil
                [4 ]Centro de Pesquisas René Rachou/Fundação Oswaldo Cruz (Fiocruz), Belo Horizonte, Minas Gerais, Brazil
                University of Wisconsin Medical School, UNITED STATES
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                The authors have declared that no competing interests exist.

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                http://orcid.org/0000-0003-3521-348X
                http://orcid.org/0000-0002-5347-8150
                http://orcid.org/0000-0002-2003-908X
                http://orcid.org/0000-0002-7966-3629
                Article
                PPATHOGENS-D-17-00191
                10.1371/journal.ppat.1006303
                5444841
                28542526
                fa74f085-0965-4537-8f67-9d9d15f66059
                © 2017 Paranaiba 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.

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                Figures: 1, Tables: 1, Pages: 5
                Funding
                This work was supported by Fundação de Amparo do Estado de Minas Gerais Programa Pesquisador Mineiro-X, PPM-00102-16 and Conselho Nacional de Pesquisa e Desenvolvimento CNPq. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
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