Molecular Epidemiology of Agents of Human Chromoblastomycosis in Brazil with the Description of Two Novel Species

The human mutilating disease chromoblastomycosis is caused by melanized members of the order Chaetothyriales. To assess population diversity among 123 clinical strains of agents of the disease in Brazil we applied sequencing of the rDNA internal transcribed spacer region, and partial cell division cycle and β-tubulin genes. Strains studied were limited to three clusters divided over the single family Herpotrichiellaceae known to comprise agents of the disease. A Fonsecaea cluster contained the most important agents, among which F. pedrosoi was prevalent with 80% of the total set of strains, followed by 13% for F. monophora, 3% for F. nubica, and a single isolate of F. pugnacius. Additional agents, among which two novel species, were located among members of the genus Rhinocladiella and Cyphellophora, with frequencies of 3% and 1%, respectively.


Introduction
Chromoblastomycosis is a chronic granulomatous infection of the skin caused by melanized fungi. It has a worldwide distribution mainly in tropical and subtropical climate zones, with a preference for humid climates with dense forestation, with Cladophialophora carrionii being the only species that is restricted to semi-arid areas with Cactaceae as main vegetation. Endemic areas are in Japan, Southeast Asia, Australia, Madagascar, as well as South and Central America [1][2][3][4][5][6][7]. In Brazil, the infection is observed in all states, with an estimated prevalence of 1/196 thousand inhabitants, but in some hyperendemic regions a considerably higher prevalence is noted [8]. Infection is assumed to occur through accidental inoculation of the fungus via contaminated plant debris, being favored by agricultural activities denoting an occupational nature of the disease. Chromoblastomycosis is one of the most frequent implantation mycoses found among rural populations [2,[8][9][10][11].
Clinically, the disease is characterized by pseudoepitheliomatous hyperplasia with epidermal microabscesses and dermal granulomata [12,13]. The disease has a slow evolution, but finally may result in disfigurement of affected body sites [8]. The initial lesion is noted as a small pink papule at the site of inoculation which gradually enlarges. Development of superficial erythematous plaques with scaly or warty appearance probably takes several months or years. As a result of acanthosis these lesions may develop into large papillomatous and verrucous warts.
Species of the humid climate are particularly members of the genus Fonsecaea, with F. pedrosoi, F. monophora and F. nubica as prevalent agents [14][15][16][17]. Recently another species, F. pugnacius was described [18]. Rhinocladiella aquaspersa is an uncommon species of humid as well as of dry climates [19]. Other reported agents such as Phialophora verrucosa and Exophiala dermatitidis [17,20] are extremely rare and mostly cause other types of infections. Fonsecaea pedrosoi is nearly exclusively isolated from chromoblastomycosis, while F. monophora repeatedly causes brain infection and F. pugnacius combines the two disorders by starting as chromoblastomycosis with cerebral dissemination in a single patient [18]. Species distinction of agents of the disease is clinically significant because of the differences in prognosis of the infection.
The present study evaluates the diversity of agents in endemic areas of Brazil based on multilocus sequence data, clinical aspects, direct mycological examination and culture. An enumeration of currently proven cases with molecular support in endemic areas in Brazil is provided.

Results
A set of 123 clinical strains from cases of chromoblastomycosis from different endemic areas in Brazil was analyzed. Judging from a reference set of partial LSU rDNA sequences of members of Chaetothyriales available at CBS, agents of chromoblastomycosis were polyphyletic within the order, being dispersed in three different clades: jeanselmei-, bantiana-and europaea-clades (Fig 1, arrows).
Multilocus sequence analyses using ITS, and partial BT2 and CDC42 genes were performed for identification and for elucidation of species identities (S1 Fig). The 123 clinical strains clustered in different clades within the Chaetothyriales, being centred around members of the genera Fonsecaea, Rhinocladiella, and Cyphellophora (Table 1). The Brazilian clinical isolates used in this study all were derived from humid climate zones; members of the Cladophialophora carrionii group were not encountered.
Fonsecaea is nested in the 'bantiana-clade' (Table 1) and contains the prevalent agents of the disease. Of the studied isolates, 98 (80%) grouped as Fonsecaea pedrosoi, followed by 16 (13%) isolates of F. monophora, 4 (3%) isolates of F. nubica and one isolate of F. pugnacius. Isolates of the Rhinocladiella group and of phialophora-like species are considered as rare agents of chromoblastomycosis in the Americas. Rhinocladiella was nested in the 'jeanselmei-clade' and the phialophora-like agent clustered in the 'europaea-clade' (presently known as Cyphellophoraceae); two unnamed species were uncovered (Fig 1).
The analyzed ITS and BT2 regions and a tree resulting from combined loci revealed identical topologies in phylogenetic analyses. The unnamed strains CMRP1287, CMRP1307, IMT776 and CMRP1317 were found to be concordantly positioned in all trees and grouped with remaining members of Rhinocladiella and Cyphellophora causing chromoblastomycosis (Figs 2 and 3). Clinical strain CMRP1317 was located at a significant distance from all reference strains of Cyphellophora, i.e with combined ITS and BT2 data the distance was 23.4%. Strains CMRP1287, CMRP1307 and IMT776 were also located at significant distance from known species in Rhinocladiella (Table 2). Consequently the strains were judged to represent novel taxa in Cyphellophora and Rhinocladiella, respectively.
We report the clinical cases caused by the novel Cyphellophora and Rhinocladiella species, which are named below as C. ludoviensis and R. tropicalis, respectively. The species showed optimal development at 30˚C and 27˚C, respectively, with a wide growth range between 18˚C and 37˚C and with residual growth at 15˚C and 38˚C and maximum growth temperature at 37˚C; no growth was observed at 40˚C (Fig 4). progressed with 3 years of evolution; muriform cells were observed in tissue (Fig 6A and 6B). Patient was treated orally with itraconazole (200 mg/day), leading to improvement of the lesions during treatment within three months. Patient abandoned treatment after 12 months and returned in 2011 with recurred lesions spreading throughout the lower limb, following a lymphatic path, with secondary infections, presenting verrucous type injuries, ulceration and crusting at the surface. The fungus was re-isolated from the recurred lesions. The patient was treated using itraconazole (200 mg/day) combined with cryosurgery. Notes: The strain clustered with members of Chaetothyriales variously classified in Cyphellophora or Phialophora. Several of these have been reported from mild infections of human skin but without presence of muriform cells. Cyphellophora ludoviensis is the only species in the 'europaea-clade' (Cyphellophoraceae) where muriform cells were observed in the lesions,  (Figs 3 and 7).
Etymology: Named after its occurrence in tropical South America. Holotype: Maranhão State, Brazil, from skin lesion of human patient, dried holotype UPCB 85593 at Department of Botany Herbarium at Federal University of Paraná (UPCB); type strain CMRP1287 = LMICRO326 = CBM17. Additional material examined listed in Table 1.
Case reports: Patient infected by R. tropicalis CMRP1287 was a 65-year-old caucasian male from Pinheiro, Maranhão, Brazil, diagnosed in 2004 with lower limb injuries showing polymorphic lesions with plaques and nodular and cicatrized lesions. Muriform cells were observed in tissue (Fig 6C and 6D). The infection evolved during a 6-year period. Treatment was started with itraconazole (200 mg/day), irregularly until 2012; subsequently regular treatment was installed but with low response. From then onwards additional cryosurgery with liquid nitrogen was applied once a week. After 4 years of therapy still some lesions with a fibrotic aspect and with few murifom cells were observed. Patient infected by R. tropicalis CMRP1307 strain was a 78-year-old afrodescendant male, from Icatu, Maranhão, Brazil, diagnosed in 2002 with lower limb injuries showing polymorphic lesions with plaques and infiltration and muriform cells in tissue (Fig 6E and 6F). The diseased showed moderate development over a 3-year period of evolution. Patient was treated with oral itraconazole (200 mg/day), initiated in 2010. Some treatment interruptions occurred because of the distance to the patient's living place and the low response to itraconazole, with worsening of the symptoms.
Both patients are still under treatment in 2016. The patient infected by R. tropicalis CMRP1287 is currently treated using itraconazole (200 mg/day) combined with cryosurgery and the patient infected by R. tropicalis CMRP1307 uses the antifungals itraconazole (400 mg/ day) and terbinafin (250 mg twice daily) in combination.
During our studies we noticed strain IMT766, isolated in 1970 from a case of chromoblastomycosis and deposited in the Institute of Tropical Medicine, São Paulo, Brazil, and supplementary material from a patient infected by strain CBS 132913, a 63-year-old male construction worker from Venezuela with an asymptomatic and localized skin lesion of the hand with a scaly, crusted, dull-red appearance, friable with hemorrhagic dots [19].
The response to treatment has been evaluated by clinical, mycological and histopathological criteria. A complete clinical response is being accompanied assuming for cure criteria after two years follow up without recurrence, with complete healing of the lesions and disappearance of itching and local pain. The patients must also be monitored by three to four consecutive biopsies to access the mycological and histopathological criteria of cure. A mycological response will be achieved after no observation of fungal elements upon direct examination and failure to isolate the causal agent from tissue fragments.
Notes: With LSU rDNA the novel species clusters close to Rhinocladiella aquaspersa and R. phaeophora in the 'jeanselmei clade' in Herpotrichiellaceae (Fig 1). Members of this cluster are morphologically outstanding by stiff, erect conidiophores packed with sympodial, non-catenate conidia. With ITS (Fig 3), distances of 5.1% were noted between R. tropicalis and R. aquaspersa, and 5.4% with R. phaeophora ( Table 2), underlining that a complex of sibling species is concerned.

Discussion
In this study, we describe two novel species of black fungi causing chromoblastomycosis infections. Among a set of 123 strains from cases of this disease, representatives of three genera were recognized, i.e. Fonsecaea, Rhinocladiella, and Cyphellophora. No member of Cladophialophora was encountered, which is explained by climatic conditions, as C. carrionii is prevalent in arid environmental conditions. In Brazil C. carrionii is rarely reported [24,25]. The prevalent species in humid tropical climates of South America remains Fonsecaea pedrosoi, followed by F. monophora [2], while the latter species is predominant in southern China [26]. All four species of genus Fonsecaea related to chromoblastomycosis were found in the Brazilian endemic area. Judging from literature data, F. pedrosoi and F. nubica seem to be pathogens that are strictly associated with chromoblastomycosis, while F. monophora and F. pugnacius show some degree of neurotropism eventually leading to dissemination to the brain and other organs [14,27].  The genus Cyphellophora is characterized by phialides producing sickle-shaped, septate conidia [28]. The group clusters with some phialidic species with small, one-celled conidia. Although the generic type species of Phialophora, P. verrucosa clusters in the 'carrionii-clade' distant from Cyphellophora, Feng et al. [22] classified them in Phialophora on morphological criteria. Later Réblová et al. [29] took phylogeny as the leading principle and reclassified all species of the 'europaea-clade' in Cyphellophora, the only genus of the newly established family Cyphellophoraceae. Since the taxonomy of Chaetothyriales is in a flux with numerous species to be added, we judge establishment of categories above the species level premature. Currently, phylogenetic data do not match with any other criterion established thus far in Chaetothyriales [21], and therefore phylogenetic genera and families in this order inevitably will remain counterintuitive.

Novel Agents of Human Chromoblastomycosis
Cyphellophora ludoviensis is not effective to produce conidia on common mycological media; it was placed in the genus based on DNA sequence analyses. Members of the genus Cyphellophora colonize different habitats including, in addition to humans, plant debris, ant nests and abiotic substrates [22]. Our species is genetically close to C. capiguarae, described as living in association with ants (Atta capiguara), and to C. oxyspora from decaying leaves [30,31]. Other members of Cyphellophora originate from mild cutaneous infections in humans, mostly from skin and nails [22]. Cyphellophora europaea in particular has been encountered globally as an agent of mild skin disease and onychomycosis [31] and was noted co-occurring with dermatophytes, mainly Trichophyton rubrum affecting the skin of diabetic patients [32]. Environmental strains of this species were found in indoor wet cells, such as bathrooms and washing machines [33,34]. Cyphellophora ludoviensis is the first species in the Cyphellophoraceae that had muriform cells in tissue and showed acanthosis rather than necrosis; on the basis of these features the infection was classified as chromoblastomycosis.
The new species Rhinocladiella tropicalis is a cryptic species close to R. phaeophora and R. aquaspersa. Rhinocladiella phaeophora was known from a single strain recovered from maize field soil in Colombia [35]. It has recently been reported from a case of human chromoblastomycosis, but the sequence of this strain was not available for comparison [36]. This report nevertheless suggests that all members of the cluster consistently are able to cause chromoblastomycosis when inoculated into human skin. Rhinocladiella aquaspersa is a classical agent of chromoblastomycosis, nearly all cases having been reported from the American continent [19], but the majority of historical clinical cases have not been verified by sequence data. Strain CBS 132913 was originally reported as R. aquaspersa but was found to be 100% identical with R. tropicalis. The three species are phenotypically and clinically similar, but their sequence diversity interferes with molecular recognition of R. aquaspersa as a single species. According to Chen et al. [37] the term 'species complex' could be applied used to indicate closely related species do not seem to differ in clinically relevant parameters. The present rhinocladiella-like lineages have sufficient molecular distance to be recognized as species, but additional studies of antifungal susceptibility, clinical course, virulence and physiology are needed to verify significance of distinction of the three agents as individual species in hospital routine.
Chromoblastomycosis is clinically highly variable, with six different clinical types [8,38]. Despite the polymorphic nature of lesions, common factor at the patient side is the absence of necrosis and often even hyper-growth of dermal tissues, which distinguishes the disease from its clinical counterpart, phaeohyphomycosis. At the fungal side, the invasive form is the muriform cell, which is likely to be the cause of the growth-promoting dermal response. As such the disease is polyphyletic within the Chaetothyriales, but has not or extremely rarely been observed outside this order. In both cases caused by these two new species here described it was encountered polymorphic lesions frequently related to clinical cases of chromoblastomycosis [8].
In the State of Maranhão, Brazil, five chaetothyrialean agents of chromoblastomycosis are endemic. A potential source of infection has been suggested [39] to be the harvest of babassu coconuts from a wild palm tree (Orbignya phalerata). A large part of the local rural population is involved in the collection of nuts to extract babassu oil, an important component for local and international beauty product manufacturers. Members of Chaetothyriales are indeed enriched on babassu shell fragments, which are considered a risk factor for developing chromoblastomycosis after trauma sustained at work [39,40]. A direct link between shells and agents of the disease has however not unambiguously been established. In other Brazilian regions the number of new cases of chromoblastomycosis is decreasing [8,41,42]. This is thought to reflect changes in agricultural practices, the extensive use of agricultural antifungals, especially azole derivatives, and the progressive mechanization of plantations resulting in a reduction of the risk of occupational exposure [8,43,44].
Our results showed that C. ludoviensis and R. tropicalis had their optimal development at 30 and 27˚C, respectively, the maximum growth temperature of all strains analyzed being at 37˚C. The chronic nature of the infection corresponds with borderline survival of the fungus in tissue. Epidermal temperatures are usual below 37˚C, allowing infection by fungi that barely support this temperature. This agrees with the clinical observation that members of the Cyphellophoraceae ('europaea-clade'), which have their maximum growth at 36˚C, cause only mild, superficial infections, having a very low degree of invasive ability and virulence [22].
According to the World Health Organization (WHO) [45] the Neglected Tropical Diseases include a series of endemic diseases that prevail in tropical or subtropical areas worldwide. The prevalence of causative microbes is linked to poverty and disadvantage. However, fungal diseases were still not included in this list, except mycetoma, another implantation mycosis [46]. Chromoblastomycosis has been reported in the literature as an overlooked disease [11]. Its global burden is comparable to or greater than that of mycetoma. Considering to its global distribution, its impact on the impoverished, and its refractoriness, it also should be considered a true neglected disease as defined by WHO.

Strains studied
Strains analyzed comprised 123 clinical isolates (

Physiology
Cardinal growth temperatures were determined on 2% MEA. Plates were incubated in the dark for 3 weeks at a 3-36˚C temperature range with intervals of 3˚C; growth was also recorded at 14, 37, 38, 39 and 40˚C. Growth rates per species were obtained by calculation of the average growth of all isolates proven to belong to that species, including the respective standard deviations. Results were plotted with temperature (˚C) versus colony diameter (mm) as parameters. Optimum range (= average ± standard deviation) and maximum growth temperatures were determined using the type strains of each species with three replicates averages of three measurements were calculated. Different temperatures were tested, at 28˚C was observed the largest number of structures to Chyphellophora and it was used to describe the species morphology.

DNA extraction and amplification
DNA extraction and quality tests were performed using glass beads (Sigma G9143) according to protocols described previously [23] and when it was required, the purification of DNA was undertaken using the UltraClean™ Microbial DNA Kit (MO Bio, Carlsbad, CA, USA) according to manufacturer's instructions. Colonies were cultivated on Sabouraud's glucose agar (SGA).
The partial large subunit of the nuclear ribosomal RNA gene (LSU) was amplified using primers NL1 and LR5 [22] for phylogenetic assessment. Three gene regions were chosen for species delimitation: rDNA Internal Transcribed Spacer (ITS), and the partial genes cell division cycle gene (CDC42) and β-tubulin (BT2). ITS amplicons were generated with primers V9G and LS266 [47,48] and were sequenced with primers ITS1 and ITS4. CDC42 amplification and sequencing was generated with cdc42w and cdc42f [49] and BT2 amplification and sequencing was generated with Bt-2a and T2 [50]. PCR was performed in a 12.5 μL volume of a reaction mixture containing 1× PCR buffer, 2.0 mM MgCl 2 , 25 μM dNTPs, 0.5 μM of each forward and reverse primers, 1 U of BioTaq DNA polymerase, and 10 ng of genomic DNA.
Amplification was performed in an ABI PRISM 2720 (Applied Biosystems, Foster City, USA) thermocycler as follows: 95˚C for 4 min, followed by 35 cycles consisting of 95˚C for 45s, 52˚C for 30s and 72˚C for 2 min, and a delay at 72˚C for 7 min. Annealing temperatures were changed to 52˚C, 55˚C and 58˚C for ITS, CDC42 and BT2 respectively. Amplicons were cleaned with Exonuclease I and Shrimp Alkaline Phosphatase (SAP) according to manufacturer's instructions. Amplicons were sequenced with a BigDye Terminator Cycle Sequencing Kit v. 3.1 (Applied Biosystems, Foster City, CA, USA) according to the manufacturer's instructions, reactions were purified with Sephadex G-50 fine (GE Healthcare Bio-Sciences, Uppsala, Sweden) and sequences were analysed on an ABI Prism 3700 DNA Sequencer (Perkin-Elmer, Norwalk, Foster City, CA, USA).

Phylogenetic analysis
Consensus sequences of the ITS region, BT2, CDC42, and the LSU were visually inspected using MEGA v.7 software [51]. The alignment of obtained sequences was performed using the online MAFFT interface [52]. The genes ITS, CDC42 and BT2 were first analyzed separately and for analysis of multilocus (S1 Fig). We did the LSU analyses to assess the phylogenetic position of the species analyzed in this study. The phylogenetic analyses of the small subunit (SSU) and LSU groups previously recognized in the Herpotrichiellaceae by de Hoog et al. [21], Feng et al. [22] and Vicente et al. [23] were taken as a basis for clade delimitation. Trees were constructed with 100 bootstrap replicates using the Maximum Likelihood Implemented in Mega v. 7 software [51], with the best evolutionary model to this dataset. Conflicts were estimated using the partition homogeneity test available in PAUP Ã v. 4.Ob10 [53]. To elucidated and explore a more detailed the clustering unnamed species, their sequences were compared to those deposited at GenBank and the CBS-KNAW sequence data sets.