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Seasonal dynamics, Leishmania diversity, and nanopore-based metabarcoding of blood meal origins in Culicoides spp. in the newly emerging focus of leishmaniasis in Northern Thailand

Parasites & Vectors volume 17, Article number: 400 (2024) Cite this article

Abstract

Background

Clinical cases of leishmaniasis caused by Leishmania (Mundinia) parasites have been increasingly reported in Southeast Asia, particularly Thailand. Recent evidence has shown that Leishmania (Mundinia) parasites successfully developed into infective metacyclic promastigotes in Culicoides biting midges, strongly supporting their putative role in disease transmission. However, Culicoides diversity, host preference, and Leishmania prevalence in endemic areas remain largely unknown.

Methods

We investigated the seasonal dynamics, infection prevalence, and blood meal identification of Culicoides collected from the emerging focus of visceral leishmaniasis in Lampang Province, Northern Thailand, during 2021–2023. Midge samples were molecularly screened for Leishmania using SSU rRNA-qPCR and ITS1-PCR, followed by Sanger plasmid sequencing, and parasite haplotype diversity was analyzed. Host blood meal origins were comparatively identified using host-specific Cytb-PCRs and a nanopore-based metabarcoding approach.

Results

A total of 501 parous and gravid females and 46 blood-engorged ones belonging to at least 17 species of five subgenera (Remmia, Trithecoides, Avaritia, Hoffmania, and Meijerehelea) and two species groups (Shortti and Calvipalpis) were collected with temporal differences in abundance. Leishmania was detected by SSU rRNA-qPCR in 31 samples of at least 11 midge species, consisting of Culicoides oxystoma, C. guttifer, C. orientalis, C. mahasarakhamense, C (Trithecoides) spp., C. innoxius, C. shortti, C. arakawae, C. sumatrae, C. actoni, and C. fulvus, with the overall infection prevalence of 5.7%. The latter six species represent the new records as putative leishmaniasis vectors in Northern Thailand. The ITS1-PCR and plasmid sequencing revealed that Leishmania martiniquensis was predominantly identified in all qPCR-positive species, whereas L. orientalis was identified only in three C. oxystoma samples. The most dominant haplotype of L. martiniquensis in Thailand was genetically intermixed with those from other geographical regions, confirming its globalization. Neutrality test statistics were also significantly negative on regional and country-wide scales, suggesting rapid population expansion or selective sweeps. Nanopore-based blood meal analysis revealed that most Culicoides species are mammalophilic, with peridomestic and wild mammals (cow, pig, deer, and goat-like species) and humans as hosts, while C. guttifer and C. mahasarakhamense fed preferentially on chickens.

Conclusions

This study revealed seasonal dynamics and sympatric circulation of L. martiniquensis and L. orientalis in different species of Culicoides. Evidence of human blood feeding was also demonstrated, implicating Culicoides as putative vectors of human leishmaniasis in endemic areas. Further research is therefore urgently needed to develop vector control strategies and assess the infection status of their reservoir hosts to effectively minimize disease transmission.

Graphical Abstract

Background

Autochthonous leishmaniasis is currently considered an important public health problem in Southeast Asia with Thailand being an endemic hotspot. Since 1996, an increasing number of clinical cases have been reported, particularly in the northern and southern provinces of the country [1]. This emerging disease has been proven to be caused by two Leishmania species of the newly classified subgenus Mundinia, namely Leishmania martiniquensis and L. orientalis [1,2,3,4,5]. Traditionally, leishmaniasis was known to be transmitted by phlebotomine sand flies [6]. Based on the positive detection of Leishmania DNA, several phlebotomine species of the genera Sergentomyia [7,8,9], Grassomyia [10], and Phlebotomus [11] were proposed as potential vectors of these two Leishmania (Mundinia) species. However, recent evidence indicates that several Leishmania (Mundinia) parasites could not successfully develop to the infective stage within the midgut of the sand fly [12,13,14]. In addition, the positive detection rates for Leishmania (Mundinia) species are relatively low in field-caught sand flies, suggesting that these emerging Leishmania (Mundinia) parasites may be transmitted by other blood-sucking dipteran vectors than sand flies [7, 9,10,11, 15].

In addition to sand flies, Culicoides biting midges are globally distributed hematophagous insects of the family Ceratopogonidae, order Diptera. Of medical and veterinary importance, species of this insect genus have been implicated as vectors of several human, domestic, and wildlife pathogens. They are involved in the transmission of several animal arboviruses, including African horse sickness, bluetongue, epizootic hemorrhagic disease, Oropouche, vesicular stomatitis, and Schmallenberg viruses [16]. Culicoides species have also been incriminated as vectors of protozoan parasites infecting mammals and birds, including Hepatocystis, Haemoproteus, Leucocytozoon, and Trypanosoma, as well as several species of filarial nematodes [17,18,19,20].

It has been previously noted that several Leishmania species, including Leishmania (Leishmania) amazonensis [21], L. (L.) infantum [22], L. (L.) mexicana [23], and L. (Viannia) braziliensis [21], have been molecularly detected in Culicoides spp. collected from different geographical origins. Nevertheless, the metacyclic development of these Leishmania species has never been demonstrated in dissections of natural Culicoides species or in laboratory experiments, which is an important criterion for confirming their vector competence [12,13,14, 24, 25]. However, recent experimental infections have shown that several strains of L. martiniquensis and L. orientalis can complete metacyclic development in Culicoides sonorensis and be successfully transmitted to mice [12, 14]. It is therefore highly likely that Culicoides biting midges play a role in the transmission of autochthonous leishmaniasis caused by these two Leishmania (Mundinia) species in endemic areas of Thailand.

Positive detection of two autochthonous Leishmania species, L. martiniquensis and L. orientalis, in certain Culicoides species has been previously reported in endemic areas of Thailand. In Northern Thailand, Culicoides mahasarakhamense has been identified as the predominant vector [26, 27], while in Southern Thailand, C. peregrinus and C. oxystoma are the main putative vectors [28]. However, more than 168 Culicoides species from different ecotypes have been described in Southeast Asian countries, and many of them feed on mammals, which may serve as parasite reservoirs [29]. Accordingly, it can be speculated that Leishmania parasites may exploit more Culicoides species as hosts than previously reported, with spatiotemporal differences in the vector species spectrum between leishmaniasis-affected localities in different geographical regions of Thailand.

Although several experimental and field studies have implicated Culicoides as putative vectors of autochthonous leishmaniasis [12, 14, 26,27,28], evidence of their feeding behaviors on human blood has never been demonstrated, particularly in endemic areas of the country. Therefore, the incrimination of Culicoides as true natural vectors of human leishmaniasis according to the Killick-Kendrick criteria [30] cannot be strengthened. Several attempts were made using Sanger sequencing to analyze blood meals in engorged Culicoides collected near human dwellings in leishmaniasis-endemic areas, but it was found that all specimens fed only on animals with domestic and peridomestic environments, without evidence of human blood [28, 31]. We speculated that these results were likely biased because Sanger sequencing can only generate a single chromatogram, representing a single blood meal source, and is therefore not suitable for characterizing multiple blood meal sources in a single specimen. Additionally, information on the composition of Culicoides with seasonal abundance, prevalence of infection, and sympatric occurrence of Leishmania parasites in the affected communities remains limited.

In the present study, we comparatively investigated the seasonal dynamics of Culicoides biting midges and the infection prevalence and genetic diversity of Leishmania in Culicoides samples collected from the residence of the leishmaniasis index case in Lampang Province, an emerging focus of visceral leishmaniasis in Northern Thailand, from 2021 to 2023. In addition, we demonstrated the application of a nanopore-based metabarcoding strategy to provide high-throughput data for the unbiased identification of multiple host species. Novel insights from this study will help us better understand the role of Culicoides in leishmaniasis transmission and facilitate effective vector management and control to interrupt disease transmission, especially in endemic areas of northern Thailand.

Methods

Investigation area, biting midge collection, and morphological identification

Culicoides biting midges were collected in Wang Nuea District, Lampang Province, Northern Thailand (19° 10′ 27.5″ N, 99° 38′ 53.0″ E), from November 2021 to May 2023 (Fig. 1). The midge collection was performed within a 50-m radius around the residence of the index case who had been previously diagnosed with visceral leishmaniasis. The Centers for Disease Control and Prevention miniature UV light traps were situated 1 m above the ground in different places near the household area and neighboring cattle sheds. The traps were installed from dusk to dawn for 3 consecutive days. All insect specimens collected the next day would be immobilized by being knocked out in the freezer for 30 min. At the field site, the collection was then inspected under a stereomicroscope (EZ4 HD, Leica, Germany) to sort female Culicoides individuals from males and other insect species, according to distinct morphological structures, i.e., non-plumose antennae and wing venation patterns. In this study, nulliparous females, which generally predominated in the traps and had never been exposed to an infectious blood meal, were discarded from the female collection. Only non-engorged (parous and gravid) and blood-engorged ones, which had fed on hosts and entered the gonotrophic cycle, were picked up for downstream analysis. All midge specimens were then morphologically identified using the illustrated keys to Culicoides of Southeast Asia formerly described by Wirth and Hubert [29] and the formal description of a new species, C. mahasarakhamense, recorded by Pramual et al. [32]. Then, the midge specimens were frozen at – 80 °C before genomic DNA isolation.

Fig. 1
figure 1

Map and geographic coordinates of Culicoides trapping site in Wang Nuea District, Lampang Province, Northern Thailand. The light traps were installed near the cattle pen and chicken coop within the patient’s housing area. The map of Thailand was obtained from the public domain (https://d-maps.com). The satellite image was modified from the Google Earth website (https://earth.google.com/web/search/Thailand)

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Genomic DNA isolation from Culicoides samples

To preserve the morphological structure of the samples, each Culicoides individual was extracted for total genomic DNA (gDNA) without sample homogenization using a non-destructive protocol previously described by Santos et al. [33]. Briefly, each sample was digested in 200 µl lysis buffer containing Proteinase K and incubated at 50 °C overnight. The lysate was then purified using the magnetic bead-based system with the GENTi™ Advanced Genomic DNA Extraction Kit (GeneAll®, Seoul, South Korea). The quality and concentration of gDNA were assessed using the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The gDNA samples obtained were stored at – 20 °C until use. Post-extracted insect remains were stored in 70% ethanol at room temperature for further species reaffirmation.

Initial screening of Leishmania DNA by SSU rRNA-qPCR

All extracted gDNA samples were first tested for the presence of Leishmania DNA using TaqMan quantitative PCR (qPCR) targeting the conserved region of the small subunit ribosomal RNA (SSU rRNA) gene of all Leishmania species, as previously described [34]. The SSU rRNA-qPCR reactions were performed using a forward primer (5′-CCAAAGTGTGGAGATCGAAG-3′), a reverse primer (5′-GGCCGGTAAAGGCCGAATAG-3′), and a TaqMan probe (5′-6FAM-ACCATTGTAGTCCACACTGC-3′-MGB-NFQ). Reaction components were prepared in a total volume of 20 µl containing 10 µl TaqMan™ Fast Advanced Master Mix (Thermo Scientific, Waltham, MA, USA), 0.5 µM each of 10 µM primers, 0.5 µl 10 µM probe, and 2 µl gDNA. All reactions were performed on the QuantStudio™ 5 Real-Time PCR System (Applied Biosystems, CA, USA) with the following thermal conditions: initial denaturation at 95 °C, 2 min and 45 cycles of denaturation at 95 °C, 15 s and annealing/extension at 60 °C, 15 s. A Ct value < 40 was considered positive.

Conventional Leishmania ITS1-PCR

The gDNA samples with positive qPCR results were used as templates for conventional PCR targeting all Leishmania species' internal transcribed spacer-1 (ITS1) region. ITS1-PCR reactions were performed using forward primer LITSR2 (5’-CTGGATCATTTTCCGATGATT-3’) and reverse primer L5.8Sinner (5’-GTTATGTGAGCCGTTATCC-3’) to generate an amplicon of approximately 272–280 bp [35]. Reaction components consisted of 4 µl gDNA, 1.5 µl each of 10 µM primers, 25 µl 2X KAPA HiFi HotStart ReadyMix (Roche, Basel, Switzerland), and nuclease-free water added to a final volume of 50 µl. Thermal conditions included initial denaturation at 95 °C, 5 min, followed by 35 cycles of denaturation at 98 °C, 30 s, annealing at 53 °C, 30 s, extension at 72 °C, 30 s, and final extension at 72 °C, 10 min. Amplification products were verified on 1.5% (w/v) agarose gel electrophoresis stained with ethidium bromide and then visualized using the Gel Doc XR + Gel Documentation System (Bio-Rad, Hercules, CA, USA).

Parasite identification by Sanger plasmid DNA sequencing

All Leishmania ITS1 amplicons were ligated into the pGEM® T-Easy cloning vector (Promega Corp., Madison, WI, USA) according to the manufacturer's specifications. The ligation products were then chemically transformed into competent Escherichia coli strain DH5α cells. Transformants were transferred onto the Luria Bertani (LB) agar plates containing ampicillin, IPTG, and X-Gal for blue/white colony selection. Five white colonies suspected of harboring the recombinant plasmids were confirmed by PCR and subsequently cultured overnight at 37 °C in LB broth medium containing ampicillin. Chimeric plasmids were extracted using the Exprep™ Plasmid SV DNA Purification Kit (GeneAll®, Seoul, Korea) and sequenced using T7 promoter primer by Macrogen, Inc. (Seoul, Korea). To identify the parasite species, the ITS1 sequences obtained were compared with GenBank references in the nucleotide collection (nr/nt) database using BLASTn (http://blast.ncbi.nlm.nih.gov/Blast.cgi) optimized for highly similar sequences.

Haplotype network analysis

The genetic variability of L. martiniquensis and L. orientalis ITS1 sequences identified in this study and those from GenBank was investigated by haplotype network analysis based on single nucleotide variation and small insertions and deletions (indels). A minimum-spanning network was constructed in RStudio version 2024.04.2+764 [36]. Briefly, the ITS1 sequences in FASTA format were converted into a DNA binary file required for network construction using the package “adegenet” version 2.1.10 [37]. The package “pegas” version 1.3 was then used to create the haplotype network from a list of DNA sequences in DNA binary format [38]. DNA sequences were compared, and each unique sequence was assigned to a specific haplotype using the 'haplotype' function in the pegas package. Genetic diversity statistics, including the number of haplotypes, haplotype diversity (Hd), nucleotide diversity (π), average number of nucleotide differences (k), and Tajima’s D statistic, were calculated using the package “pegas” version 1.3. Fu and Li’s D statistics were calculated using the package “PopGenome” version 2.7.5 [39]. P-values < 0.05 were considered statistically significant.

PCR amplification of mammalian and avian cytochrome b regions

The gDNA extracted from engorged specimens was used as a template for PCR targeting the vertebrate cytochrome b (Cytb) region for mammalian and avian host identification as described elsewhere. For mammalian hosts, multiplex PCR reactions were set up in a total volume of 25 µl consisting of 3 µl gDNA template, 0.9 µl 10 µM forward primer (Human741F, Cow121F, Dog368F, Pig573F), and universal reverse primer (UNREV1025) [40], 12.5 µl 2X KAPA HiFi HotStart ReadyMix, and 5 µl nuclease-free water. Additionally, singleplex PCR reactions were performed for the avian host using L15557 and H16065 primers [41]. Thermal conditions included initial denaturation at 95 °C, 5 min; 35 cycles of denaturation at 95 °C, 1 min, annealing at 58 °C (for mammals) and 50 °C (for avian), 1 min, extension at 72 °C, 1 min, and final extension at 72 °C, 7 min. PCR products were verified by 1.5% (w/v) agarose gel electrophoresis with staining and visualization as previously described. The expected amplicon sizes were 334, 561, 680, 453, and 508 bp for human, bovine, canine, porcine, and avian, respectively.

Vertebrate COI-PCR and MinION® amplicon sequencing

To identify additional hosts not detected by Cytb-PCR, nanopore amplicon sequencing was performed on all engorged samples. The partial cytochrome c oxidase subunit I (COI) gene of approximately 395 bp was amplified using VertCOI_7194_F (5’-CGMATRAAYAAYATRAGCTTCTGAY-3’) and Mod_RepCOI_R (5’-TTCDGGRTGNCCRAARAATCA-3’) [42]. The amplification reactions were set up in a total volume of 25 µl consisting of 3 µl gDNA template, 0.75 µl of each 10 µM primer, and 12.5 µl 2X KAPA HiFi HotStart ReadyMix. Thermal conditions were programmed as follows: 95 °C for 3 min, 40 cycles of denaturation at 95 °C, 40 s, annealing at 48.5 °C, 30 s, extension at 72 °C, 1 min, and final extension at 72 °C for 7 min. Each amplicon sample was then purified using Agencourt AMPure XP beads (Beckman Coulter, CA, USA).

For DNA library preparation, 200 fmol purified amplicon per sample was end-repaired using the NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs, MA, USA). End-prepped DNA samples were ligated with native barcodes provided in the Native Barcoding Kit 96 V14 (Cat. No. SQK-NBD114.96, Oxford Nanopore Technologies, Didcot, UK) using NEB Blunt/TA Ligase Master Mix (New England Biolabs). For multiplexing, barcoded samples were pooled and ligated to the sequencing adaptor using the NEBNext Quick Ligation Module (New England Biolabs). After removing the excess adaptor, 50 fmol of the final preparation was loaded into the MinION® R10.4.1 flow cell for 10 h. The Dorado version 7.3.11 was used for super-accuracy base calling using the dna_r10.4.1_e8.2_400bps_sup@v.4.3.0 model, demultiplexing, and adaptor-barcode trimming. Sequenced reads with Q scores < 20 were filtered out using Chopper version 0.7.0 [43], and reads between 300–500 bp were analyzed. Reads of similar sequence and length were clustered using amplicon_sorter.py (version 2024_02_20) [44] and then error-polished with raw reads using Medaka version 1.11.3 to generate all accurate consensus sequences for each sample. For the taxonomic assignment, the obtained consensus sequences of each sample were compared to GenBank references using BLASTn optimized for highly similar sequences.

Results

Index case description

On 11 January 2021, a 60-year-old male living in Wang Nuea District, Lampang Province, presented with a 1-month history of fatigue and leg myalgia. Physical examination revealed markedly pale conjunctiva, consistent with anemia. Hematological investigations revealed pancytopenia with a hemoglobin level of 5.0 g/dl, hematocrit of 16%, white blood cell count of 2040 cells/mm3 (neutrophil, 38%; lymphocyte, 56%; monocyte, 3%; eosinophil, 2%; basophil, 1%), and platelet count of 72,000 platelets/mm3. His HIV serology was negative. He then received several blood transfusions without significant improvement in his symptoms, and huge splenomegaly developed. In August 2021, a bone marrow biopsy showed several macrophages full of intracellular amastigotes. ITS1-PCR and Sanger sequencing confirmed the final diagnosis of visceral leishmaniasis caused by L. martiniquensis. The DNA sequence obtained was submitted to GenBank under accession no. OR917763. The patient improved clinically following a 1-week course of intravenous amphotericin B (1 mg/kg/day) with seven doses of filgrastim (300 mcg/day) by subcutaneous injection every 2 days.

Seasonal abundance of Culicoides species

Culicoides biting midges were caught three times around the patient’s household in November 2021, March 2022, and May 2023. In total, our collection consisted of 501 non-engorged (parous and gravid) females and 51 blood-engorged females caught only in November 2021. All Culicoides samples were taxonomically identified as at least 17 different species belonging to five subgenera, namely Remmia, Trithecoides, Avaritia, Hoffmania, Meijerehelea, and two species groups, namely Shortti and Calvipalpis, mainly based on the characteristic wing pigmentation patterns (Table 1, Fig. 2). With temporal variability, C. (Trithecoides) spp. were prevalent in November 2021, whereas C. innoxius and C. oxystoma were the most abundant species in March 2022 and May 2023, respectively. Only a single specimen of Culicoides imicola, C. huffi, and C. liui were found sporadically during these three collection periods. The three most abundant species of the entire collection were C. oxystoma, C. (Trithecoides) spp., and C. shortti, representing 29.3%, 15.5%, and 11.9% of all Culicoides midges, respectively.

Table 1 Species diversity with temporal and overall variability in the relative abundance of Culicoides biting midges collected from the vicinity of the patient’s residence during three collection periods from November 2021 to May 2023
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Fig. 2
figure 2

Wing morphology and pigmentation patterns of Culicoides species from the trap collections, shown in descending order of total relative abundance. The scale bar represents 200 µM

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Infection prevalence in Culicoides and parasite identification

Of 501 non-engorged and 46 blood-engorged Culicoides samples tested, Leishmania SSU rRNA-qPCR was positive in 27 non-engorged and 4 engorged individuals, consisting of C. oxystoma (n = 6), C. innoxius (n = 4), C. shortti (n = 4), C. guttifer (n = 3), C. orientalis (n = 3), C. mahasarakhamense (n = 3), C. arakawae (n = 2), C. sumatrae (n = 2), C. (Trithecoides) spp. (n = 2), C. actoni (n = 1), and C. fulvus (n = 1), with an overall prevalence of 5.7%. Leishmania was temporally detected with the highest frequency in C. orientalis, C. innoxius, and C. oxystoma in November 2021, March 2022, and May 2023, respectively, as shown in Table 2. Conventional ITS1-PCR successfully amplified all qPCR-positive samples. Plasmid DNA sequencing and BLASTn analysis revealed that L. martiniquensis was commonly detected in 24 samples of these positive Culicoides species, whereas L. orientalis was only amplified in three samples of C. oxystoma. None of the samples showed co-infection with these two Leishmania (Mundinia) species. The Leishmania ITS1 sequences obtained from non-engorged and blood-engorged samples were deposited in GenBank under accession nos. OR917764-OR917790 and PQ014661-PQ014664, respectively.

Table 2 Parasite identification and accession numbers of Leishmania sequences obtained from the patient and field-caught Culicoides biting midges by conventional ITS1-PCR and plasmid sequencing in this study
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Haplotype diversity and neutrality statistics of detected Leishmania

A total of 167 Leishmania ITS1 sequences, including 29 L. martiniquensis and 3 L. orientalis sequences amplified from the index case and Culicoides samples in our collection and 135 pre-exisitng sequences from the GenBank database, consisting of L. martiniquensis (n = 88) and L. orientalis (n = 47), were included in the haplotype diversity analysis. As shown in Fig. 3, the star-like network consisted of 32 and 27 unique haplotypes of L. martiniquensis and L. orientalis, respectively, circulating in Culicoides biting midges, animal hosts (cow, horse, and black rat), and leishmaniasis patients from Thailand and other geographical regions, as detailed in Supplementary File 1.

Fig. 3
figure 3

Haplotype diversity of Leishmania (Mundinia) species from different geographical origins based on ITS1 sequences. The size of the circle indicates the number of each unique haplotype. Hatch marks between the circles represent the number of nucleotide polymorphisms between haplotypes. Blue-green circles represent unique haplotypes of L. martiniquensis and L. orientalis identified in the present study

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For L. martiniquensis, H01 was the most common haplotype shared by 72 sequences worldwide from several leishmaniasis-affected areas of Thailand, including Chanthaburi, Chiang Mai, Chiang Rai, Lampang (in this study), Lamphun, Nakhon Si Thammarat, Satun, Trang, and Songkhla Provinces, and other countries, namely Martinique Island, Myanmar, and the USA. The remaining descendant haplotypes were less common with varying degrees of regional area specificity. As shown in Tables 3 and 4, eight unique haplotypes with 14 polymorphic sites were identified from all L. martiniquensis sequences in our collection, with most sequences grouped into the dominant haplotype H01. The haplotype diversity for our collection and populations of L. martiniquensis in the northern provinces and the whole country was relatively high with values of 0.5556–0.6133. In contrast, nucleotide diversity for these three populations was exceptionally low with values of 0.0050–0.0063. In addition, neutrality tests showed significantly negative Tajima’s D values of −2.3353 and −2.5642 for the latter two populations and a significantly negative Fu and Li’s D value of −4.8110 for the whole country population.

Table 3 Haplotypes of 32 Leishmania ITS1 sequences amplified from the index case and Culicoides biting midges collected in this study
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Table 4 Genetic diversity and neutrality statistics of Leishmania martiniquensis and L. orientalis populations identified in Culicoides vectors and humans in different geographic localities of Thailand based on ITS1 region
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For L. orientalis, the H33 haplotype was the most dominant with 14 sequences from Chiang Rai and Nan in Northern Thailand and Trang Province in Southern Thailand. Two haplotypes (H41 and H44) with five polymorphic sites were identified in our collection. Two haplotypes, H44 and H49, could be found in different geographical locations. H44 was shared by four individuals from Lampang, Nakhon Si Thammarat, and Trang Provinces, while H49 was shared by five individuals from Chiang Rai, Trang, and Songkhla Provinces. This suggests possible gene flow across these sites. The haplotype diversity value for our collection was 0.6667, while those of L. orientalis populations in the northern region and the whole country were remarkably higher with values of 0.9569 and 0.9094, respectively. The lower degree of genetic differentiation of L. orientalis in our collection was probably due to the considerably small effective population size. As with L. martiniquensis, nucleotide diversity values for these groups ranged from 0.0080 to 0.0086. Neutrality tests were also significantly negative, with Tajima’s D values of − 2.4975 and − 2.3052 for the northern region and the whole country populations, respectively, and Fu and Li’s D value of − 2.9282 for the whole country population.

Blood meal source identification by host-specific Cytb-PCRs

A total of 46 blood-engorged females of nine Culicoides species were collected in November 2021 as detailed in Table 1. The Cytb-PCR reactions targeting mammalian and avian DNA were successfully performed on all engorged samples. Of these, four kinds of vertebrate hosts were identified with the following detection frequencies: cow (n = 41), human (n = 7), bird (n = 4), and pig (n = 1). Forty-one samples with cows as hosts consisted of Culicoides shortti (n = 18), C. fulvus (n = 7), C. orientalis (n = 4), C. actoni (n = 5), C. (Trithecoides) spp. (n = 5), C. jacobsoni (n = 1), and C. insignipennis (n = 1). Of these 41 samples, six samples of four species, namely C. shortti (n = 3), C. fulvus (n = 1), C. orientalis (n = 1), and C. actoni (n = 1), were found to feed on both cows and humans. Pig blood was detected in only one sample of C. orientalis, while none of the samples tested positive for dogs. Four samples of two Culicoides species, C. guttifer (n = 2) and C. mahasarakhamense (n = 2), were recorded as feeding on birds, and one of these two C. guttifer samples also fed on humans.

MinION® amplicon sequencing

A metabarcoding approach using nanopore-based COI amplicon sequencing was also used to generate high-throughput data, greatly facilitating the identification of multiple host species. COI-PCR was also successfully performed on all the engorged samples in which host-specific Cytb-PCRs were obtained. After filtering out low-quality reads, 739,245 high-quality reads with Q scores ≥ 20 were obtained from all individuals in the engorged collection. The resulting high-quality reads from each sample were clustered and error-polished to generate highly accurate consensus sequences. In total, 71 consensus sequences were generated and aligned against GenBank references using BLASTn for the host taxonomic assignment of each sample as detailed in Table 5. As shown in Fig. 4, six vertebrate host species were identified with the following detection frequencies: Bos indicus (cow, n = 41), Homo sapiens (human, n = 16), Gallus gallus (chicken, n = 5), Cervus sp. (deer, n = 4), and Sus scrofa (pig, n = 1), with high similarity percentages ranging from 94.7–99.3%, and unknown species related to Rupicapra sp. (goat-like species, n = 4) with similarity percentages of 89.9–90.5%.

Table 5 The information on sources of blood meals in 46 blood-engorged Culicoides samples identified by host-specific Cytb-PCR and MinION® amplicon sequencing
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Fig. 4
figure 4

(A) Circos plot illustrating the association between blood meal origins and each Culicoides species. (B) Bar chart showing the relative abundance of sequenced reads in 46 blood-engorged Culicoides samples analyzed by MinION® amplicon sequencing in this study

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Performance comparison between host-specific Cytb-PCR and MinION® amplicon sequencing

Although there were differences in the frequency of hosts detected between host-specific Cytb-PCR and nanopore amplicon sequencing, the most common host was cow, identified in 41 of 46 samples (89.1%) by both techniques. The second most common host was human, 15.2% by host-specific Cytb-PCR and 34.8% by amplicon deep sequencing. The superiority of amplicon deep sequencing in generating the high-throughput sequenced read dataset allowed the identification of additional hosts not detected by host-specific Cytb-PCR and showed evidence of multiple blood meal origins within certain individuals of the engorged collection as shown in Table 5. Cytb-PCR showed evidence of two host species in only seven samples (15.2%). In contrast, amplicon deep sequencing identified 19 samples (41.3%) with multiple hosts, including 14 with two hosts, four with three hosts, and one with four hosts. Peridomestic species (cow, chicken, and pig), humans, and wildlife (deer and unknown species related to Rupicapra sp.) were identified as host species in Culicoides samples with evidence of multiple blood meals. Of the 11 samples with cow and human as a blood source, four samples, consisting of two C. shortti, one C. actoni, and one C. fulvus, were found positive for L. martiniquensis.

Discussion

The increasing prevalence of autochthonous human leishmaniasis, particularly in transmission areas of Thailand, has highlighted the importance of identifying vector and animal reservoir species and developing vector management strategies for effective transmission interruption. Recent experimental evidence has demonstrated successful promastigote development of several Leishmania (Mundinia) strains in laboratory-colonized C. sonorensis, suggesting that Culicoides biting midges are the imperative vectors of Leishmania (Mundinia) species rather than phlebotomine sand flies, which are traditionally known to be vectors of leishmaniasis [12,13,14]. However, biological information on the species diversity, population dynamics, infection prevalence, and host feeding patterns of Culicoides vectors remains poorly understood.

Temporal variability in species composition and abundance was observed in this study, suggesting that seasonality may influence the availability of favorable habitats for larvae of each Culicoides species. All Culicoides species were caught with the lowest abundance in summer with C. innoxius as the dominant species, whereas C. oxystoma and C. (Trithecoides) spp. were found to be the dominant species during the rainy season and winter, respectively. This could be because the summer could have contributed to the dryness of the soil habitats, strongly affecting immature Culicoides which require a moist environment and optimal environmental factors for their oviposition, larval development, and adult emergence [45,46,47], thus reducing the number of Culicoides populations during this period. In addition to seasonality, host availability and wind speed may also have influenced the species richness and abundance of Culicoides during these three collection periods [48,49,50,51].

This study demonstrated the concordance between SSU rRNA-qPCR and conventional ITS1-PCR results, showing Leishmania prevalence in at least 11 midge species, namely C. oxystoma, C. guttifer, C. orientalis, C. mahasarakhamense, C (Trithecoides) spp., C. innoxius, C. shortti, C. arakawae, C. sumatrae, C. actoni, and C. fulvus, with an overall prevalence of infection of 5.7%. Culicoides mahasarakhamense was first recorded as a vector of L. martiniquensis in Lamphun Province, Northern Thailand, in 2021 [26]. More recently, C. mahasarakhamense, C. guttifer, C. (Trithecoides) spp., C. jacobsoni, C. oxystoma, and C. orientalis have been implicated in the transmission of leishmaniasis in Chiang Rai Province, the most endemic area of leishmaniasis in Northern Thailand [27]. Therefore, the detection of Leishmania in the latter six species in our study represents the new records in Northern Thailand. Of note, L. martiniquensis was ubiquitously detected in all positive species over three seasonal periods with a high prevalence in the rainy season, followed by winter, whereas L. orientalis was only positive in three samples of C. oxystoma in the rainy season. Importantly, our finding indicates the sympatric occurrence of these two Leishmania (Mundinia) species circulating in the major livestock-associated biting midges in the emerging focus of leishmaniasis in Northern Thailand, suggesting that they may share Culicoides vector species for transmission to humans and animal reservoirs.

It could also be observed that Leishmania was detected with the highest frequency in the predominant species at a given collection time. It can be assumed that Leishmania parasites are transmitted to mammalian hosts through the bites of infected vectors; therefore, the maintenance of parasite transmission in nature appears to be closely associated with vector abundance [28, 47, 52, 53]. On the other hand, dominant vector species are more likely to increase the opportunities for pathogen transmission than less abundant species. Our findings are also consistent with the previous literature, which reported that the most abundant Culicoides species identified on cattle farms in Southern Ireland were associated with the transmission of arboviral diseases, including bluetongue and Schmallenberg viruses [54].

The intraspecific genetic diversity of L. martiniquensis and L. orientalis circulating in Culicoides biting midges, humans, and animal reservoirs in Thailand and other countries was revealed by the haplotype network of the ITS1 region in this study. Intriguingly, the haplotype network of each parasite species exhibited a star-like distribution with a dominant central haplotype and its multiple descendant lineages with few base differences, suggesting demographic expansion following the genetic bottleneck effect [55]. Negative neutrality statistics also signified that populations of these two parasites, particularly at regional and country levels, were likely to have undergone recent selective sweeps or population expansions [56, 57]. Essentially, the genetic divergence of the dominant core haplotype into novel descendent haplotypes appears to represent an evolutionary process by which the parasites have successfully adapted to a wide range of insect and mammalian host species in different geographical locations [58, 59].

For L. martiniquensis, the dominant haplotype H01 was the most ancestral and widespread globally, being shared by several individuals from different geographical origins. The existence of allopatric L. martiniquensis isolates with the H01 haplotype in different geographical locations strongly supports the hypothesis of a supercontinent origin, suggesting that the species divergence of the subgenus Mundinia occurred before the break-up of Gondwana [60, 61]. More importantly, haplotype H01 contained the sequences amplified from Culicoides samples in our collection and all leishmaniasis patients in Northern Thailand recorded to date, including the index case in this study. This genetic similarity confirms that natural Culicoides individuals are infected with the same Leishmania parasites circulating in humans in the same transmission area. Contrarily, L. orientalis was identified exclusively in Thailand [5], with populations of this species in the Northern region and throughout the country exhibiting significantly higher haplotype diversity than those of L. martiniquensis. Our results are consistent with previous literature showing considerable genetic differentiation of L. orientalis populations circulating in Culicoides and asymptomatic seropositive individuals in Chiang Rai Province [27, 62].

As previously published, the characterization of blood meal sources of Culicoides collected from different geographical locations in Thailand was based on conventional PCR targeting the mitochondrial Cytb and COI genes [28, 31, 48, 63] or the nuclear prepronociceptin (PNOC) gene [64], followed by Sanger sequencing. To our knowledge, domestic and peridomestic animals, including cattle, dogs, goats, and chickens, were identified as hosts of Culicoides species collected from areas of leishmaniasis endemicity [28, 31]. Notably, only three species, Culicoides brevitarsis, C. imicola, and C. oxystoma, collected from non-endemic areas, were recorded as opportunistic human blood-feeders [48, 64]. Thus, evidence of human blood feeding in leishmaniasis-endemic areas has never been demonstrated. As mentioned in the Background section, Sanger-based blood meal identification appears to be more prone to bias because this traditional sequencing method could only generate a single sequence for an individual sample. Multiplex Cytb-PCR is another good option for the identification of common vertebrate host species due to its high sensitivity and accuracy. However, this assay cannot identify wildlife species because of the limited number of primer pairs used. We therefore circumvent this by using a nanopore-based metabarcoding approach, which can differentiate long-read amplicon populations in samples of multiple origins to identify host species with higher taxonomic resolution without bias.

The vertebrate COI metabarcoding dataset revealed that all nine Culicoides species in our study are predominantly maintained by cows, followed by humans, chickens, deer, goat-like species, and pigs. Seven Culicoides species, namely C. shortti, C. fulvus, C. orientalis, C. actoni, C. (Trithecoides) sp., C. guttifer, and C. jacobsoni, represent the new records of feeding on human blood with percentages of human sequence reads ranging from 1.4 to 31.3% and exceptionally 51.5% in one sample of C. guttifer. However, most human feeding samples have a low percentage of human sequence reads, reflecting that human feeding is less frequent or opportunistic. This may be because most Culicoides species tend to be crepuscular in activity [29, 65]. They forage most actively at dawn and dusk and also bite at night when humans are in settlements and unlikely to be exposed to their bites. Our metabarcoding data are consistent with previous studies [31, 48, 63], showing that two C. guttifer and two C. mahasarakhamense samples in our engorged collection are ornithophilic and feed mainly on chickens.

Previously, L. martiniquensis has been reported to cause cutaneous leishmaniasis in cattle in Switzerland [66] and horses in Germany [67] and the USA [68]. In addition to cattle and horses, L. martiniquensis was molecularly detected in the visceral tissues of black rats captured in the endemic area of Songkhla Province, Southern Thailand [69], and in the buffy coat of a black rat from the patient’s residence in Chiang Rai Province [11]. Furthermore, Leishmania antibodies were also found in water buffaloes, dogs, and black rats from Chiang Rai Province [11]. These molecular and serological findings implicated domestic and peridomestic animals as reservoirs of autochthonous Leishmania parasites. In this study, blood-engorged Culicoides samples were also analyzed for Leishmania to shed light on the role of vertebrate hosts in the transmission cycle. Interestingly, four samples in our engorged collection, consisting of two C. shortti, one C. fulvus, one C. actoni, contained cow and human blood and all tested positive for L. martiniquensis. This strongly suggests that cattle may serve as an animal reservoir for L. martiniquensis, posing the risk of zoonotic transmission in this transmission area.

Our nanopore-based blood meal analysis provided promising evidence that Culicoides in leishmaniasis-endemic areas feed on humans and animal reservoirs, supporting the first criterion of Killick-Kendrick [30]. In addition, Leishmania parasites identified in Culicoides in this study were found to be genetically identical to those from patients in the same geographical area. This finding confirms Killick-Kendrick’s third criterion, which states that parasites from vectors and vertebrate hosts are indistinguishable [30]. Accordingly, our molecular evidence supports the role of positive Culicoides species as putative vectors of leishmaniasis. However, it remains insufficient to incriminate Culicoides as true natural vectors of Leishmania (Mundinia) parasites in Thailand, as parasite DNA may be detectable after host feeding, but parasite development and transmission may not occur [24]. To prove the major involvement of Thai Culicoides species in leishmaniasis transmission cycles, the full development of Leishmania (Mundinia) parasites in incriminated Culicoides species, at least by dissection of field-caught specimens and more ideally in controlled laboratory experiments, and the capability to transmit to the vertebrate hosts need to be demonstrated, which will also fulfill the second and fourth criteria of Killick-Kendrick [12,13,14, 24, 25, 30]. Therefore, colonization, experimental infection, and transmission of suspected vector species will be the next steps to confirm Culicoides as proven vectors responsible for the autochthonous transmission of Leishmania (Mundinia) parasites in Thailand.

Finally, our results revealed the seasonal population dynamics and host preference of Culicoides midge populations, as well as the infection prevalence, and haplotype diversity of two Leishmania (Mundinia) species sympatrically circulating in different Culicoides vector species in the newly emerging focus of leishmaniasis in Northern Thailand. The novel data from this study are an important step towards a more complete understanding of Culicoides midges and their medical importance in the transmission of leishmaniasis in areas of endemicity in Thailand as well as effective prevention and control of this neglected parasitic disease.

Conclusions

In this research, we investigated the species diversity, seasonal dynamics of Culicoides biting midges, and infection prevalence and genetic diversity of L. martiniquensis and L. orientalis circulating in different Culicoides species in the emerging focus of visceral leishmaniasis in Lampang Province, Northern Thailand. Our molecular findings revealed that L. martiniquensis was ubiquitously identified in at least 11 Culicoides species, whereas L. orientalis was only detected in C. oxystoma. Haplotype diversity analysis indicated recent population divergence of these two parasite species. The L. martiniquensis isolate identified in our index case was genetically identical to those circulating in Culicoides in the same area. Evidence of human blood feeding has been demonstrated, supporting the putative role of Culicoides in the autochthonous transmission of human leishmaniasis in Thailand. Blood meal analysis also suggested that peridomestic and wild animals, including cattle, deer, goat-like species, and pigs, may serve as parasite reservoirs with a risk of zoonotic transmission. Confirmation of metacyclic development by dissection of field-caught specimens, as well as colonization of Thai Culicoides species and experimental infection with Leishmania (Mundinia) parasites under laboratory conditions, will be performed in the next study. Essentially, the novel information from this study will facilitate a better understanding of the complexity of leishmaniasis transmission in endemic areas of Thailand and be a step towards developing vector control strategies to mitigate the endemicity of this neglected tropical disease effectively.

Availability of data and materials

All data supporting the findings of this study are available within the paper and its Supplementary Information. The Leishmania ITS1 sequences obtained in this study have been uploaded into GenBank with assigned accession numbers OR917763-OR917790 and PQ014661-PQ014664.

Abbreviations

UV:

Ultraviolet

RNA:

Ribonucleic acid

DNA:

Deoxyribonucleic acid

qPCR:

Quantitative polymerase chain reaction

PCR:

Polymerase chain reaction

Ct:

Cycle threshold

IPTG:

Isopropyl-beta-D-1-thiogalactopyranoside

X-gal:

5-Bromo-4-chloro-3-indolyl-beta-D-galactoside

HIV:

Human immunodeficiency virus

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Acknowledgements

We sincerely thank the staff members of the Center of Excellence in Vector Biology and Vector-Borne Disease and the Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand, for facilitating us with instrumentation and laboratory assistance.

Funding

This work has been supported by the Ratchadapiseksompote Fund, Graduate Affairs, Faculty of Medicine, Chulalongkorn University, Grant number GA68/001), the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.

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Authors and Affiliations

  1. Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok, Thailand

    Chulaluk Promrangsee

  2. Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand

    Sira Sriswasdi

  3. Center for Artificial Intelligence in Medicine, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand

    Sira Sriswasdi

  4. Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

    Sira Sriswasdi

  5. Center of Excellence in Vector Biology and Vector-Borne Disease, Chulalongkorn University, Bangkok, Thailand

    Sakone Sunantaraporn, Rungfar Boonserm, Rinnara Ampol, Padet Siriyasatien & Kanok Preativatanyou

  6. Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand

    Sakone Sunantaraporn, Chatuthanai Savigamin, Thanapat Pataradool, Chatchapon Sricharoensuk, Rungfar Boonserm, Rinnara Ampol, Padet Siriyasatien & Kanok Preativatanyou

  7. Division of Medical Technical and Academic Affairs, Department of Medical Services, Ministry of Public Health, Nonthaburi, Thailand

    Pitchayaporn Pruenglampoo

  8. Department of Parasitology, Phramongkutklao College of Medicine, Bangkok, Thailand

    Mathirut Mungthin

  9. Bernhard-Nocht-Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, Hamburg, Germany

    Jonas Schmidt-Chanasit

  10. Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany

    Jonas Schmidt-Chanasit

Authors
  1. Chulaluk Promrangsee
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  2. Sira Sriswasdi
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  13. Kanok Preativatanyou
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Contributions

KP conceptualized the idea of the study and designed the experiments. KP, CP, SSu, RB, PP and PS collected specimens. CP, SSu, CSa, TP, CSri, RA, MM, JS, PS and KP performed laboratory investigations. CP, SSri and KP analyzed the data. KP and CP wrote the paper. KP revised the manuscript. All authors have read and approved the final version of the manuscript.

Corresponding author

Correspondence to Kanok Preativatanyou.

Ethics declarations

Ethics approval and consent to participate

The procedures and research methodology for clinical specimen collection, entomological investigation and molecular analysis were approved by the Institutional Review Board of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (IRB No. 0613/67, COE No. 048/2024) and the animal research ethics committee of Chulalongkorn University Animal Care and Use Protocol (CU-ACUP), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (COA no. 004/2564).

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Not applicable.

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The authors declare no competing interests.

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Supplementary Information

13071_2024_6487_MOESM1_ESM.docx

Additional file 1: Table S1. The information on 167 ITS1 sequences of Leishmania martiniquensis and L. orientalis isolates in humans, Culicoides biting midges, and animal hosts from Thailand and other geographical regions.

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Promrangsee, C., Sriswasdi, S., Sunantaraporn, S. et al. Seasonal dynamics, Leishmania diversity, and nanopore-based metabarcoding of blood meal origins in Culicoides spp. in the newly emerging focus of leishmaniasis in Northern Thailand. Parasites Vectors 17, 400 (2024). https://doi.org/10.1186/s13071-024-06487-z

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Keywords

Parasites & Vectors

ISSN: 1756-3305

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