Identification of wild-caught phlebotomine sand flies from Crete and Cyprus using DNA barcoding

Surveillance of sand flies (Psychodidae, Phlebotominae) from Mexico: Altitudinal and climatic patterns after historical and new geographic records in endemic areas of leishmaniasis

This study updates knowledge on historical geographic distribution of sand fly species through identifying altitudinal and bioclimatic patterns in leishmaniasis endemic areas in Mexico. We analyze and identify sand fly specimens obtained through national efforts by the Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE, Mexico), collected between 1995 and 2001, 2008-2012, and 2017-2023, and add bibliographic information (427 additional records). After a principal components analysis of WorldClim variables and altitudinal ranges, variables that better explain the distribution of sand fly species were chosen (BIO6, BIO12, and BIO16, explaining 72 % of variation). A total of 1,187 specimens of 22 species were retrieved from eight states, providing 29 new municipalities and 48 new localities, being Lutzomyia cruciata, Micropygomyia chiapanensis, and Psathyromyia shannoni the most common species. We presented new historical records of distribution for sand fly species from Morelos (3), Oaxaca (7) and Tabasco (1). The 82.7 % of sand fly species analyzed were distributed in areas with altitudinal ranges below 420 m. The anthropophilic species Psathyromyia shannoni, and Lutzomyia cruciata showed the greatest variability regarding altitudinal range, and climatic preferences, while several wild species showed abiotic preferences. It is likely that the effect of urbanization and climate change generate new beneficial biotopes for the proliferation of the vector sand fly species. Complementary studies that consider seasonality, vegetation types, and change in land use could provide new information to better understand the spread of vector-borne diseases.

Entomological surveillance and spatiotemporal risk assessment of sand fly-borne diseases in Cyprus

Visceral and cutaneous leishmaniases are important public health concerns in Cyprus. Although the diseases, historically prevalent on the island, were nearly eradicated by 1996, an increase in frequency and geographical spread has recently been recorded. Upward trends in leishmaniasis prevalence have largely been attributed to environmental changes that amplify the abundance and activity of its vector, the phlebotomine sand flies. Here, we performed an extensive field study across the island to map the sand fly fauna and compared the presence and distribution of the species found with historical records. We mapped the habitat preferences of Phlebotomus papatasi and P. tobbi, two medically important species, and predicted the seasonal abundance of P. papatasi at unprecedented spatiotemporal resolution using a climate-sensitive population dynamics model driven by high-resolution meteorological forecasting. Our compendium holds a record of 18 species and the locations of a subset, including those of potential public and veterinary health concern. We confirmed that P. papatasi is widespread, especially in densely urbanized areas, and predicted that its abundance uniformly peaks across the island at the end of summer. We identified potential hotspots of P. papatasi activity even after this peak. Our results form a foundation to inform public health planning and contribute to the development of effective, efficient, and environmentally sensitive strategies to control sand fly populations and prevent sand fly-borne diseases.

Mitochondrial COI and Cytb gene as valid molecular identification marker of sandfly species (Diptera: Psychodidae) in China

The accurate identification of sandfly species is crucial because some species transmit medically significant diseases, including leishmaniasis, bartonellosis and sandfly fever. However, due to the high similarity of the external morphology in sandfly species, identification can only be performed using internal morphological characteristics after dissection, which is time consuming and requires highly experienced staff. Thus, the introduction of suitable molecular markers may solve these identification problems. This study screened suitable DNA barcodes to identify common sandfly species in China. The phlebotomine sandflies were collected from Sichuan, Henan and Hainan Provinces from 2014 to 2016. The species were identified by the morphological characteristics of the pharyngeal armature and spermatheca. The genomic DNA of sandfly was extracted individually, and mitochondrial DNA (mtDNA) cytochrome C oxidase subunit I (COI) and cytochrome B (Cytb) as well as the 18S subunit of ribosomal DNA (rDNA) were amplified using polymerase chain reaction (PCR). Additionally, intraspecific and interspecific differences (p-distance) were calculated to evaluate the feasibility of the three gene fragments as a DNA barcode. The phylogeny trees of all sandfly species in this study were constructed using neighbor joining (NJ) method. Six species were identified by the morphological features, belonging to Phlebotomus and Sergentomyia, as Ph. chinensis s. l., Ph. stantoni, Se. bailyi, Se. iyengari, Se. squamirostris, and Se. squamipleuris. Analysis based on three gene fragments revealed some degree of intraspecific polymorphism among these sandfly species in China. The largest intraspecific variation occurred in Ph. chinensis s. l. (mtDNA COI, p-distance = 0.042; mtDNA Cytb, p-distance = 0.071), but the 18S rDNA fragment showed a small variation (p-distance = 0.005). The ranges of interspecific p-distances for mtDNA COI and mtDNA Cytb were 0.138 - 0.231 and 0.128 - 0.274, respectively. However, the interspecific p-distances of 18S rDNA are relatively low ranging from 0.003 to 0.055. Both mitochondrial COI and Cytb gene fragments are valid molecular identification markers in theses sandfly species. The topological structure of phylogeny trees based on mtDNA COI, mtDNA Cytb and 18S rDNA genes were all consistent with morphological classification. And we also found there were significant intraspecies differences within Ph. chinensis s. l. (0.006-0.071) and Se. bailyi (0.002-0.032) based on mtDNA Cytb gene fragment. Sequence alignment data suggested that Ph. chinensis s. l. from Sichuan should be Ph. sichuanensis, and the sandfly specimen collected from Henan was Ph. chinensis s. s.. There could be cryptic species in Se. bailyi from China.

Molecular taxonomy of phlebotomine sand flies (Diptera, Psychodidae) with emphasis on DNA barcoding: A review

The taxonomy and systematics of sand flies (Diptera, Psychodidae, Phlebotominae) are one of the pillars of research aimed to identifying vector populations and the agents transmitted by these insects. Traditionally, the use of morphological traits has been the main line of evidence for the definition of species, but the use of DNA sequences is useful as an integrative approach for their delimitation. Here, we discuss the current status of the molecular taxonomy of sand flies, including their most sequenced molecular markers and the main results. Only about 37% of all sand fly species have been processed for any molecular marker and are publicly available in the NCBI GenBank or BOLD Systems databases. The genera Phlebotomus, Nyssomyia, Psathyromyia and Psychodopygus are well-sampled, accounting for more than 56% of their sequenced species. However, less than 34% of the species of Sergentomyia, Lutzomyia, Trichopygomyia and Trichophoromyia have been sampled, representing a major gap in the knowledge of these groups. The most sequenced molecular markers are those within mtDNA, especially the DNA barcoding fragment of the cytochrome c oxidase subunit I (coi) gene, which has shown promising results in detecting cryptic diversity within species. Few sequences of conserved genes have been generated, which hampers higher-level phylogenetic inferences. We argue that sand fly species should be sequenced for at least the coi DNA barcoding marker, but multiple markers with different mutation rates should be assessed, whenever possible, to generate multilocus analysis.

Mitochondrial DNA barcoding of mosquito species (Diptera: Culicidae) in Thailand

The correct identification of mosquito species is important for effective mosquito vector control. However, the standard morphological identification of mosquito species based on the available keys is not easy with specimens in the field due to missing or damaged morphological features during mosquito collections, often leading to the misidentification of morphologically indistinguishable. To resolve this problem, we collected mosquito species across Thailand to gather genetic information, and evaluated the DNA barcoding efficacy for mosquito species identification in Thailand. A total of 310 mosquito samples, representing 73 mosquito species, were amplified using mitochondrial cytochrome c oxidase subunit I (COI) primers. The average maximum intraspecific genetic variation of the 73 mosquito species was 1% ranged from 0–5.7%. While, average minimum interspecific genetic variation (the distance to the nearest neighbour) of the 73 mosquito species was 7% ranged from 0.3–12.9%. The identification of success rates based on the “Best Match,” “Best Close Match,” and “All Species Barcodes” methods were 97.7%, 91.6%, and 81%, respectively. Phylogenetic analyses of Anopheles COI sequences demonstrated a clear separation between almost all species (except for those between An. baimaii and An. dirus), with high bootstrap support values (97%–99%). Furthermore, phylogenetic analyses revealed potential sibling species of An. annularis, An. tessellatus, and An. subpictus in Thailand. Our results indicated that DNA barcoding is an effective molecular approach for the accurate identification of mosquitoes in Thailand.

Concurrent molecular characterization of sand flies and Leishmania parasites by amplicon-based next-generation sequencing

BACKGROUND

Phlebotomine sand flies are vectors of Leishmania parasites, which are the causative agents of leishmaniasis. Herein, we developed an amplicon-based next-generation sequencing (Amp-NGS) to characterize sand flies and Leishmania parasites simultaneously targeting partial fragments of 18S rDNA and ITS1 genes, respectively.

METHODS

Our assay was optimized using reference sand fly (n = 8) and Leishmania spp. (n = 9) samples and validated using wild-caught sand flies from Palestine. The assay was highly specific, and all DNA references were successfully identified to the species level.

RESULTS

Among the wild-caught sand flies (n = 187), Phlebotomus spp. represented 95% of the collected samples (177/187), including Ph. sergenti (147/187, 79%), Ph. papatasi (19/187, 10.2%), Ph. perfiliewi (3/187, 1.6%), Ph. tobbi (2/187, 1.2%) and Ph. syriacus (6/187, 3.2%). Sergentomyia spp. represented only 5% (10/187) of the collected samples and included S. dentata (n = 6), S. fallax (n = 2), S. schwetzi (n = 1) and S. ghesquiere (n = 1). The study observed strong positive correlation between sand fly identification results of the Amp-NGS and morphological identification method (r = 0.84, df = 185, P < 0.001). Some discrepancies between the two methods in the identification of closely related species (i.e. Ph. perfiliewi, Ph. tobbi and Ph. syriacus) were observed. Leishmania DNA was detected and identified as L. tropica in 14 samples (14/187, 7.5%).

CONCLUSIONS

Our assay was sensitive to detect (limit of detection was 0.0016 ng/reaction) and identify Leishmania DNA in sand flies, thus representing a new tool for studying sand flies and their associated Leishmania parasites in endemic areas.

Sand fly fauna of South-Eastern Romania, with the description of Phlebotomus (Transphlebotomus) simonahalepae n. sp. (Diptera: Psychodidae)

Background

An entomological study was conducted in the Canaraua Fetii Special Protection Area in the Dobrogea region, South-Eastern Romania. Four sand fly species were recorded at this location between 1968 and 1970: Phlebotomus neglectus, Ph. balcanicus, Ph. sergenti and Sergentomyia minuta. The most abundant sand fly species recorded at that time were Ph. balcanicus and Se. minuta. In the context of a countrywide study to update the sand fly species diversity, we surveyed the same area, recording also a previously unknown Ph. (Transphlebotomus) sp., for which we provide a formal description here.

Methods

Sand flies were collected between July and August in 2018 and 2019 in three sites from Canaraua Fetii, Dobrogea region, Romania. The general aspect of the landscape is of a canyon (vertical, narrow walls and deep valleys). Species identification was done using both morphological and molecular analyses.

Results

Out of 645 collected sand flies, 644 (99.8%) were morphologically identified as Ph. neglectus, while one female specimen (0.2%) was assigned to a previously unknown species, belonging to the subgenus Transphlebotomus. The morphological and molecular examination of this specimen showed that it is a previously unknown species which we formally describe here as Phlebotomus (Transphlebotomus) simonahalepae n. sp. Also, Ph. balcanicus, Ph. sergenti, and Se. minuta (previously recorded in this location) were not present.

Conclusions

The study revealed for the first time the presence of sand flies of the subgenus Transphlebotomus in Romania. Moreover, a new species, Ph. simonahalepae n. sp., was described based on a female specimen, raising the number of species in this subgenus to six. In the investigated natural habitat, the predominant species was Ph. neglectus instead of Ph. balcanicus and Se. minuta (recorded as the predominant species in 1968–1970).

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04929-6.

Phlebotomine sand fly survey in the Republic of Moldova: species composition, distribution and host preferences

BACKGROUND

Phlebotomine sand flies (Diptera: Psychodiae) in the Republic of Moldova have been understudied for decades. Our study provides a first update on their occurrence, species composition and bloodmeal sources after 50 years.

METHODS

During 5 seasons (2013-2017), 58 localities from 20 regions were surveyed for presence of sand flies using CDC light traps and manual aspirators. Species identification was done by a combination of morphological and molecular approaches (DNA barcoding, MALDI-TOF MS protein profiling). In engorged females, host blood was identified by three molecular techniques (RFLP, cytb sequencing and MALDI-TOF peptide mass mapping). Population structure of most abundant species was studied by cox1 haplotyping; phylogenetic analyses of ITS2 and cox1 genetic markers were used to resolve relationships of other detected species.

RESULTS

In total, 793 sand flies were collected at 30 (51.7%) localities from 12 regions of Moldova. Three species were identified by an integrative morphological and molecular approach: Phlebotomus papatasi, P. perfiliewi and Phlebotomus sp. (Adlerius), the first being the most abundant and widespread, markedly anthropophilic based on bloodmeal analyses, occurring also indoors and showing low population structure with only five haplotypes of cox1 detected. Distinct morphological and molecular characters of Phlebotomus sp. (Adlerius) specimens suggest the presence of a yet undescribed species.

CONCLUSIONS

Our study revealed the presence of stable sand fly populations of three species in Moldova that represent a biting nuisance as well as a potential threat of pathogen transmission and shall be further studied.

Development of a next generation DNA sequencing-based multi detection assay for detecting and identifying Leishmania parasites, blood sources, plant meals and intestinal microbiome in phlebotomine sand flies

Leishmaniasis is a disease caused by Leishmania parasites transmitted by phlebotomine sand flies (Diptera: Psychodidae). Human infections with different Leishmania species cause characteristic clinical manifestations; cutaneous or visceral leishmaniasis. Here we describe the development and application of a Miseq Next GenerationSequencing (NGS)-based Multi Detection Assay (MDA) designed to characterize metagenomics parameters pertinent to the sand fly vectors which may affect their vectorial capacity for Leishmania. For this purpose, we developed a MDA by which, DNA fragments were amplified through polymerase chain reactions (PCR) and then sequenced by MiSeq/NGS. PCR amplification was achieved using some published and some new primers designed specifically for identifying Leishmania spp. (ITS1), sand fly spp. (cytochrome oxidase I), vertebrate blood (Cytochrome b), plant DNA ribulose-1,5-bisphosphate carboxylase large subunit gene (rbcL), and prokaryotic micobiome (16 s rRNA). This MDA/NGS analysis was performed on two species of wild-caught sand flies that transmit different Leishmania spp. in two ecologically distinct, but geographically neighboring locations. The results were analyzed to identify, quantitate and correlate the measured parameters in order to assess their putative importance in the transmission dynamics of leishmaniasis.

Revision of the species composition and distribution of Turkish sand flies using DNA barcodes

Background

Currently, knowledge regarding the phlebotomine sand fly (Diptera: Psychodidae) fauna of Turkey is restricted to regions with endemic leishmaniasis. However, rapidly changing environmental and social conditions highlight concerns on the possible future expansion of sand fly-borne diseases in Turkey, promoting risk assessment through biosurveillance activities in non-endemic regions. Traditional morphological approaches are complicated by extensive cryptic speciation in sand flies, thus integrated studies utilizing DNA markers are becoming increasingly important for correct sand fly identification. This study contributes to the knowledge of the sand fly fauna in understudied regions of Turkey, and provides an extensive DNA barcode reference library of expertly identified Turkish sand fly species for the first time.

Methods

Fly sampling was conducted at 101 locations from 29 provinces, covering all three biogeographical regions of Turkey. Specimens were morphologically identified using available keys. Cytochrome c oxidase I (cox1) barcode sequences were analyzed both for morphologically distinct species and those specimens with cryptic identity. A taxon identity tree was obtained using Neighbor Joining (NJ) analysis. Species boundaries among closely related taxa evaluated using ABGD, Maximum Likelihood (ML) and haplotype network analyses. Sand fly richness of all three biogeographical regions were compared using nonparametric species richness estimators.

Results

A total of 729 barcode sequences (including representatives of all previously reported subgenera) were obtained from a total of 9642 sand fly specimens collected in Turkey. Specimens belonging to the same species or species complex clustered together in the NJ tree, regardless of their geographical origin. The species delimitation methods revealed the existence of 33 MOTUs, increasing the previously reported 28 recorded sand fly species by 17.8%. The richest sand fly diversity was determined in Anatolia, followed by the Mediterranean, and then the Black Sea regions of the country.

Conclusions

A comprehensive cox1 reference library is provided for the sand fly species of Turkey, including the proposed novel taxa discovered herein. Our results have epidemiological significance exposing extensive distributions of proven and suspected sand fly vectors in Turkey, including those areas currently regarded as non-endemic for sand fly-borne disease.

Electronic supplementary material

The online version of this article (10.1186/s13071-019-3669-3) contains supplementary material, which is available to authorized users.

The Prevalence of Antibodies against Sandfly Fever Viruses and West Nile Virus in Cyprus

BACKGROUND

Sandfly fever is an incapacitating disease caused by sandfly-borne Phleboviruses that can lead to meningitis, encephalitis or meningoencephalitis. West Nile virus (WNV), a mosquito-borne Flavivirus, can induce neuroinvasive disease manifested by meningitis, encephalitis or acute flaccid paralysis. Both vectors are endemic in Cyprus and very active during summer. The aims of this study were to determine first the prevalence of sandfly fever viruses (SFV) and WNV infections in Cyprus and second, to investigate their role in central nervous system (CNS) infections.

METHODS

For the prevalence study, 327 sera collected in 2013 and 2014 were tested for anti-SFV and anti-WNV IgG using indirect immunofluorescence assay and ELISA, respectively. In order to investigate a possible role of SFV and WNV in CNS infections, 127 sera of patients presenting symptoms of SFV or WNV infections were screened for IgM specific to SFV and WNV.

RESULTS

The overall anti-SFV IgG seroprevalence was 28% and was increasing with age (P< 0.01). The seroprevalence rate for anti-WNV IgG in Cyprus was 5%. Concerning the role of SFVs in CNS infections, anti-SFV IgM was detected in 8 out of 127 sera from selected patients presenting relevant symptoms of infections during vector's active period. In addition, anti-WNV IgM were detected in 17 out of the 127 patients with compatible symptoms.

CONCLUSION

The findings confirm the presence of sandfly fever and WNV in Cyprus and should, therefore, be considered in the differential diagnosis of patients with febrile illness/meningitis.