The species concept in parasites and other pathogens: a pragmatic approach?

Haplotypic analysis of cox1 from Toxocara canis demonstrates five distinct clades that are not geographically defined

BACKGROUND

Toxocara canis is a cosmopolitan parasite of dogs that is transmitted transplacentally to puppies resulting in widespread shedding of eggs in the environment. However, it is not clear if there are dominant parasite genotypes that are more common, pathogenic, or likely to be zoonotic.

METHODS/PRINCIPLE FINDINGS

Sequences of mitochondrial cox1 gene from adult worms were used to compare parasites from the United States with submitted sequences from parasites isolated from dogs in different countries. Our analysis revealed at least 55 haplotypes. While we expected the North American worms to form a distinct cluster, we found haplotypes of T. canis reported elsewhere existing in this population. Interestingly, combining the sequence data from our study with the available GenBank data, analysis of cox1 sequences results in five distinct clades that are not geographically defined.

CONCLUSIONS

The five clades of T. canis revealed in this study potentially have unique life histories, traits, or host preferences. Additional investigation is needed to see if these distinct clades represent cryptic species with clinically useful attributes or genotypes with taxonomic value. Evaluation of common mitochondrial genes may reveal distinct populations of zoonotic T. canis.

Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism

BACKGROUND

The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T rubrum sensu stricto and T violaceum, as well as other less well-established or debatable taxa like T soudanense, T kuryangei and T megninii. Our previous study provided limited evidence in favour of the existence of two genetic lineages in the Russian T rubrum sensu stricto population.

OBJECTIVES

We aimed to study the genetic structure of the Russian population of T rubrum and to identify factors shaping this structure.

METHODS

We analysed the polymorphism of 12 simple sequence repeat (SSR or microsatellite) markers and single nucleotide polymorphism in the TERG_02941 protein-coding gene in 70 T rubrum isolates and performed a phylogenomic reconstruction.

RESULTS

All three types of data provided conclusive evidence that the population consists of two genetic lineages. Clustering, performed by means of microsatellite length polymorphism analysis, was strongly dependent on the number of nucleotide repeats in the 5'-area of the fructose-1,6-bisphosphate aldolase gene. Analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22%-48% of the variability was among groups within T rubrum. There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression or urease activity.

CONCLUSION

Our results suggest that the Russian population of T rubrum consists of two cosmopolitan genetic lineages.

DNA topoisomerase 2 gene polymorphism in dermatophytes

BACKGROUND

Dermatophytes are a group of keratinophilic fungi of medical importance. Despite a relatively long history of molecular taxonomic studies, there is still a need for information on genetic polymorphism in wider variety of genomic loci.

OBJECTIVES

Our goal was to study partial DNA topoisomerase 2 gene (TOP2) polymorphism in dermatophytes.

METHODS

We performed DNA sequencing of TOP2 in 26 dermatophyte species along with ribosomal internal transcribed spacer (ITS) sequencing.

RESULTS

The number of polymorphic sites in TOP2 data set was similar to that one in ITS data set. Nannizzia species formed paraphyletic group in TOP2 tree. Trichophyton simii was paraphyletic in concatenated TOP2-ITS tree, one of its two clades contained solely Iranian isolates.

CONCLUSIONS

Our results revealed several unresolved problems in the taxonomy of dermatophytes, including probable polyphyly of the genus Nannizzia and the species T simii.

Next-Generation Molecular Surveillance of TriTryp Diseases

Elimination programs targeting TriTryp diseases (Leishmaniasis, Chagas' disease, human African trypanosomiasis) significantly reduced the number of cases. Continued surveillance is crucial to sustain this progress, but parasite molecular surveillance by genotyping is currently lacking. We explain here which epidemiological questions of public health and clinical relevance could be answered by means of molecular surveillance. Whole-genome sequencing (WGS) for molecular surveillance will be an important added value, where we advocate that preference should be given to direct sequencing of the parasite's genome in host tissues instead of analysis of cultivated isolates. The main challenges here, and recent technological advances, are discussed. We conclude with a series of recommendations for implementing whole-genome sequencing for molecular surveillance.

Phylogenetic insights on Leishmania detected in cats as revealed by nucleotide sequence analysis of multiple genetic markers

Cats have been found infected by the same Leishmania species that also infect dogs and humans in both the New and Old Worlds, and their role as additional reservoir hosts of L. infantum has been previously suggested. Currently, the genetic diversity of Leishmania spp. detected in cats is poorly understood. In this cross-sectional study, the partial nucleotide sequences of four gene markers (cytB, g6pdh, hsp70 and ITS-rDNA) were explored to investigate the genetic diversity and the phylogenetic relationships of Leishmania parasites detected in cats. A total of 25 cat buffy coat samples where the presence of Leishmania SSU-rDNA was revealed by PCR (from a convenience sample of 465 cats screened), as well as six Leishmania strains previously isolated from cats, were included in this study. Phylogenetic analyses showed that the majority of Leishmania parasites detected in cats did not display distinctive genetic features, sharing the same genetic types with L. infantum strains isolated from humans, dogs and phlebotomine sand flies. Unexpectedly, DNA of L. major and/or of a L. major/L. donovani sensu lato hybrid was detected in buffy coat samples of two cats from different regions of Portugal. However, a mix infection hypothesis cannot be formally excluded. To our knowledge, this study represents the first evidence for the presence of DNA of Leishmania hybrid parasites in cats. The results reported here not only reinforce the idea that cats play a role in the epidemiology of zoonotic leishmaniosis but also indicate the circulation of L. major and/or L. major/L. donovani s.l. hybrid parasites in Portugal. Also, whenever sequencing of whole Leishmania genomes regularly cannot be accomplished, and while their complete genomes remain under-represented in the nucleotide sequence databases, the combined use of multiple genetic markers, including kinetoplast maxicircle DNA, seems to be essential for typing of Leishmania parasites.

Morphological, ultrastructural, and phylogenetic analysis of two novel Myxobolus species (Cnidaria: Myxosporea) parasitizing bryconid fish from São Francisco River, Brazil

Twelve Myxobolus species have been previously described to parasitize Bryconidae fish in South America. Here, we describe two novel myxosporean species that parasitize economically important Bryconidae from the São Francisco River basin in Brazil. Myxospores morphometry, morphology, small-subunit ribosomal DNA - ssrDNA sequences, and other biological traits were used in the taxonomic analysis. Phylogenetic analysis was performed to assess the position of the new Myxobolus species among the closest Myxobolus/Henneguya. Myxobolus iecoris n. sp. was found infecting the liver of Salminus franciscanus (dourado). Myxospores were oval with the anterior region aculiform in frontal view and biconvex in lateral view and measured 11.4-14.2 (12.8 ± 0.8) μm long, 7.7-9.9 (8.7 ± 0.6) μm wide, 6.5-7.5 (6.9 ± 0.4) μm thick. Two pyriform and equal-sized polar capsules measuring 4.9-7.4 (5.9 ± 0.5) μm long and 2.3-3.5 (3.0 ± 0.2) μm wide contained polar tubules with 8-9 turns. Myxobolus lienis n. sp. was found infecting the spleen of Brycon orthotaenia (matrinxã). Myxospores were round to oval in frontal view and biconvex in lateral view and measured 10.3-13.8 (12 ± 0.6) μm long, 6.8-9.3 (8.3 ± 0.5) μm wide, and 6.9-7.0 (7.0 ± 0.6) μm thick. Two oval and equal-sized polar capsules measured 3.9-5.8 (4.6 ± 0.5) μm long and 2.0-3.5 (2.8 ± 0.3) μm wide contained polar tubules with 5-6 turns. Ultrastructural analysis revealed asynchronous sporogenesis with germinative cells and young sporogonic stages in the periphery of the plasmodia. A connective tissue capsule was observed surrounding Myxobolus lienis n. sp., but it was absent for Myxobolus iecoris n. sp. Maximum likelihood and Bayesian inferences showed the two novel species clustering in a well-supported subclade composed by Myxobolus spp. of bryconids. Myxobolus iecoris n. sp. appeared as a sister species of M. aureus and Myxobolus lienis n. sp. as sister to M. umidus.

Medical Parasitology Taxonomy Update: January 2012 to December 2015

Parasites of medical importance have long been classified taxonomically by morphological characteristics. However, molecular-based techniques have been increasingly used and relied on to determine evolutionary distances for the basis of rational hierarchal classifications. This has resulted in several different classification schemes for parasites and changes in parasite taxonomy. The purpose of this Minireview is to provide a single reference for diagnostic laboratories that summarizes new and revised clinically relevant parasite taxonomy from January 2012 through December 2015.

Phylogenetic position of Leishmania isolates from Khyber Pakhtunkhwa province of Pakistan

Several species of the genus Leishmania are causative agents of cutaneous leishmaniasis in Pakistan. This study aimed to determine phylogenetic placement of Leishmania species causing cutaneous leishmaniasis in Khyber Pakhtunkhwa province, Pakistan (34 Leishmania tropica, 3 Leishmania infantum), in-relation to species from other geographical areas using gene sequences encoding cytochrome b (cytb) and internal transcribed spacer 2 (its2). Based on cytochrome b sequence analysis, L. tropica strains from Pakistan and other geographical regions were differentiated into two genotype groups, A and B. Within the province, five distinct L. tropica genotypes were recognized; two in group A, three in group B. Two L. infantum isolates from the province were closely associated with both Afro-Eurasian and American species of the Leishmania donovani complex, including Leishmania chagasi, L. infantum and L. donovani from Sudan and Ethiopia; while a third L. infantum isolate could not be differentiated from visceralizing Kenyan and Indian L. donovani. We observed apposite phylogenetic placement of CL-causing L. tropica and L. infantum from Khyber Pakhtunkhwa. Affinities ascribed to Leishmania spp. From the region are valuable in tracing potential importation of leishmaniasis.

A review of Theileria diagnostics and epidemiology

•

Serological and molecular assays exist for most economic important Theileria species.

•

Molecular assays are constantly being improved with regard to sensitivity and specificity.

•

The concept of what constitute a Theileria species impacts on accurate diagnostics.

•

Analytical specificity of molecular assays are >800 000 parasites/L blood.

•

Parasitemia ranges may determine practical limits of detection.

An extensive range of serological and molecular diagnostic assays exist for most of the economically important Theileira species such as T. annulata, T. equi, T. lestoquardi, T. parva, T. uilenbergi and other more benign species. Diagnostics of Theileria is considered with regard to sensitivity and specificity of current molecular and serological assays and their use in epidemiology. In the case of serological assays, cross-reactivity of genetically closely related species reduces the use of the gold standard indirect fluorescent antibody test (IFAT). Development of antigen-specific assays does not necessarily address this problem, since closely related species will potentially have similar antigens. Even so, serological assays remain an important line of enquiry in epidemiological surveys. Molecular based assays have exploded in the last decade with significant improvements in sensitivity and specificity. In this review, the current interpretation of what constitute a species in Theileria and its impact on accurate molecular diagnostics is considered. Most molecular assays based on conventional or real-time PCR technology have proven to be on standard with regard to analytical sensitivity. However, consideration of the limits of detection in regard to total blood volume of an animal indicates that most assays may only detect >400,000 parasites/L blood. Even so, natural parasitaemia distribution in carrier-state animals seems to be above this limit of detection, suggesting that most molecular assays should be able to detect the majority of infected individuals under endemic conditions. The potential for false-negative results can, however, only be assessed within the biological context of the parasite within its vertebrate host, i.e. parasitaemia range in the carrier-state that will support infection of the vector and subsequent transmission.

Hidden diversity and evolutionary trends in malacosporean parasites (Cnidaria: Myxozoa) identified using molecular phylogenetics

Malacosporeans represent a small fraction of myxozoan biodiversity with only two genera and three species described. They cycle between bryozoans and freshwater fish. In this study, we (i) microscopically examine and screen different freshwater/marine fish species from various geographic locations and habitats for the presence of malacosporeans using PCR; (ii) study the morphology, prevalence, host species/habitat preference and distribution of malacosporeans; (iii) perform small subunit/large subunit rDNA and Elongation factor 2 based phylogenetic analyses of newly gathered data, together with all available malacosporean data in GenBank; and (iv) investigate the evolutionary trends of malacosporeans by mapping the morphology of bryozoan-related stages, host species, habitat and geographic data on the small subunit rDNA-based phylogenetic tree. We reveal a high prevalence and diversity of malacosporeans in several fish hosts in European freshwater habitats by adding five new species of Buddenbrockia and Tetracapsuloides from cyprinid and perciform fishes. Comprehensive phylogenetic analyses revealed that, apart from Buddenbrockia and Tetracapsuloides clades, a novel malacosporean lineage (likely a new genus) exists. The fish host species spectrum was extended for Buddenbrockia plumatellae and Buddenbrockia sp. 2. Co-infections of up to three malacosporean species were found in individual fish. The significant increase in malacosporean species richness revealed in the present study points to a hidden biodiversity in this parasite group. This is most probably due to the cryptic nature of malacosporean sporogonic and presporogonic stages and mostly asymptomatic infections in the fish hosts. The potential existence of malacosporean life cycles in the marine environment as well as the evolution of worm- and sac-like morphology is discussed. This study improves the understanding of the biodiversity, prevalence, distribution, habitat and host preference of malacosporeans and unveils their evolutionary trends.

Further observations on in vitro hybridization of hemosporidian parasites: patterns of ookinete development in Haemoproteus spp

Increasingly frequent outbreaks of zoonotic infections call for studies of wildlife parasites to reach a better understanding of the mechanisms of host switch, leading to the evolution of new diseases. However, speciation processes have been insufficiently addressed in experimental parasitology studies, primarily due to difficulties in determining and measuring mate-recognition signals in parasites. We investigated patterns of sexual process and ookinete development in avian Haemoproteus (Parahaemoproteus) spp. (Haemosporida, Haemoproteidae) using in vitro experiments on between-lineage hybridization. Eleven mitochondrial cytochrome b (cyt b) lineages belonging to 9 species of hemoproteid were isolated from naturally infected passerine birds. The parasites were identified to species on the basis of morphology of their gametocytes and polymerase chain reaction amplification of segments of the cyt b gene. Sexual process and ookinete development were initiated in vitro by mixing blood containing mature gametocytes with a 3.7% solution of sodium citrate and exposing the mixture to air. Ookinetes of all lineages except Haemoproteus payevskyi (lineage hRW1) and Haemoproteus nucleocondensus (hGRW1) developed; the 2 latter species did not exflagellate. Between-lineage hybridization was initiated by mixing blood containing mature gametocytes of 2 different parasites; the following experiments were performed: (1) Haemoproteus pallidus (lineage hPFC1) × Haemoproteus minutus (lineage hTURDUS2); (2) H. pallidus (hPFC1) × Haemoproteus tartakovskyi (hSISKIN1); (3) Haemoproteus belopolskyi (hHIICT3) × Haemoproteus lanii (hRB1); (4) Haemoproteus balmorali (hSFC1) × H. pallidus (hPFC1); (5) H. belopolskyi (hHIICT1) × Haemoproteus parabelopolskyi (hSYBOR1); (6) H. tartakovskyi (hHAWF1) × H. tartakovskyi (hSISKIN1); (7) H. pallidus (hPFC1) × H. lanii (hRB1); (8) H. tartakovskyi (hHAWF1) × H. parabelopolskyi (hSYBOR1). We report 4 patterns of between-lineage interactions that seem to be common and might prevent mixing lineages during simultaneous sexual process in wildlife: (1) the blockage of ookinete development of both parasites; (2) the development of ookinetes of 1 parasite and blockage of ookinete development of the other; (3) selective within-lineage mating resulting in ookinete development of both parent species and absence of hybrid organisms; (4) absence of selective within-lineage mating resulting in presence of ookinetes of both parents and also development of hybrid organisms with unclear potential for further sporogony. The present study indicates directions for collection of source material in the investigation of mechanisms of reproductive isolation leading to speciation in these parasites. The next steps in these studies should be the development of nuclear markers for distinguishing hemosporidian hybrid organisms and the experimental observation of further development of hybrid ookinetes in vectors.

Babesia: a world emerging

Babesia are tick-transmitted hemoprotozooans that infect mammals and birds, and which are acknowledged for their major impact on farm and pet animal health and associated economic costs worldwide. Additionally, Babesia infections of wildlife can be fatal if associated with stressful management practices; and human babesiosis, also transmitted by blood transfusion, is an increasing public-health concern. Due to the huge diversity of species reported to serve as Babesia hosts, all vertebrates might be potential carriers, as long as they are adequate hosts for Babesia-vector ticks. We here provide a comprehensive overview of the most relevant Babesia species, and a discussion of the classical taxonomic criteria. Babesia, Cytauxzoon and Theileria parasites are closely related and collectively referred to as piroplasmids. A possible scenario for the history of piroplasmids is presented in the context of recent findings, and its implications for future research avenues are outlined. Phylogenetic trees of all available 18S rRNA and hsp70 genes were generated, based on which we present a thoroughly revised molecular classification, comprising five monophyletic Babesia lineages, one Cytauxzoon clade, and one Theileria clade. Updated 18S rRNA and beta-tubulin gene trees of the B. microti isolates agree with those previously reported. To reconcile estimates of the origin of piroplasmids and ticks (~300 Ma, respectively), and mammalian radiation (60 Ma), we hypothesize that the dixenous piroplasmid life cycle evolved with the origin of ticks. Thus, the observed time gap between tick origin and mammalian radiation indicates the existence of hitherto unknown piroplasmid lineages and/or species in extant vertebrate taxa, including reptiles and possibly amphibians. The development and current status of the molecular taxonomy of Babesia, with emphasis on human-infecting species, is discussed. Finally, recent results from population genetic studies of Babesia parasites, and their implications for the development of pathogenicity, drug resistance and vaccines, are summarized.

Species delimitation and phylogenetic relationships of Chinese Leishmania isolates reexamined using kinetoplast cytochrome oxidase II gene sequences

Leishmaniasis is a geographically widespread disease caused by protozoan parasites belonging to the genus Leishmania and transmitted by certain species of sand fly. This disease still remains endemic in China, especially in the west and northwest frontier regions. A recent ITS1 phylogeny of Chinese Leishmania isolates has challenged some aspects for their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within Chinese Leishmania isolates highlights the need for additional data and analyses. Here, we test the phylogenetic relationships among Chinese isolates and their relatives by analyzing kinetoplast cytochrome oxidase II (COII) gene sequences, including 14 Chinese isolates and three isolates from other countries plus 17 sequences retrieved from GenBank. The COII gene might have experienced little substitution saturation, and its evolutionary process was likely to have been stationary, reversible, and homogeneous. Both neighbor-joining and Bayesian analyses reveal a moderately supported group comprising ten newly determined isolates, which is closely related to Leishmania tarentolae and Endotrypanum monterogeii. In combination with genetic distance analysis as well as Bayesian hypothesis testing, this further corroborates the occurrence of an undescribed species of Leishmania. Our results also suggest that (1) isolate MHOM/CN/93/GS7 and isolate IPHL/CN/77/XJ771 are Leishmania donovani; (2) isolate MHOM/CN/84/JS1 is Leishmania tropica; (3) the status referring to an isolate MRHO/CN/62/GS-GER20 from a great gerbil in Gansu, China, as Leishmania gerbilli, formerly based on multilocus enzyme electrophoresis, is recognized; and (4) E. monterogeii is nested within the genus Leishmania, resulting in a paraphyletic Leishmania. In addition, the results of this study enrich our understanding of the heterogeneity and relationships of Chinese Leishmania isolates.

African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum

Plasmodium reichenowi, a chimpanzee parasite, was until very recently the only known close relative of Plasmodium falciparum, the most virulent agent of human malaria. Recently, Plasmodium gaboni, another closely related chimpanzee parasite, was discovered, suggesting that the diversity of Plasmodium circulating in great apes in Africa might have been underestimated. It was also recently shown that P. reichenowi is a geographically widespread and genetically diverse chimpanzee parasite and that the world diversity of P. falciparum is fully included within the much broader genetic diversity of P. reichenowi. The evidence indicates that all extant populations of P. falciparum originated from P. reichenowi, likely by a single transfer from chimpanzees. In this work, we have studied the diversity of Plasmodium species infecting chimpanzees and gorillas in Central Africa (Cameroon and Gabon) from both wild-living and captive animals. The studies in wild apes used noninvasive sampling methods. We confirm the presence of P. reichenowi and P. gaboni in wild chimpanzees. Moreover, our results reveal the existence of an unexpected genetic diversity of Plasmodium lineages circulating in gorillas. We show that gorillas are naturally infected by two related lineages of parasites that have not been described previously, herein referred to as Plasmodium GorA and P. GorB, but also by P. falciparum, a species previously considered as strictly human specific. The continuously increasing contacts between humans and primate populations raise concerns about further reciprocal host transfers of these pathogens.

Populations, hybrids and the systematic concepts of species and subspecies in Chagas disease triatomine vectors inferred from nuclear ribosomal and mitochondrial DNA

In Chagas disease, triatomine vectors are the main target for control measures because of the absence of effective drugs. The broad usefulness of nuclear rDNA and mtDNA sequences explains why triatomine studies using these markers have increased so pronouncedly in recent years. This indicates the appropriateness of an updated review about these molecular markers, concentrating on aspects useful for research on Chagas disease vectors. A comparative analysis is presented on the efficiency, weight of their different characteristics, limitations and problems of each of the different DNA markers in the light of the results obtained in studies on populations, hybrids, subspecies and species of the subfamily Triatominae. The use of a standardized composite haplotype code nomenclature for both nuclear rDNA and mtDNA markers is strongly encouraged to avoid difficulties in comparative studies. Triatomine aspects related to concerted evolution, microsatellites, minisatellites and insertions/deletions in nuclear rDNA and silent/non-silent mutations, pseudogenes and weaknesses of partial sequences in mtDNA are analysed. Introgression and hybrids, nuclear and mitochondrial DNA strengths, and compared evolutionary rates of nuclear rDNA and mtDNA in triatomines are discussed. Many conclusions are obtained thanks to the availability, for the first time in triatomines, of a complete sequence of a protein-coding mtDNA gene as ND1 from very numerous triatomine species covering from different populations of a species up to members belonging to different tribes. The evolutionary rates of each nuclear rDNA marker and mtDNA marker are analysed by comparison at subspecies level (intrapopulational, interpopulational, between morphs, and between subspecies) and species level (close and distant species of the same genus, species of different genera, and species of different tribes). Weaknesses of mtDNA for systematic-taxonomic purposes detected recently and newly in insects and triatomines, respectively, are discussed in detail. Emphasis is given to taxonomic units and biological entities presenting well-known problematics, both from the systematic-taxonomic and/or epidemiological-control points of view, as well as to molecular situations which can give rise to erroneous conclusions. All these aspects constitute the background on which the key question about the systematic concepts of species and subspecies in triatomines is focused. The global purpose is to facilitate future work on triatomines by highlighting present gaps, how better choice the appropriate markers, and marker aspects which should be taken into account. Key characteristics as alpha, CI and transformation rate matrices ought to be obtained and noted to get appropriate results and allow correct interpretations. The main aim is to offer a baseline for future fundamental research on triatomines and applied research on transmission, epidemiology and control measures related to Chagas disease vectors.

Microbial molecular epidemiology: an overview

In this introductory chapter, I stress one more time the urgency to better connect molecular epidemiology and evolutionary biology. I show how much population genetics and phylogenetic analyses can confer a considerable added value to all attempts to characterize strains and species of pathogens. The problems dealing with the mere definition of basic concepts, such as species, subspecies, or strains, are briefly summarized. Last, I show the important contribution of molecular epidemiology to our knowledge of the basic biology of pathogens and insist on the necessity not to separate the studies dealing with pathogens from those that concern the hosts and the vectors, in the case of vector-borne diseases.