Dermacentor (Indocentor) auratus Supino 1897: Potential geographic range, and medical and veterinary significance

Dermacentor (Indocentor) auratus Supino, 1897 occurs in many regions of Southeast Asia and South Asia. In many regions of Southeast Asia and South Asia, targeted tick sampling and subsequent screening of collected D. auratus ticks have detected pathogenic bacteria and viruses in D. auratus. These disease-causing pathogens that have been detected in D. auratus include Anaplasma, Bartonella, Borrelia, Rickettsia (including spotted fever group rickettsiae), African swine fever virus, Lanjan virus, and Kyasanur forest disease virus. Although D. auratus predominantly infests wild pigs, this tick is also an occasional parasite of humans and other animals. Indeed, some 91 % of human otoacariasis cases in Sri Lanka were due to infestation by D. auratus. With the propensity of this tick to feed on multiple species of hosts, including humans, and the detection of pathogenic bacteria and viruses from this tick, D. auratus is a tick of medical, veterinary, and indeed zoonotic concern. The geographic range of this tick, however, is not well known. Therefore, in the present paper, we used the species distribution model, BIOCLIM, to project the potential geographic range of D. auratus, which may aid pathogen and tick-vector surveillance. We showed that the potential geographic range of D. auratus is far wider than the current geographic distribution of this tick, and that regions in Africa, and in North and South America seem to have suitable climates for D. auratus. Interestingly, in Southeast Asia, Borneo and Philippines also have suitable climates for D. auratus, but D. auratus has not been found in these regions yet despite the apparent close proximity of these regions to Mainland Southeast Asia, where D. auratus occurs. We thus hypothesize that the geographic distribution of D. auratus is largely dependent on the movement of wild pigs and whether or not these wild pigs are able to overcome dispersal barriers. We also review the potential pathogens and the diseases that may be associated with D. auratus and provide an updated host index for this tick.

Insights from entire mitochondrial genome sequences into the phylogeny of ticks of the genera Haemaphysalis and Archaeocroton with the elevation of the subgenus Alloceraea Schulze, 1919 back to the status of a genus

We used entire mitochondrial (mt) genome sequences (14.5-15 kbp) to resolve the phylogeny of the four main lineages of the Haematobothrion ticks: Alloceraea, Archaeocroton, Bothriocroton and Haemaphysalis. In our phylogenetic trees, Alloceraea was the sister to Archaeocroton sphenodonti, a tick of an archetypal reptile, the tuatara, from New Zealand, to the exclusion of the rest of the species of Haemaphysalis. The mt genomes of all four of the Alloceraea species that have been sequenced so far had a substantial insert, 132-312 bp, between the tRNA-Glu (E) gene and the nad1 gene in their mt genomes. This insert was not found in any of the other eight subgenera of Haemaphysalis. The mt genomes of 13 species of Haemaphysalis from NCBI GenBank were added to the most recent data set on Haemaphysalis and its close relatives to help resolve the phylogeny of Haemaphysalis, including five new subgenera of Haemaphysalis not previously considered by other authors: Allophysalis (structurally primitive), Aboimisalis (structurally primitive), Herpetobia (structurally intermediate), Ornithophysalis (structurally advanced) and Segalia (structurally advanced). We elevated Alloceraea Schulze, 1919 to the status of genus because Alloceraea Schulze, 1919 is phylogenetically distinct from the other subgenera of Haemaphysalis. Moreover, we propose that the subgenus Allophysalis is the sister to the rest of the Haemaphysalis (14 subgenera) and that the 'structurally primitive' subgenera Hoogstraal and Kim comprise early diverging lineages. Our matrices of the pairwise genetic difference (percent) of mt genomes and partial 16S rRNA sequences indicated that the mt genome sequence of Al. kitaokai (gb# OM368280) may not be Al. kitaokai Hoogstraal, 1969 but rather another species of Alloceraea. In a similar way, the mt genome sequence of H. (Herpetobia) nepalensis Hoogstraal, 1962 (gb# NC_064124) was only 2% genetically different to that of H. (Allophysalis) tibetensis Hoogstraal, 1965 (gb# OM368293): this indicates to us that they are the same species. Alloceraea cretacea may be better placed in a genus other than Alloceraea Schulze, 1919. Reptiles may have been the host to the most recent common ancestor of Archaeocroton and Alloceraea.

Unraveling the phylogenetics of genetically closely related species, Haemaphysalis japonica and Haemaphysalis megaspinosa, using entire tick mitogenomes and microbiomes

Ticks have a profound impact on public health. Haemaphysalis is one of the most widespread genera in Asia, including Japan. The taxonomy and genetic differentiation of Haemaphysalis spp. is challenging. For instance, previous studies struggled to distinguish Haemaphysalis japonica and Haemaphysalis megaspinosa due to the dearth of nucleotide sequence polymorphisms in widely used barcoding genes. The classification of H. japonica japonica and its related sub-species Haemaphysalis japonica douglasi or Haemaphysalis jezoensis is also confused due to their high morphological similarity and a lack of molecular data that support the current classification. We used mitogenomes and microbiomes of H. japonica and H. megaspinosa to gain deeper insights into the phylogenetic relationships and genetic divergence between two species. Phylogenetic analyses of concatenated nucleotide sequences of protein-coding genes and ribosomal DNA genes distinguished H. japonica and H. megaspinosa as monophyletic clades, with further subdivision within the H. japonica clade. The 16S rRNA and NAD5 genes were valuable markers for distinguishing H. japonica and H. megaspinosa. Population genetic structure analyses indicated that genetic variation within populations accounted for a large proportion of the total variation compared to variation between populations. Microbiome analyses revealed differences in alpha and beta diversity between H. japonica and H. megaspinosa: H. japonica had the higher diversity. Coxiella sp., a likely endosymbiont, was found in both Haemaphysalis species. The abundance profiles of likely endosymbionts, pathogens, and commensals differed between H. japonica and H. megaspinosa: H. megaspinosa was more diverse.

The geographic limits and life history of the tropical brown dog tick, Rhipicephalus linnaei (Audouin, 1826), in Australia with notes on the spread of Ehrlichia canis

The tropical brown dog tick, Rhipicephalus linnaei, is a tick of much medical, veterinary, and zoonotic importance. This tick has a nearly world-wide distribution due to its ability to survive and propagate in kennels and houses. Rhipicephalus linnaei is the vector of Ehrlichia canis, the causative agent of canine monocytic ehrlichiosis, an often debilitating disease of canids and, occasionally, humans. To prevent incursion of E. canis into Australia, dogs entering Australia have been required to have a negative immunofluorescence antibody test for E. canis. In May 2020 however, E. canis was detected in Western Australia. The detection of E. canis in Australia prompted disease investigation and concerted surveillance for R. linnaei and E. canis in regions across Australia. These investigations revealed that R. linnaei was established far beyond the previously recognised geographic range limits of this tick. In the present paper, using records from various collections, published data, and data from our network of veterinarian collaborators and colleagues, we update the current geographic range of R. linnaei in Australia. Our analyses revealed that the geographic range of R. linnaei in Australia is much wider than was previously supposed, particularly in Western Australia, and in South Australia. We also map, for the first time, where E. canis has been detected in Australia. Last, we discuss the possible routes of incursion and subsequently the factors which may have aided the spread of E. canis in Australia which led to the establishment of this pathogen in Australia.

New insights into the molecular phylogeny, biogeographical history, and diversification of Amblyomma ticks (Acari: Ixodidae) based on mitogenomes and nuclear sequences

BACKGROUND

Amblyomma is the third most diversified genus of Ixodidae that is distributed across the Indomalayan, Afrotropical, Australasian (IAA), Nearctic and Neotropical biogeographic ecoregions, reaching in the Neotropic its highest diversity. There have been hints in previously published phylogenetic trees from mitochondrial genome, nuclear rRNA, from combinations of both and morphology that the Australasian Amblyomma or the Australasian Amblyomma plus the Amblyomma species from the southern cone of South America, might be sister-group to the Amblyomma of the rest of the world. However, a stable phylogenetic framework of Amblyomma for a better understanding of the biogeographic patterns underpinning its diversification is lacking.

METHODS

We used genomic techniques to sequence complete and nearly complete mitochondrial genomes -ca. 15 kbp- as well as the nuclear ribosomal cluster -ca. 8 kbp- for 17 Amblyomma ticks in order to study the phylogeny and biogeographic pattern of the genus Amblyomma, with particular emphasis on the Neotropical region. The new genomic information generated here together with genomic information available on 43 ticks (22 other Amblyomma species and 21 other hard ticks-as outgroup-) were used to perform probabilistic methods of phylogenetic and biogeographic inferences and time-tree estimation using biogeographic dates.

RESULTS

In the present paper, we present the strongest evidence yet that Australasian Amblyomma may indeed be the sister-group to the Amblyomma of the rest of the world (species that occur mainly in the Neotropical and Afrotropical zoogeographic regions). Our results showed that all Amblyomma subgenera (Cernyomma, Anastosiella, Xiphiastor, Adenopleura, Aponomma and Dermiomma) are not monophyletic, except for Walkeriana and Amblyomma. Likewise, our best biogeographic scenario supports the origin of Amblyomma and its posterior diversification in the southern hemisphere at 47.8 and 36.8 Mya, respectively. This diversification could be associated with the end of the connection of Australasia and Neotropical ecoregions by the Antarctic land bridge. Also, the biogeographic analyses let us see the colonization patterns of some neotropical Amblyomma species to the Nearctic.

CONCLUSIONS

We found strong evidence that the main theater of diversification of Amblyomma was the southern hemisphere, potentially driven by the Antarctic Bridge's intermittent connection in the late Eocene. In addition, the subgeneric classification of Amblyomma lacks evolutionary support. Future studies using denser taxonomic sampling may lead to new findings on the phylogenetic relationships and biogeographic history of Amblyomma genus.

The weather determines the number of cases of tick paralysis in dogs and cats in eastern Australia, caused by Ixodes holocyclus, the eastern paralysis tick

We studied over 222,000 cases of emergency veterinary consultations in four regions along the eastern coast of Australia. We found that cases of tick paralysis (TP) caused by the eastern paralysis tick, Ixodes holocyclus, accounted for 7.5% of these cases: >16,000 cases. The season of TP and the number (prevalence) of TP cases varied among regions and over the years. Our study of the association between weather and (i) the start of the season of TP, and (ii) the number of TP cases revealed much about the intricate relationship between the weather and I. holocyclus. We studied the effect of the hypothetical availability of isoxazoline-containing tick-preventative medicines and found that an increase in the availability of these medicines had significantly contributed to the decrease in TP cases. We found that the weather in winter accounted for the time of the year the season of TP starts whereas the weather in summer accounted for the number of TP cases in the TP season. Last, through a study of the effects of shifts in the climate under four hypothetical scenarios (warmer/cooler and drier/wetter than average), we propose that the start of the season of TP depends on how soon the weather in winter becomes suitable for the activity (e.g. host-seeking) and the development of I. holocyclus nymphs, and that the number of TP cases during the TP season depends on how many engorged female ticks and their eggs survive during summer.

A new subgenus, Australixodes n. subgen. (Acari: Ixodidae), for the kiwi tick, Ixodes anatis Chilton, 1904, and validation of the subgenus Coxixodes Schulze, 1941 with a phylogeny of 16 of the 22 subgenera of Ixodes Latreille, 1795 from entire mitochondrial genome sequences

A new subgenus, Australixodes n. subgen., is described for the kiwi tick, Ixodes anatis Chilton, 1904. The subgenus Coxixodes Schulze, 1941 is validated for the platypus tick, Ixodes (Coxixodes) ornithorhynchi Lucas, 1846, sister group of the subgenus Endopalpiger Schulze, 1935. A phylogeny from mitochondrial genomes of 16 of the 22 subgenera of Ixodes (32 spp.) indicates, for the first time, the relationships of the subgenera of Ixodes Latreille, 1795, the largest genus of ticks.

Seventy-eight entire mitochondrial genomes and nuclear rRNA genes provide insight into the phylogeny of the hard ticks, particularly the Haemaphysalis species, Africaniella transversale and Robertsicus elaphensis

Hoogstraal and Kim (1985) proposed from morphology, three groups of Haemaphysalis subgenera: (i) the "structurally advanced"; (ii) the "structurally intermediate"; and (iii) the "structurally primitive" subgenera. Nuclear gene phylogenies, however, did not indicate monophyly of these morphological groups but alas, only two mitochondrial (mt) genomes from the "structurally intermediate" subgenera had been sequenced. The phylogeny of Haemaphysalis has not yet been resolved. We aimed to resolve the phylogeny of the genus Haemaphysalis, with respect to the subgenus Alloceraea. We presented 15 newly sequenced and annotated mt genomes from 15 species of ticks, five species of which have not been sequenced before, and four new 18S rRNA and 28S rRNA nuclear gene sequences. Our datasets were constructed from 10 mt protein-coding genes, cox1, and the 18S and 28S nuclear rRNA genes. We found a 132-bp insertion between tRNA-Glu (E) gene and the nad1 gene in the mt genome of Haemaphysalis (Alloceraea) inermis that resembles insertions in H. (Alloceraea) kitaokai and Rhipicephalus (Boophilus) geigyi. Our mt phylogenies had the three species of Amblyomma (Aponomma) we sequenced embedded in the main clade of Amblyomma: Am. (Aponomma) fimbriatum, Am. (Aponomma) gervaisi and Am. (Aponomma) latum. This is further support for the hypothesis that the evolution of eyes appears to have occurred in the most-recent-common-ancestor of Amblyocephalus (i.e. Amblyomminae plus Rhipicephalinae) and that eyes were subsequently lost in the most-recent-common-ancestor of the subgenus Am. (Aponomma). Either Africaniella transversale or Robertsicus elaphensis, or perhaps Af. transversale plus Ro. elaphensis, appear to be the sister-group to the rest of the metastriate Ixodida. Our cox1 phylogenies did not indicate monophyly of the "structurally primitive", "structurally intermediate" nor the "structurally advanced" groups of Haemaphysalis subgenera. Indeed, the subgenus Alloceraea may be the only monophyletic subgenus of the genus Haemaphysalis sequenced thus far. All of our mt genome and cox1 phylogenies had the subgenus Alloceraea in a clade that was separate from the rest of the Haemaphysalis ticks. If Alloceraea is indeed the sister to the rest of the Haemaphysalis subgenera this would resonate with the argument of Hoogstraal and Kim (1985), that Alloceraea was a subgenus of "primitive" Haemaphysalis. Alectorobius capensis from Japan had a higher genetic-identity to A. sawaii, which was also from Japan, than to the A. capensis from South Africa. This indicates that A. capensis from Japan may be a cryptic species with respect to the A. capensis from South Africa.

Two seasons of tick paralysis in Victoria yet one season in Queensland and New South Wales, Australia

We studied 22,840 cases of tick paralysis in dogs and cats that were attributable to infestation with the eastern paralysis tick, Ixodes holocyclus. We report that the mortality rates from the holocyclotoxins of the tick or from euthanasia due to complications arising from tick paralysis in dogs and cats were 10% and 8%, respectively. The distribution of cases of tick paralysis among the 52 weeks of 22 years (1999 to 2020, inclusive) in four regions along the eastern coast of Australia revealed much about how the life-cycle of this tick varied among regions. The four regions in our study were: (i) Cairns, Innisfail, and surrounding postcodes in Far North Queensland; (ii) South East Queensland; (iii) Northern Beaches of Sydney in New South Wales; and (iv) the Shire of East Gippsland in Victoria. We found that the season of tick paralysis started earlier in more northerly latitudes than in more southerly latitudes. We also found that Victoria has two seasons of tick paralysis, one from approximately the third week of February to the first week of May, and another from approximately the third week of September to the third week of December, whereas all of the other regions we studied in eastern Australia only had one season of tick paralysis. When we studied the two seasons of tick paralysis in Victoria, we found a statistically significant negative correlation between the number of cases of tick paralysis between the two seasons: the more cases in one season, the fewer the cases in the next season. One possible explanation for the negative correlation may be immunity to I. holocyclus acquired by dogs and cats in the first season.

Rediscovery of Ixodes confusus in Australia with the first description of the male from Australia, a redescription of the female and the mitochondrial (mt) genomes of five species of Ixodes

We: (i) report the rediscovery of Ixodes (Sternalixodes) confusus Roberts, 1960 in Australia; (ii) redescribe the male and female of I.confusus; (iii) describe the mitochondrial (mt) genome of I. confusus from five ticks from four localities in Far North Queensland; and (iv) present the first substantial phylogeny of the subgenera of the Ixodes. The mt genomes of I.confusus, I. cornuatus, I. hirsti, I. myrmecobii and I. trichosuri are presented here for the first time. In our phylogeny from entire mt genomes (ca. 15 kb), the subgenus Endopalpiger was the sister-group to subgenera Sternalixodes plus Ceratixodes plus Exopalpiger whereas Exopalpiger was the sister to Sternalixodes plus Ceratixodes. [i.e. ((Endopalpiger) (Sternalixodes, Ceratixodes and Exopalpiger))]. Finally, we show that Ixodes anatis, the kiwi tick, may be closely related to the ticks of marsupials of Australia and Papua New Guinea.

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Rediscovery in Australia of the tick, Ixodes confusus.

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First description of the male of Ixodes confusus from Australia.

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Nine new mitochondrial genomes of Ixodes ticks from Australia and first substantial phylogeny of the subgenera of Ixodes.

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Ixodes anatis, a tick of the kiwi bird of NZ may be a closely related to the ticks of marsupials of Australia and PNG.

Comparative mitogenomics elucidates the population genetic structure of Amblyomma testudinarium in Japan and a closely related Amblyomma species in Myanmar

Ticks are the second most important vector capable of transmitting diseases affecting the health of both humans and animals. Amblyomma testudinarium Koch 1844 (Acari: Ixodidae), is a hard tick species having a wide geographic distribution in Asia. In this study, we analyzed the composition of A. testudinarium whole mitogenomes from various geographical regions in Japan and investigated the population structure, demographic patterns, and phylogeographic relationship with other ixodid species. In addition, we characterized a potentially novel tick species closely related to A. testudinarium from Myanmar. Phylogeographic inference and evolutionary dynamics based on the 15 mitochondrial coding genes supported that A. testudinarium population in Japan is resolved into a star‐like haplogroup and suggested a distinct population structure of A. testudinarium from Amami island in Kyushu region. Correlation analysis using Mantel test statistics showed that no significant correlation was observed between the genetic and geographic distances calculated between the A. testudinarium population from different localities in Japan. Finally, demographic analyses, including mismatch analysis and Tajima’s D test, suggested a possibility of recent population expansion occurred within Japanese haplogroup after a bottleneck event. Although A. testudinarium has been considered widespread and common in East and Southeast Asia, the current study suggested that potentially several cryptic Amblyomma spp. closely related to A. testudinarium are present in Asia.

Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification

High-throughput sequencing (HTS) technology has profoundly been involved in sequencing whole genomes of several organisms in a fast and cost-effective manner. Although HTS provides an alternative biomonitoring method to the time-consuming and taxonomy-expertise dependent morphological approach, still we cannot rule out the possibility of the impediment and misidentification biases. In this article we aim to retrieve whole mitochondrial genome (mitogenome) sequences from publicly available raw sequencing data for phylogenetic comparison of Ixodes persulcatus. For this comparison, we sequenced whole mitogenomes of four I. persulcatus ticks from Japan and constructed mitogenomes from raw sequencing data of 74 I. persulcatus ticks from China. Bayesian phylogenetic trees were inferred by the concatenated fifteen mitochondrial genes. We further tested our results by the phylogenetic analysis of cytochrome c oxidase subunit 1 (cox1) gene and internal transcribed spacer 2 (ITS2) sequences. Our findings showed that 70 constructed mitogenomes from China were clustered with the sequenced four mitogenomes of I. persulcatus from Japan. We also revealed that mitogenome sequences retrieved from two data sets CRR142297 and CRR142298 were clustered with Ixodes nipponensis. Moreover, other two mitogenome sequences from CRR142310 and CRR142311 formed a clade with Ixodes pavlovskyi. The phylogenetic analysis of cox1 gene and ITS2 sequences confirmed the identification errors of these four samples. The overall phylogenetics in our study concluded that accurate morphological identification is necessary before implementing HTS to avoid any misidentification biases.

Climatic requirements of the southern paralysis tick, Ixodes cornuatus, with a consideration of its host, Vombatus ursinus, and the possible geographic range of the tick up to 2090

The southern paralysis tick, Ixodes cornuatus, is a tick of veterinary and medical importance in Australia. We use two methods, CLIMEX, and an envelope-model approach which we name the 'climatic-range method' to study the climatic requirements of I. cornuatus and thus to attempt to account for the geographic distribution of I. cornuatus. CLIMEX and our climatic-range method allowed us to account for 94% and 97% of the records of I. cornuatus respectively. We also studied the host preferences of I. cornuatus which we subsequently used in conjunction with our species distribution methods to account for the presence and the absences of I. cornuatus across Australia. Our findings indicate that the actual geographic distribution of I. cornuatus is smaller than the potential geographic range of this tick, and thus, that there are regions in Australia which may be suitable for I. cornuatus where this tick has not been recorded. Although our findings indicate that I. cornuatus might be able to persist in these currently unoccupied regions, our findings also indicate that the potential geographic range of I. cornuatus may shrink by 51 to 76% by 2090, depending on which climate change scenario comes to pass.

Climatic requirements of the eastern paralysis tick, Ixodes holocyclus, with a consideration of its possible geographic range up to 2090

The eastern paralysis tick, Ixodes holocyclus, is an ectoparasite of medical and veterinary importance in Australia. The feeding of I. holocyclus is associated with an ascending flaccid paralysis which kills many dogs and cats each year, with the development of mammalian meat allergy in some humans, and with the transmission of Rickettsia australis (Australian scrub typhus) to humans. Although I. holocyclus has been well studied, it is still not known exactly why this tick cannot establish outside of its present geographic distribution. Here, we aim to account for the presence as well as the absence of I. holocyclus in regions of Australia. We modelled the climatic requirements of I. holocyclus with two methods, CLIMEX, and a new envelope-model approach which we name the 'climatic-range method'. These methods allowed us to account for 93% and 96% of the geographic distribution of I. holocyclus, respectively. Our analyses indicated that the geographic range of I. holocyclus may not only shift south towards Melbourne, but may also expand in the future, depending on which climate-change scenario comes to pass.

Phylogenies from mitochondrial genomes of 120 species of ticks: Insights into the evolution of the families of ticks and of the genus Amblyomma

The evolution and phylogenetic relationships of the ticks at both the family and genus levels are contested. The genus Amblyomma and its subgenera are in a state of flux; moreover, the relationships among the three tick families are controversial due to conflicting phylogenetic support for different arrangements of the three families of living ticks. With 18 newly sequenced mitochondrial (mt) genomes of ticks included, we executed the largest mt genome phylogenetic study of ticks so far. Phylogenetic trees were inferred from one sea spider mt genome, one horseshoe crab, five mite mt genomes and 146 tick mt genomes from 120 species: 153 mt genomes in total. Sixteen phylogenetic trees were inferred from 10 datasets using both maximum likelihood and Bayesian inference methods. We describe the first novel mt gene-arrangement for the metastriate Ixodidae in Amblyomma (Africaniella) transversale. Also, three unusual partial 16S rRNA gene inserts were found in the mt genome of Haemaphysalis (Alloceraea) kitaokai: we consider the possible role of past genome translocation events in the formation of these inserts. Our phylogenies revealed evidence that: (i) the genus Amblyomma is polyphyletic with respect to Amblyomma (Africaniella) transversale; (ii) the subgenus Aponomma is apparently embedded in the genus Amblyomma; (iii) Haemaphysalis (Segalia) parva and Haemaphysalis (Alloceraea) kitaokai form a clade to the exclusion of other Haemaphysalis species; and (iv) the phylogenetic position of the family Nuttalliellidae is unstable among phylogenies from different datasets.

Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

BACKGROUND

In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)-evolutionarily related to MGTV-were reported.

RESULTS

In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China's Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia.

CONCLUSIONS

To the best of our knowledge, this is the first study in which 5' and 3' sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.

International recommendations for an effective control of head louse infestations

Head louse infestations continue to be a concern of public health in most countries, including the most developed ones. The present recommendations are intended to inform and stress the role and impact of the different authorities, institutions, industry, and the public in the control of head lice in order to reduce the prevalence of this parasite. We encourage health authorities to pursue more effective methods to correctly identify such infestations, and evaluate existing and new pediculicides, medical devices, louse repellents, and louse- and nit-removal remedies. Pediculicides and medical devices must have verifiable claims in the instructions for use and should be tested periodically to document current levels of resistance by lice to the active ingredients and to the formulated products. Where the prevalence of lice is claimed to be epidemic, children should be periodically evaluated objectively to document the actual level of prevalence. Continuing education for health providers and the general population promises to correct misinformation regarding the biology, prevention, and management of lice. Parents should regularly inspect their children for head lice and treat as necessary. Health authorities are encouraged to eliminate policies and practices that rely upon school exclusion as a means to reduce incidence and prevalence, e.g., the 'no-nit' policy which lacks scientific justification, and are counterproductive to the health and welfare of children.

Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element

Background

In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal (e.g. Dermacentor silvarum) containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) detect and analyze mt DNA variation within an individual tick.

Results

These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins.

Conclusions

We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals

In the present study, we applied our 'precise annotation' to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5' and 3' end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.

Survey of cases of tick-paralysis and the presence of the eastern paralysis tick, Ixodes holocyclus, and the southern paralysis tick, Ixodes cornuatus, in the Greater Melbourne Area

OBJECTIVE

The objective of this study was to test the hypothesis that the paralysis ticks, Ixodes holocyclus and Ixodes cornuatus, are epizootic and/or enzootic in the Greater Melbourne Area (GMA).

METHODS

We examined the ticks in the museum collections of Australia, wrote to, phoned and visited veterinarians and other colleagues in the GMA to gather information about the cases of tick paralysis and to request the ticks for identification.

RESULTS

We present evidence of I. holocyclus at 24 postcodes and I. cornuatus at 28 postcodes in the GMA.

CONCLUSIONS

We found evidence that I. holocyclus is epizootic at four postcodes in the GMA: at East Melbourne, Williamstown, Moonee Ponds and Hoppers Crossing. We did not find evidence that I. holocyclus is enzootic in the GMA. I. cornuatus is apparently enzootic in the GMA at Bullengarook, Kinglake, Chum Creek and Healesville. Our hypothesis is that I. cornuatus is also enzootic at Mt Macedon, Gisborne and at other bushy postcodes in the GMA. Since this tick is apparently enzootic in the GMA, it may also be epizootic at postcodes adjacent to busy postcodes such as Bullengarook, Kinglake, Chum Creek and Healesville. The concept of hitch-hiker larvae, nymphs and adult female ticks may explain many of the cases of tick paralysis due to I. holocyclus in the GMA. The accurate assessment of the risk of tick paralysis in dogs and cats in the GMA requires a more detailed map of the distribution of I. holocyclus and I. cornuatus in Victoria.

A transcriptome-based phylogenetic study of hard ticks (Ixodidae)

Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.

Potential Spatial Distribution of the Newly Introduced Long-horned Tick, Haemaphysalis longicornis in North America

The North American distributional potential of the recently invaded tick, Haemaphysalis longicornis, was estimated using occurrence data from its geographic range in other parts of the world and relevant climatic data sets. Several hundred candidate models were built using a correlative maximum entropy approach, and best-fitting models were selected based on statistical significance, predictive ability, and complexity. The median of the best-fitting models indicates a broad potential distribution for this species, but restricted to three sectors—the southeastern United States, the Pacific Northwest, and central and southern Mexico.

Rickettsia fournieri sp. nov., a novel spotted fever group rickettsia from Argas lagenoplastis ticks in Australia

Strain AUS118^T was isolated from an Argas lagenoplastis tick collected from the nest of a Petrochelidon ariel (fairy martin) in Australia in 2013. Microscopic observation of infected cell cultures indicated this strain had a morphology and intracellular location typical of Rickettsiaspecies. Phylogenetic analysis of this strain based firstly on multi-locus sequence analysis and subsequently on whole genome analysis demonstrated that AUS118^T was most closely related to, but divergent from Rickettsia japonica and Rickettsia heilongjiangensis. We therefore propose the creation of a novel species, Rickettsia fournieri sp. nov, with the type strain AUS118^T (DSM 28985 and CSUR R501).

The Mitochondrial Genome of the Guanaco Louse, Microthoracius praelongiceps: Insights into the Ancestral Mitochondrial Karyotype of Sucking Lice (Anoplura, Insecta)

Fragmented mitochondrial (mt) genomes have been reported in 11 species of sucking lice (suborder Anoplura) that infest humans, chimpanzees, pigs, horses, and rodents. There is substantial variation among these lice in mt karyotype: the number of minichromosomes of a species ranges from 9 to 20; the number of genes in a minichromosome ranges from 1 to 8; gene arrangement in a minichromosome differs between species, even in the same genus. We sequenced the mt genome of the guanaco louse, Microthoracius praelongiceps, to help establish the ancestral mt karyotype for sucking lice and understand how fragmented mt genomes evolved. The guanaco louse has 12 mt minichromosomes; each minichromosome has 2-5 genes and a non-coding region. The guanaco louse shares many features with rodent lice in mt karyotype, more than with other sucking lice. The guanaco louse, however, is more closely related phylogenetically to human lice, chimpanzee lice, pig lice, and horse lice than to rodent lice. By parsimony analysis of shared features in mt karyotype, we infer that the most recent common ancestor of sucking lice, which lived ∼75 Ma, had 11 minichromosomes; each minichromosome had 1-6 genes and a non-coding region. As sucking lice diverged, split of mt minichromosomes occurred many times in the lineages leading to the lice of humans, chimpanzees, and rodents whereas merger of minichromosomes occurred in the lineage leading to the lice of pigs and horses. Together, splits and mergers of minichromosomes created a very complex and dynamic mt genome organization in the sucking lice.

Ticks in Australia: endemics; exotics; which ticks bite humans?

At least 71 species of ticks occur in Australia; a further 33 or so species are endemic to its neighbours, New Guinea and New Zealand. The ticks of Australia and other parts of Australasia are phylogenetically distinct. Indeed, there are at least two lineages of ticks that are unique to Australasia: the genus Bothriocroton Klompen, Dobson & Barker, 2002; and the new genus Archaeocroton Barker & Burger, 2018. Two species of ticks that are endemic to Australia are notorious for feeding on humans: (i) Ixodes holocyclus, the eastern paralysis tick, in eastern Australia; and (ii) Amblyomma triguttatum triguttatum, the ornate kangaroo tick, in Western Australia, at one place in South Australia, and in parts of Queensland. Three of the other endemic species of ticks that feed on humans in Australia are also noteworthy: (i) Bothriocroton hydrosauri, the southern reptile tick, which is a vector of Rickettsia honei (Flinders Island spotted fever); (ii) Haemaphysalis novaeguineae, the New Guinea haemaphysalid; and (iii) Ornithodoros capensis, the seabird soft tick. Here, we present images of female Ixodes holocyclus, Amblyomma t. triguttatum, Bothriocroton hydrosauri and Haemaphysalis novaeguineae and our latest maps of the geographic distributions of Ixodes holocyclus, Amblyomma t. triguttatum and Bothriocroton hydrosauri. None of the five exotic species of ticks in Australia typically feed on humans.

Ovicidal Efficacy of Abametapir Against Eggs of Human Head and Body Lice (Anoplura: Pediculidae)

Studies were undertaken to determine the ovicidal efficacy of 5,5'-dimethyl-2,2'-bipyridyl (abametapir) against eggs of both human head and body lice. Head lice eggs of different ages (0-2, 3-5, and 6-8-d-old eggs) were exposed to varying concentrations of abametapir in isopropanol and concentration-dependent response relationships established based on egg hatch. One hundred percent of all abametapir-treated eggs failed to hatch at the 0.74 and 0.55% concentrations, whereas 100% of 6-8-d-old head louse eggs failed to hatch only at the 0.74% concentration. The LC₅₀ value for abametapir varied, depending on the age of the head lice eggs, from ∼0.10% recorded for 0-2-d-old eggs and increasing to ∼0.15% for 6-8-d-old eggs. Abametapir was also evaluated once formulated into a lotion referred to as Xeglyze (0.74% abametapir) and serial dilutions made. Ovicidal efficacies were determined against head lice eggs 0-8-d-old. Results indicated 100% ovicidal activity at the 0.74, 0.55, 0.37, and 0.18% concentrations. Additional studies undertaken using body lice eggs also demonstrated that abametapir was 100% ovicidal against eggs of all ages when evaluated at a concentration of 0.37 and 0.55%. Given that ovicidal activity is a critical component of any effective treatment regime for louse control, the data presented in this study clearly demonstrate the ability of abametapir to inhibit hatching of both head and body louse eggs as assessed in vitro.

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

The mitochondrial genome of the chimpanzee louse, Pediculus schaeffi: insights into the process of mitochondrial genome fragmentation in the blood-sucking lice of great apes

Background

Blood-sucking lice in the genera Pediculus and Pthirus are obligate ectoparasites of great apes. Unlike most bilateral animals, which have 37 mitochondrial (mt) genes on a single circular chromosome, the sucking lice of humans have extensively fragmented mt genomes. The head louse, Pediculus capitis, and the body louse, Pe. humanus, have their 37 mt genes on 20 minichromosomes. The pubic louse, Pthirus pubis, has its 34 mt genes known on 14 minichromosomes. To understand the process of mt genome fragmentation in the sucking lice of great apes, we sequenced the mt genome of the chimpanzee louse, Pe. schaeffi, and compared it with the three human lice.

Results

We identified all of the 37 mt genes typical of bilateral animals in the chimpanzee louse; these genes are on 18 types of minichromosomes. Seventeen of the 18 minichromosomes of the chimpanzee louse have the same gene content and gene arrangement as their counterparts in the human head louse and the human body louse. However, five genes, cob, trnS₁, trnN, trnE and trnM, which are on three minichromosomes in the human head louse and the human body louse, are together on one minichromosome in the chimpanzee louse.

Conclusions

Using the human pubic louse, Pt. pubis, as an outgroup for comparison, we infer that a single minichromosome has fragmented into three in the lineage leading to the human head louse and the human body louse since this lineage diverged from the chimpanzee louse ~6 million years ago. Our results provide insights into the process of mt genome fragmentation in the sucking lice in a relatively fine evolutionary scale.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1843-3) contains supplementary material, which is available to authorized users.

SNPs in Entire Mitochondrial Genome Sequences (≈15.4 kb) and cox1 Sequences (≈486 bp) Resolve Body and Head Lice From Doubly Infected People From Ethiopia, China, Nepal, and Iran But Not France

Some people host lice on the clothing as well as the head. Whether body lice and head lice are distinct species or merely variants of the same species remains contentious. We sought to ascertain the extent to which lice from these different habitats might interbreed on doubly infected people by comparing their entire mitochondrial genome sequences. Toward this end, we analyzed two sets of published genetic data from double-infections of body lice and head lice: 1) entire mitochondrial coding regions (≈15.4 kb) from body lice and head lice from seven doubly infected people from Ethiopia, China, and France; and 2) part of the cox1 gene (≈486 bp) from body lice and head lice from a further nine doubly infected people from China, Nepal, and Iran. These mitochondrial data, from 65 lice, revealed extraordinary variation in the number of single nucleotide polymorphisms between the individual body lice and individual head lice of double-infections: from 1.096 kb of 15.4 kb (7.6%) to 2 bps of 15.4 kb (0.01%). We detected coinfections of lice of Clades A and C on the scalp hair of three of the eight people from Nepal: one person of the two people from Kathmandu and two of the six people from Pokhara. Lice of Clades A and B coinfected the scalp hair of one person from Atherton, Far North Queensland, Australia. These findings argue for additional large-scale studies of the body lice and head lice of double-infected people.

A list of the 70 species of Australian ticks; diagnostic guides to and species accounts of Ixodes holocyclus (paralysis tick), Ixodes cornuatus (southern paralysis tick) and Rhipicephalus australis (Australian cattle tick); and consideration of the place of Australia in the evolution of ticks with comments on four controversial ideas

Seventy species of ticks are known from Australia: 14 soft ticks (family Argasidae) and 56 hard ticks (family Ixodidae). Sixteen of the 70 ticks in Australia may feed on humans and domestic animals (Barker and Walker 2014). The other 54 species of ticks in Australia feed only on wild mammals, reptiles and birds. At least 12 of the species of ticks in Australian also occur in Papua New Guinea. We use an image-matching system much like the image-matching systems of field guides to birds and flowers to identify Ixodes holocyclus (paralysis tick), Ixodes cornuatus (southern paralysis tick) and Rhipicephalus (Boophilus) australis (Australian cattle tick). Our species accounts have reviews of the literature on I. holocyclus (paralysis tick) from the first paper on the biology of an Australian tick by Bancroft (1884), on paralysis of dogs by I. holocyclus, to papers published recently, and of I. cornuatus (southern paralysis tick) and Rhipicephalus (Boophilus) australis (Australian cattle tick). We comment on four controversial questions in the evolutionary biology of ticks: (i) were labyrinthodont amphibians in Australia in the Devonian the first hosts of soft, hard and nuttalliellid ticks?; (ii) are the nuttalliellid ticks the sister-group to the hard ticks or the soft ticks?; (iii) is Nuttalliella namaqua the missing link between the soft and hard ticks?; and (iv) the evidence for a lineage of large bodied parasitiform mites (ticks plus the holothyrid mites plus the opiliocarid mites).

Fragmented mitochondrial genomes are present in both major clades of the blood-sucking lice (suborder Anoplura): evidence from two Hoplopleura rodent lice (family Hoplopleuridae)

Background

The suborder Anoplura contains 540 species of blood-sucking lice that parasitize over 840 species of eutherian mammals. Fragmented mitochondrial (mt) genomes have been found in the lice of humans, pigs, horses and rats from four families: Pediculidae, Pthiridae, Haematopinidae and Polyplacidae. These lice, eight species in total, are from the same major clade of the Anoplura. The mt genomes of these lice consist of 9–20 minichromosomes; each minichromosome is 1.5–4 kb in size and has 1–8 genes. To understand mt genome fragmentation in the other major clade of the Anoplura, we sequenced the mt genomes of two species of rodent lice in the genus Hoplopleura (family Hoplopleuridae).

Results

We identified 28 mt genes on 10 minichromosomes in the mouse louse, Ho. akanezumi; each minichromosome is 1.7–2.7 kb long and has 1–6 genes. We identified 34 mt genes on 11 minichromosomes in the rat louse, Ho. kitti; each minichromosome is 1.8–2.8 kb long and has 1–5 genes. Ho. akanezumi also has a chimeric minichromosome with parts of two rRNA genes and a full-length tRNA gene for tyrosine. These two rodent lice share the same pattern for the distribution of all of the protein-coding and rRNA genes but differ in tRNA gene content and gene arrangement in four minichromosomes. Like the four genera of blood-sucking lice that have been investigated in previous studies, the Hoplopleura species have four minichromosomes that are only found in this genus.

Conclusions

Our results indicate that fragmented mt genomes were present in the most recent common ancestor of the two major clades of the blood-sucking lice, which lived ~75 million years ago. Intra-genus variation in the pattern of mt genome fragmentation is common in the blood-sucking lice (suborder Anoplura) and genus-specific minichromosomes are potential synapomorphies. Future studies should expand into more species, genera and families of blood-sucking lice to explore further the phylogenetic utility of the novel features associated with fragmented mt genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-751) contains supplementary material, which is available to authorized users.

Second-generation sequencing of entire mitochondrial coding-regions (∼15.4 kb) holds promise for study of the phylogeny and taxonomy of human body lice and head lice

The Illumina Hiseq platform was used to sequence the entire mitochondrial coding-regions of 20 body lice, Pediculus humanus Linnaeus, and head lice, P. capitis De Geer (Phthiraptera: Pediculidae), from eight towns and cities in five countries: Ethiopia, France, China, Australia and the U.S.A. These data (∼310 kb) were used to see how much more informative entire mitochondrial coding-region sequences were than partial mitochondrial coding-region sequences, and thus to guide the design of future studies of the phylogeny, origin, evolution and taxonomy of body lice and head lice. Phylogenies were compared from entire coding-region sequences (∼15.4 kb), entire cox1 (∼1.5 kb), partial cox1 (∼700 bp) and partial cytb (∼600 bp) sequences. On the one hand, phylogenies from entire mitochondrial coding-region sequences (∼15.4 kb) were much more informative than phylogenies from entire cox1 sequences (∼1.5 kb) and partial gene sequences (∼600 to ∼700 bp). For example, 19 branches had > 95% bootstrap support in our maximum likelihood tree from the entire mitochondrial coding-regions (∼15.4 kb) whereas the tree from 700 bp cox1 had only two branches with bootstrap support > 95%. Yet, by contrast, partial cytb (∼600 bp) and partial cox1 (∼486 bp) sequences were sufficient to genotype lice to Clade A, B or C. The sequences of the mitochondrial genomes of the P. humanus, P. capitis and P. schaeffi Fahrenholz studied are in NCBI GenBank under the accession numbers KC660761-800, KC685631-6330, KC241882-97, EU219988-95, HM241895-8 and JX080388-407.

Ticks of Australia. The species that infest domestic animals and humans

The book Australian Ticks by F.H.S. Roberts (1970) is a land-mark in Australian tick biology. But it is time for a new and improved book on the ticks of Australia. The present book has identification guides and accounts of the biology and diseases associated with the 16 species of ticks that may feed on domestic animals and humans in Australia. These comprise five argasid (soft) ticks: Argas persicus (poultry tick), Argas robertsi (Robert's bird tick), Ornithodoros capensis (seabird soft tick), O. gurneyi (kangaroo soft tick), Otobius megnini (spinose ear tick); and 11 ixodid (hard) ticks, Amblyomma triguttatum (ornate kangaroo tick), Bothriocroton auruginans (wombat tick), B. hydrosauri (southern reptile tick), Haemaphysalis bancrofti (wallaby tick), H. longicornis (bush tick), Ixodes cornuatus (southern paralysis tick), I. hirsti (Hirst's marsupial tick), I. holocyclus (paralysis tick), I. tasmani (common marsupial tick), Rhipicephalus (Boophilus) australis (Australian cattle tick) and R. sanguineus (brown dog tick).  We use an image-matching system to identify ticks, much like the image-matching systems used in field-guides for birds and flowers. Ticks may be identified by drawings that emphasise unique matrices of uniformly defined morphological characters that, together, allow these 16 ticks to be identified by morphology unequivocally. The species accounts have seven sections: (i) General; (ii)  Differential diagnosis; (iii) Hosts; (iv) Life-cycle and seasonality; (v) Disease; (vi) Habitat and geographic distribution; (vii) Genes and genomes; and (viii) Other information. There are 71 figures and tables, including a glossary character matrices, drawings of life-cycles, drawings of genera, species, and colour photographs of tick biology.

Detection of Bartonella quintana in African body and head lice

Currently, the body louse is the only recognized vector of Bartonella quintana, an organism that causes trench fever. In this work, we investigated the prevalence of this bacterium in human lice in different African countries. We tested 616 head lice and 424 body lice from nine African countries using real-time polymerase chain reaction targeting intergenic spacer region 2 and specific B. quintana genes. Overall, B. quintana DNA was found in 54% and 2% of body and head lice, respectively. Our results also show that there are more body lice positive for B. quintana in poor countries, which was determined by the gross domestic product, than in wealthy areas (228/403 versus 0/21, P < 0.001). A similar finding was obtained for head lice (8/226 versus 2/390, P = 0.007). Our findings suggest that head lice in Africa may be infected by B. quintana when patients live in poor economic conditions and are also exposed to body lice.

Variation in mitochondrial minichromosome composition between blood-sucking lice of the genus Haematopinus that infest horses and pigs

BACKGROUND

The genus Haematopinus contains 21 species of blood-sucking lice, parasitizing both even-toed ungulates (pigs, cattle, buffalo, antelopes, camels and deer) and odd-toed ungulates (horses, donkeys and zebras). The mitochondrial genomes of the domestic pig louse, Haematopinus suis, and the wild pig louse, Haematopinus apri, have been sequenced recently; both lice have fragmented mitochondrial genomes with 37 genes on nine minichromosomes. To understand whether the composition of mitochondrial minichromosomes and the gene content and gene arrangement of each minichromosome are stable within the genus, we sequenced the mitochondrial genome of the horse louse, Haematopinus asini.

METHODS

We used a PCR-based strategy to amplify four mitochondrial minichromosomes in near full-length, and then amplify the entire coding regions of all of the nine mitochondrial minichromosomes of the horse louse. These amplicons were sequenced with an Illumina Hiseq platform.

RESULTS

We identified all of the 37 mitochondrial genes typical of bilateral animals in the horse louse, Haematopinus asini; these genes are on nine circular minichromosomes. Each minichromosome is 3.5-5.0 kb in size and consists of a coding region and a non-coding region except R-nad4L-rrnS-C minichromosome, which contains two coding regions and two non-coding regions. Six of the nine minichromosomes of the horse louse have their counterparts in the pig lice with the same gene content and gene arrangement. However, the gene content and arrangement of the other three minichromosomes of the horse louse, including R-nad4L-rrnS-C, are different from that of the other three minichromosomes of the pig lice.

CONCLUSIONS

Comparison between the horse louse and the pig lice revealed variation in the composition of mitochondrial minichromosomes within the genus Haematopinus, which can be accounted for by gene translocation events between minichromosomes. The current study indicates that inter-minichromosome recombination plays a major role in generating the variation in the composition of mitochondrial minichromosomes and provides novel insights into the evolution of fragmented mitochondrial genomes in the blood-sucking lice.

Substantial variation in the extent of mitochondrial genome fragmentation among blood-sucking lice of mammals

Blood-sucking lice of humans have extensively fragmented mitochondrial (mt) genomes. Human head louse and body louse have their 37 mt genes on 20 minichromosomes. In human pubic louse, the 34 mt genes known are on 14 minichromosomes. To understand the process of mt genome fragmentation in the blood-sucking lice of mammals, we sequenced the mt genomes of the domestic pig louse, Haematopinus suis, and the wild pig louse, H. apri, which diverged from human lice approximately 65 Ma. The 37 mt genes of the pig lice are on nine circular minichromosomes; each minichromosome is 3–4 kb in size. The pig lice have four genes per minichromosome on average, in contrast to two genes per minichromosome in the human lice. One minichromosome of the pig lice has eight genes and is the most gene-rich minichromosome found in the sucking lice. Our results indicate substantial variation in the rate and extent of mt genome fragmentation among different lineages of the sucking lice.

Borrelia recurrentis in head lice, Ethiopia

Since the 1800s, the only known vector of Borrelia recurrentis has been the body louse. In 2011, we found B. recurrentis DNA in 23% of head lice from patients with louse-borne relapsing fever in Ethiopia. Whether head lice can transmit these bacteria from one person to another remains to be determined.

Heteroplasmy in the mitochondrial genomes of human lice and ticks revealed by high throughput sequencing

The typical mitochondrial (mt) genomes of bilateral animals consist of 37 genes on a single circular chromosome. The mt genomes of the human body louse, Pediculus humanus, and the human head louse, Pediculus capitis, however, are extensively fragmented and contain 20 minichromosomes, with one to three genes on each minichromosome. Heteroplasmy, i.e. nucleotide polymorphisms in the mt genome within individuals, has been shown to be significantly higher in the mt cox1 gene of human lice than in humans and other animals that have the typical mt genomes. To understand whether the extent of heteroplasmy in human lice is associated with mt genome fragmentation, we sequenced the entire coding regions of all of the mt minichromosomes of six human body lice and six human head lice from Ethiopia, China and France with an Illumina HiSeq platform. For comparison, we also sequenced the entire coding regions of the mt genomes of seven species of ticks, which have the typical mitochondrial genome organization of bilateral animals. We found that the level of heteroplasmy varies significantly both among the human lice and among the ticks. The human lice from Ethiopia have significantly higher level of heteroplasmy than those from China and France (Pt<0.05). The tick, Amblyomma cajennense, has significantly higher level of heteroplasmy than other ticks (Pt<0.05). Our results indicate that heteroplasmy level can be substantially variable within a species and among closely related species, and does not appear to be determined by single factors such as genome fragmentation.

Evolution of extensively fragmented mitochondrial genomes in the lice of humans

Bilateral animals are featured by an extremely compact mitochondrial (mt) genome with 37 genes on a single circular chromosome. The human body louse, Pediculus humanus, however, has its mt genes on 20 minichromosomes. We sequenced the mt genomes of two other human lice: the head louse, P. capitis, and the pubic louse, Pthirus pubis. Comparison among the three human lice revealed the presence of fragmented mt genomes in their most recent common ancestor, which lived ∼7 Ma. The head louse has exactly the same set of mt minichromosomes as the body louse, indicating that the number of minichromosomes, and the gene content and gene arrangement in each minichromosome have remained unchanged since the body louse evolved from the head louse ∼107,000 years ago. The pubic louse has the same pattern of one protein-coding or rRNA gene per minichromosome (except one minichromosome with two protein-coding genes, atp6 and atp8) as the head louse and the body louse. This pattern is apparently ancestral to all human lice and has been stable for at least 7 Myr. Most tRNA genes of the pubic louse, however, are on different minichromosomes when compared with their counterparts in the head louse and the body louse. It is evident that rearrangement of four tRNA genes (for leucine, arginine and glycine) was due to gene-identity switch by point mutation at the third anticodon position or by homologous recombination, whereas rearrangement of other tRNA genes was by gene translocation between minichromosomes, likely caused by minichromosome split via gene degeneration and deletion.

International guidelines for clinical trials with pediculicides

Pediculosis capitis, infestation with head lice, is common in all human societies. Chemical pediculicides are often used to control head louse infestations, particularly in wealthy communities. A significant number of different protocols have been used to test the efficacy and safety of pediculicides in clinical trials; this constrains scientific comparison of the evidence for efficacy of the different pediculicides. Here we recommend protocols for clinical trials of the efficacy and safety of single-, two-, and three-treatment interventions.

Multispacer sequence typing relapsing fever Borreliae in Africa

BACKGROUND

In Africa, relapsing fevers are neglected arthropod-borne infections caused by closely related Borrelia species. They cause mild to deadly undifferentiated fever particularly severe in pregnant women. Lack of a tool to genotype these Borrelia organisms limits knowledge regarding their reservoirs and their epidemiology.

METHODOLOGY/PRINCIPAL FINDINGS

Genome sequence analysis of Borrelia crocidurae, Borrelia duttonii and Borrelia recurrentis yielded 5 intergenic spacers scattered between 10 chromosomal genes that were incorporated into a multispacer sequence typing (MST) approach. Sequencing these spacers directly from human blood specimens previously found to be infected by B. recurrentis (30 specimens), B. duttonii (17 specimens) and B. crocidurae (13 specimens) resolved these 60 strains and the 3 type strains into 13 species-specific spacer types in the presence of negative controls. B. crocidurae comprised of 8 spacer types, B. duttonii of 3 spacer types and B. recurrentis of 2 spacer types.

CONCLUSIONS/SIGNIFICANCE

Phylogenetic analyses of MST data suggested that B. duttonii, B. crocidurae and B. recurrentis are variants of a unique ancestral Borrelia species. MST proved to be a suitable approach for identifying and genotyping relapsing fever borreliae in Africa. It could be applied to both vectors and clinical specimens.

The multipartite mitochondrial genome of Liposcelis bostrychophila: insights into the evolution of mitochondrial genomes in bilateral animals

Booklice (order Psocoptera) in the genus Liposcelis are major pests to stored grains worldwide and are closely related to parasitic lice (order Phthiraptera). We sequenced the mitochondrial (mt) genome of Liposcelis bostrychophila and found that the typical single mt chromosome of bilateral animals has fragmented into and been replaced by two medium-sized chromosomes in this booklouse; each of these chromosomes has about half of the genes of the typical mt chromosome of bilateral animals. These mt chromosomes are 8,530 bp (mt chromosome I) and 7,933 bp (mt chromosome II) in size. Intriguingly, mt chromosome I is twice as abundant as chromosome II. It appears that the selection pressure for compact mt genomes in bilateral animals favors small mt chromosomes when small mt chromosomes co-exist with the typical large mt chromosomes. Thus, small mt chromosomes may have selective advantages over large mt chromosomes in bilateral animals. Phylogenetic analyses of mt genome sequences of Psocodea (i.e. Psocoptera plus Phthiraptera) indicate that: 1) the order Psocoptera (booklice and barklice) is paraphyletic; and 2) the order Phthiraptera (the parasitic lice) is monophyletic. Within parasitic lice, however, the suborder Ischnocera is paraphyletic; this differs from the traditional view that each suborder of parasitic lice is monophyletic.

An ex vivo, assessor blind, randomised, parallel group, comparative efficacy trial of the ovicidal activity of three pediculicides after a single application--melaleuca oil and lavender oil, eucalyptus oil and lemon tea tree oil, and a "suffocation" pediculicide

Background

There are two components to the clinical efficacy of pediculicides: (i) efficacy against the crawling-stages (lousicidal efficacy); and (ii) efficacy against the eggs (ovicidal efficacy). Lousicidal efficacy and ovicidal efficacy are confounded in clinical trials. Here we report on a trial that was specially designed to rank the clinical ovicidal efficacy of pediculicides. Eggs were collected, pre-treatment and post-treatment, from subjects with different types of hair, different coloured hair and hair of different length.

Method

Subjects with at least 20 live eggs of Pediculus capitis (head lice) were randomised to one of three treatment-groups: a melaleuca oil (commonly called tea tree oil) and lavender oil pediculicide (TTO/LO); a eucalyptus oil and lemon tea tree oil pediculicide (EO/LTTO); or a "suffocation" pediculicide. Pre-treatment: 10 to 22 live eggs were taken from the head by cutting the single hair with the live egg attached, before the treatment (total of 1,062 eggs). Treatment: The subjects then received a single treatment of one of the three pediculicides, according to the manufacturers' instructions. Post-treatment: 10 to 41 treated live eggs were taken from the head by cutting the single hair with the egg attached (total of 1,183 eggs). Eggs were incubated for 14 days. The proportion of eggs that had hatched after 14 days in the pre-treatment group was compared with the proportion of eggs that hatched in the post-treatment group. The primary outcome measure was % ovicidal efficacy for each of the three pediculicides.

Results

722 subjects were examined for the presence of eggs of head lice. 92 of these subjects were recruited and randomly assigned to: the "suffocation" pediculicide (n = 31); the melaleuca oil and lavender oil pediculicide (n = 31); and the eucalyptus oil and lemon tea tree oil pediculicide (n = 30 subjects). The group treated with eucalyptus oil and lemon tea tree oil had an ovicidal efficacy of 3.3% (SD 16%) whereas the group treated with melaleuca oil and lavender oil had an ovicidal efficacy of 44.4% (SD 23%) and the group treated with the "suffocation" pediculicide had an ovicidal efficacy of 68.3% (SD 38%).

Conclusion

Ovicidal efficacy varied substantially among treatments, from 3.3% to 68.3%. The "suffocation" pediculicide and the melaleuca oil and lavender oil pediculicide (TTO/LO) were significantly more ovicidal than eucalyptus oil and lemon tea tree oil pediculicide (EO/LTTO) (P < 0.0001). Ranking: 1. "Suffocation" pediculicide (68.3% efficacy against eggs); 2. Melaleuca oil and lavender oil (44.4%) pediculicide; 3. Eucalyptus oil and lemon tea tree oil (3.3%) pediculicide. The "suffocation" pediculicide and TTO/LO are also highly efficacious against the crawling-stages. Thus, the "suffocation" pediculicide and TTO/LO should be recommended as first line treatments.

Trial Registration

The study was listed at the Australian/New Zealand Clinical Trial Registry (ANZCTR): reg. no. 12609000884202.

Chimeric mitochondrial minichromosomes of the human body louse, Pediculus humanus: evidence for homologous and non-homologous recombination

The mitochondrial (mt) genome of the human body louse, Pediculus humanus, consists of 18 minichromosomes. Each minichromosome is 3 to 4 kb long and has 1 to 3 genes. There is unequivocal evidence for recombination between different mt minichromosomes in P. humanus. It is not known, however, how these minichromosomes recombine. Here, we report the discovery of eight chimeric mt minichromosomes in P. humanus. We classify these chimeric mt minichromosomes into two groups: Group I and Group II. Group I chimeric minichromosomes contain parts of two different protein-coding genes that are from different minichromosomes. The two parts of protein-coding genes in each Group I chimeric minichromosome are joined at a microhomologous nucleotide sequence; microhomologous nucleotide sequences are hallmarks of non-homologous recombination. Group II chimeric minichromosomes contain all of the genes and the non-coding regions of two different minichromosomes. The conserved sequence blocks in the non-coding regions of Group II chimeric minichromosomes resemble the "recombination repeats" in the non-coding regions of the mt genomes of higher plants. These repeats are essential to homologous recombination in higher plants. Our analyses of the nucleotide sequences of chimeric mt minichromosomes indicate both homologous and non-homologous recombination between minichromosomes in the mitochondria of the human body louse.

A randomised, assessor blind, parallel group comparative efficacy trial of three products for the treatment of head lice in children--melaleuca oil and lavender oil, pyrethrins and piperonyl butoxide, and a "suffocation" product

Background

There are many different types of pediculicides available OTC in Australia. In this study we compare the efficacy and safety of three topical pediculicides: a pediculicide containing melaleuca oil (tea tree oil) and lavender oil (TTO/LO); a head lice "suffocation" product; and a product containing pyrethrins and piperonyl butoxide (P/PB).

Method

This study was a randomised, assessor-blind, comparative, parallel study of 123 subjects with live head lice. The head lice products were applied according to the manufacturer's instructions (the TTO/LO product and the "suffocation" product were applied three times at weekly intervals according to manufacturers instructions (on Day 0, Day 7 and Day 14) and the P/PB product was applied twice according to manufacturers instructions (on Day 0 and Day 7)). The presence or absence of live lice one day following the last treatment was determined.

Results

The percentage of subjects who were louse-free one day after the last treatment with the product containing tea tree oil and lavender oil (41/42; 97.6%) and the head lice "suffocation" product (40/41, 97.6%) was significantly higher compared to the percentage of subjects who were louse-free one day after the last treatment with the product containing pyrethrins and piperonyl butoxide (10/40, 25.0%; adj. p < 0.0001).

Conclusion

The high efficacy of the TTO/LO product and the head lice "suffocation" product offers an alternative to the pyrethrins-based product.

Trial Registration

The study was entered into the Australian/New Zealand Clinical Trial Registry, ACTRN12610000179033.