Genomic comparison of Rickettsia honei strain RBT and other Rickettsia Species

Rickettsia honei strain RB(T) was isolated from a febrile patient on Flinders Island, Australia, in 1991 and has been demonstrated to be the agent of Flinders Island spotted fever, a disease transmitted to humans by ticks. The comparison of this 1.27-Mb genome with other Rickettsia genomes provides additional insight into the mechanisms of evolution in Rickettsia species.     

Characteristics of in vitro infection of human monocytes,by Rickettsia helvetica

Eighteen species of rickettsiae are reported to cause infections in humans. One of these is Rickettsia helvetica, which is endemic in European and Asian countries and transmitted by the tick Ixodes ricinus. Besides fever, it has been demonstrated to cause meningitis and is also associated with perimyocarditis. One of the initial targets for rickettsiae after inoculation by ticks is the macrophage/monocyte. How rickettsiae remain in the macrophages/monocytes before establishing their infection in vascular endothelial cells remains poorly understood. The main aim of the present study was to investigate the impact on and survival of R. helvetica in a human leukemic monocytic cell line, THP-1. Our results show that R. helvetica survives and propagates in the THP-1 cells. The infection in monocytes was followed for seven days by qPCR and for 30 days by TEM, where invasion of the nucleus was also observed as well as double membrane vacuoles containing rickettsiae, a finding suggesting that R. helvetica might induce autophagy at the early stage of infection. Infected monocytes induced TNF-α which may be important in host defence against rickettsial infections and promote cell survival and inhibiting cell death by apoptosis. The present findings illustrate the importance of monocytes to the pathogenesis of rickettsial disease.     

Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae

Rickettsia typhi, the causative agent of murine typhus, is an obligate intracellular bacterium with a life cycle involving both vertebrate and invertebrate hosts. Here we present the complete genome sequence of R. typhi (1,111,496 bp) and compare it to the two published rickettsial genome sequences: R. prowazekii and R. conorii. We identified 877 genes in R. typhi encoding 3 rRNAs, 33 tRNAs, 3 noncoding RNAs, and 838 proteins, 3 of which are frameshifts. In addition, we discovered more than 40 pseudogenes, including the entire cytochrome c oxidase system. The three rickettsial genomes share 775 genes: 23 are found only in R. prowazekii and R. typhi, 15 are found only in R. conorii and R. typhi, and 24 are unique to R. typhi. Although most of the genes are colinear, there is a 35-kb inversion in gene order, which is close to the replication terminus, in R. typhi, compared to R. prowazekii and R. conorii. In addition, we found a 124-kb R. typhi-specific inversion, starting 19 kb from the origin of replication, compared to R. prowazekii and R. conorii. Inversions in this region are also seen in the unpublished genome sequences of R. sibirica and R. rickettsii, indicating that this region is a hot spot for rearrangements. Genome comparisons also revealed a 12-kb insertion in the R. prowazekii genome, relative to R. typhi and R. conorii, which appears to have occurred after the typhus (R. prowazekii and R. typhi) and spotted fever (R. conorii) groups diverged. The three-way comparison allowed further in silico analysis of the SpoT split genes, leading us to propose that the stringent response system is still functional in these rickettsiae.     

Genomic Analysis of Rickettsia japonica Strain YHT

Rickettsia japonica strain YH, isolated in 1984 in Japan, is the type strain of R. japonica, the tick-borne agent of Japanese spotted fever. Here, we report the 1.33-Mb genome of this rickettsial species.     

Molecular Investigations of Rickettsia helvetica Infection in Dogs,Foxes, Humans,and Ixodes Ticks

Rickettsia helvetica, a tick-borne member of the spotted-fever-group rickettsiae, is a suspected pathogen in humans; however, its role in animals is unknown. The aims of this study were to establish a R. helvetica-specific real-time TaqMan PCR assay and apply it to the analysis of tick vectors (to determine potential exposure risk) and blood samples from Canidae and humans (to determine prevalence of infection). The newly designed 23S rRNA gene assay for R. helvetica was more sensitive than a published citrate synthase gene (gltA) assay for several rickettsiae. Blood samples from 884 dogs, 58 foxes, and 214 human patients and 2,073 ticks (Ixodes spp.) collected from either vegetation or animals were analyzed. Although the maximal likelihood estimate of prevalence was 12% in unfed ticks and 36% in ticks collected from animals, none of the 1,156 blood samples tested PCR positive. Ticks from cats were more frequently PCR positive than ticks from dogs. Sequencing of the 23S rRNA and/or the gltA gene of 17 tick pools confirmed the presence of R. helvetica. Additionally, Rickettsia monacensis, which has not been previously found in Switzerland, was identified. In conclusion, R. helvetica was frequently detected in the tick population but not in blood samples. Nevertheless, due to the broad host range of Ixodes ticks and the high rate of infestation with this agent (i.e., R. helvetica was 13 times more frequent in unfed ticks than the tick-borne encephalitis virus), many mammals may be exposed to R. helvetica. The PCR assay described here represents an important tool for studying this topic.Tick-borne rickettsioses are caused by intracellular bacteria belonging to the spotted fever group (SFG) of the genus Rickettsia. The latter comprises more than 20 different species, of which an increasing number are known to be associated with human and animal diseases. The SFG rickettsiae are distributed worldwide, and their distribution depends upon the occurrence of tick species. The most common tick in Europe is Ixodes ricinus, which was found to harbor Rickettsia helvetica. R. helvetica is transmitted not only transstadially but also transovarially in I. ricinus. Therefore, this tick is both a vector and a reservoir for R. helvetica. Due to the broad host range of I. ricinus, many mammalian species, including humans, can serve as hosts. Therefore, these host species may potentially be exposed to R. helvetica. R. helvetica is a suspected pathogen in humans, and the symptoms described for infections in humans include fever, headache, arthralgia, and myalgia (1, 3, 7, 21, 34). The agent also has been implicated in two cases of fatal perimyocarditis (20, 22).Interestingly, despite the wide distribution of I. ricinus ticks and the high rate of infection of these ticks with R. helvetica that has been reported in several European countries (2, 9, 18, 19, 25, 29, 35, 42), larger studies discussing the prevalence of the infection in humans and animals are scarce. No studies evaluating the importance of R. helvetica in pets or farm animals are available as yet. It is unknown whether these animals can serve as a reservoir or develop clinical signs after infection.Rickettsial infections have been reported to represent the third most common vector-borne disease acquired during international travel and are therefore considered a common cause of fever of unknown origin in returned travelers (24). As the occurrence of tick-borne infectious diseases, and particularly rickettsial infections, is increasing in humans worldwide (26), it may be assumed that the same holds true for companion animals. In dogs, fever of unknown origin that is responsive to antibiotic treatment is frequently observed. In these cases, an infectious agent is suspected but rarely, if ever, confirmed. R. helvetica infections may be the underlying cause in some of these cases, even if the patient does not have a travel history, since exposure to R. helvetica-infected I. ricinus ticks may have occurred locally.To date, the diagnosis of rickettsial infection has most often been confirmed by serological testing. However, antibodies are not detectable prior to the second week of illness for any rickettsial disease studied thus far. Moreover, except for detection of seroconversion or a fourfold increase in titer, a positive serology result does not necessarily indicate an acute infection. A standardized sensitive and specific molecular method for the confirmation of R. helvetica infections would facilitate not only its diagnosis but also prevalence studies. This in turn could increase the awareness of physicians and veterinarians who are confronted with diseased individuals.Therefore, the aims of the present study were as follows: first, to establish a sensitive real-time PCR assay specific for R. helvetica; second, to study tick vectors for R. helvetica to assess the potential exposure risk for animals and humans; and third, to evaluate blood samples from Canidae and humans to assess the occurrence of R. helvetica infections.(These studies were conducted by A. Perreten as partial fulfillment of the requirements for a doctoral thesis at the Vetsuisse Faculty, University of Zurich.)     

Genomic sequence of the class II region of the canine MHC: comparison with the MHC of other mammalian species

The domestic dog, Canis familiaris, is an excellent model species in which to study complex inherited diseases, having over 200 recognized breeds, each of which represents a closed gene pool. Overlapping canine genomic BAC clones were sequenced to obtain 711,521 bp of the canine classical and extended MHC class II regions. Analysis and annotation of this sequence reveals that it contains 45 loci, of which 29 are predicted to be functionally expressed. Comparison of the DLA class II sequence with those of the cat, human, and mouse highlights regions of syntenic conservation and species-specific gene rearrangement and duplication and gives an insight into the evolution of the DR region in the order Carnivora. Elucidation of functionally important dog class II genes and the identification of 23 microsatellite markers spanning this region will contribute significantly to the study of canine diseases that have an immune component.     

Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

Background

Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis, Nipponia nippon. Once widespread across North-East Asia, by 1981 only seven individuals from two breeding pairs remained in the wild. The recovering crested ibis populations thus provide an excellent example for conservation genomics since every individual bird has been recruited for genomic and demographic studies.

Results

Using high-quality genome sequences of multiple crested ibis individuals, its thriving co-habitant, the little egret, Egretta garzetta, and the recently sequenced genomes of 41 other avian species that are under various degrees of survival threats, including the bald eagle, we carry out comparative analyses for genomic signatures of near extinction events in association with environmental and behavioral attributes of species. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes contribute to the major genetic defects of the endangered species. We further identify that genetic inbreeding and loss-of-function genes in the crested ibis may all constitute genetic susceptibility to other factors including long-term climate change, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to facilitate sustainable recovery of endangered species.

Conclusions

These findings demonstrate common genomic signatures of population decline across avian species and pave a way for further effort in saving endangered species and enhancing conservation genomic efforts.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0557-1) contains supplementary material, which is available to authorized users.     

Ultrastructure of a Japanese Rickettsial strain genetically identified as Rickettsia helvetica which was originally found in Europe

A rickettsial strain IO-1 has been isolated from a tick, Ixodes ovatus, in Japan and genetically identified as Rickettsia helvetica, a member of the spotted fever group rickettsiae. Ultrastructural observations were made on the microorganism. The ultrastructure of R. helvetica IO-1 appeared to be generally the same as that previously shown for other rickettsiae of the spotted fever and typhus groups. The rickettsiae were primarily found free in the cytoplasm of L929 cultured cells. Occasionally, the rickettsiae may also invade the host cell nucleus; however, the frequency of the nuclear localization was very low.     

Ticks Parasitizing Wild Birds in Portugal: Detection of Rickettsia aeschlimannii, R. helvetica and R. massiliae

From January 2002 to December 2004, 152 ticks were collected from 40 wild birds recovered in Santo André Natural Reserve and Monsanto Forestal Park, Portugal mainland. Five ticks species were identified from 22 species of birds, and new host record were provided for some species. In addition, 32 (21%) ticks were screened by PCR to detect infections with agents belonging to order Rickettsiales: Anaplasma phagocytophilum, Ehrlichia chaffeensis, and Rickettsia spp. PCR amplicons were obtained in 5 (15.6%) tick samples. Rickettsia DNA exhibiting gltA sequences similar to those of Rickettsia aeschilimannii, R. helvetica and R. massiliae were identified in Hyalomma marginatum, Ixodes ventalloi and in Rhipicephalus turanicus, respectively. This is the first report of rickettsiae infections in ticks collected from wild birds in Portugal. Giving the results presented above wild birds play an important role in the maintenance and dissemination of several tick species and associated rickettsiae.     

Sequence comparison of gamma-crystallins from the reptilian and other vertebrate species

Lens crystallins were isolated from homogenates of reptilian eye lenses (Caiman crocodylus apaporiensis) by gel-permeation chromatography and characterized by gel electrophoresis, and amino acid and N-terminal sequence analyses. Four fractions corresponding to alpha-, delta/epsilon/beta-, beta- and gamma-crystallins were identified on the basis of their electrophoretic patterns as revealed by SDS gel electrophoresis. Comparison of the amino acid contents of reptilian crystallins with those of mammals suggests that each orthologous class of crystallins from the evolutionarily distant species still exhibits similarity in their amino acid compositions and probably sequence homology as well. All fractions except that of gamma-crystallin were found to be N-terminally blocked. N-terminal sequence analysis of the purified gamma-crystallin subfractions showed extensive homology between the reptilian gamma-crystallin polypeptides themselves and also those from other vertebrate species, suggesting the existence of a multigene family and their close relatedness to gamma-crystallins of other vertebrates.     

Analytical comparison of gums from Acacia hebeclada and other gummiferae species

Analysis of the arabinogalactan-protein isolated from a specimen of Acacia hebeclada gum has shown major differences in composition between this and a specimen previously examined in another laboratory. In its much lower proportions of protein and uronic acid, and higher arabinose content, the present specimen of A. hebeclada gum resembles more closely gum from the taxonomically related species A. tortilis, this similarity extending to the modes of linkage of the constituent sugar and uronic acid residues. The hydroxyproline content of the protein moiety is also close to that in A. tortilis gum. The wide variation in composition between different specimens of A. hebeclada gum is comparable with that of the gums of A. karroo and A. erioloba, from the same series (Gummiferae Benth.).     

Detection of Rickettsia helvetica DNA from peripheral blood of Sika deer (Cervus nippon yesoensis) in Japan

Partial nucleotide sequences of the citrate synthase and 17-kDa genes of Rickettsia helvetica were detected from peripheral blood samples of Sika deer (Cervus nippon yesoensis) in Hokkaido, Japan. Results suggest the presence of a rickettsiemia associated with R. helvetica. This is the first evidence of R. helvetica infection in Sika deer and indicates that this species may represent a potential reservoir host of R. helvetica in Japan.     

ESCCAR international congress on Rickettsia and other intracellular bacteria

The European Society for the study of Chlamydia, Coxiella, Anaplasma and Rickettsia (ESCCAR) held his triennial international meeting in Lausanne. This meeting gathered 165 scientists from 28 countries and all 5 continents, allowing efficient networking and major scientific exchanges.Topics covered include molecular and cellular microbiology, genomics, as well as epidemiology, veterinary and human medicine. Several breakthroughs have been revealed at the meeting, such as (i) the presence of CRISPR (the “prokaryotic immune system”) in chlamydiae, (ii) an Anaplasma effector involved in host chromatin remodelling, (iii) the polarity of the type III secretion system of chlamydiae during the entry process revealed by cryo-electron tomography.Moreover, the ESCCAR meeting was a unique opportunity to be exposed to cutting-edge science and to listen to comprehensive talks on current hot topics.     

Human adipose tissue hormone-sensitive lipase: identification and comparison with other species

The mRNA for human hormone-sensitive lipase (HSL) was identified using Northern blot analysis and a cDNA-probe for rat HSL. As in the rat, human adipose tissue expresses a single mRNA species of 3.3 kb. Using Western blotting with a polyclonal rabbit antibody towards rat adipose tissue HSL, the corresponding enzyme in human adipose tissue was identified with an apparent 88 kDa polypeptide, thus slightly larger than the rat and bovine 84 kDa, and the mouse and guinea-pig 82 kDa species. Additional evidence for the identification was provided by the inhibition of HSL diacylglycerol lipase activity by the anti-rat HSL antibody, and by NaF, DFP and Hg2+, known inhibitors of HSL. The concentration of the enzyme, as reflected by its activity per g tissue and the specific activity was about two thirds of that in the rat adipose tissue (200 g rats). The identification of the human enzyme protein made it possible to directly demonstrate its phosphorylation by cAMP-dependent protein kinase, thus extending the previous report regarding activation of the lipase with this kinase and ATP-Mg2+ in human adipose tissue extracts (Khoo, J.C., Aquino, A.A. and Steinberg, D. (1974) J. Clin. Invest. 53, 1124-1131).     

Chromosome C-banding of the teosinte Zea nicaraguensis and comparison to other Zea species

The Nicaraguan teosinte Zea nicaraguensis was studied cytologically to determine its chromosome number and C-banding pattern. The C-banding pattern was compared with that of the close relative Zea luxurians as well as with Zea diploperennis and cultivated maize, Zea mays ssp. mays. Karyograms were constructed for the four Zea species. It is shown that Z. nicaraguensis, like most other Zea species, is a diploid with 2n=20 chromosomes. The C-banding pattern shows that Z. nicaraguensis is very similar to Z. luxurians and more similar to Z. luxurians than to Z. diploperennis and cultivated maize. Whether or not Z. nicaraguensis and Z. luxurians should be regarded as subspecies instead of individual species is, however, not possible to conclude from this study.     

Isoenzyme analysis of Echinostoma liei: comparison and hybridization with other African species

Isoenzyme analysis was carried out on the laboratory strain of Echinostoma liei. The results were compared with those from a preliminary study on Echinostoma caproni, Echinostoma togoensis, and Echinostoma sp. (A. Voltz, J. Richard, B. Pesson, and J. Jourdane, 1986, Annales de Parasitologie Humaine et Comparée, 61, 617-623). Isoelectrofocusing showed characteristic phenotypes for phosphoglucomutase (PGM, EC 5.4.2.2) and glucosephosphate isomerase (GPI, EC 5.3.1.9). The four experimental strains were monomorphic. Their genotypes were defined. Isoenzyme analysis of F1-hybrids and their F2 descendants indicated the subunit structure of both isoenzymes and showed that they were encoded by independent genes. Finally, it also suggested that the four strains corresponded to variants of the same species.