Discovery of a novel spotted fever group Rickettsia, "Candidatus Rickettsia kedanie," in unfed larval chigger mites, Leptotrombidium scutellare.

Spotted fever group (SFG) rickettsia, the causative agent of SFG rickettsiosis, is predominantly carried by ticks, whereas Orientia tsutusgamushi, the causative agent of scrub typhus, is primarily transmitted by chigger mites in Japan. In this study, we attempted to isolate intracellular eubacteria from Leptotrombidium scutellare, a major vector of O. tsutsugamushi; moreover, we isolated an SFG rickettsia using a mosquito-derived cell line. Draft genome sequences of this unique isolate, by applying criteria for species delimitation, classified this isolate as a novel strain, proposed as "Rickettsia kedanie." Further genetic analysis identified conserved virulence factors, and the isolate successfully propagated in mammalian cells, suggesting its ability to cause diseases in humans. The presence of SFG rickettsia in unfed larvae implies potential dual-pathogen carriage and reflects a symbiotic relationship similar to that between the mites and O. tsutsugamushi, indicating possibility of its transovarial transmission from female adults. Furthermore, conserved genomic similarity of the novel isolate to known SFG rickettsia suggests potential multiple hosts, including chiggers and ticks. In the natural environment, ticks, chigger mites, and wild animals may carry new isolates, complicating the infection cycle and increasing the transmission risks to humans. This discovery challenges the conventional association of SFG rickettsia with ticks, emphasizing its implications for research and disease control. However, this study was confined to a particular species of chigger mites and geographic area, underscoring the necessity for additional studies to comprehend the ecological dynamics, host interactions, and health implications linked to this newly identified SFG rickettsia.

Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events.

Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages.

Masqueraders Around Disaster: Clinical Features of Scrub Typhus in Fukushima, Japan.

Background: Scrub typhus (ST) is endemic in Fukushima, with the largest number of cases reported in Japan from 2009 to 2010. Although ST is highly treatable, its atypical clinical presentation impedes diagnosis, causing delays in treatment. Methods: We review the clinical features of ST in adults from 2008 to 2017 at Ohta Nishinouchi General Hospital in Fukushima, Japan. Results: Fifty-five cases (serotype Karp 24, Irie/Kawasaki 21, Hirano/Kuroki 10) of ST were confirmed via serology based on elevated immunoglobulin (Ig)M and IgG and polymerase chain reaction positivity of eschar samples. The mean age was 69 years, and 64% were female. The case fatality rate was 1.8% (1/55). Approximately 70% of cases (38/55) were not diagnosed as ST upon the initial clinic visit. Inappropriate use of antibiotics was identified in 22% of cases (12/55). In terms of atypical clinical features, 1 or more of the manifestations, fever, rash, and eschar, was absent in 31% of cases (17/55). Approximately 11% of cases presented without eschar (6/55; Karp 1, Irie/Kawasaki 1, Hirano/Kuroki 4). Moreover, severe complications were observed with shock and disseminated intravascular coagulation in 7% of cases (4/55), Thus, while 53% of cases presented with the typical triad (29/55), unusual complications and atypical features occurred in 40% (22/55). Conclusions: Diagnosis of ST becomes clinically challenging in the absence of typical features. In Fukushima, an endemic area of ST, an atypical presentation involving multisystem disease is common.

GENETIC VARIATION OF LEPTOTROMBIDIUM (ACARI: TROMBICULIDAE) MITES CARRYING ORIENTIA TSUTSUGAMUSHI, THE BACTERIAL PATHOGEN CAUSING SCRUB TYPHUS.

Leptotrombidium (Acari: Trombiculidae) mites are carriers of Orientia tsutsugamushi, the bacterial pathogen causing scrub typhus in humans. Classification of Leptotrombidium is vital because limited mite species carry O. tsutsugamushi. Generally, Leptotrombidium at the larval stage (approximately 0.2 mm in size) are used for morphological identification. However, morphological identification is often challenging because it requires considerable skills and taxonomic expertise. In this study, we found that the full-length sequences of the mitochondrial cytochrome c oxidase subunit 1 gene varied among the significant Leptotrombidium. On the basis of these, we modified the canonical deoxyribonucleic acid (DNA) barcoding method for animals by redesigning the primer set to be suitable for Leptotrombidium. Polymerase chain reaction with the redesigned primer set drastically increased the detection sensitivity, especially against Leptotrombidium scutellare (approximately 17% increase), one of the significant mites carrying O. tsutsugamushi. Phylogenetic analysis showed that the samples morphologically classified as L. scutellare and Leptotrombidium pallidum were further split into 3 and 2 distinct subclusters respectively. The mean genetic distance (p-distance) between L. scutellare and L. pallidum was 0.2147, whereas the mean distances within each species were 0.052 and 0.044, respectively. Within L. scutellare, the mean genetic distances between the 3 subclusters were 0.1626-0.1732, whereas the distances within each subcluster were 0.003-0.017. Within L. pallidum, the mean genetic distance between the 2 subclusters was 0.1029, whereas the distances within each subcluster were 0.010-0.013. The DNA barcoding uncovered a broad genetic diversity of Leptotrombidium, especially of L. scutellare and L. pallidum, the notable species carrying O. tsutsugamushi. We conclude that the DNA barcoding using our primers enables precise and detailed classification of Leptotrombidium and implies the existence of a subgenotype in Leptotrombidium that had not been found by morphological identification.

First detection and characterization of rat hepatitis E Virus (HEV-C1) in Japan.

Rat hepatitis E virus (HEV-C1) in the Orthohepevirus C species has been reported to cause zoonotic infection and hepatitis in humans. HEV-C1 strains have been detected from wild rats in many countries in Europe, Asia, and North America. However, in Japan, no HEV-C1 strains have been identified. In the present study, 5 (1.2%) of 428 wild rats (Rattus norvegicus or R. rattus) were positive for anti-HEV-C1 IgG. Although all 428 rat sera were negative for HEV-C1 RNA, it was detectable in 20 (19.8%) of 101 rat fecal samples collected on a swine farm, where HEV (genotype 3b, HEV-3b) was prevalent and wild rats were present. In addition, HEV-C1 RNA was detectable in the intestinal contents and liver tissues of 7 (18.9%) of 37 additional rats captured on the same farm. The HEV-C1 strain (ratEJM1703495L) obtained in this study shared only 75.8-84.7% identity with reported HEV-C1 strains over the entire genome but propagated efficiently in cultured cells. HEV-3b strains were detected in the rats' intestinal contents, with 97.3-99.5% identity to those in pigs on the same farm, but were undetectable in rat liver tissues, suggesting that wild rats do not support the replication of HEV-3b of swine origin.

Obligate intracellular bacteria diversity in unfed Leptotrombidium scutellare larvae highlights novel bacterial endosymbionts of mites.

It is well known that the mite Leptotrombidium scutellare carries the pathogen of scrub typhus, Orientia tsutsugamushi. However, our understanding of other bacterial endosymbionts of mites is limited. This study investigated the diversity of the obligate intracellular bacteria carried by L. scutellare using 16S rRNA gene amplicon analysis with next-generation sequencing. The results showed that the detected bacteria were classified into the genera Rickettsia, Wolbachia, and Rickettsiella and an unknown genus of the order Rickettsiales. For further classification of the detected bacteria, a representative read that was most closely related to the assigned taxonomic classification was subjected to homology search and phylogenic analysis. The results showed that some bacteria of the genus Rickettsia were identical or very close to the human pathogens Rickettsia akari, Rickettsia aeschlimannii, Rickettsia felis, and Rickettsia australis. The genetic distance between the genus Wolbachia bacteria in the present study and in previous reports is highly indicative that the bacteria in the present study can be classified as a new taxon of Wolbachia. This study detected obligate intracellular bacteria from unfed mites; thus, the mites did not acquire bacteria from infected animals or any other infectious sources. Finally, the present study demonstrated that various and novel bacterial endosymbionts of mites, in addition to O. tsutsugamushi, might uniquely evolve with the host mites throughout overlapping generations of the mite life cycle. The roles of the bacteria in mites and their pathogenicity should be further examined in studies based on bacterial isolation.

Integrative taxonomic approach of trypanosomes in the blood of rodents and soricids in Asian countries, with the description of three new species.

Trypanosoma lewisi (Kinetoplastea: Trypanosomatida: Trypanosomatidae) with a cosmopolitan distribution is the type species of the subgenus Herpetosoma, which includes ca. 50 nominal species isolated mainly from rodents. Since members of Herpetosoma in different host species have an almost identical morphology of bloodstream forms, these trypanosomes are referred to as 'T. lewisi-like', and the molecular genetic characterization of each species is necessary to verify their taxonomy. In the present study, we collected blood samples from 89 murid rodents of 15 species and 11 soricids of four species in Indonesia, Philippines, Vietnam, Taiwan, and mainland China for the detection of hemoprotozoan infection. T. lewisi and T. lewisi-like trypanosomes were found in the blood smears of 10 murid animals, which included Bandicota indica (two rats), Rattus argentiventer (one rat), and Rattus tiomanicus (two rats) in Indonesia; Rattus rattus (one rat) in the Philippines; and Niviventer confucianus (four rats) in mainland China. Furthermore, large- or medium-sized non-T. lewisi-like trypanosomes were detected in two soricids, Crocidura dracula in Vietnam and Anourosorex yamashinai in Taiwan, respectively. Molecular genetic characterization of the small subunit (SSU) ribosomal RNA gene (rDNA) and glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) gene indicated that the trypanosomes from all the murid hosts had identical SSU rDNA or gGAPDH gene nucleotide sequences except for those in N. confucianus in mainland China. These N. confucianus-infecting trypanosomes also showed several unique morphological features such as smaller bodies, anteriorly positioned nuclei, and larger rod-shaped kinetoplasts when compared with T. lewisi trypomastigotes. Trypanosoma (Herpetosoma) niviventerae n. sp. is erected for this new species. Similarly, based on morphological and molecular genetic characterization, Trypanosoma sapaensis n. sp. and Trypanosoma anourosoricis n. sp. are proposed for the trypanosomes in C. dracula in Vietnam and A. yamashinai in Taiwan, respectively. More effort directed toward the morphological and molecular genetic characterization of the trypanosomes of rodents and soricids is required to fully understand the real biodiversity of their hemoflagellates.

Tick surveillance for Borrelia miyamotoi and phylogenetic analysis of isolates in Mongolia and Japan.

Borrelia miyamotoi, recently recognized as a human pathogenic spirochete, was isolated from Ixodes persulcatus and I. ovatus in northern Mongolia and Honshu Island, a major island in Japan. Although no human B. miyamotoi infections have been reported in Mongolia, the prevalence of B. miyamotoi in ticks from Mongolia is higher than that in ticks from Hokkaido, Japan, where human cases have been reported. Moreover, the multi-locus sequence analysis of cultured isolates revealed that B. miyamotoi isolates in Mongolia belong to the Siberian type, a sequence type that was originally reported from isolates from I. persulcatus in Hokkaido. Thus, there is a possibility of unrecognized human B. miyamotoi infections in Mongolia. Moreover our data support the hypothesis of clonal expansion of the Siberian type B. miyamotoi. In contrast, although the isolates were found to belong to the Siberian type B. miyamotoi, two isolates from I. persulcatus in Honshu Island were identified to be of a different sequence type. Furthermore, B. miyamotoi isolates from I. ovatus were distinguishable from those from I. ricinus complex ticks, according to genetic analysis. In this study, we show that there may be some genetic diversity among B. miyamotoi in ticks from Honshu Island.

PREVALENCE AND DIVERSITY OF BARTONELLA SPECIES IN WILD SMALL MAMMALS IN ASIA.

We collected 641 small mammals belonging to 17 species of Rodentia and four species of Soricomorpha in Japan, Korea, Russia, Taiwan, and Thailand and investigated the prevalence and genetic diversity of Bartonella species. Apodemus (field mice) and Rattus (rats) were the most-common genera captured, making up 56.0% and 23.1% of the total specimens, respectively. Bartonellae were isolated from 54.6% of the collected animals, and the prevalence varied depending on the host species and the country of origin. The isolates were identified to the species level based on gltA and rpoB sequences. Although most Bartonella species were shared by more than two host species, the distribution patterns of Bartonella species clearly differed among the four most-common host genera: Apodemus, Rattus, Myodes (voles), and Suncus (shrews). The predominant Bartonella species were Bartonella grahamii in Apodemus, Bartonella tribocorum in Rattus, B. grahamii and Bartonella taylorii in Myodes, and an unclassified Bartonella sp. in Suncus.

A novel Bunyavirus from the soft tick, Argas vespertilionis, in Japan.

Soft ticks, Argas vespertilionis, were collected from feces of bats in Japan. Cytopathic effect (CPE) was observed after inoculating the homogenates of ticks to Vero cells. Sequencing of RNA extracted from the cell supernatant was performed by next generation sequencer. The contigs had identity to segments of Bunyaviruses, Issyk-Kul virus. The identities of segment L, M and S were only 77, 76 and 79% to Issyk-Kul virus, respectively. Therefore, we named this novel virus Soft tick bunyavirus (STBV). In the phylogenetic tree, segment L of STBV was closely related to a cluster consisting of the genus Nairovirus of the family Bunyaviridae.

Isolation of pathogenic Yersinia enterocolitica 1B/O:8 from Apodemus mice in Japan.

Yersinia enterocolitica was isolated from 15.7% (88/560) of wild rodents captured in 15 prefectures in Japan. Prevalences by rodent species were 18.0% (70/388) in Japanese field mice (Apodemus speciosus), 20% (14/71) in small Japanese field mice (Apodemus argenteus), and 11% (4/38) in gray red-backed vole (Myodes rufocanus bedfordiae), suggesting that these rodent species are important reservoirs of Y. enterocolitica. Although most of the isolates were identified as biotype 1A, the pathogenic bioserotype 1B/O:8 was detected in one of the A. speciosus and in three of the A. argenteus captured in Aomori Prefecture. It is suggested that Apodemus mice may be an important reservoir of Y. enterocolitica, and that there are foci of the pathogenic bioserotype 1B/O:8 in Aomori Prefecture, because human sporadic cases by the serotype have been reported in this prefecture.

Case of tick-associated rash illness caused by Amblyomma testudinarium.

We report a case of tick-associated rash illness (TARI), a new clinical entity of erythema migrans associated with a tick bite without infection of Lyme borreliosis agent. The patient, a 53-year-old man, went hiking in a mountainous area of Minoh City, Osaka Prefecture in October 2012. An erythematous macule with itching and a biting tick was found on his left thigh 2 days later, which gradually expanded. On the first visit to our department at the fifth day after hiking, an erythematous macule of 10 cm was recognized around the bite site. He had no systemic symptoms, and laboratory data were within normal limits. The tick was identified as a nymph of Amblyomma testudinarium. Histopathologically, perivascular infiltrates, mainly consisting of T lymphocytes, were seen in the dermis. The skin rash disappeared within 2 weeks with no treatment. Serum antibody titers against Lyme disease borrelial and rickettsial agents on the first visit and 2 weeks later were negative. These results indicate that the skin lesion of TARI was not associated with borrelial or rickettsial infection but a T-cell-mediated allergic reaction to salivary gland substances of the tick.

Detection of Anaplasma phagocytophilum and Anaplasma bovis in small wild mammals from Taichung and Kinmen Island, Taiwan.

A total of 138 animals from 7 species (Apodemus agrarius, Bandicota indica, Crocidura suaveolens, Mus caroli, Mus formosanus, Rattus losea, and Suncus murinus) captured in Taichung, located in central Taiwan, and Kinmen Island, an island off the shore of China, were examined for the presence of Anaplasma phagocytophilum. The presence of the bacteria, which causes human granulocytic anaplasmosis, was examined by nested PCR targeting the16S rDNA. Twelve animals (8.7%) from M. caroli and R. losea, and 25 (18.1%) from A. agrarius, B. indica, M. caroli, and R. losea were infected with A. phagocytophilum and Anaplasma bovis, respectively. Phylogenetic analysis revealed that partial 16S rDNA sequences in the 12 aforementioned animals showed higher similarity to the sequences related to A. phagocytophilum detected in wild rodents (Rattus and Niviventer) from southeast China. The sequences of the other 25 animals belonged to the A. bovis clade. We demonstrated that small wild mammals were infected with A. phagocytophilum and A. bovis in Taichung and Kinmen Island, Taiwan.

Significantly higher cytokine and chemokine levels in patients with Japanese spotted fever than in those with Tsutsugamushi disease.

Tetracyclines are administered to cure Japanese spotted fever (JSF) and tsutsugamushi disease (TD). It is generally said that the clinical course of JSF is worse than that of TD despite antibiotic treatment. The precise mechanism underlying the more severe clinical course of JSF is not fully understood. We therefore examined whether the differential cytokine profile between these two infectious diseases contributes to the difference in clinical severity. The serum concentrations of various cytokines (tumor necrosis factor alpha [TNF-α], interleukin-6 [IL-6], and gamma interferon [IFN-γ]) and chemokines (IL-8, interferon-inducible protein 10 [IP-10], monocyte chemoattractant protein 1 [MCP-1], macrophage inflammatory protein 1α [MIP-1α], MIP-1ß, and eotaxin) were measured in 32 TD and 21 JSF patients. The results showed that serum levels of TNF-α in the acute phases of TD and JSF were significantly increased, with a higher concentration of TNF-α in patients with JSF (mean, 39.9 pg/ml) than in those with TD (mean, 13.8 pg/ml). Comparatively higher levels of other cytokines and chemokines (IL-6, IFN-γ, IL-8, IP-10, MCP-1, MIP-1α, and MIP-1ß) were also observed in the acute phase of JSF. The clinical severity score (3.67 ± 1.71) of JSF patients was higher than that of TD patients (1.47 ± 0.77). Our findings revealed that the cytokine and chemokine levels in the acute phase of JSF were significantly higher than those in the acute phase of TD. The differential cytokine levels may be related to the difference in clinical severity between JSF and TD.

PCR detection of Anaplasma phagocytophilum and Borrelia burgdorferi in Ixodes persulcatus ticks in Mongolia.

A molecular epidemiological survey was conducted to identify the tick-borne disease agents Anaplasma phagocytophilum and Borrelia burgdorferi sensu lato in Selenge Province, Mongolia. The survey was in response to a suspected A. phagocytophilum infection in a patient. In 2012, a total of 129 questing Ixodes persulcatus adult ticks were sampled by flagging vegetation. A. phagocytophilum and Borrelia spp. were detected by PCR, targeting the 16S rDNA (rrs) and 5S-23S intergenic spacer region, respectively. Infection rates for A. phagocytophilum and B. burgdorferi sensu lato spp. were 6.2% and 55.0%, respectively. Six of the 129 ticks (4.9%) were coinfected with A. phagocytophilum and B. burgdorferi sensu lato. Among Borrelia spp., the highest prevalence rate was that for B. garinii 20047 type (26.3%), followed by B. afzelii (7.8%) and B. garinii NT29 type (7.0%). Furthermore, ticks were detected that were dually infected with B. afzelii and B. garinii 20047 type (7.8%) and B. garinii NT29 and 20047 types (6.2%).

Molecular phylogenetic analysis of Orientia tsutsugamushi based on the groES and groEL genes.

DNA sequences encoding the GroES and GroEL proteins of Orientia tsutsugamushi were amplified by the PCR and sequenced. Pairwise alignment of full-length groES and groEL gene sequences indicated high sequence similarity (90.4-100% and 90.3-100%) in O. tsutsugamushi, suggesting that these genes are good candidates for the molecular diagnosis and phylogenetic analysis of scrub typhus. Comparisons of the 56-kD type-specific antigen (TSA) protein gene and the groES and groEL genes showed that genotypes based on the 56-kD TSA gene were not related to a cluster containing the groES and groEL genes in a dendrogram, suggesting that a gene rearrangement may be associated with homologous recombination in mites.

Multilocus sequence typing and DNA similarity analysis implicates that a Borrelia valaisiana-related sp. isolated in Japan is distinguishable from European B. valaisiana.

Lyme disease Borrelia spp. are transmitted by Ixodes ticks, and more than 10 species of borreliae have been identified around the world. Recently, another Borrelia sp. has been reported in Asia (Japan, Korea, China, Taiwan and Thailand) as Borrelia valaisiana-related sp. In the present study, we obtained and genetically characterized 19 B. valaisiana-related sp. strains from mammals and ticks. Genetic analyses showed that the Borrelia strains were distinct from B. valaisiana found in Europe. Multilocus sequence typing revealed that these Borrelia isolates formed a monophyletic group with B. yangtze strains in China. Some of the strains were isolated from the bladders of small mammals, and also two strains were experimentally confirmed to be infectious in C3H/HeN mice. We observed that the Borrelia sp. was maintained in the Ixodes granulatus tick after molting. These results suggested that small mammals and I. granulatus were possible reservoir hosts and the vector tick for the Borrelia sp., respectively. B. valaisiana, originally found in Europe, was transmitted mainly by I. ricinus, and birds were mainly thought to be reservoir hosts. Our results suggested that Japanese isolates of B. yangtze (formerly B. valaisiana-related sp.) were distinguishable from B. valaisiana according to the reservoir host and its vector tick. In this study, we also deposited borrelia strain Okinawa-CW62 into bioresource centers as a reference strain of B. yangtze(=DSM 24625, JCM 17189).

Tsutsugamushi disease caused by Shimokoshi-type Orientia tsutsugamushi: the first report in Western Japan.

An 85-year-old female farmer was admitted to our hospital for fever, general fatigue, and skin rash. Cephalosporin was not effective and minocycline was dramatically effective. An eschar was discovered on her inguinal region after the defervescence. Laboratory examination of serum taken 12 days after onset of the illness showed elevated titers of antibodies against the Shimokoshi strain of Orientia tsutsugamushi. The gene sequence analysis of specimen from the patient's eschar revealed high similarity to the Shimokoshi strain by nested polymerase chain reaction. Therefore, this patient was diagnosed as a case of Shimokoshi-type tsutsugamushi disease, which has not previously been reported in Western Japan. Recently, cases of this type have also been confirmed in northeastern Japan, suggesting the need for further epidemiological studies.