Whole genome sequence and comparative genomic analysis of novel Rickettsia koreansis strain CNH17-7 isolated from human.

PURPOSE: To determine the genomic feature of novel spotted fever-causing Rickettsia koreansis strain CNH17-7, which is different from R. japonica that is a causative agent for Japanese spotted fever (JSF), and to perform its comparative genomic analysis. METHODS: Whole genome sequencing (WGS) was performed on R. koreansis strain CNH17-7 by using the Illumina Miseq system. After WGS, assembly and annotation were done by SPAdes. Then, its genomic features were compared with 19 different Rickettsia species. Based on the average nucleotide identity (ANI) value, an unweighted pair group method with an arithmetic mean (UPGMA) dendrogram was generated. Following the dendrogram analysis, pan-and core-genome analysis was performed. Then additional comparative analyses with two genetically closest Rickettsia species were conducted based on gene repertoire. RESULTS: R. koreansis strain CNH17-7 has a chromosome consisting of 1,392,633 bp with GC content of 32.4%. The ANI-derived UPGMA showed that R. koreansis strain CNH17-7 is genetically close to R. japonica YH and R. heilongjiangensis 054 but is distinctively differentiated. The ANI value of R. koreansis strain CNH17-7 to R. japonica YH and R. heilongjiangensis 054 are 98.14% and 98.04% respectively, indicating R. koreansis strain CNH17-7 is sufficient to be classified as a new species. Other than ANI, R. koreansis strain CNH17-7 also contains novel CDS and its COG functional category proportion which is distinct compared to R. japonica YH and R. heilongjiangensis 054. CONCLUSION: We have revealed genomic features of the novel R. koreansis strain CNH17-7. Hence, we propose R. koreansis strain CNH17-7 as new Rickettsia species.

Distribution of Rickettsia spp. in Ticks from Northwestern and Southwestern Provinces, Republic of Korea.

This study was done to characterize distribution of Rickettsia spp. in ticks in the northwestern and southwestern provinces in the Republic of Korea. A total of 2,814 ticks were collected between May and September 2009. After pooling, 284 tick DNA samples were screened for a gene of Rickettsia-specific 17-kDa protein using nested PCR (nPCR), and produced 88 nPCR positive samples. Of these positives, 75% contained 190-kDa outer membrane protein gene (ompA), 50% 120-kDa outer membrane protein gene (ompB), and 64.7% gene D (sca4). The nPCR products of ompA, ompB, and sca4 genes revealed close relatedness to Rickettsia japonica, R. heilongjiangensis, and R. monacensis. Most Rickettsia species were detected in Haemaphysalis longicornis. This tick was found a dominant vector of rickettsiae in the study regions in the Republic of Korea.

Geographical distribution of Orientia tsutsugamushi strains in chiggers from three provinces in Korea.

Chiggers were collected from the central and southern parts of South Korea between April and November, 2009 with the aim of investigating the seasonal and geographical distribution of Or. A total of 1136 chiggers were identified. They included eight species belonging to four genera, as follows: Leptotrombidium scutellare (27.2%, n = 309), L. pallidum (54.6%, n = 621), L. orientale (6.25%, n = 71), L. palpale (1.59%, n = 18), L. zetum (2.0%, n = 23), Euschoengastia koreaensis (1.5%, n = 17), Cheladonta ikaoensis (0.08%, n = 1) and Neotrombicula japonica (1.05%, n = 12). The density of L. pallidum was high from April to May, whereas L. scutallare was not found in spring, being observed from October. Serotype-specific nested PCR targeting the 56 kDa protein gene and sequencing analysis identified that the strains of 1136 O. tsutsugamushi in the chiggers as Boryong (6.8%), Kanda (0.4%), Oishi (0.3%), Jecheon (0.1%), Youngworl (0.1%) and Wonju (0.1%). Our findings indicate that L. pallidum and L. scutellare are dominant species in Korea and have geographical and seasonal variations.

First isolation of Rickettsia monacensis from a patient in South Korea.

A Rickettsia sp. was isolated from the blood of a patient with an acute febrile illness using the shell vial technique; the isolate was named CN45Kr and was identified by molecular assay as Rickettsia monacensis, which was first recognized as a pathogen in Spain. Sequencing analysis showed that the gltA sequence of the isolate was identical to that of Rickettsia sp. IRS3. The ompA-5mp fragment sequence showed 100% identity to those of R. monacensis and Rickettsia sp. In56 and ompA-3pA In56 and 100% identity to that of Rickettsia sp. IRS3. The ompB sequence was found to have 99.9% similarity to that of R. monacensis IrR/Munich. This study confirms the pathogenicity of this agent and provides additional information about its geographic distribution.

Larval chigger mites collected from small mammals in 3 provinces, Korea.

A total of 9,281 larval chigger mites were collected from small mammals captured at Hwaseong-gun, Gyeonggi-do (Province) (2,754 mites from 30 small mammals), Asan city, Chungcheongnam-do (3,358 mites from 48 mammals), and Jangseong-gun, Jeollanam-do (3,169 for 62 mammals) from April-November 2009 in the Republic of Korea (= Korea) and were identified to species. Leptotrombidium pallidum was the predominant species in Hwaseong (95.8%) and Asan (61.2%), while Leptotrombidium scutellare was the predominant species collected from Jangseong (80.1%). Overall, larval chigger mite indices decreased from April (27.3) to June (4.9), then increased in September (95.2) and to a high level in November (169.3). These data suggest that L. pallidum and L. scutellare are the primary vectors of scrub typhus throughout their range in Korea. While other species of larval chigger mites were also collected with some implications in the transmission of Orientia tsutsugamushi, they only accounted for 11.2% of all larval chigger mites collected from small mammals.

Spotted fever group rickettsia closely related to Rickettsia monacensis isolated from ticks in South Jeolla province, Korea.

Rickettsia monacensis, a spotted fever group rickettsia, was isolated from Ixodes nipponensis ticks collected from live-captured small mammals in South Jeolla province, Korea in 2006. Homogenates of tick tissues were inoculated into L929 and Vero cell monolayers using shell vial assays. After several passages, Giemsa staining revealed rickettsia-like organisms in the inoculated Vero cells, but not the L929 cells. Sequencing analysis revealed that the ompA-small part (25-614 bp region), ompA-large part (2849-4455 bp region), nearly full-length ompB (58-4889 bp region) and gltA (196-1236 bp region) of the isolates had similarities of 100%, 99.8%, 99.3% and 99.5%, respectively, to those of R. monacensis. Furthermore, phylogenetic analysis showed that the isolate was grouped into the cluster in the same way as R. monacensis in the trees of all genes examined. These results strongly suggest that the isolate is closely related to R. monacensis. As far as is known, this is the first report of isolation of R. monacensis from ticks in Korea.

Detection of Rickettsia monacensis from Ixodes nipponensis collected from rodents in Gyeonggi and Gangwon Provinces, Republic of Korea.

A total of 1,305 ticks were collected from wild rodents captured monthly, except July and August, during 2008 at three US-ROK operated military training sites and three US military installations in Gyeonggi and Gangwon Provinces, the Republic of Korea (ROK). Ixodes nipponensis was the most frequently collected tick (n = 1,299, 99.5 %), followed by Ixodes pomerantzevi (n = 6, 0.5 %). The ticks were pooled (1-15/sample) and tested by nested polymerase chain reaction (nPCR) for spotted fever group (SFG) rickettsiae with primer sets targeting the outer membrane protein B (ompB), citrate synthase (gltA), and 17-kDa antigen gene loci. A total of 115/197 (58.4 %) pools were positive by nPCR for the outer membrane protein ompB. Nucleotide sequence analysis of 105/115 (91.3 %) ompB targeted nPCR positive products showed a high degree of similarity to Rickettsia monacensis (99.3-100 %, n = 87) and R. japonica (99.5-100 %, n = 18). From the 87 positive samples demonstrating a high degree of similarity to R. monacensis, 15 were selected and analyzed by nPCR for gltA and the 17-kDa genes. A total of 12/15 pooled samples were positive for by nPCR for gltA, with amplicons demonstrating a high degree of similarity to R. monacensis (99.3-99.7 %). A total of 13/15 pooled samples were positive by nPCR for the 17-kDa gene, with amplicons demonstrating a high degree of similarity to R. monacensis (99.4-100 %). These findings demonstrate that R. monacensis is distributed throughout Gyeonggi and Gangwon Provinces in the ROK. Furthermore, data suggest a relative high prevalence of R. monacensis in the tick, I. nipponensis.

Molecular Typing on Human Blood Reveals the Borrelia afzelii Infection in Korea.

Lyme disease is a tick-borne infection in Korea. Here, clinical samples were collected from a 72-year old patient, with sudden onset of fever on April, 2018. The patient was passed away after 3rd day of doxycycline administration. The molecular diagnostic tests, nested polymerase chain reaction targeting 5S-23S rRNA intergenic spacer region (IGS) and multilocus sequence typing (MLST), showed positive for Borrelia afzelii from blood. Further, mutations in both 5S - 23S IGS and pepX allele of MLST were determined. Herein, we report the expected first death case by B. afzelii infection in Korea.

Tick-borne rickettsiae in Midwestern region of Republic of Korea.

To identify spotted fever group (SFG) rickettsiae among ticks collected by dragging at eight sites in three provinces of the midwestern region of the Republic of Korea (ROK), genus- and species-specific quantitative real-time PCR (qPCR) assays and sequencing were performed. DNA was extracted from a total of 2,312 ticks that were assayed individually (n=140) or in pools (n=444), resulting in a total of 584 individual and pooled tick samples. The 584 tick samples were screened with the genus-specific qPCR assay (Rick17b) and produced 265 (45.38%) positive reactions [individual (n=64) and pooled (n=101) samples]. Of these genus-specific positive samples, 57 (21.51%) were identified as Candidatus Rickettsia longicornii and 48 (18.11%) were identified as R. monacensis by species-specific qPCR assays. Subsequently, nested PCR (nPCR) was performed with 120 samples, which tested positive samples for genus-specific, but not species-specific, qPCR assays. The sequences of ompA and ompB genes showed how many close relatedness to Ca. R. longicornii and Ca. R. jingxinensis isolate Xian Hl-79, uncultured Rickettsia sp. Y27-1, Ca. R. tasmanensis strain T152, R. endosymbiont of H. longicornis tick 47, and R. koreansis strain CNH17-7. In conclusion, we successfully detected specific rickettsial agents using qPCR and a sequence-based analysis approach that demonstrated the prevalence of various tick-borne Rickettsia spp. in midwestern ROK.

Molecular genetic analysis and clinical characterization of Rickettsia species isolated from the Republic of Korea in 2017.

Rickettsia sp. CNH17-7 was isolated from patients' blood and identified by gene analysis as a species distinct from Rickettsia japonica. In addition, similar rickettsial infection was confirmed in two species (Haemaphysalis longicornis and Ixodes nipponensis) of ticks and rodents in northeastern and southwestern provinces, Republic of Korea. Subsequently, the analysis of 16S rRNA, ompA, ompB and sca4 genes of isolate CNH17-7 revealed 100%, 99.68%, 99.57% and 99.44% sequence similarity with Rickettsia sp. HlR/D91 and Candidatus R. longicornii ROK-HL727. In this study, we report the isolation of a new Rickettsia sp. CNH17-7 and infection of different types of ticks with the same rickettsial agents.

Diagnosis of scrub typhus by immunohistochemical staining of Orientia tsutsugamushi in cutaneous lesions.

We assessed the clinical usefulness of immunohistochemical staining on skin biopsy specimens for the diagnosis of scrub typhus compared with indirect immunofluorescent antibody assay (IFA), the definitive diagnostic method for scrub typhus, in a prospective study of 125 patients with possible scrub typhus in 2005 and 2006. Skin biopsy specimens were obtained from 63 patients. To minimize the effects caused by antibiotics on immunohistochemical results, 46 patients were assessed before antibiotic administration (4 patients received antibiotic therapy before admission; 13 underwent skin biopsy after antibiotic administration at our hospital). Compared with IFA results, immunohistochemical results on maculopapular skin lesions demonstrated a sensitivity of 0.65 and a specificity of 1. Immunohistochemical results on eschars demonstrated a sensitivity of 1 and a specificity of 1. For immunohistochemical staining performed on skin lesions within 3 or 4 days of administration of antibiotics that are effective for Rickettsia, the antibiotics did not greatly influence diagnostic sensitivity. Immunohistochemical staining of skin biopsy specimens, particularly that of eschars, is sensitive and specific, and this technique can be reliable for confirming the diagnosis of scrub typhus.

Reclassification of Borrelia spp. Isolated in South Korea Using Multilocus Sequence Typing.

Here, we used multilocus sequence typing (MLST) to evaluate 3 intergenic genes (16S rRNA, ospA, and 5S-23S IGS) in Borrelia isolated from South Korea to analyze the relationships between host, vector, and molecular background. We identified B. afzelii, B. yangtzensis, B. garinii, and B. bavariensis. This study is the first report for the identification of B. yangtzensis using MLST in South Korea.

Severe scrub typhus confirmed early via immunohistochemical staining.

We describe a case of interstitial pneumonia that was confirmed as scrub typhus by immunohistochemical (IHC) staining of an eschar. When a patient presents with interstitial pneumonia accompanied by generalized lymphadenopathy on the thoracic CT scan, clinicians should suspect scrub typhus, especially when the patient has a history of travel to a scrub typhus-endemic area. IHC staining on an eschar revealed invasion by Orientia tsutsugamushi coccobacilli of the patient's sweat ducts and glands as well as vascular endothelium. IHC staining of an eschar could be used as an early-confirmation diagnostic method to establish scrub typhus.

Low-molecular weight mannogalactofucans prevent herpes simplex virus type 1 infection via activation of Toll-like receptor 2.

Low-molecular-weight mannogalactofucans (LMMGFs, <4000g/mol) were prepared by the enzymatic degradation of Undaria pinnatifida sporophyll galactofucan (MF) and evaluated or their antiviral activities and underlying action mechanisms against herpes simplex virus type 1 (HSV-1). The 50% inhibitory concentrations (IC50) of LMMGFs and MF were 2.64 and 2.42µg/mL, respectively. LMMGFs inhibited the viral entry on the host cell surface and also exhibited inhibitory activity directly against viral particles, as observed in a virucidal assay. LMMGFs dose-dependently enhanced the mRNA expression of Toll-like receptor 2 (TLR2) and stimulated the phosphorylation of Akt and JNK in Vero cells. These results clearly demonstrated that LMMGFs use TLR2 as their receptor, preventing HSV-1 infection on the host cell surface and antagonizing viral adsorption via TLR2 pathway activation in Vero cells.

PIAS1 enhances SUMO-1 modification and the transactivation activity of the major immediate-early IE2 protein of human cytomegalovirus.

The protein inhibitor of activated STAT1 (PIAS1), known to be a small ubiquitin-like modifier (SUMO) E3 ligase, was found to interact with the human cytomegalovirus IE2 protein. We found that the sumoylation of IE2 was markedly enhanced by wild-type PIAS1 but not by a mutant containing a Cys to Ser substitution at position 351 (C351S) within the RING finger-like domain. In target reporter gene assays, wild-type PIAS1, but not the C351S mutant, enhanced the IE2-mediated transactivations of viral polymerase promoter and cellular cyclin E promoter and this augmentation required the intact sumoylation sites of IE2. Our results suggest that PIAS1 acts as a SUMO E3 ligase toward IE2 and that it may regulate the transactivation function of IE2. To our knowledge, IE2 is the first viral target found to be regulated by a SUMO E3 ligase.

Differentiation of Borrelia burgdorferi sensu lato through groEL gene analysis.

The nucleotide sequences (310 bp) of the groEL gene, which encode the 60-kDa heat shock protein GroEL from 31 reference strains of Borrelia were determined and compared. More than 92.3% similarity was observed among Borrelia burgdorferi sensu lato strains. In the phylogenetic tree constructed with the maximum-likelihood method, each species of B. burgdorferi sensu lato was differentiated as a distinct entity. We developed polymerase chain reaction-restriction fragment length polymorphism analysis using a specific single amino acid variation [N(213) (AAT)-->S (AGC or AGT)] between B. burgdorferi sensu stricto strains and the other B. burgdorferi sensu lato strains. These results showed that the groEL gene is useful for differentiation of B. burgdorferi sensu lato.

A case of scrub typhus requiring maintenance hemodialysis.

Renal failure caused by scrub typhus is known to be reversible. In most cases, renal function is almost fully restored after appropriate antibiotic treatment. A 71-year-old man was diagnosed with scrub typhus complicated by renal failure. A renal biopsy revealed histopathologic findings consistent with acute tubulointerstitial nephritis. Renal function did not improve 18 months after discharge and the patient required continuous hemodialysis. Although severe renal failure requiring dialysis is a rare complication of scrub typhus, we describe a case of scrub typhus requiring maintenance hemodialysis. To the best of our knowledge, this is the first such report.

Comparison study between MAST CLA and OPTIGEN.

BACKGROUND: The MAST-CLA system (Hitachi Chemical Diagnostics, Inc., Mountain View, CA) is an in vitro diagnostic test for the simultaneous determination of specific IgE to different allergens. Recently, a new generation of MAST-CLA was developed (OPTIGEN; Hitachi Chemical Diagnostics). The purpose of this study was to determine the performance of these two tests for the diagnosis of allergic rhinitis. METHODS: Suspicious allergic rhinitis patients were divided into four groups and their medical records were reviewed: group 1 patients were tested with the MAST-CLA and skin-prick tests (251 patients), group 2 patients were tested with the OPTIGEN and skin-prick tests (319 patients), group 3 patients were tested with the MAST-CLA and CAP (104 patients) tests, and group 4 patients were tested with the OPTIGEN and CAP tests (270 patients). The correlation between MAST-CLA and OPTIGEN to skin-prick and CAP tests was determined. RESULTS: The positivity percentage of MAST-CLA results was higher than with skin-prick and CAP tests, and the results for the OPTIGEN test were comparable with skin-prick test and CAP. This suggests that the MAST-CLA test might have a slightly higher rate of giving false positive results. The OPTIGEN test correlated better with the skin-prick test and CAP. CONCLUSION: The OPTIGEN test performed better than the MAST-CLA test for diagnosing allergic rhinitis.

Activation of mitogen-activated protein kinases is involved in the induction of interferon beta gene in macrophages infected with Orientia tsutsugamushi.

We investigated the role of MAPK in IFN-beta gene expression in macrophages after infection with Orientia tsutsugamushi. ERK1/2 became phosphorylated in Orientia-stimulated macrophages. Selective inhibition of ERK1/2 and p38 MAPK could all significantly reduce Orientia-stimulated IFN-beta mRNA expression. Orientia inactivation by heat abolished IFN-beta mRNA induction only, whereas cytochalasin D treatment completely blocked both IFN-beta and chemokine expression, suggesting requirement of cellular internalization by viable bacteria for IFN-beta gene induction. In conclusion, our data indicate that MAPK pathways are required to induce maximal IFN-beta gene expression in macrophages during Orientia infection.

Development of recombinant OmpA and OmpB proteins as diagnostic antigens for rickettsial disease.

In this study the diagnostic potential of Rickettsia conorii recombinant antigens was analyzed. For this, site-specific PCR primers were used to clone the OmpA and OmpB genes of R. conorii into pMAL-c2X plasmids. Six fragments of OmpA and four of OmpB were expressed as fusion proteins with maltose-binding protein in Escherichia coli. OmpA(1350-1784), OmpB(801-1269,) and OmpB(1227-1634) regions from truncated proteins were selected as diagnostic candidate antigens by ELISA using control sera. ELISA results of three antigens were compared to the results obtained by using a commercial ELISA kit which contained whole OmpA and OmpB antigens from R. conorii. For this analysis, 40 serum samples taken from febrile patients and uninfected controls were tested. Of the 20 R. conorii test results which were positive with the commercial kit, 18 were shown to be positive by ELISA using OmpA(1350-1784) (a sensitivity of 90%). The specificity of the ELISA was 100%; all of the 20 samples shown to be negative using the commercial kit were also negative in our assay. The sensitivities of the ELISA using the OmpB(801-1269) and OmpB(1227-1634) were 90% and 95%, respectively. The specificities of the OmpB(801-1269) and the OmpB(1227-1634) were 100% and 95%, respectively. These results suggest that specific regions of OmpA and OmpB effectively detect antibodies against R. conorii, and the truncated recombinant antigens could be used for development of diagnostic tools for rickettsial disease.