High prevalence of Rickettsia spp. in ticks from wild hedgehogs rather than domestic bovine in Jiangsu province, Eastern China

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.

Molecular Identification of Spotted Fever Group Rickettsiae in Ticks in the Republic of Korea

The Rickettsia species transmitted by ticks are mostly classified within the spotted fever group rickettsiae (SFGR), which causes tick-borne rickettsiosis. Although efforts have been made to investigate their prevalence in the Republic of Korea (ROK), research has been limited to certain areas. Furthermore, the pooling method for ticks does not fully reflect the exact infection rate. Therefore, we aimed to perform molecular identification of SFGR in ticks to elucidate the current prevalence of tick-borne rickettsiosis in the ROK. The SFGR of ticks was identified using polymerase chain reaction targeting the 17 kDa antigen, ompA, and gltA, followed by sequencing for species identification and phylogenetic analysis. In total, 302 ticks belonging to four species (Haemaphysalis flava, H. longicornis, Ixodes nipponensis, and Amblyomma testudinarium) were collected between April and November 2022. The overall SFGR infection rate was 26.8% (81/302 patients). Both adult and nymphal ticks and the SFGR infection rate increased during April-May, reaching their peaks in June, followed by a marked decline in August and July, respectively. Phylogenetic analysis revealed three species (R. monacensis, R. heilongjiangensis, and Candidatus R. jingxinensis) of SFGR. Thus, our results emphasize the importance of tick surveys for the prevention and management of tick-borne rickettsiosis.

Infestation prevalence, spatio-temporal distribution, phylogenetic positioning, and pathogen investigation of Argas persicus ticks in domestic hens (Gallus gallus domesticus) from Pakistan

Soft ticks pose significant health risks as vectors of various pathogens. This study explored the spatio-temporal distribution and genetic relationships of the soft tick species Argas persicus infesting domestic hens (Gallus gallus domesticus) across different districts in Pakistan. An examination of 778 hens revealed a notable tick infestation prevalence of 70.82%, with a total of 1299 ticks collected from 551 hens. The overall mean intensity was 2.19 soft ticks per infested chicken, and the overall mean abundance was 1.61 soft ticks per examined hen. Morphological identification confirmed all collected ticks (n = 1210) as A. persicus, comprising 719 males, 333 females, 121 nymphs, and 38 larvae. The Haveli, Muzaffarabad, and Kotli districts had the highest infestation rates, while Bagh had the lowest. Molecular analyses of tick DNA, focusing on 16S rDNA and 12S rDNA sequences, revealed genetic similarities among A. persicus soft ticks from Pakistan and other regions, providing insights into their evolutionary history. Importantly, no Babesia, Rickettsia, or Anaplasma infections were detected in the examined samples. These findings enhance the understanding of soft tick infestation patterns and the genetic diversity of A. persicus in the studied region.

Complete genome sequencing and comparative genomic analyses of a new spotted-fever Rickettsia heilongjiangensis strain B8

Rickettsia heilongjiangensis, a tick-borne obligate intracellular bacterium and causative agent of spotted fever in China, has attracted increasing concern regarding its capability in causing human rickettsiosis. Here, we conducted a genomic analysis of a new R. heilongjiangensis strain B8 (B8) isolated from the serum of a patient who had been bitten by a Haemaphysalis longicornis tick in Anhui Province, China. The present study sought to identify exclusive genes that might be associated with the pathogenicity of B8 using comparative genomics. Specifically, the sequences of B8 were assembled into one circular chromosome of 1,275,081 bp and predicted to contain 1447 genes. Comparative genome analyses were performed based on the genome of B8 and 28 spotted fever group (SFG) rickettsial genomes deposited in NCBI. Phylogenomic analyses indicated the B8 strain was clustered within the R. heilongjiangensis species; however, a sum of 112 and 119 B8-unique genes was identified when compared with R. heilongjiangensis and R. japonica strains, respectively. Functional annotation analyses revealed that these B8-unique genes were mainly annotated to defence mechanisms, lipid transport and metabolism, cell wall/membrane/envelope biogenesis. These data indicate B8 rather represents a previously undescribed human-pathogenic SFG rickettsia lineage, which may be an intermediate lineage of R. heilongjiangensis and R. japonica. Overall, this study isolated a new strain of R. heilongjiangensis in East-Central China for the first time, and provided potential B8-unique genetic loci that could be used for the discrimination of B8 from other R. heilongjiangensis and closely related SFG Rickettsial strains.

Applying next generation sequencing to detect tick-pathogens in Dermacentor nuttalli, Ixodes persulcatus, and Hyalomma asiaticum collected from Mongolia

Ticks and tick-borne diseases represent major threats to the public health of the Mongolian population, of which an estimated 26% live a traditional nomadic pastoralist lifestyle that puts them at increased risk for exposure. Ticks were collected by dragging and removal from livestock in Khentii, Selenge, Tuv, and Umnugovi aimags (provinces) during March-May 2020. Using next-generation sequencing (NGS) with confirmatory PCR and DNA sequencing, we sought to characterize the microbial species present in Dermacentor nuttalli (n = 98), Hyalomma asiaticum (n = 38), and Ixodes persulcatus (n = 72) tick pools. Rickettsia spp. were detected in 90.4% of tick pools, with Khentii, Selenge, and Tuv tick pools all having 100% pool positivity. Coxiella spp. were detected at an overall pool positivity rate of 60%, while Francisella spp. were detected in 20% of pools and Borrelia spp. detected in 13% of pools. Additional confirmatory testing for Rickettsia-positive pools demonstrated Rickettsia raoultii (n = 105), Candidatus Rickettsia tarasevichiae (n = 65) and R. slovaca/R. sibirica (n = 2), as well as the first report of Candidatus Rickettsia jingxinensis (n = 1) in Mongolia. For Coxiella spp. reads, most samples were identified as a Coxiella endosymbiont (n = 117), although Coxiella burnetii was detected in eight pools collected in Umnugovi. Borrelia species that were identified include Borrelia burgdorferi sensu lato (n = 3), B. garinii (n = 2), B. miyamotoi (n = 16), and B. afzelii (n = 3). All Francisella spp. reads were identified as Francisella endosymbiont species. Our findings emphasize the utility of NGS to provide baseline data across multiple tick-borne pathogen groups, which in turn can be used to inform health policy, determine regions for expanded surveillance, and guide risk mitigation strategies.

Phylogenetic Analysis of Spotted Fever Group Rickettsia Gene from Ticks and Human Patients in Tottori Prefecture, Japan

Background

Japanese spotted fever (JSF) is a tick-borne bacterial febrile disease caused by Rickettsia japonica characterized by fever, rash, and occasional death. The number of patients in Japan and the Tottori Prefecture has been increasing over the past 20 years. Most cases were found in Eastern Tottori; however, the distribution of patients has expanded to the Central and Western regions. Ticks carried by wild animals may be the cause, but the prevalence of R. japonica in ticks has not yet been analyzed.

Methods

Ticks were collected by flagging-dragging from 16 sites in Tottori, Japan. The ticks were morphologically classified and DNA was extracted. The 17-kDa antigen gene was amplified using nested PCR. PCR amplicons from ticks and JSF patients were sequenced and phylogenetically compared.

Results

In total, 177 ticks were collected and identified as Haemahysalis, Ixodes, Amblyomma, and Dermcentor. The Spotted Fever Group Rickettsia (SFGR) was detected in Haemahysalis and Amblyomma spp. using PCR, with positivity rates of 36.8% and 33.3%, respectively. DNA sequencing and phylogenetic analysis revealed that positive ticks harbored R. japonica, P. raoultii, and other Rickettsiae species; however, the patient's samples were restricted to R. japonica. Similar to the incidence of JSF, the rate of R. japonica-positive ticks was higher in the Eastern region; however, R. japonica-positive ticks were also detected in the Western region.

Conclusion

R. japonica sequences had been found in ticks collected in Tottori Prefecture. Ticks harboring R. japonica were found in the Eastern and Western parts of Tottori Prefecture and the sequences were identical to the human cases. Only the R. japonica sequence has been detected in patients with spotted fever symptoms, even though ticks were harboring various SFGRs.

Human pathogens in ticks removed from humans in Hebei, China

Ticks are the hosts or vectors of many human pathogens, including viruses, bacteria and protozoa, and can transmit these causative agents to humans when feeding on human bodies. In this study, 26 ticks removed from humans in Hebei, China were tested for the presence of human-pathogenic microorganisms by Polymerase Chain Reaction (PCR) or Reversed Transcript PCR (RT-PCR). As a result, 11 ticks tested positive for at least one human pathogen. Specifically, four validated human pathogens, including Rickettsia raoultii, Candidatus Rickettsia tarasevichiae, Babesia venatorum, and Borrelia garinii, as well as Anaplasma ovis with zoonotic potential, were identified in Ixodes persulcatus, Dermacentor silvarum and Haemaphysalis concinna. Importantly, this is the first report of Anaplasma and Babesia species pathogenic to humans in Hebei province. Moreover, the co-infections, including double infection and quadruple infection were observed. In addition, Candidatus R. principis with unknown pathogenicity was identified in one tick, which may be the same species as Candidatus R. hongyuanensis based on the nucleotide identity and phylogenetic analysis. Concluding, four validated tick-borne pathogens and one with zoonotic potential were identified in ticks parasitizing humans, suggesting the potential high public health risk in the local human population.

Exploring the Potential of Big Data Analytics in Urban Epidemiology Control: A Comprehensive Study Using CiteSpace

In recent years, there has been a growing amount of discussion on the use of big data to prevent and treat pandemics. The current research aimed to use CiteSpace (CS) visual analysis to uncover research and development trends, to help academics decide on future research and to create a framework for enterprises and organizations in order to plan for the growth of big data-based epidemic control. First, a total of 202 original papers were retrieved from Web of Science (WOS) using a complete list and analyzed using CS scientometric software. The CS parameters included the date range (from 2011 to 2022, a 1-year slice for co-authorship as well as for the co-accordance assessment), visualization (to show the fully integrated networks), specific selection criteria (the top 20 percent), node form (author, institution, region, reference cited, referred author, journal, and keywords), and pruning (pathfinder, slicing network). Lastly, the correlation of data was explored and the findings of the visualization analysis of big data pandemic control research were presented. According to the findings, "COVID-19 infection" was the hottest cluster with 31 references in 2020, while "Internet of things (IoT) platform and unified health algorithm" was the emerging research topic with 15 citations. "Influenza, internet, China, human mobility, and province" were the emerging keywords in the year 2021-2022 with strength of 1.61 to 1.2. The Chinese Academy of Sciences was the top institution, which collaborated with 15 other organizations. Qadri and Wilson were the top authors in this field. The Lancet journal accepted the most papers in this field, while the United States, China, and Europe accounted for the bulk of articles in this research. The research showed how big data may help us to better understand and control pandemics.

Diversity of Rickettsiales bacteria in five species of ticks collected from Jinzhai County, Anhui Province, China in 2021-2022

The order Rickettsiales in the class Alphaproteobacteria comprises vector-borne pathogens of both medical and veterinary importance. Ticks, as a group, are second only to mosquitoes as vectors of pathogens to humans, playing a critical role in the transmission of rickettsiosis. In the present study, 880 ticks collected from Jinzhai County, Lu'an City, Anhui Province, China in 2021-2022 were identified as belonging to five species from three genera. DNA extracted from individual ticks was examined using nested polymerase chain reaction targeting the 16S rRNA gene (rrs), and the gene fragments amplified were sequenced to detect and identify Rickettsiales bacteria in the ticks. For further identification, the rrs-positive tick samples were further amplified by PCR targeting the gltA and groEL gene and sequenced. As a result, 13 Rickettsiales species belonging to the genera Rickettsia, Anaplasma, and Ehrlichia were detected, including three tentative species of Ehrlichia. Our results reveal the extensive diversity of Rickettsiales bacteria in ticks from Jinzhai County, Anhui Province. There, emerging rickettsial species may be pathogenic and cause under-recognized diseases. Detection of several pathogens in ticks that are closely related to human diseases may indicate a potential risk of infection in humans. Therefore, additional studies to assess the potential public health risks of the Rickettsiales pathogens identified in the present study are warranted.

Plasma-derived exosomal miRNA as potential biomarker for diagnosis and prognosis of vector-borne diseases: A review

Early disease diagnosis is critical for better management and treatment outcome of patients. Therefore, diagnostic methods should ideally be accurate, consistent, easy to perform at low cost and preferably non-invasive. In recent years, various biomarkers have been studied for the detection of cardiovascular diseases, cerebrovascular diseases, infectious diseases, diabetes mellitus and malignancies. Exosomal microRNA (miRNA) are small non-coding RNA molecules that influence gene expression after transcription. Previous studies have shown that these types of miRNAs can potentially be used as biomarkers for cancers of the breast and colon, as well as diffuse large B-cell lymphoma. It may also be used to indicate viral and bacterial infections, such as the human immunodeficiency virus (HIV), tuberculosis and hepatitis. However, its use in the diagnosis of vector-borne diseases is rather limited. Therefore, this review aims to introduce several miRNAs derived from exosomal plasma that may potentially serve as a disease biomarker due to the body's immune response, with special focus on the early detection of vector-borne diseases.

Identification of Bacterial Communities and Tick-Borne Pathogens in Haemaphysalis spp. Collected from Shanghai, China

Ticks can carry and transmit a large number of pathogens, including bacteria, viruses and protozoa, posing a huge threat to human health and animal husbandry. Previous investigations have shown that the dominant species of ticks in Shanghai are Haemaphysalis flava and Haemaphysalis longicornis. However, no relevant investigations and research have been carried out in recent decades. Therefore, we investigated the bacterial communities and tick-borne pathogens (TBPs) in Haemaphysalis spp. from Shanghai, China. Ixodid ticks were collected from 18 sites in Shanghai, China, and identified using morphological and molecular methods. The V3-V4 hypervariable regions of the bacterial 16S rRNA gene were amplified from the pooled tick DNA samples and subject to metagenomic analysis. The microbial diversity in the tick samples was estimated using the alpha diversity that includes the observed species index and Shannon index. The Unifrac distance matrix as determined using the QIIME software was used for unweighted Unifrac Principal coordinates analysis (PCoA). Individual tick DNA samples were screened with genus-specific or group-specific nested polymerase chain reaction (PCR) for these TBPs and combined with a sequencing assay to confirm the results of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. We found H. flava and H. longicornis to be the dominant species of ticks in Shanghai in this study. Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are the main bacterial communities of Haemaphysalis spp. The total species abundances of Proteobacteria, Firmicutes and Bacteroidetes, are 48.8%, 20.8% and 18.1%, respectively. At the level of genus analysis, H. longicornis and H. flava carried at least 946 genera of bacteria. The bacteria with high abundance include Lactobacillus, Coxiella, Rickettsia and Muribaculaceae. Additionally, Rickettsia rickettsii, Rickettsia japonica, Candidatus Rickettsia jingxinensis, Anaplasma bovis, Ehrlichia ewingii, Ehrlichia chaffeensis, Coxiella spp. and Coxiella-like endosymbiont were detected in Haemaphysalis spp. from Shanghai, China. This study is the first report of bacterial communities and the prevalence of some main pathogens in Haemaphysalis spp. from Shanghai, China, and may provide insights and evidence for bacterial communities and the prevalence of the main pathogen in ticks. This study also indicates that people and other animals in Shanghai, China, are exposed to several TBPs.