Skin infectome of patients with a tick bite history

Distribution prediction of the habitat of Jingmen tick virus in China

Jingmen tick virus (JMTV) is widely distributed in China, and human cases have been reported. Therefore, the objectives of this study were to understand the distribution of the JMTV in suitable areas in China under the current and projected future climates. We used two pairs of JMTV primers to detect ticks in Guizhou Province via PCR and obtained data on JMTV detection in other regions through literature research. We obtained climate data from China. Finally, maximum entropy, a boosted regression tree model, and a random forest model were used for prediction. The predictive performance of the model was evaluated by the area under the curve (AUC) of the receiver operating characteristic (ROC) curve. The JMTV positivity rate in Guizhou Province was 11.02%, which was lower than the overall national positivity rate of 16.9%. The predicted probability increased monotonically with increasing monthly mean temperature. China's high JMTV habitat is concentrated in the Daxinganling region of Heilongjiang, Shanghai, and Hainan Provinces, with the total area of high JMTV habitat accounting for 1.94% of the country's total land area. In the future, from 2021 to 2040, the area of JMTV habitat area in China will show an expanding trend. Our maps of JMTV distributions provide effective early warning information for monitoring JMTV and rapidly detecting outbreaks. The potential distribution of JMTV in China is expected to increase in size in the future, requiring continuous attention and surveillance.IMPORTANCESince the first detection of the Jingmen tick virus (JMTV) in ticks in 2014, it has been detected on several continents around the world. JMTV has also been detected in several regions of China, and human cases have been reported. JMTV has many types of hosts, including ticks, mice, bats, and turtles. It can be spread with these hosts in close proximity or over long distances. As a segmented virus, JMTV is capable not only of genetic mutation and recombination but also of genetic reassortment, resulting in changes in viral infectivity or pathogenicity. However, many uninvestigated areas still exist in China. Therefore, we investigated ticks carrying JMTV in Guizhou Province. We also predicted the distribution of JMTV in China by combining previous data.

From castaways to discoveries: unveiling treasures in skin RNAseq using a novel multidimensional data processing workflow including infection-host dynamics

Defining physiology and methods to measure biological mechanisms is essential. Extensive datasets such as RNA sequencing are used with little analysis of the knowledge gained from the various methodologies. Within this work, we have processed publicly available NCBI RNAseq datasets using a combination of bioinformatics tools for the largest physiological organ, the skin. In many datasets, we identify the quality of the sample, human transcript mapping, the sex of each sample, foreign RNA from bacteria/viruses/protists, and the presence of B/T-cell immune repertoire. Processing 8,274 samples from 132 different experiments for skin samples identifies common flora of skin with elevation of protists (such as Leishmania), bacteria (Staphylococcus, Cutibacterium acnes), and viruses [Human alphaherpesvirus (HSV), Human papillomavirus (HPV)] that may be involved in physiological differences. We observed samples with the Heilongjiang tick virus, human T-cell leukemia virus type I, and equine infectious anemia virus that likely play pathological roles in physiology. Integrating the various biomarkers identified five ideal datasets for skin pathologies that elucidated a novel correlation between the normal skin flora bacterium Bacillus megaterium with major histocompatibility complex (MHC) regulation and the immune repertoire clonal expansion, particularly in patients with hidradenitis suppurativa. Finally, we show that in multiple independent experiments, biological sex is associated with multiple sex chromosome gene differences, highlighting the importance of future work in studying sex differences in skin. Data integrations and multidimensional data mapping are critical for physiological omics advancements, and this work highlights the exciting ability to apply these tools to skin physiology.NEW & NOTEWORTHY Complex bioinformatics mapping to skin RNA sequencing datasets can simultaneously map biological sex, skin-specific genes, bacteria, viruses, protists, and the acquired immune response. The integration of these datasets elucidated bacterial signatures from common skin flora while identifying novel insights on Bacillus megaterium in the acquired immune response and novel viral signatures for Heilongjiang tick virus and equine infectious anemia virus.

Strange relatives: the enigmatic arbo-jingmenviruses and orthoflaviviruses

Arthropod - and vertebrate-associated jingmenviruses (arbo-JMV) have segmented positive-strand RNA genomes and are provisional members of the genus Orthoflavivirus (family Flaviviridae). Current investigations have described arbo-JMV infection in vertebrate hosts in proximity to humans. This raises concerns about the virus host range and public health implications. This review explores the genomic and evolutionary relationship between arbo-JMV and orthoflaviviruses and evaluates the potential of arbo-JMV to pose a public health threat.

Virome specific to tick genus with distinct ecogeographical distribution

BACKGROUND

The emergence of tick-borne pathogens poses a serious threat to both human and animal health. There remains controversy about virome diversity in relation to tick genus and ecogeographical factors.

RESULTS

We conducted the meta‑transcriptomic sequencing of 155 pools of ticks encompassing 7 species of 3 genera collected from diverse geographical fauna of Ningxia Province, China. Two species of Dermacentor genus were distributed in the predominantly grassland areas of the central and eastern regions, with the lowest viral diversity. Two species of Hyalomma ticks were found in the predominantly desert areas of the northern regions, with intermediate viral diversity. Three species of Haemaphysalis ticks were concentrated in the predominantly forested areas of the southern regions, exhibiting the highest viral diversity. We assembled 348 viral genomes of 63 species in 14 orders, including 26 novel viruses. The identified viruses were clearly specific to tick genus: 22 virus species were exclusive to Dermacentor, 12 to Hyalomma, and 27 to Haemaphysalis.

CONCLUSIONS

The associations between tick genera and geographical distribution, viral richness, and composition provide new insights into tick-virus interactions, offering clues to identify high-risk regions for different tick-borne viruses. Video Abstract.

Exploring the microbiomes of camel ticks to infer vector competence: insights from tissue-level symbiont-pathogen relationships

Ticks are blood-feeding ectoparasites that harbor diverse pathogens and endosymbionts. Their microbial communities vary based on tick species, stage, sex, geographical location, surrounding environment, and tissue type. Understanding tick microbiota at the tissue level is crucial for unraveling how microbiomes are distributed in tick tissues and influence pathogen transmission. We used V1-V2 16 S rRNA gene sequencing to analyze tissue-specific bacterial compositions (hemolymph, saliva, salivary glands, and midgut) of Amblyomma gemma, Rhipicephalus pulchellus, Hyalomma dromedarii, and Hyalomma rufipes ticks collected from camels in Marsabit County, northern Kenya. The V1-V2 region of the 16 S rRNA gene effectively differentiated 43 Rickettsia africae and 16 Rickettsia aeschlimannii tick samples from other rickettsial species, as well as Coxiella endosymbionts from Coxiella burnetii. In contrast, the V3-V4 region sequences of these species could not be clearly distinguished. Coxiella endosymbionts were most common in Am. gemma and Rh. pulchellus, while Francisella endosymbionts predominated in Hyalomma ticks; both were primarily localized in the salivary glands. High abundances of Coxiella endosymbionts, as well as Pseudomonas, were associated with the absence or low abundance of Rickettsia pathogens in both Am. gemma and Rh. pulchellus, suggesting competitive interactions between these microbes. Additionally, Proteus mirabilis, an opportunistic pathogen of the urinary tract in humans, was found predominantly in Hyalomma ticks, except for the salivary glands, which were most abundant with Francisella endosymbionts. Furthermore, we detected the Acinetobacter, Pseudomonas, and Corynebacterium genera in all the tick tissues, supporting the hypothesis that these bacteria might circulate between camel blood and ticks. Saliva and hemolymph generally harbored more extracellular bacteria than the salivary glands and midgut. This study provides a new approach to unravel tick-endosymbiont-pathogen interactions by examining the tissue localization of tick-borne pathogens and symbionts in Am. gemma, Rh. pulchellus, Hy. dromedarii, and Hy. rufipes from camels in northern Kenya. Our findings establish a baseline for developing an understanding of the functional capacities of symbionts and for designing symbiont-based control strategies.

Microbial community variations in adult Hyalomma dromedarii ticks from single locations in Saudi Arabia and Tunisia

Introduction

The camel-infesting tick, Hyalomma dromedarii, is a prominent ectoparasite in the Middle East and North Africa (MENA) region, critically impacting camel health and acting as a vector for tick-borne pathogens. Despite prior studies on its microbiota, the effects of geographic origin and sex on microbial community structure and functional stability remain poorly understood.

Methods

To address this, we characterized the bacterial microbiota of H. dromedarii ticks collected from camels in Tunisia (TUN) and Saudi Arabia (SA) using 16S rRNA gene sequencing, microbial network analysis, and metabolic pathway prediction.

Results

Our findings indicate a dominant presence of Francisella endosymbionts in Tunisian ticks, suggesting adaptive roles of H. dromedarii ticks in arid ecosystems. Keystone taxa, particularly Staphylococcus and Corynebacterium, were identified as central to microbial network structure and resilience. Moreover, network robustness analyses demonstrated enhanced ecological stability in the Tunisian tick microbiota under perturbation, indicative of higher resilience to environmental fluctuations compared to Saudi Arabian ticks. Additionally, functional pathway predictions further revealed geographically distinct metabolic profiles between both groups (Tunisia vs. Saudi Arabia and males vs. females), underscoring environmental and biological influences on H. dromedarii microbiota assembly.

Discussion

These results highlight region-specific and sex-specific microbial adaptations in H. dromedarii, with potential implications for pathogen transmission dynamics and vector resilience. Understanding these microbial interactions may contribute to improved strategies for tick control and tick-borne disease prevention.

Tertiary Structures of Haseki Tick Virus Nonstructural Proteins Are Similar to Those of Orthoflaviviruses

Currently, a large number of novel tick-borne viruses potentially pathogenic to humans are discovered. Studying many of them by classical methods of virology is difficult due to the absence of live viral particles or a sufficient amount of their genetic material. In this case, the use of modern methods of bioinformatics and synthetic and structural biology can help. Haseki tick virus (HSTV) is a recently discovered tick-borne unclassified ssRNA(+) virus. HSTV-positive patients experienced fever and an elevated temperature. However, at the moment, there is no information on the tertiary structure and functions of its proteins. In this work, we used AlphaFold 3 and other bioinformatic tools for the annotation of HSTV nonstructural proteins, based on the principle that the tertiary structure of a protein is inextricably linked with its molecular function. We were the first to obtain models of tertiary structures and describe the putative functions of HSTV nonstructural proteins (NS3 helicase, NS3 protease, NS5 RNA-dependent RNA-polymerase, and NS5 methyltransferase), which play a key role in viral genome replication. Our results may help in further taxonomic identification of HSTV and the development of direct-acting antiviral drugs, POC tests, and vaccines.

Severe fever with thrombocytopenia syndrome virus infection shapes gut microbiome of the tick vector Haemaphysalis longicornis

BACKGROUND

Ticks serve as vectors for a diverse array of pathogens, including viruses responsible for both human and livestock diseases. Symbiotic bacteria hold significant potential for controlling tick-borne disease. However, the alteration of tick gut bacterial community in response to pathogen infection has not been analyzed for any tick-borne viruses. Here, the impact of severe fever with thrombocytopenia syndrome virus (SFTSV) infection on bacterial diversity in the gut of Haemaphysalis longicornis is investigated.

METHODS

Unfed tick females were artificially infected with SFTSV. The gut samples were collected and the genomic DNA was extracted. We then investigated alterations in gut bacterial composition in response to SFTSV infection through 16S rRNA gene sequencing.

RESULTS

The study found that a reduction in the number of operational taxonomic units (OTUs) in the tick gut following SFTSV infection. However, there were no significant changes in alpha diversity indices upon infection. Four genera, including Corynebacterium, Arthrobacter, Sphingomonas, and Escherichia, were identified as biomarkers for the tick gut without SFTSV infection. Notably, the predicted correlation network indicated that the biomarkers Sphingomonas and Escherichia exhibited positive correlations within the same subcommunity, which was altered upon viral infection.

CONCLUSIONS

These findings revealed that the change in tick gut bacterial composition upon SFTSV infection and could facilitate the discovery new target for tick-borne viral disease control.

Prokaryotic and eukaryotic skin microbiota modifications triggered by Leishmania infection in localized Cutaneous Leishmaniasis

Cutaneous Leishmaniasis (CL) is a tropical disease characterized by cutaneous ulcers, sometimes with satellite lesions and nodular lymphangitis. Leishmania parasites, transmitted by sandfly vectors, cause this widespread public health challenge affecting millions worldwide. CL's complexity stems from diverse Leishmania species and intricate host interactions. Therefore, this study aims to shed light on the spatial-temporal distribution of Leishmania species and exploring the influence of skin microbiota on disease progression. We analyzed 40 samples from CL patients at three military bases across Colombia. Using Oxford Nanopore's Heat Shock Protein 70 sequencing, we identified Leishmania species and profiled microbiota in CL lesions and corresponding healthy limbs. Illumina sequencing of 16S-rRNA and 18S-rRNA genes helped analyze prokaryotic and eukaryotic communities. Our research uncovered a spatial-temporal overlap between regions of high CL incidence and our sampling locations, indicating the coexistence of various Leishmania species. L. naiffi emerged as a noteworthy discovery. In addition, our study delved into the changes in skin microbiota associated with CL lesions sampled by scraping compared with healthy skin sampled by brushing of upper and lower limbs. We observed alterations in microbial diversity, both in prokaryotic and eukaryotic communities, within the lesioned areas, signifying the potential role of microbiota in CL pathogenesis. The significant increase in specific bacterial families, such as Staphylococcaceae and Streptococcaceae, within CL lesions indicates their contribution to local inflammation. In essence, our study contributes to the ongoing research into CL, highlighting the need for a multifaceted approach to decipher the intricate interactions between Leishmaniasis and the skin microbiota.

Jingmen tick virus: an emerging arbovirus with a global threat

Jingmen tick virus (JMTV), belonging to the Flaviviridae family, is a novel segmented RNA virus identified in 2014 in the Jingmen region of Hubei Province, China. Up to now, JMTV has been detected in a variety of countries or regions in Asia, Europe, Africa, and the Americas, involving a wide range of arthropods and mammals, and even humans. The JMTV genome is composed of four linear RNA segments, two of which are derived from flaviviruses, while the other two segments are unique to JMTV and has no matching virus. Currently, JMTV has been shown to have a pathogenic effect on humans. Humans who had been infected would develop viremia and variable degrees of clinical symptoms. However, the pathogenic mechanism of JMTV has not been elucidated yet. Therefore, it is crucial to strengthen the epidemiological surveillance and laboratory studies of JMTV.