Metagenomic Investigation of Ticks From Kenyan Wildlife Reveals Diverse Microbial Pathogens and New Country Pathogen Records

Detection of multiple novel viruses in argasid and ixodid ticks in Mexico

We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.

First detection and molecular characterization of Jingmen tick virus with a high occurrence in Rhipicephalus (Boophilus) microplus collected from livestock in Cameroon (2024)

BACKGROUND

Jingmen tick virus (JMTV) is a novel tick-borne virus detected for the first time in Rhipicephalus (Boophilus) microplus in China. To date, there is no information regarding the circulation of JMTV in ticks collected from livestock in Cameroon. As part of the surveillance for arboviral circulation, this study aimed to assess the presence of JMTV in ticks collected from livestock (cattle and sheep) in an area of the Akonolinga health district, Center Region, Cameroon.

METHODS

A cross sectional study was carried out during the dry season between 5 and 14 March 2024. Ticks were collected from cattle and sheep in six sampling sites in an area approximately 30 km long and 18 km wide along the Nyong River, in central Cameroon. Ticks were identified morphologically and molecularly. Total RNA/DNA was extracted from tick pools and screened for JMTV RNA using a segment 2 RT-qPCR system. Positive JMTV pools were sequenced for partial JMTV-Segment 1 and full genome analyses.

RESULTS

A total of 622 ticks, organized into 251 pools were collected from 155 cattle and nine sheep. They consisted of five species covering three genera: R. (B.) microplus (472; 75.9%), Amblyomma variegatum (118; 19.0%), Hyalomma truncatum (13; 2.1%), Hyalomma rufipes (2; 0.3%), and other Rhipicephalus spp. (17; 2.7%). The quantitative reverse transcription polymerase chain reaction (qRT-PCR) screening of 251 tick pools yielded 61 JMTV-positive pools, of which 58 corresponded to R. (B.) microplus. Multiple sequence analysis revealed that JMTV from the Akonolinga area shared > 95% identity with strains from Guinea, and that these strains clustered phylogenetically together.

CONCLUSIONS

We provide molecular evidence of the presence of JMTV in R. (B.) microplus and A. variegatum collected from cattle and sheep from an area not yet recognized as endemic for this virus, confirming its wide geographical distribution.

Ticks as vectors of Trypanosomatidae with medical or veterinary interest: Insights and implications from a comprehensive systematic review and meta-analysis

Since the 20th century, numerous studies have detected or isolated parasites from the Trypanosomatidae family in various tick species. However, the status of ticks as vectors for medically or veterinary significant Trypanosoma and Leishmania remains unclear. We conducted a systematic review and meta-analysis to provide new insights into the potential vector status of these pathogens, which have significant medical and veterinary implications. We searched three databases (PubMed, Google Scholar, and Web of Science) from 1912 to June 30, 2023, resulting in 94 papers included in the qualitative analysis and 86 papers in the quantitative analysis. All identified field studies were conducted in endemic areas and investigated the presence of Trypanosoma and Leishmania parasites, DNA, or antigens in ticks. We recorded a pooled prevalence of Trypanosomatidae detection in ticks at 15.48 % [7.99-24.61 %], with significant variations depending on the year, detection method, and geographical area. Most of the infected tick species belonged to the genera Amblyomma, Hyalomma, Ixodes, and Rhipicephalus. Experimental laboratory work on transmission routes demonstrated potential vector competence in both the Argasidae and Ixodidae tick families. Although our systematic review and meta-analysis provide compelling evidence of the natural infection of ticks by Trypanosomatidae parasites, along with some evidence of non-traditional transmission routes, they do not offer conclusive evidence regarding the role of ticks as biological or mechanical vectors for Trypanosomatidae species of veterinary and medical interest. This highlights the urgent need for additional investigations to address this point.

Identification and phylogenetic analysis of Jingmen tick virus in ticks and sheep from Henan Province, China

Jingmen tick virus (JMTV) is a novel segmented Flavivirus that was first identified from Rhipicephalus microplus in the Jingmen region of Hubei Province, China, in 2010. Subsequently, it was detected in a variety of countries and regions around the world. Meanwhile, JMTV has been proved to be pathogenic to humans and animals and could cause viremia in animals. However, the pathogenic mechanism of JMTV and what role animals play in the viral cycle have not yet been elucidated. In this study, 38 sheep sera were collected from Xinyang region of Henan Province, China and 204 ticks attached to the sheep were collected. The qRT-PCR and nested PCR were used to confirm the presence of JMTV in serum and tick samples. The results showed that the positive rate of JMTV in serum and ticks was 13.16% (5/38) and 7.84% (16/204), respectively. Phylogenetic analysis showed that JMTV sequences in sheep and ticks shared a high degree of identity with each other, and JMTV was relatively conserved in evolution. These results enriched the evidence for the prevalence of JMTV in animals and further deepened our understanding of the mechanisms and routes of JMTV transmission.

Prevalence and genotyping of Toxoplasma gondii in questing Ixodes ricinus ticks from forest areas of Northern Poland

Toxoplasma gondii occurs in a wide range of intermediate hosts, whose blood may be a meal for different tick species. A few studies have examined the role of ticks in the life cycle of T. gondii. This one includes the largest number and all stages of Ixodes ricinus collected from the widest area, covering seven recreational localities within a forest biotope in Northern Poland. This study aimed to determine the prevalence of T. gondii DNA in 2144 collected questing ticks to establish whether they may be involved in T. gondii life cycle. The additional goal was to genotype the detected T. gondii, as knowledge about its genotypes occurring in European ticks is insufficient. A further purpose was to detect coinfection with T. gondii and Borreliaceae in the collected ticks, as all of them have previously been tested for the presence of bacteria DNA. Nested PCR and sequencing of the obtained B1 gene fragment were conducted. T. gondii DNA was detected in 0.9% of all ticks (1.1% of nymphs and 0.7% of larvae). The presence of T. gondii in unfed larvae and nymphs may indicate the possibility of its vertical transmission. The prevalence of T. gondii DNA in ticks collected from individual sites was focal (0-4.3%) and seems to depend on local climatic conditions. Among all examined ticks, 0.3% were coinfected with T. gondii and Borreliella spp., vs. 0.6% of specimens with a single T. gondii infection. The obtained B1 sequences showed the greatest similarity (99.71-100%) to the sequence representing type III.

Deciphering the microbial communities in ticks of Inner Mongolia: ecological determinants and pathogen profiles

BACKGROUND

Ticks are vectors of numerous pathogens, with their bacterial composition, abundance, diversity, and interaction influencing both their growth and disease transmission efficiency. Despite the abundance of ticks in Inner Mongolia, China, comprehensive data on their microbial communities are lacking. This study aims to analyze the microbial communities within ticks from Inner Mongolia to inform innovative control strategies for interrupting pathogen transmission.

METHODS

Tick samples were collected from animals and vegetation in multiple locations across Inner Mongolia and stored at - 80 °C. Ticks were identified using morphological keys and molecular biology methods. Full-length 16S rRNA gene sequencing was performed on collected samples. Bacterial community composition and diversity were mainly analyzed using bioinformatic tools such as QIIME, phyloseq, and DESeq2. Alpha diversity was assessed using Chao1, ACE, and Shannon indices, while beta diversity was evaluated using Bray-Curtis dissimilarity matrices. LEfSe analysis was applied to identify taxa associated with ecological and biological variables.

RESULTS

A total of 5,048,137 high-quality read counts were obtained, forming an average of 789.3 OTUs per sample. Proteobacteria, Firmicutes, and Bacteroidetes were the most dominant phyla. Bacterial community composition varied significantly with geography, with Dermacentor nuttalli showing a higher abundance of Rickettsia in Xilingol League, while other regions had different dominant genera. The microbial community also differed based on the feeding status of ticks. Additionally, the microbiota of engorged ticks showed organ specificity. Pathogen detection efforts revealed the presence of nine pathogens across all three tick species. D. nuttalli was found to carry a significantly higher burden of pathogenic bacteria, making it the most potentially threatening tick species in Inner Mongolia.

CONCLUSIONS

The study highlights significant variations in tick microbiomes influenced by geographic location, feeding status, and tick species. It underscores the importance of enhancing tick and tick-borne disease surveillance in Inner Mongolia for early detection and control of emerging pathogens.

Detection and prevalence of a novel Bandavirus related to Guertu virus in Amblyomma gemma ticks and human populations in Isiolo County, Kenya

INTRODUCTION

Emerging tick-borne viruses of medical and veterinary importance are increasingly being reported globally. This resurgence emphasizes the need for sustained surveillance to provide insights into tick-borne viral diversity and associated potential public health risks. We report on a virus tentatively designated Kinna virus (KIV) in the family Phenuiviridae and genus Bandavirus. The virus was isolated from a pool of Amblyomma gemma ticks from Kinna in Isiolo County, Kenya. High throughput sequencing of the virus isolate revealed close relatedness to the Guertu virus. The virus genome is consistent with the described genomes of other members of the genus Bandavirus, with nucleotides lengths of 6403, 3332 and 1752 in the Large (L), Medium (M) and Small (S) segments respectively. Phylogenetic analysis showed that the virus clustered with Guertu virus although it formed a distinct and well supported branch. The RdRp amino acid sequence had a 93.3% identity to that of Guertu virus, an indication that the virus is possibly novel. Neutralizing antibodies were detected in 125 (38.6%, 95% CI 33.3-44.1%) of the human sera from the communities in this region. In vivo experiments showed that the virus was lethal to mice with death occurring 6-9 days post-infection. The virus infected mammalian cells (Vero cells) but had reduced infectivity in the mosquito cell line (C636) tested.

CONCLUSION

Isolation of this novel virus with the potential to cause disease in human and animal populations necessitates the need to evaluate its public health significance and contribution to disease burden in the affected regions. This also points to the need for continuous monitoring of vector and human populations in high-risk ecosystems to update pathogen diversity.

Coxiella burnetii serostatus in dromedary camels (Camelus dromedarius) is associated with the presence of C. burnetii DNA in attached ticks in Laikipia County, Kenya

AIMS

Q fever is a globally distributed, neglected zoonotic disease of conservation and public health importance, caused by the bacterium Coxiella burnetii. Coxiella burnetii normally causes subclinical infections in livestock, but may also cause reproductive pathology and spontaneous abortions in artiodactyl species. One such artiodactyl, the dromedary camel (Camelus dromedarius), is an increasingly important livestock species in semi-arid landscapes. Ticks are naturally infected with C. burnetii worldwide and are frequently found on camels in Kenya. In this study, we assessed the relationship between dromedary camels' C. burnetii serostatus and whether the camels were carrying C. burnetii PCR-positive ticks in Kenya. We hypothesized that there would be a positive association between camel seropositivity and carrying C. burnetii PCR-positive ticks.

METHODS AND RESULTS

Blood was collected from camels (N = 233) from three herds, and serum was analysed using commercial ELISA antibody test kits. Ticks were collected (N = 4354), divided into pools of the same species from the same camel (N = 397) and tested for C. burnetii and Coxiella-like endosymbionts. Descriptive statistics were used to summarize seroprevalence by camel demographic and clinical variables. Univariate logistic regression analyses were used to assess relationships between serostatus (outcome) and tick PCR status, camel demographic variables, and camel clinical variables (predictors). Camel C. burnetii seroprevalence was 52%. Across tick pools, the prevalence of C. burnetii was 15% and Coxiella-like endosymbionts was 27%. Camel seropositivity was significantly associated with the presence of a C. burnetii PCR-positive tick pool (OR: 2.58; 95% CI: 1.4-5.1; p = 0.0045), increasing age class, and increasing total solids.

CONCLUSIONS

The role of ticks and camels in the epidemiology of Q fever warrants further research to better understand this zoonotic disease that has potential to cause illness and reproductive losses in humans, livestock, and wildlife.

Hard ticks (Ixodida: Ixodidae) in the Colombian Caribbean harbor the Jingmen tick virus: an emerging arbovirus of public health concern

BACKGROUND

Ticks are obligate hematophagous ectoparasites involved in transmitting viruses of public health importance. The objective of this work was to identify the Jingmen tick virus in hard ticks from the Colombian Caribbean, an arbovirus of importance for public health.

METHODS

Ticks were collected in rural areas of Córdoba and Cesar, Colombia. Taxonomic identification of ticks was carried out, and pools of 13 individuals were formed. RNA extraction was performed. Library preparation was performed with the MGIEasy kit, and next-generation sequencing (NGS) with MGI equipment. Bioinformatic analyses and taxonomic assignments were performed using the Galaxy platform, and phylogenetic analyses were done using IQ-TREE2.

RESULTS

A total of 766 ticks were collected, of which 87.33% (669/766) were Rhipicephalus microplus, 5.4% (42/766) Dermacentor nitens, 4.2% (32/766) Rhipicephalus linnaei, and 3.0% (23/766) Amblyomma dissimile. Complete and partial segments 1, 2, 3, and 4 of Jingmen tick virus (JMTV) were detected in the metatranscriptome of the species R. microplus, D. nitens, and A. dissimile. The JMTVs detected are phylogenetically related to JMTVs detected in Aedes albopictus in France, JMTVs detected in R. microplus in Trinidad and Tobago, JMTVs in R. microplus and A. variegatum in the French Antilles, and JMTVs detected in R. microplus in Colombia. Interestingly, our sequences clustered closely with JMTV detected in humans from Kosovo.

CONCLUSIONS

JMTV was detected in R. microplus, D. nitens, and A. dissimile. JMTV could pose a risk to humans. Therefore, it is vital to establish epidemiological surveillance measures to better understand the possible role of JMTV in tropical diseases.

Comparison of test performance of a conventional PCR and two field-friendly tests to detect Coxiella burnetii DNA in ticks using Bayesian latent class analysis

Introduction

Coxiella burnetii (C. burnetii)-infected livestock and wildlife have been epidemiologically linked to human Q fever outbreaks. Despite this growing zoonotic threat, knowledge of coxiellosis in wild animals remains limited, and studies to understand their epidemiologic role are needed. In C. burnetii-endemic areas, ticks have been reported to harbor and spread C. burnetii and may serve as indicators of risk of infection in wild animal habitats. Therefore, the aim of this study was to compare molecular techniques for detecting C. burnetii DNA in ticks.

Methods

In total, 169 ticks from wild animals and cattle in wildlife conservancies in northern Kenya were screened for C. burnetii DNA using a conventional PCR (cPCR) and two field-friendly techniques: Biomeme's C. burnetii qPCR Go-strips (Biomeme) and a new C. burnetii PCR high-resolution melt (PCR-HRM) analysis assay. Results were evaluated, in the absence of a gold standard test, using Bayesian latent class analysis (BLCA) to characterize the proportion of C. burnetii positive ticks and estimate sensitivity (Se) and specificity (Sp) of the three tests.

Results

The final BLCA model included main effects and estimated that PCR-HRM had the highest Se (86%; 95% credible interval: 56-99%), followed by the Biomeme (Se = 57%; 95% credible interval: 34-90%), with the estimated Se of the cPCR being the lowest (24%, 95% credible interval: 10-47%). Specificity estimates for all three assays ranged from 94 to 98%. Based on the model, an estimated 16% of ticks had C. burnetii DNA present.

Discussion

These results reflect the endemicity of C. burnetii in northern Kenya and show the promise of the PCR-HRM assay for C. burnetii surveillance in ticks. Further studies using ticks and wild animal samples will enhance understanding of the epidemiological role of ticks in Q fever.

Fecal thyroid hormone metabolites in wild ungulates: a mini-review

This review aims to analyse the fluctuations of fecal thyroid hormone metabolites (FTMs) related to environmental and individual variables in different species of wild ungulates and provide a collection of assay methods. The great advantage of fecal sampling is being completely non-invasive. A systemic search was conducted from 2019 to 2024, using data sources PubMed, Scopus, Web of Science, and the World Wide Web, and ten studies were found on this topic. Three studies used the radioimmunoassay method for FTMs analysis, while the others used a less expensive enzyme-linked immunosorbent assay. Most of these papers validated the method for the species-specific matrix. Related to the studied variables, some authors analysed FTM fluctuations only concerning individual variables, and others in response to both. Temperature and fecal cortisol metabolites (FCMs) were the most studied environmental and individual variables, respectively. Since FTMs are an integrative measure of plasma thyroid hormones, the information obtained from a non-invasive-assay method regarding wild ungulate physiology is becoming of great interest to the scientific community.

Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics

Ticks are arachnid ectoparasites that rank second only to mosquitoes in the transmission of human diseases including bacteria responsible for anaplasmosis, ehrlichiosis, spotted fevers, and Lyme disease among other febrile illnesses. Due to the paucity of data on bacteria transmitted by ticks in Kenya, this study undertook a bacterial metagenomic-based characterization of ticks collected from Isiolo, a semi-arid pastoralist County in Eastern Kenya, and Kwale, a coastal County with a monsoon climate in the southern Kenyan border with Tanzania. A total of 2,918 ticks belonging to 3 genera and 10 species were pooled and screened in this study. Tick identification was confirmed through the sequencing of the Cytochrome C Oxidase Subunit 1 (COI) gene. Bacterial 16S rRNA gene PCR amplicons obtained from the above samples were sequenced using the MinION (Oxford Nanopore Technologies) platform. The resulting reads were demultiplexed in Porechop, followed by trimming and filtering in Trimmomatic before clustering using Qiime2-VSearch. A SILVA database pretrained naïve Bayes classifier was used to classify the Operational Taxonomic Units (OTUs) taxonomically. The bacteria of clinical interest detected in pooled tick assays were as follows: Rickettsia spp. 59.43% of pools, Coxiella burnetii 37.88%, Proteus mirabilis 5.08%, Cutibacterium acnes 6.08%, and Corynebacterium ulcerans 2.43%. These bacteria are responsible for spotted fevers, query fever (Q-fever), urinary tract infections, skin and soft tissue infections, eye infections, and diphtheria-like infections in humans, respectively. P. mirabilis, C. acnes, and C. ulcerans were detected only in Isiolo. Additionally, COI sequences allowed for the identification of Rickettsia and Coxiella species to strain levels in some of the pools. Diversity analysis revealed that the tick genera had high levels of Alpha diversity but the differences between the microbiomes of the three tick genera studied were not significant. The detection of C. acnes, commonly associated with human skin flora suggests that the ticks may have contact with humans potentially exposing them to bacterial infections. The findings in this study highlight the need for further investigation into the viability of these bacteria and the competency of ticks to transmit them. Clinicians in these high-risk areas also need to be appraised for them to include Rickettsial diseases and Q-fever as part of their differential diagnosis.

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.

Phlebovirus diversity in ticks from livestock in arid ecologies in Kenya

Phleboviruses are emerging pathogens of public health importance. However, their association with ticks is poorly described, particularly in Africa. Here, adult ticks infesting cattle, goats and sheep were collected in two dryland pastoralist ecosystems of Kenya (Baringo and Kajiado counties) and were screened for infection with phleboviruses. Ticks mainly belonged to the species Rhipicephalus appendiculatus, Hyalomma impeltatum, and Hyalomma rufipes. A fragment of the RNA-dependent RNA polymerase (RdRp) gene was identified in thirty of 671 tick pools, of which twenty-nine were from livestock sampled in Baringo county. Phylogenetic analyses revealed that twenty-five sequences were falling in three clades within the group of tick-associated phleboviruses. The sequences of the three clades showed nucleotide distances 8%, 19% and 22%, respectively, to previously known viruses suggesting that these sequence fragments may belong to three distinct viruses. Viruses of the group of tick-associated phleboviruses have been found in several countries and continents but so far have not been associated with disease in humans or animals. In addition, five sequences were found to group with the sandfly-associated phleboviruses Bogoria virus, Perkerra virus and Ntepes virus recently detected in the same region. Further studies are needed to investigate the transmission and maintenance cycles of these viruses, as well as to assess their potential to infect vertebrates.

Canine Distemper Virus in Autochtonous and Imported Dogs, Southern Italy (2014–2021)

Simple Summary

In the period 2014–2021, the circulation of CDV in dogs of Southern Italy was investigated. In this time span a reduction in the circulation of CDV was observed, with a higher frequency of detection of the pathogen in imported dogs (18.4%) compared to stray (7.4%) and household (3.9%) animals. These results underline the effectiveness of the prophylaxis strategy on autochthonous dogs as well as the importance of continuous surveillance of CDV, especially in imported dogs.

Abstract

This study aims to investigate the presence of canine distemper virus (CDV) infection in 949 autochthonous or illegally imported dogs from Southern Italy, over a period of eight years (2014–2021). CDV RNA was detected in 6.8% (65/949) of the animals tested, with no detection of CDV in dogs sampled in 2020–2021. The frequency of CDV detection was higher in imported dogs (19/103, 18.3%) with respect to stray (27/365, 7.4%) and household dogs (19/481, 3.9%). On sequence and phylogenetic analyses of selected strains, the analyzed viruses belonged to the Arctic clade, which has already been reported in Italy and in Europe. The results of our study may suggest a reduction of CDV circulation in Southern Italy, while at the same time highlighting the need for strict controls on dog importation, in order to prevent the introduction of viruses from endemic countries.