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

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.

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.