scholarly journals iSeq100 for metagenomic pathogen screening in ticks

2021 ◽  
Author(s):  
Ju Yeong Kim ◽  
Myung-hee Yi ◽  
Alghurabi Areej Sabri Mahdi ◽  
Tai-Soon Yong
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Haemaphysalis Longicornis ◽  
Conventional Pcr ◽  
Control Programs ◽  
Blood Sucking ◽  
Pathogen Screening ◽  
Vector Borne ◽  
Severe Fever

Abstract Background: Ticks are blood sucking ectoparasites that play a pivotal role in the transmission of various pathogens to humans and animals. In Korea, Haemaphysalis longicornis is the predominant tick species and is recognized as the vector of pathogens causing various diseases such as babesiosis, borreliosis, rickettsiosis, and severe fever with thrombocytopenia syndrome. Methods: In this study, we developed a method to screen bacterial pathogens in H. longicornis using targeted high-throughput sequencing of the 16S rRNA V4 region using the state-of-the-art sequencing instrument, iSeq 100, and compared the findings with those of conventional PCR with specific primers. Results: Rickettsia spp. were detected in 18 out of 39 samples using iSeq 100 but in only 14 samples using conventional PCR. In the phylogenetic analysis using gltA and ompA sequences of the detected Rickettsia, the highest sequence similarity was found with Candidatus Rickettsia jingxinensis isolate Xian-Hl-79, Ca. R. jingxinensis isolate F18, and Ca. R. longicornii isolate ROK-HL727. In the microbiome study, Coxiella AB001519, a known tick symbiont, was detected in all 39 tick samples. The Actinomycetospora chiangmaiensis group was more abundant in Rickettsia spp.-positive samples than in Rickettsia spp.-negative samples. Conclusions: Thus, we demonstrated that iSeq100 can rapidly and economically screen potential pathogens in ticks and can be applied to large-scale pathogen screening in arthropods for vector-borne disease control programs.

scholarly journals iSeq 100 for metagenomic pathogen screening in ticks

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ju Yeong Kim ◽  
Myung-hee Yi ◽  
Alghurabi Areej Sabri Mahdi ◽  
Tai-Soon Yong
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Haemaphysalis Longicornis ◽  
Differential Abundance ◽  
Control Programs ◽  
Blood Sucking ◽  
Pathogen Screening ◽  
Vector Borne ◽  
Differential Abundance Analysis

Abstract Background Ticks are blood-sucking ectoparasites that play a pivotal role in the transmission of various pathogens to humans and animals. In Korea, Haemaphysalis longicornis is the predominant tick species and is recognized as the vector of pathogens causing various diseases such as babesiosis, borreliosis, rickettsiosis, and severe fever with thrombocytopenia syndrome. Methods In this study, the targeted high-throughput sequencing of the 16S rRNA V4 region was performed using the state-of-the-art sequencing instrument, iSeq 100, to screen bacterial pathogens in H. longicornis, and the findings were compared with those using conventional PCR with specific primers. Microbiome analyses were performed with EzBioCloud, a commercially available ChunLab bioinformatics cloud platform. ANOVA-Like Differential Expression tool (ALDEx2) was used for differential abundance analysis. Results Rickettsia spp. were detected in 16 out of 37 samples using iSeq 100, and this was confirmed using a PCR assay. In the phylogenetic analysis using gltA and ompA sequences of the detected Rickettsia, the highest sequence similarity was found with ‘Candidatus Rickettsia jingxinensis’ isolate Xian-Hl-79, ‘Ca. R. jingxinensis’ isolate F18, and ‘Ca. R. longicornii‘ isolate ROK-HL727. In the microbiome study, Coxiella AB001519, a known tick symbiont, was detected in all 37 tick samples. Actinomycetospora chiangmaiensis was more abundant in Rickettsia-positive samples than in Rickettsia-negative samples. Conclusions In this study, iSeq 100 was used to investigate the microbiome of H. longicornis, and the potentially pathogenic Rickettsia strain was detected in 16 out of 37 ticks. We believe that this approach will aid in large-scale pathogen screening of arthropods to be used in vector-borne disease control programs. Graphical Abstract

scholarly journals Nationwide Temporal and Geographical Distribution of Tick Populations and Phylogenetic Analysis of Severe Fever with Thrombocytopenia Syndrome Virus in Ticks in Korea, 2020

2021 ◽  
Vol 9 (8) ◽  
pp. 1630
Author(s):  
Min-Goo Seo ◽  
Byung-Eon Noh ◽  
Hak Seon Lee ◽  
Tae-Kyu Kim ◽  
Bong-Goo Song ◽  
...  
Keyword(s):  
Tick Species ◽  
Temporal Distribution ◽  
Epidemiological Studies ◽  
Haemaphysalis Longicornis ◽  
Geographical Regions ◽  
Control And Prevention ◽  
Amblyomma Testudinarium ◽  
High Degree ◽  
Severe Fever ◽  
Minimum Infection Rate

Since 2010, the Korea Disease Control and Prevention Agency has established centers at 16 locations to monitor disease vectors and pathogens. Here, we examined tick populations to understand the geographical and temporal distribution of severe fever with thrombocytopenia syndrome virus (SFTSV) vectors in 2020. From April to November, 63,376 ticks were collected from traps to monitor tick populations, with a trap index of 41.3. Tick incidence varied from April to October, with population peaks observed for nymphs in May, adults in July, and larvae in September. The predominant tick species were Haemaphysalis longicornis, Haemaphysalis spp., H. flava, Ixodes spp., Amblyomma testudinarium, and Ixodes nipponensis. Approximately 50% of the collected ticks were pooled into 2973 groups to detect the rate of SFTSV infection in ticks. The minimum infection rate (MIR) of SFTSV was 0.2%, and Andong had the highest MIR for SFTSV (4.0%). The B3 genotype was the most prevalent (52.2%) followed by B2 (28.6%), B5 (15.9%), B4 (1.6%), and B6 (1.6%). We identified widely distributed tick species and a high degree of diversity in SFTSV strains in ticks from different geographical regions. The results may provide a basis for future epidemiological studies and risk assessments for tick-borne diseases.

Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 141-155 ◽  
Author(s):  
H H Yan ◽  
J Mudge ◽  
D-J Kim ◽  
R C Shoemaker ◽  
D R Cook ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Glycine Max ◽  
Medicago Truncatula ◽  
Physical Mapping ◽  
Large Scale ◽  
Sequence Similarity ◽  
Artificial Chromosome ◽  
Bac Contig ◽  
Cross Hybridization ◽  
Bac Contigs

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

scholarly journals Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 234 ◽  
Author(s):  
Eric A. Griffin ◽  
Joshua G. Harrison ◽  
Melissa K. McCormick ◽  
Karin T. Burghardt ◽  
John D. Parker
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tree Diversity ◽  
Trophic Levels ◽  
Community Diversity ◽  
And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

scholarly journals Molecular detection of vector borne pathogens in anemic and thrombocytopenic dogs in southern Brazil

2018 ◽  
Vol 27 (4) ◽  
pp. 505-513 ◽  
Author(s):  
Anna Cláudia Baumel Mongruel ◽  
Priscila Ikeda ◽  
Keyla Carstens Marques de Sousa ◽  
Jyan Lucas Benevenute ◽  
Margarete Kimie Falbo ◽  
...  
Keyword(s):  
18S Rrna ◽  
Molecular Detection ◽  
Phylogenetic Analyses ◽  
Southern Brazil ◽  
Conventional Pcr ◽  
Pathogenic Potential ◽  
Vector Borne ◽  
Pcr Assays ◽  
Etiological Agents ◽  
Positive Results

Abstract Arthropod-borne pathogens are medically important because of their ability to cause diseases in their hosts. The purpose of this study was to detect the occurrence of Ehrlichia spp., piroplasmids and Hepatozoon spp. in dogs with anemia and thrombocytopenia in southern Brazil. EDTA-whole blood was collected from 75 domestic dogs presenting anemia or/and thrombocytopenia from Guarapuava, state of Paraná, Brazil. DNA samples were subjected to conventional PCR assays for Ehrlichia spp. (dsb), piroplasmids (18S rRNA) and Hepatozoon spp. (18S rRNA), followed by sequencing and phylogenetic analyses. Among the 75 dogs, one (1.33%) was positive for Hepatozoon sp. and six (8%) were positive for piroplasmids in 18S rRNA cPCR assays. None of the dogs showed positive results in Ehrlichia spp.-cPCR targeting dsb gene. The phylogenetic analyses revealed that three piroplasm sequences were clustered with Rangellia vitalii, while one sequence was grouped with B. vogeli. The only sequence obtained from Hepatozoon spp.-PCR protocol was pooled with H. canis. Therefore, there is urgent need for differential molecular diagnosis of the two piroplasm species cited as etiological agents in clinical cases of canine hemoparasitic diseases, given the higher pathogenic potential of R. vitalii than of B. vogeli.

scholarly journals MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 806
Author(s):  
Shambhu G. Aralaguppe ◽  
Anoop T. Ambikan ◽  
Manickam Ashokkumar ◽  
Milner M. Kumar ◽  
Luke Elizabeth Hanna ◽  
...  
Keyword(s):  
Drug Resistance ◽  
High Throughput ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Polymorphism Analysis ◽  
Resistance Mutations ◽  
Subtype C ◽  
Bioinformatics Pipeline ◽  
Drug Resistance Mutations ◽  
Hiv 1

The detection of drug resistance mutations (DRMs) in minor viral populations is of potential clinical importance. However, sophisticated computational infrastructure and competence for analysis of high-throughput sequencing (HTS) data lack at most diagnostic laboratories. Thus, we have proposed a new pipeline, MiDRMpol, to quantify DRM from the HIV-1 pol region. The gag-vpu region of 87 plasma samples from HIV-infected individuals from three cohorts was amplified and sequenced by Illumina HiSeq2500. The sequence reads were adapter-trimmed, followed by analysis using in-house scripts. Samples from Swedish and Ethiopian cohorts were also sequenced by Sanger sequencing. The pipeline was validated against the online tool PASeq (Polymorphism Analysis by Sequencing). Based on an error rate of <1%, a value of >1% was set as reliable to consider a minor variant. Both pipelines detected the mutations in the dominant viral populations, while discrepancies were observed in minor viral populations. In five HIV-1 subtype C samples, minor mutations were detected at the <5% level by MiDRMpol but not by PASeq. MiDRMpol is a computationally as well as labor efficient bioinformatics pipeline for the detection of DRM from HTS data. It identifies minor viral populations (<20%) of DRMs. Our method can be incorporated into large-scale surveillance of HIV-1 DRM.

scholarly journals Classification of Tick Species and Detection of Tick-borne Pathogens in Yanbian, China

2020 ◽  
Author(s):  
Jixu Li ◽  
Shuang Zhang ◽  
Wanfeng Liang ◽  
Shaowei Zhao ◽  
Hao Wang ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
North Korea ◽  
Tick Species ◽  
Spotted Fever ◽  
Ixodes Persulcatus ◽  
Spotted Fever Group ◽  
Haemaphysalis Longicornis ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Severe Fever

Abstract BackgroundYanbian is located at the junction between China, Russia, and North Korea. We aimed to determine the species distribution and pathogens carried by ticks in Yanbian.MethodsA total of 2673 unattached ticks were collected from eight counties and cities in Yanbian and classified morphologically. Candidatus Rickettsia tarasevichiae (CRT), spotted fever group Rickettsia (SFGR), severe fever thrombocytopenia syndrome virus (SFTSV), Theileria, and other pathogens were detected using polymerase chain reaction (PCR) and real-time quantitative polymerase chain reaction followed by phylogenetic and genotypic analyses.ResultsAccording to the morphological classification, the main tick species in Yanbian were Haemaphysalis longicornis, Ixodes persulcatus, Dermacentor silvarum, Haemaphysalis japonica, and Haemaphysalis concinna. Candidatus Rickettsia tarasevichiae, spotted fever group Rickettsia, severe fever thrombocytopenia syndrome virus, and Theileria orientalis were detected in H. longicornis, Candidatus Rickettsia tarasevichiae, spotted fever group Rickettsia, and severe fever thrombocytopenia syndrome virus were detected in I. persulcatus, H. japonica, and D. silvarum, but only severe fever thrombocytopenia syndrome virus was detected in H. concinna. Mixed infection with Candidatus Rickettsia tarasevichiae and severe fever thrombocytopenia syndrome virus was found in I. persulcatus and H. japonica. The gene sequences of all tested pathogens exhibited 95.7%–100% homology with sequences registered in GenBank. Phylogenetic analysis showed that different spotted fever group Rickettsia and severe fever thrombocytopenia syndrome virus genotypes were closely related to the Korean strains. We provide the first evidence for the presence of the spotted fever group Rickettsia genotypes of Candidatus Rickettsia longicornii, ompA, ompB, sca4, and rrs, in Haemaphysalis longicornis in Yanbian. ConclusionsThese results provide epidemiological data to support the prevention and control of ticks and tick-borne diseases in the border areas of China, North Korea, and Russia.

scholarly journals A Field Efficacy Evaluation of In2Care Mosquito Traps in Comparison with Routine Integrated Vector Management at Reducing Aedes aegypti

2021 ◽  
Vol 37 (4) ◽  
pp. 242-249
Author(s):  
Eva A. Buckner ◽  
Katie F. Williams ◽  
Samantha Ramirez ◽  
Constance Darrisaw ◽  
Juliana M. Carrillo ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Large Scale ◽  
Pathogen Transmission ◽  
Small Scale ◽  
Integrated Vector Management ◽  
Control Programs ◽  
Vector Management ◽  
Scale Field ◽  
Large Scale Field ◽  
Eggs And Larvae

ABSTRACT Aedes aegypti is the predominant vector of dengue, chikungunya, and Zika viruses. This mosquito is difficult to control with conventional methods due to its container-inhabiting behavior and resistance to insecticides. Autodissemination of pyriproxyfen (PPF), a potent larvicide, has shown promise as an additional tool to control Aedes species in small-scale field trials. However, few large-scale field evaluations have been conducted. We undertook a 6-month-long large-scale field study to compare the effectiveness and operational feasibility of using In2Care Mosquito Traps (In2Care Traps, commercially available Aedes traps with PPF and Beauveria bassiana) compared to an integrated vector management (IVM) strategy consisting of source reduction, larviciding, and adulticiding for controlling Ae. aegypti eggs, larvae, and adults. We found that while the difference between treatments was only statistically significant for eggs and larvae (P &lt; 0.05 for eggs and larvae and P &gt; 0.05 for adults), the use of In2Care Traps alone resulted in 60%, 57%, and 57% fewer eggs, larvae, and adults, respectively, collected from that site compared to the IVM site. However, In2Care Trap deployment and maintenance were more time consuming and labor intensive than the IVM strategy. Thus, using In2Care Traps alone as a control method for large areas (e.g., &gt;20 ha) may be less practical for control programs with the capacity to conduct ground and aerial larviciding and adulticiding. Based on our study results, we conclude that In2Care Traps are effective at suppressing Ae. aegypti and have the most potential for use in areas without sophisticated control programs and within IVM programs to target hotspots with high population levels and/or risk of Aedes-borne pathogen transmission.

Sign in / Sign up

Export Citation Format

Share Document