iSeq 100 for metagenomic pathogen screening in ticks
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 babesio...
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doaj-f2c514f723e443cfa3eaa5f079bf95d62021-07-04T11:33:13ZengBMCParasites & Vectors1756-33052021-06-0114111010.1186/s13071-021-04852-wiSeq 100 for metagenomic pathogen screening in ticksJu Yeong Kim0Myung-hee Yi1Alghurabi Areej Sabri Mahdi2Tai-Soon Yong3Department of Environmental Medical Biology, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of MedicineDepartment of Environmental Medical Biology, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of MedicineDepartment of Global Health Security, Graduate School of Public Health, Yonsei UniversityDepartment of Environmental Medical Biology, Institute of Tropical Medicine, Arthropods of Medical Importance Resource Bank, Yonsei University College of MedicineAbstract 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 Abstracthttps://doi.org/10.1186/s13071-021-04852-wHaemaphysalis longicornisiSeq 100Next generation sequencingRickettsiaVector-borne disease |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ju Yeong Kim Myung-hee Yi Alghurabi Areej Sabri Mahdi Tai-Soon Yong |
spellingShingle |
Ju Yeong Kim Myung-hee Yi Alghurabi Areej Sabri Mahdi Tai-Soon Yong iSeq 100 for metagenomic pathogen screening in ticks Parasites & Vectors Haemaphysalis longicornis iSeq 100 Next generation sequencing Rickettsia Vector-borne disease |
author_facet |
Ju Yeong Kim Myung-hee Yi Alghurabi Areej Sabri Mahdi Tai-Soon Yong |
author_sort |
Ju Yeong Kim |
title |
iSeq 100 for metagenomic pathogen screening in ticks |
title_short |
iSeq 100 for metagenomic pathogen screening in ticks |
title_full |
iSeq 100 for metagenomic pathogen screening in ticks |
title_fullStr |
iSeq 100 for metagenomic pathogen screening in ticks |
title_full_unstemmed |
iSeq 100 for metagenomic pathogen screening in ticks |
title_sort |
iseq 100 for metagenomic pathogen screening in ticks |
publisher |
BMC |
series |
Parasites & Vectors |
issn |
1756-3305 |
publishDate |
2021-06-01 |
description |
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 |
topic |
Haemaphysalis longicornis iSeq 100 Next generation sequencing Rickettsia Vector-borne disease |
url |
https://doi.org/10.1186/s13071-021-04852-w |
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