Nanopore-based metagenomics reveal a new Rickettsia in Europe
Accurate identification of tick-borne bacteria, including those associated with rickettsioses, pose significant challenges due to the polymicrobial and polyvectoral nature of the infections. We aimed to carry out a comparative evaluation of a non-targeted metagenomic approach by nanopore sequencing...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2024-03-01
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| Series: | Ticks and Tick-Borne Diseases |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1877959X23001863 |
| _version_ | 1797320969944039424 |
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| author | Suppaluck Polsomboon Nelson Koray Ergunay Brian P. Bourke Drew D. Reinbold-Wasson Laura Caicedo-Quiroga Giorgi Kirkitadze Tamar Chunashvili Cynthia L. Tucker Yvonne-Marie Linton |
| author_facet | Suppaluck Polsomboon Nelson Koray Ergunay Brian P. Bourke Drew D. Reinbold-Wasson Laura Caicedo-Quiroga Giorgi Kirkitadze Tamar Chunashvili Cynthia L. Tucker Yvonne-Marie Linton |
| author_sort | Suppaluck Polsomboon Nelson |
| collection | DOAJ |
| description | Accurate identification of tick-borne bacteria, including those associated with rickettsioses, pose significant challenges due to the polymicrobial and polyvectoral nature of the infections. We aimed to carry out a comparative evaluation of a non-targeted metagenomic approach by nanopore sequencing (NS) and commonly used PCR assays amplifying Rickettsia genes in field-collected ticks. The study included a total of 310 ticks, originating from Poland (44.2 %) and Bulgaria (55.8 %). Samples comprised 7 species, the majority of which were Ixodes ricinus (62.9 %), followed by Dermacentor reticulatus (21.2 %). Screening was carried out in 55 pools, using total nucleic acid extractions from individual ticks. NS and ompA/gltA PCRs identified Rickettsia species in 47.3 % and 54.5 % of the pools, respectively. The most frequently detected species were Rickettsia asiatica (27.2 %) and Rickettsia raoultii (21.8 %), followed by Rickettsia monacensis (3.6 %), Rickettsia helvetica (1.8 %), Rickettsia massiliae (1.8 %) and Rickettsia tillamookensis (1.8 %). Phylogeny construction on mutS, uvrD, argS and virB4 sequences and a follow-up deep sequencing further supported R. asiatica identification, documented in Europe for the first time. NS further enabled detection of Anaplasma phagocytophilum (9.1 %), Coxiella burnetii (5.4 %) and Neoehrlichia mikurensis (1.8 %), as well as various endosymbionts of Rickettsia and Coxiella. Co-detection of multiple rickettsial and non-rickettsial bacteria were observed in 16.4 % of the pools with chromosome and plasmid-based contigs. In conclusion, non-targeted metagenomic sequencing was documented as a robust strategy capable of providing a broader view of the tick-borne bacterial pathogen spectrum. |
| first_indexed | 2024-03-08T04:50:46Z |
| format | Article |
| id | doaj.art-855f48990c9d48cb873b2e82046987ad |
| institution | Directory Open Access Journal |
| issn | 1877-9603 |
| language | English |
| last_indexed | 2024-03-08T04:50:46Z |
| publishDate | 2024-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Ticks and Tick-Borne Diseases |
| spelling | doaj.art-855f48990c9d48cb873b2e82046987ad2024-02-08T05:07:29ZengElsevierTicks and Tick-Borne Diseases1877-96032024-03-01152102305Nanopore-based metagenomics reveal a new Rickettsia in EuropeSuppaluck Polsomboon Nelson0Koray Ergunay1Brian P. Bourke2Drew D. Reinbold-Wasson3Laura Caicedo-Quiroga4Giorgi Kirkitadze5Tamar Chunashvili6Cynthia L. Tucker7Yvonne-Marie Linton8Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USAWalter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USA; Hacettepe University, Faculty of Medicine, Ankara, Turkey; Corresponding author: Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA.Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USAU.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, GeorgiaWalter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USAU.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, GeorgiaU.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, GeorgiaWalter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USAWalter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA; Smithsonian Institution, Department of Entomology, National Museum of Natural History (NMNH), Washington, DC, USAAccurate identification of tick-borne bacteria, including those associated with rickettsioses, pose significant challenges due to the polymicrobial and polyvectoral nature of the infections. We aimed to carry out a comparative evaluation of a non-targeted metagenomic approach by nanopore sequencing (NS) and commonly used PCR assays amplifying Rickettsia genes in field-collected ticks. The study included a total of 310 ticks, originating from Poland (44.2 %) and Bulgaria (55.8 %). Samples comprised 7 species, the majority of which were Ixodes ricinus (62.9 %), followed by Dermacentor reticulatus (21.2 %). Screening was carried out in 55 pools, using total nucleic acid extractions from individual ticks. NS and ompA/gltA PCRs identified Rickettsia species in 47.3 % and 54.5 % of the pools, respectively. The most frequently detected species were Rickettsia asiatica (27.2 %) and Rickettsia raoultii (21.8 %), followed by Rickettsia monacensis (3.6 %), Rickettsia helvetica (1.8 %), Rickettsia massiliae (1.8 %) and Rickettsia tillamookensis (1.8 %). Phylogeny construction on mutS, uvrD, argS and virB4 sequences and a follow-up deep sequencing further supported R. asiatica identification, documented in Europe for the first time. NS further enabled detection of Anaplasma phagocytophilum (9.1 %), Coxiella burnetii (5.4 %) and Neoehrlichia mikurensis (1.8 %), as well as various endosymbionts of Rickettsia and Coxiella. Co-detection of multiple rickettsial and non-rickettsial bacteria were observed in 16.4 % of the pools with chromosome and plasmid-based contigs. In conclusion, non-targeted metagenomic sequencing was documented as a robust strategy capable of providing a broader view of the tick-borne bacterial pathogen spectrum.http://www.sciencedirect.com/science/article/pii/S1877959X23001863RickettsiaNanopore sequencingTicksPolandBulgaria |
| spellingShingle | Suppaluck Polsomboon Nelson Koray Ergunay Brian P. Bourke Drew D. Reinbold-Wasson Laura Caicedo-Quiroga Giorgi Kirkitadze Tamar Chunashvili Cynthia L. Tucker Yvonne-Marie Linton Nanopore-based metagenomics reveal a new Rickettsia in Europe Ticks and Tick-Borne Diseases Rickettsia Nanopore sequencing Ticks Poland Bulgaria |
| title | Nanopore-based metagenomics reveal a new Rickettsia in Europe |
| title_full | Nanopore-based metagenomics reveal a new Rickettsia in Europe |
| title_fullStr | Nanopore-based metagenomics reveal a new Rickettsia in Europe |
| title_full_unstemmed | Nanopore-based metagenomics reveal a new Rickettsia in Europe |
| title_short | Nanopore-based metagenomics reveal a new Rickettsia in Europe |
| title_sort | nanopore based metagenomics reveal a new rickettsia in europe |
| topic | Rickettsia Nanopore sequencing Ticks Poland Bulgaria |
| url | http://www.sciencedirect.com/science/article/pii/S1877959X23001863 |
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