Nanopore-based metagenomics reveal a new Rickettsia in Europe

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

Ticks and Tick-Borne Diseases (Mar 2024)

Nanopore-based metagenomics reveal a new Rickettsia in Europe

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

Affiliations

Suppaluck Polsomboon Nelson: 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, USA
Koray Ergunay: 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, USA; Hacettepe University, Faculty of Medicine, Ankara, Turkey; Corresponding author: Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA.
Brian P. Bourke: 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, USA
Drew D. Reinbold-Wasson: U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia
Laura Caicedo-Quiroga: 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, USA
Giorgi Kirkitadze: U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia
Tamar Chunashvili: U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia
Cynthia L. Tucker: Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
Yvonne-Marie Linton: 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, USA

Journal volume & issue: Vol. 15, no. 2
p. 102305

Abstract

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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.

Published in Ticks and Tick-Borne Diseases

ISSN: 1877-9603 (Online)
Publisher: Elsevier
Country of publisher: Germany
LCC subjects: Medicine: Internal medicine: Infectious and parasitic diseases
Website: https://www.sciencedirect.com/journal/ticks-and-tick-borne-diseases

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