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

doi:10.1016/j.ttbdis.2023.102305

Nanopore-based metagenomics reveal a new Rickettsia in Europe

Ticks Tick Borne Dis. 2024 Mar;15(2):102305. doi: 10.1016/j.ttbdis.2023.102305. Epub 2023 Dec 27.

Authors

Suppaluck Polsomboon Nelson¹, Koray Ergunay², Brian P Bourke¹, Drew D Reinbold-Wasson³, Laura Caicedo-Quiroga¹, Giorgi Kirkitadze³, Tamar Chunashvili³, Cynthia L Tucker⁴, Yvonne-Marie Linton¹

Affiliations

¹ 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.
² 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. Electronic address: ekoray@hacettepe.edu.tr.
³ U.S. Army Medical Research Directorate - Georgia (USAMRD-G), Tbilisi, Georgia.
⁴ Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA; Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA.

PMID: 38150911
DOI: 10.1016/j.ttbdis.2023.102305

Abstract

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.

Keywords: Bulgaria; Nanopore sequencing; Poland; Rickettsia; Ticks.

MeSH terms

Animals
Europe
Ixodes* / microbiology
Nanopores*
Rickettsia Infections* / epidemiology
Rickettsia Infections* / microbiology
Rickettsia* / genetics