Targeted Metagenomics for Clinical Detection and Discovery of Bacterial Tick-Borne Pathogens

Abstract

Tickborne diseases, due to a diversity of bacterial pathogens, represent a significant and increasing public health threat throughout the northern hemisphere. A high-throughput 16S V1-V2 rDNA-based metagenomics assay was developed and evaluated using >13,000 residual samples from patients suspected of tickborne illness and >1000 controls. Taxonomic predictions for tickborne bacteria were exceptionally accurate, as independently validated by secondary testing. Overall, 881 specimens were positive for bacterial tickborne agents. Twelve tickborne bacterial species were detected, including two novel pathogens, representing a 100% increase in the number of tickborne bacteria identified compared to what was possible by initial PCR testing. In three blood specimens, two tickborne bacteria were simultaneously detected. Seven bacteria, not known to be tick-transmitted, were also confirmed unique to samples from persons suspected of tickborne illness. These results indicate 16S V1-V2 metagenomics can greatly simplify diagnosis and accelerate discovery of bacterial tickborne pathogens.

Borrelia miyamotoi Meningoencephalitis in an Immunocompetent Patient

“…New B. miyamotoi immunoreactive antigens have been developed and can improve antibody assay sensitivity and specificity [ 19 ]. Newer diagnostic testing approaches using metagenomic next-generation sequencing may provide a useful alternative to serodiagnosis and aid in the detection of several tick-borne zoonoses, including those caused by Borrelia [ 20 , 21 ].…”

Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases

“…Many laboratories have validated and implemented LDTs for deep amplicon sequencing with both bacterial and fungal identification [ 130 , 131 ], with one group even demonstrating a useful pipeline to incorporate both [ 127 ]. In addition, 16S deep amplicon sequencing has made it easier to identify the more difficult to grow organisms including tick-borne bacteria that usually are not detected with conventional bacterial culture (e.g., Borrelia , Anaplasmsa , Ehrlichia , and Rickettsia ) [ 132 ]. Specifically, for 16S gene amplification, there has been clinical utility demonstrated for a variety of specimen types including joint fluid [ 133 ], blood [ 134 ], and cerebrospinal fluid (CSF) [ 135 ].…”

New Technological Developments in Identification and Monitoring of New and Emerging Infections

“…PCR amplification and sequencing of 16s rRNA have been used to identify multiple bacteria belonging to the families Rickettsiaceae , Enterobacteriaceae, and Pseudomonadaceae ( Lambert et al, 2019 ; Sperling et al, 2017 ). A similar approach also allows for the metagenomic identification of tick-borne bacteria in blood from patients ( Kingry et al, 2020 ; Rodino et al, 2021 ).…”