Genomic Confirmation of <i>Borrelia garinii</i>, United States
Bibliographic record
Abstract
L yme disease is a multisystem disorder caused by infection with bacteria of the Borrelia burgdorferi sensu lato species complex.Three members of this complex, B. burgdorferi sensu stricto, B. garinii, and B. afzelii, are responsible for most cases of Lyme disease worldwide (1,2).B. burgdorferi s.l. is the only one of these 3 species that is found widely in North America, although B. garinii has been identified on islands off the coast of Newfoundland and Labrador, Canada (3-5).We describe the isolation and genome sequencing characterization of a South Carolina B. garinii isolate from a repository of strains from rodent hosts and tick vectors in the southeastern United States that had been identified as B. burgdorferi s.l.A second B. garinii isolate from the same B. burgdorferi s.l.strain repository was identified on the basis of multilocus sequence typing (MLST).Phylogenetic analysis showed that these 2 strains from the southeastern United States were most closely related to a group of B. garinii isolates from Europe but were not derived from strains from Canada, or vice versa (3). Methods Sources, Cultivation, and Analyses of Borrelia spp.The 2 Borrelia isolates described were isolated from ear biopsy specimens from a cotton mouse (Peromyscus gossypinus) (SCCH-7) trapped in Charleston County, South Carolina, in 1995 and from an eastern woodrat (Neotoma floridana) (SCGH-19) trapped in Georgetown County, South Carolina, in 1996 (Appendix, https://wwwnc.cdc.gov/EID/article/29/1/22-0930-App1.pdf)(6).We performed Borrelia culture in Barbour-Stoenner-Kelly H medium, DNA purification, and PCR analyses as described (7).We detected B. burgdorferi s.l. in samples by amplification of the 5S-23S intergenic region (8) (Appendix) by using species-specific PCR and primers designed on the basis of the ospA gene, which confirmed the presence of multiple spirochete species (9).Cultures in which B. garinii was confirmed were plated on solid medium, and clonal single colonies were isolated according to a modified protocol (10) (Appendix). Whole-Genome Sequencing and Genome AssemblyWe performed whole-genome sequencing by using the Pacific Biosciences Sequel II system (https:// www.pacb.com).We performed genome assembly by using the Genome Assembly tool in PacBio SMRTLink version 10.2 and 150 Mb of the HiFi reads >5 kb (Appendix).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".