Genome sequence of Mycobacterium yongonense RT 955-2015 isolate from a patient misdiagnosed with multidrug-resistant tuberculosis: First clinical detection in Tanzania
Bibliographic record
Abstract
BACKGROUND: Mycobacterium yongonense is a recently described novel species belonging to Mycobacterium avium complex, which is the most prevalent aetiology of non-tuberculous mycobacteria associated with pulmonary infections, and poses tuberculosis diagnostic challenges in high-burden, resource-constrained settings. METHODS: Whole genome shotgun sequencing and comparative microbial genomic analyses were used to characterize the isolate from a patient diagnosed with multidrug-resistant tuberculosis (MDR-TB) after relapse. RESULTS: The genome sequence of the first case of M. yongonense (M. yongonense RT 955-2015) in Tanzania is presented. Sequence analysis revealed that the RT 955-2015 strain had a high similarity to M. yongonense 05-1390(T) (98.74%) and Mycobacterium chimaera DSM 44623(T) (98%). Its 16S rRNA showed similarity to Mycobacterium paraintracellulare KCTC 290849(T) (100%), Mycobacterium intracellulare ATCC 13950(T) (100%), M. chimaera DSM 44623(T) (99.9%), and M. yongonense 05-1390(T) (98%). The strain exhibited a substantially different rpoB sequence to that of M. yongonense 05-1390 (95.16%), but closely related to that of M. chimaera DSM 44623(T) (99.86%), M. intracellulare ATCC 13950(T), (99.53%), and M. paraintracellulare KCTC 290849(T) (99.53%). CONCLUSIONS: In light of the OrthoANI algorithm and phylogenetic analysis, it was concluded that the isolate was M. yongonense Type II genotype, which is an indication that the patient was misdiagnosed with TB/MDR-TB and received inappropriate treatment.
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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 | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".