Population-based microbiological characterization of <i>Nocardia</i> strains causing invasive infections during a multiyear period in a large Canadian healthcare region
Bibliographic record
Abstract
ABSTRACT The role of specific Nocardia species in human infections continues to expand as advanced methods enable species/species complex identification. We conducted a multiyear population-based (2010–2022) characterization of invasive Nocardia spp. Isolates were analyzed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing. A total of 94 cases and 117 unique 16S rRNA gene sequences were evaluated from pulmonary (53%), skin and soft tissues (SSTIs) (29%), central nervous system (CNS) (7%), bloodstream (6%), and other sites of infection. Infections were mainly caused by three species complexes: N. farcinica ( n = 20, 21.3%), N. cyriacigeorgica ( n = 16, 17%), and N. nova ( n = 15, 16%). Phylogenetic analysis correlated with the clinical site of infection. Most N. cyriciageorgica (92%) complex isolates caused SSTIs or pulmonary infections, and most N. farcinica complex (67%) and N. nova complex (69%) isolates caused pulmonary and CNS infections, respectively. Several other unique Nocardia spp. rarely caused invasive infections (≤5 cases): (i) pulmonary ( N. abscessus complex, N. amamiensis , N. asteroides , N. otitidiscaviarum complex, N. sputorum , N. transvalensis complex, Nocardiopsis spp., Pseudonocardia spp.); (ii) SSTIs ( N. otitidiscaviarum complex); and (iii) CNS ( N. flavorosea and N. paucivorans complex). Nocardia species were highly susceptible to amikacin, trimethoprim-sulfamethoxazole, moxifloxacin, and linezolid. Imipenem resistance occurred in the N. farcinica complex and N. nova complex, while ceftriaxone resistance only occurred in the former. Antibiotic profiles varied for rare Nocardia spp. Species-level Nocardia identification using MALDI-TOF MS and 16S rRNA gene sequencing improves understanding of these organisms’ unique roles in causing invasive disease. IMPORTANCE Nocardia spp. are a rare cause of invasive infections, particularly in immunocompromised patients. The role of specific Nocardia species in human infections continues to expand as advanced methods enable species/species complex identification. We conducted a multiyear population-based (2010–2022) characterization of invasive Nocardia spp. Isolates were analyzed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing. A total of 94 cases included pulmonary infections (53%), skin and soft tissue infections (29%), central nervous system infections (7%), bloodstream infections (6%), and septic arthritis and intra-abdominal infections (5%). One hundred seventeen unique 16S rRNA gene sequences from clinical isolates were analyzed. Phylogenetic analysis correlated with the clinical site of infection. Nocardia species were highly susceptible to amikacin, trimethoprim-sulfamethoxazole, moxifloxacin, and linezolid. Imipenem resistance only occurred in N. farcinica complex and N. nova complex strains, and ceftriaxone resistance only occurred in the former. Species-level Nocardia identification using MALDI-TOF MS and 16S sequencing improves understanding of these organisms’ unique roles in invasive disease.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 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) | 0.000 | 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 teacher head, 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".