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 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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 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".