Comparative genome analysis investigation of nosocomial and community-acquired cases of Legionnaires’ disease caused by ST2858 and ST378
Bibliographic record
Abstract
ABSTRACT Eight cases of Legionnaires’ disease caused by Legionella pneumophila serogroup 1 sequence type (ST) ST2858 were detected within 4 years in Montréal, Canada. Most cases were associated with a single healthcare facility, and one of them presented with a co-infection, from which ST378 was isolated as well. The source of ST2858 was not identified, despite extensive environmental sampling. The goal of this study was to determine the diversity of both STs and confirm the source of each by matching clinical to environmental isolates. Comparative genome analysis was performed to investigate the genetic relatedness of the isolates. Long- and short-read hybrid assembly was used to produce high-quality closed genomes. A PCR assay, amplifying a unique gene of ST2858, was also developed. None of the 599 environmental isolates screened by PCR was ST2858. The ST2858 clinical isolates had a maximum of two single nucleotide polymorphisms in pairwise comparison, suggesting a common source. ST378 isolates had higher genomic diversity, and the isolate from the co-infection was similar to environmental ST378 from the healthcare facility’s hot water distribution system. The isolate from the co-infection harbored a plasmid conferring increased copper resistance. Understanding genomic diversity could help identify potential sources and should be considered for matching clinical with environmental isolates. Phenotypic diversity may be relevant for outbreak investigation, surveillance, and management. IMPORTANCE Legionnaires’ disease (LD) is transmitted to humans by inhalation of aerosols contaminated with Legionella . When an outbreak occurs, identification of the source allows public officials to make sure the source is controlled to prevent further cases. In this study, whole genome sequencing was used to investigate the relatedness between clinical and environmental isolates collected during the epidemiological investigation of cases of LD centered around a single healthcare facility, providing valuable information about the diversity of Legionella within water systems and similarity thresholds for matching clinical and environmental strains. The genomic data were also used to design a methodology to rapidly screen hundreds of historical isolates and DNA extracts, which could benefit source identification in other outbreaks. Furthermore, Legionella isolates may differ in their ability to resist disinfection methods and potentially acquire novel genetic determinants, and water system characteristics may select for specific Legionella strains.
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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 | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| 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".