Characteristics of an uncommon sequence type of serotype b Haemophilus influenzae causing an increase in invasive disease in British Columbia, Canada
Bibliographic record
Abstract
BACKGROUND: Since introduction of conjugate vaccines against serotype b Haemophilus influenzae (Hib), invasive Hib disease in British Columbia (BC), Canada has been rare (average 2.8 cases per year). However, between 2021 and 2024, 62 cases of culture confirmed cases were documented. This study examined Hib isolates from BC between January 1, 2010 to December 31, 2024. METHODS: Hib were characterized by whole genome sequencing. Demographics of Hib cases as well as clinical presentation inferred from bacteriological isolation sites were obtained from BC Centre for Disease Control. RESULTS: Ninety-eight case isolates of Hib (9.3 %) were identified from all invasive H. influenzae disease (n = 1047). The most common Hib sequence type (ST) was ST-231 (68 isolates or 69.4 %). SNVPhyl analysis clustered ST-231 Hib as uniquely different from all other Hib isolates, and also grouped them into an early E1 (from 2011 to 2008), a late L2 (from 2022 to 2023) and a late L3 (from 2017 to 2023) clusters. Core-genome multi-locus sequence typing (cgMLST) and Life Identification Numbers (LIN) assigned by PubMLST showed that the ST-231 Hib were highly similar (with five or fewer core gene differences). Only four non-Canadian Hib isolates identified by LIN and cgMLST to cluster distantly with ST-231 Hib were showing 110 core gene differences. Most (91.2 %) ST-231 Hib cases occurred in adults aged ≥ 30 years, and no case in children ≤ five years old. Most (94.1 %) cases showed positive blood culture. Temporal and geographical variations of Hib STs were found by linking Hib cases to their Health Regions. CONCLUSION: This study documented an increase of Hib cases in adults due to an uncommon ST, which was very different from other Hib found in the PubMLST databsae. ST-231 Hib cases were initially found in only two Health Regions, subsequent cases spread to cover four Health Regions suggesting community spread and endemicity in the province.
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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 | 0.001 | 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 | 0.000 |
| 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".