Whole Genome Sequencing in Tracking Intergenus Klebsiella Pneumoniae Carbapenemase (KPC) Gene Transmission in a Tertiary Care Center
Bibliographic record
Abstract
Background. An outbreak is traditionally suspected when a cluster of cases associated with a common organism is observed. Outbreaks due to carbapenemase-producing organisms challenge traditional infection control approaches as the focus shifts to resistance genes transmitted between different genera and species. Whole genome sequencing (WGS) is a new tool that allows for the genetic typing of isolates and for tracking of mobile resistance elements. Methods. In a 637-bed university teaching hospital in Montréal, Canada, detection of a new case of a nosocomially acquired KPC-producing Enterobacter cloacae (Ec1) prompted the application of WGS analysis to epidemiologically-linked clinical and surveillance samples harbouring the KPC gene (n = 9). blaKPC gene presence was confirmed by PCR. Pulsed-field gel electrophoresis using XbaI, plasmid fingerprinting (pRFLP) using Bgl II and PCR to detect plasmid incompatibility groups (Inc) was conducted. Whole genome sequencing (WGS) was conducted using Illumina technology on a Miseq with assembly using Spades. Analysis of the genomes was conducted by single variant polymorphisms (SVP), MLST and mapping of Tn4401 to a referencing using Bowtie. Results. In all, 9 isolates from 5 subjects were sequenced: 5 K. pneumoniae, 1 E.coli, 1 K. oxytoca and 2 E. cloacae (Ec1 and the only other known KPC-producing E. cloacae detected at the hospital in the previous year). SNP analysis of Tn4401 and pRFLP revealed 3 transposon types (Tn4401-type1-3), incorporated into 6 distinct plasmids (A1, A2, B1, C1, D1, E1), belonging to IncN, IncP,L/M, IncFllk or IncFIA(H1). Tn4401-type1 was identified in 3 plasmids (A2, D1, E1), found in 3 species, K. pneumoniae, E. cloacae and K. oxytoca. A2, an IncN plasmid, associated with Tn4401-type1 was identified in Ec1 and in a K. pneumoniae suggesting that the isolates are linked. Conclusion. WGS is a promising tool to aid in investigating and tracking transmission of both organisms and their highly mobile genetic determinants of resistance. As demonstrated here, its application in the setting of nosocomial transmission supports re-thinking of when and how to implement infection control practices and endorses WGS on a larger scale to optimize the management of nosocomial outbreaks. Disclosures. All authors: No reported disclosures.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| 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".