Genomic epidemiology revealed the emergence and worldwide dissemination of ST383 carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> and hospital acquired infections of ST196 <i>Klebsiella quasipneumoniae</i> in Qatar
Bibliographic record
Abstract
Abstract The emergence of carbapenem-resistant (CR) hypervirulent Klebsiella pneumoniae (hvKp) is a new threat to healthcare. In this study, we studied the molecular epidemiology of CR Klebsiella isolates in Qatar using whole genome sequence data. We also characterised the prevalence and genetic basis of hypervirulent phenotypes, and established the virulence potential using a Galleria mellonella model. One hundred CR Klebsiella isolates were recovered, and NDM and OXA-48 were the most common carbapenemases. Phylogenetic analysis indicated the presence of diverse sequence types and clonal lineages; one of them belonged to K. quaisipneumoniae ST196 that may be disseminated among several health care centres. Ten K. pneumoniae isolates carrying rmpA and/or rmpA2 , and 2 isolates belonged to KL2, indicating the prevalence of classical hypervirulent (hv) isolates was not high. Isolates carrying CR and hv genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated the bla NDM was located on an IncHI1B type plasmid (pFQ61_ST383_NDM-5), which also harbored several virulence factors, including the regulator of the mucoid phenotype ( rmpA ), the regulator of mucoid phenotype 2 ( rmpA2 ), and aerobactin ( iucABCD and iutA ), likely resulting from inversion and recombination events. In contrast, bla OXA-48 was located in an IncL-type plasmid. Comparative genomes indicated the recent evolution and emergence of CR-hv Kp ST383 via the acquisition of hybrid plasmids with both carbapenemase and virulence genes. CR-hv K. pneumoniae ST383 pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| 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) | 0.002 | 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".