Genomic analysis of virulent, multidrug resistant Klebsiella pneumoniae and Klebsiella oxytoca from bloodstream infections, South Africa
Bibliographic record
Abstract
The study investigated the resistome, virulome and mobilome of multidrug resistant (MDR) Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates. A total of 46 suspected Klebsiella species ( spp .) were collected from blood cultures within the uMgungundlovu District in the KwaZulu-Natal Province. Antibiotic susceptibility was determined against a panel of 19 antibiotics using the disk diffusion test. A subset of 14 MDR K. pneumoniae (n=10) and K. oxytoca (n=4) isolates were selected based on their antibiograms and subjected to whole genome sequencing (WGS). The sequence types (STs), resistome, virulome, mobilome, capsule loci (KLs) were analysed using relevant WGS and bioinformatics tools. Of the 10 K. pneumoniae sequence types (ST) identified, the most common were ST25 (n=3), ST101 (n=3), and 4 K. oxytoca belonged to ST450 (n=3). The two high-risk K. pneumoniae clones ST15, and ST17 were identified. O and K capsule types were identified, with predominance of KL2, KL17, KL29, O1/O2v2, O1/O2v1, and OL104 respectively. The majority of isolates displayed multidrug resistance predominantly carrying β-lactamase genes, including bla CTX-M-15 , bla TEM-1B , bla SHV , and bla OXA-1 , and bla OXY including the carbapenemase bla OXA-181 in two (14.3%) study isolates. Other resistance genes included: aac(6 ' )-lb-cr , aac(3) , aac, aph, aad, dfr , tet(A) , and tet(D), mph(A) , sul1 , sul2, oqx , qnr , acrR, ramR, parC , gyrA, arr-3 , cat , fosA , qacE genes conferring resistance to aminoglycosides, trimethoprim, tetracycline, macrolide, sulfonamides, fluoroquinolones, rifampicin phenicols, fosfomycin, and quaternary ammonium compound disinfectant. Virulence factors related to hypervirulence: encoding aerobactin ( iuc , iutA ), salmochelin ( iro ), yersiniabactin ( ybt ), enterobactin ( ent ), type 1 and 3 ( mrk and fim ), and capsule synthesis ( rcsA and rcsB ) were identified. IncF, IncR, and Col plasmid replicon types and class I integrons were detected, with IncFIB(K) predominance. The bla CTX-M-15 and bla TEM-1 genes were bracketed by Tn3 transposons, ISEc9, recombinase and IS91 insertion sequences. Conclusions : The convergence of multidrug resistance and hypervirulence genes in Klebsiella strains is a potential clinical concern. Carbapenemase, ESBL screening and genomic surveillance are urgently required in hospital environments.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| 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".