Whole Genome Sequencing of Carbapenem-Resistant Pseudomonas aeruginosa from Clinical and Screening Samples in Indonesia
Bibliographic record
Abstract
To determine the resistance profiles, genetic diversity and transmission of carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates from Indonesia. CRPA poses a significant global health threat due to high mortality and limited treatment options. Whole genome sequencing (WGS) provides a comprehensive approach to understanding the genetic determinants of resistance and transmission dynamics of CRPA. CRPA isolates were collected from clinical and screening samples at a national reference hospital in Jakarta, Indonesia. Screening samples were collected from patients on admission and from healthy volunteers living nearby. Identification and antimicrobial susceptibility testing were performed using VITEK. WGS was performed using Oxford Nanopore and Illumina platforms, followed by hybrid assembly using NanoLite v1.1, and AMR genes were detected using the latest version of the CARD database. Genomic data were analysed to determine sequence types, carbapenemase genes and resistance determinants. The screening included 573 patients and 243 healthy individuals. A total of 110 CRPA isolates were analysed (71 clinical samples, 35/573 patients on admission samples and 4/243 healthy screening samples). Antimicrobial susceptibility patterns were diverse, with high rates of resistance to multiple antibiotics (Table 1-2). The carbapenemase genes IMP and VIM were not found in screening samples but were found in clinical isolates (Table 3). WGS revealed some clusters of CRPA clones, suggesting possible transmission. This study highlights the prevalence of CRPA in both hospital and community settings in Jakarta. WGS is critical for identifying genetic diversity and potential transmission links, highlighting its crucial role in informing effective infection control strategies.
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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) | 0.001 | 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".