Molecular epidemiology of carbapenemase-producing <i>Acinetobacter</i> spp. from Israel, 2001-2006: earliest report of <i>bla</i> <sub>NDM</sub> predating the oldest known <i>bla</i> <sub>NDM</sub> -positive strains
Bibliographic record
Abstract
Abstract Background Carbapenem-resistant Acinetobacter baumannii (CRAb) is a WHO priority 1 critical pathogen. Despite early emergence of elevated CRAb rates in Israel, limited molecular data from this location are available. We searched for carbapenemases among 198 clinical Acinetobacter spp. from Israel between 2001 and 2006. Methods Strains from 3 archives underwent whole-genome sequencing (Illumina NovaSeq on all, MinION on a subset) and computational analyses: assembly (Unicycler), annotation (prokka), identification (Kraken, rpoB similarity), search for carbapenemases (ResFinder, BLDB curation). Findings A. baumannii (Ab) represented 179 (90·4%) Acinetobacter spp. Eighty-four Ab (46·9%) carried a carbapenemase: 38 (45·2%) bla OXA-72 ( bla OXA-24-like ); 28 (33·3%) bla OXA-23-like (20 bla OXA-23 and 8 bla OXA-225 ); 18 (21·5%) bla OXA-58 (16 from 2001-2). Carbapenemase rates increased yearly from 2002 (32%) to 2006 (67%). Eight species of non- baumannii Acinetobacter (NbA) accounted for 19 isolates (9·6%). Two of three A. junii contained bla OXA-58 , one of which, Ajun-H1-3, isolated in January 2004, also possessed bla NDM-1 . The pNDM-Ajun-H1-3 plasmid matched numerous NDM-positive plasmids reported from 2005 onwards in Acinetobacter spp. as well as Enterobacterales . Interpretation We assessed carbapenemase diversity among Acinetobacter spp. in Israel from 2001-2006. Findings in Ab predate observations elsewhere: rapidly rising carbapenemase rates, driven by bla OXA-23-like and bla OXA-24-like genes replacing bla OXA-58 . Among NbA, an A. junii isolated in 2004 carried bla NDM-1 , making it the earliest NDM-positive isolate reported to date, preceding those from 2005 in India. Further research into bla NDM ’s emergence is warranted, in order to shed light on the evolution and spread of this and other antibiotic-resistance genes. Funding Centre de recherche Charles-Le Moyne; Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke; Fonds de recherche du Québec – Santé; New Frontiers in Research Fund Grant NFRFE-2019-00444; CIFAR-Azrieli Global Scholars Program.
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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 | 0.001 | 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".