ArticleThe Journal of infectious diseases2025
Phylogenetic Context of Antibiotic Resistance Provides Insights into the Dynamics of Resistance Emergence and Spread.
Article in The Journal of infectious diseases, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Defining thebioRxiv : the preprint server for biology · 2026Article
- Resolving competing evolutionary histories in joint ancestral state reconstruction.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Review
- Antibiotic-resistance plasmid amplified among MRSA cases in an urban jail and its connected communities.Nature communications · 2025Article
- Antibiotic-resistance plasmid amplified among MRSA cases in an urban jail and its connected communities.medRxiv : the preprint server for health sciences · 2025Article
- Uncertainty in joint Ancestral State Reconstruction: Improving accuracy and biological interpretability of ancestral state prediction.bioRxiv : the preprint server for biology · 2025Article
- Identifying drivers of β-lactam/β-lactamase inhibitor resistance emergence and spread before their clinical deployment.medRxiv : the preprint server for health sciences · 2025Article
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7 authors.
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Abstract
backgroundTo ameliorate the antibiotic resistance crisis, the drivers of resistance emergence and resistance spread must be better understood.
methodsWhole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant Klebsiella pneumoniae isolates collected from August 2014 to July 2015 across 12 long-term acute care hospitals. Ancestral state reconstruction partitioned patients with resistant strains into those that likely acquired resistance via de novo evolution or cross-transmission. Logistic regression was used to evaluate the associations between patient characteristics/exposures and these 2 pathways: resistance due to predicted within-host emergence of resistance and resistance due to predicted cross-transmission. This framework is available in the user-friendly R package, phyloAMR (https://github.com/kylegontjes/phyloAMR).
resultsPhylogenetic analysis of 386 epidemic lineage carbapenem-resistant K. pneumoniae sequence type 258 isolates revealed differences in the relative contribution of de novo evolution and cross-transmission to the burden of resistance to 5 antibiotics. Clade-specific variations in rates of resistance emergence and their frequency and magnitude of spread were detected for each antibiotic. Phylogenetically informed regression modeling identified distinct clinical risk factors associated with each pathway. Exposure to the cognate antibiotic was an independent risk factor for resistance emergence (trimethoprim-sulfamethoxazole, colistin, and novel beta-lactam/beta-lactamase inhibitors) and resistance spread (trimethoprim-sulfamethoxazole, amikacin, and colistin). In addition to antibiotic exposures, comorbidities (eg, stage IV + decubitus ulcers) and indwelling medical devices (eg, gastrostomy tubes) were detected as unique risk factors for resistance spread.
conclusionsPhylogenetic contextualization generated insights and hypotheses into how bacterial genetic background, patient characteristics, and clinical practices influence the emergence and spread of antibiotic resistance.
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