Genomic insights into antimicrobial resistance and isolation source classification of Cronobacter sakazakii from infant and toddler food in the United States
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ID: 317420
2026
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Abstract
Cronobacter sakazakii is an opportunistic foodborne pathogen associated with severe infections in infants, linked to powdered infant formula and related products. We conducted genomic profiling of C. sakazakii (n = 209) from infant and toddler food in the United States, comprising all publicly available genomes for this source, through the integration of antimicrobial resistance (AMR), plasmid replicon, phylogenetic, and pan-genome analyses. We further applied a machine learning (ML)-driven isolation source classification approach based on pan-genome features to distinguish food and clinical isolates. AMR analysis revealed a conserved resistome dominated by three β-lactam resistance genes (blaCSA, blaCSA-1, and blaCSA-2). Independent co-occurrence and pairwise association analyses of AMR genes and plasmid replicons indicated sparse and gene-specific relationships, suggesting that observed AMR patterns were more consistent with conserved resistance determinants than extensive plasmid-mediated dissemination. Phylogenetic analysis identified two major clades, while pan-genome assessment demonstrated an open genome dominated by accessory genes. Using gene presence/absence profiles, a random forest classifier achieved high accuracy in distinguishing food and clinical isolates, highlighting the classification power of pan-genome signatures within the dataset. These findings provide insights into the genomic structure of food-associated C. sakazakii and the utility of integrating comparative genomics with ML for food safety surveillance.
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| Authors | Zhao Chen, Meiwen Cui |
| Journal | letters in applied microbiology |
| Year | 2026 |
| DOI |
10.1093/lambio/ovag054
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| URL | |
| Keywords | Keywords not found |
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