Fingerprinting study links multidrug-resistant E. coli across clinical, environmental and food sources

Multidrug-resistant Escherichia coli recovered from hospitals, the environment and food share similar resistance gene profiles and lack clear source-specific clustering, according to a new study published in Annals of Microbiology. The findings suggest possible genetic relatedness among isolates from these different ecological niches and support the use of molecular fingerprinting for antimicrobial resistance surveillance within a One Health framework.

The research team recovered a total of 120 E. coli isolates and selected 68 multidrug-resistant (MDR) isolates for detailed analysis: 21 from clinical sources, 23 from environmental sources and 24 from food. Each selected isolate underwent antimicrobial susceptibility testing, determination of the multiple antibiotic resistance (MAR) index, PCR detection of β-lactamase and carbapenemase genes, and molecular fingerprinting using two methods, ERIC-PCR and (GTG)₅-PCR. Genetic relationships among the isolates were then analysed by dendrogram construction and principal component analysis.

High levels of multidrug resistance were observed across all three sources. The reported MDR prevalence was 100 percent among clinical isolates, 91.3 percent among environmental isolates and 79.2 percent among food isolates. The authors note that the emergence and dissemination of MDR E. coli across clinical, environmental and food sources poses a major public health challenge within the One Health framework, which considers human, animal and environmental health as interconnected.

Both fingerprinting methods revealed substantial genetic diversity among the isolates, while several clusters exhibited moderate genetic similarity across different sample sources. Notably, the analysis found no clear source-specific clustering, meaning that isolates from hospitals, the environment and food did not separate neatly into distinct genetic groups by origin. The authors state that the widespread occurrence of MDR E. coli, the presence of similar resistance gene profiles across the studied sources, and the absence of clear source-specific clustering together suggest possible genetic relatedness among isolates from different sources.

The two fingerprinting techniques did not perform identically. Among clinical isolates, by contrast, both ERIC-PCR and (GTG)₅-PCR showed comparable discriminatory ability.

The study compared the antimicrobial resistance, genetic diversity and molecular relatedness of E. coli isolates from the three ecological niches using the two PCR-based fingerprinting approaches. The authors combined these patterns with dendrogram construction and principal component analysis to visualise the relationships among the 68 MDR isolates.

The authors conclude that these findings support the application of molecular fingerprinting for antimicrobial resistance surveillance within a One Health framework. Because resistance genes such as blaNDM appeared across clinical, environmental and food isolates, the study illustrates how fingerprinting methods can help trace potential connections between reservoirs of resistant bacteria. The article was published on 19 October 2026 as an open access original article, and the version shared at publication is subject to further edits before the final version of record.

Subject of Research: Comparative fingerprinting of multidrug-resistant E. coli from clinical, environmental and food sources

Article Title: Comparative evaluation of ERIC-PCR and (GTG)₅-PCR for genetic diversity analysis of multidrug-resistant Escherichia coli from clinical, environmental, and food sources

Article References: Sinha, A., Roy, A., Sahoo, A., Sahu, M. C., & Pati, S. (2026). Comparative evaluation of ERIC-PCR and (GTG)₅-PCR for genetic diversity analysis of multidrug-resistant Escherichia coli from clinical, environmental, and food sources. Annals of Microbiology. https://doi.org/10.1186/s13213-026-01884-4

Image Credits: AI Generated

DOI: 10.1186/s13213-026-01884-4

Keywords: Escherichia coli, multidrug resistance, ERIC-PCR, (GTG)5-PCR, blaNDM, One Health, genetic diversity, molecular fingerprinting, antimicrobial resistance surveillance, carbapenemase genes, MAR index, dendrogram