Antibiotics | Comparative Genome-Wide Analysis of DH5α-Inhibiting Escherichia coli Isolates Reveals Common Co-Occurrence of Bacteriocin Genes with Antibiotic Resistance and Virulence Factors

This study demonstrates that Escherichia coli strains isolated from healthy individuals' feces carry bacteriocin genes alongside widespread antibiotic resistance and virulence factors, indicating their potential role in intestinal microbial ecology and resistance transmission. The genomic characteristics of these strains provide new insights into the interplay between antibiotic resistance, virulence, and bacteriocin production, supporting the development of targeted probiotics or alternative antimicrobial strategies.

 

Literature Overview
This study published in the journal Antibiotics titled 'Comparative Genomics of DH5α-Inhibiting Escherichia coli Isolates from Feces of Healthy Individuals Reveals Common Co-Occurrence of Bacteriocin Genes with Virulence Factors and Antibiotic Resistance Genes' summarizes the genome-wide features of DH5α-inhibiting strains isolated from healthy individuals. It focuses on the co-occurrence of bacteriocin genes, antibiotic resistance genes (ARGs), and virulence factors, providing new clues for understanding their ecological roles in the gut microbiota and potential impact on resistance dissemination.

Background Knowledge
Escherichia coli represents a critical component of the intestinal microbiota, with strains harboring bacteriocins, antibiotic resistance genes, and virulence factors widely existing in healthy populations. Bacteriocins (e.g., colicins and microcins) are species-specific antimicrobial proteins that may influence intestinal microbial competition and homeostasis. The spread of resistance genes poses major global health challenges, particularly concerning their role as potential reservoirs in non-clinical populations. Through large-scale screening and whole-genome sequencing of 38 DH5α-inhibiting strains, this study reveals their genomic diversity, resistance profiles, virulence characteristics, and widespread bacteriocin gene distribution, laying the foundation for future research on microbial community dynamics and horizontal gene transfer.

 

 

Research Methods and Experiments
Researchers collected 109 fecal samples from the Singapore Integrative Omics Study (2018) and screened 3,107 Escherichia coli strains for DH5α-inhibiting activity using a large-scale spot-on-lawn assay, ultimately selecting 38 representative strains for whole-genome sequencing. Bacteriocin genes, antibiotic resistance genes, and virulence factors were predicted using BAGEL4, ResFinder, and VirulenceFinder. A phylogenetic tree based on 81 core genes was constructed to evaluate phylogenetic relationships, while distribution patterns of bacteriocin genes, resistance genes, and virulence factors were analyzed.

Key Conclusions and Perspectives

• 92% of strains carry at least one bacteriocin gene, predominantly colicins and microcins, with some strains harboring the hcp-et3-4 gene cluster encoding T6SS-related effector proteins.
• About 40% of sequenced strains exhibit multidrug resistance (MDR), with strain D96 resistant to up to 8 antibiotic classes. Resistance genes are primarily plasmid-borne, though some strains show chromosomal integration.
• 55.3% of strains meet ExPEC (Extraintestinal Pathogenic Escherichia coli) criteria, carrying ≥2 virulence factors. Group I (primarily B2 and F types) strains typically harbor ≥3 virulence factors.
• Bacteriocins may play significant roles in intestinal microbial competition, while their coexistence with resistance genes could facilitate horizontal resistance transfer, posing challenges for probiotic development.

Research Significance and Prospects
This study reveals complex genomic features in Escherichia coli strains from healthy individuals, providing new perspectives for understanding their ecological roles. Future research should evaluate these strains' in vivo efficacy against multidrug-resistant pathogens and explore their potential as probiotics. Investigating chromosomal-mediated resistance evolution will also help predict resistance gene dissemination risks within microbial communities.

 

 

Conclusion
DH5α-inhibiting Escherichia coli strains isolated from healthy individuals exhibit high genomic diversity and commonly carry bacteriocin genes, antibiotic resistance determinants, and virulence factors. These features suggest adaptive advantages in intestinal microbial competition and potential roles as horizontal gene transfer vectors. This work emphasizes comprehensive safety and genetic stability assessments for bacteriocin-producing strains in probiotic development to prevent horizontal transfer of resistance and virulence genes. The study provides baseline data for resistance gene dissemination mechanisms in healthy populations and informs future evaluations of probiotic candidate strains' feasibility and risks.

 

Shuan Er, Yichen Ding, Linda Wei Lin Tan, Niranjan Nagarajan, and Henning Seedorf. Comparative Genomics of DH5α-Inhibiting Escherichia coli Isolates from Feces of Healthy Individuals Reveals Common Co-Occurrence of Bacteriocin Genes with Virulence Factors and Antibiotic Resistance Genes. Antibiotics.