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Genomic Profiling of Multidrug-Resistant Swine Escherichia coli and Clonal Relationship to Human Isolates in Peru
Luis Alvarez1, Dennis Carhuaricra2, Joel Palomino-Farfan1
1Laboratory of Veterinary Bacteriology and Mycology, Faculty of Veterinary Medicine, National University of San Marcos, Lima 15021, Peru.
Abstract:
The misuse of antibiotics is accelerating antimicrobial resistance (AMR) in Escherichia coli isolated from farm animals. The genomes of ten multidrug-resistant (MDR) E. coli isolates from pigs were analyzed to determine their sequence types, serotypes, virulence, and AMR genes (ARGs). Additionally, the relationship was evaluated adding all the available genomes of Peruvian E. coli from humans using the cgMLST + HierCC scheme. Two aEPEC O186:H11-ST29 were identified, of which H11 and ST29 are reported in aEPEC isolates from different sources. An isolate ETEC-O149:H10-ST100 was identified, considered a high-risk clone that is frequently reported in different countries as a cause of diarrhea in piglets. One ExPEC O101:H11-ST167 was identified, for which ST167 is an international high-risk clone related to urinary infections in humans. We identified many ARGs, including extended-spectrum β-lactamase genes, and one ETEC harboring the mcr-1 gene. CgMLST + HierCC analysis differentiated three clusters, and in two, the human isolates were grouped with those of swine in the same cluster. We observed that Peruvian swine MDR E. coli cluster with Peruvian E. coli isolates from healthy humans and from clinical cases, which is of great public health concern and evidence that AMR surveillance should be strengthened based on the One Health approach.
Insights
Antimicrobial resistance (AMR) in Escherichia coli from Peruvian pigs is a public health concern. Swine AMR E. coli strains closely resemble those found in humans, highlighting the need for integrated One Health surveillance.
Area of Science:
- Microbiology
- Genomics
- Public Health
Background:
- Antibiotic misuse accelerates antimicrobial resistance (AMR) in Escherichia coli from farm animals.
- Multidrug-resistant (MDR) E. coli poses a significant threat to both animal and human health.
Purpose of the Study:
- To analyze the genomes of MDR E. coli from Peruvian pigs.
- To determine sequence types, serotypes, virulence, and AMR genes (ARGs).
- To evaluate the relationship between swine and human E. coli isolates in Peru.
Main Methods:
- Whole-genome sequencing of ten MDR E. coli isolates from pigs.
- Comparative analysis with available Peruvian human E. coli genomes.
- Core genome multilocus sequence typing (cgMLST) combined with Hierarchical Clustering (HierCC) for phylogenetic analysis.
Main Results:
- Identified high-risk E. coli clones, including aEPEC O186:H11-ST29, ETEC O149:H10-ST100, and ExPEC O101:H11-ST167.
- Detected numerous ARGs, including extended-spectrum β-lactamase genes, and the mcr-1 gene in an ETEC isolate.
- cgMLST + HierCC analysis revealed clustering of swine and human E. coli isolates, indicating potential transmission.
Conclusions:
- Peruvian swine MDR E. coli strains are closely related to human isolates, posing a public health risk.
- AMR surveillance must be strengthened using a One Health approach to address interspecies transmission.
- Genomic epidemiology is crucial for understanding AMR dissemination and informing control strategies.
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