Genetic diversity and antimicrobial resistance in commensal Escherichia coli from pigs and broiler chickens

PhD student: Shahana Ahmed,

Department of Veterinary and Animal Sciences, Section of Veterinary Clinical Microbiology

Background and aim

Escherichia coli is an important part of the gut flora of all warm-blooded vertebrates. So far research has focused on the few types of E. coli that cause disease, while the large group of harmless, commensal E. coli has been neglected. We do not know how diverse this group is, what determines its diversity, and to which extend it is a reservoir for antimicrobial resistance genes and genes that can enhance the disease potential of pathogenic E. coli. This PhD study was conducted in order to improve our understanding of the commensal E. coli population in pigs and broilers.


Commensal E. coli populations in Danish pigs and in Bangladesh broilers both showed high diversity, and diversity varied according to age. Surprisingly, the diversity in pigs was highest right after weaning, where the flora is in unbalance, challenging the concept that high diversity is a sign of gut health. DNA sequence-analysis revealed that commensal E. coil from pigs are not clearly separated from the pathogenic types and that they frequently carried virulence and antimicrobial resistance genes. Interestingly, particular sequence types appeared to be adopted to pigs. Literature suggests that this is also the case in other countries and that the types overlap between countries. Treatment of pigs with antimicrobials (tetracycline and colistin) caused short increase in concentration of commensal E. coli with resistance to these drugs, but the resistance quickly disappeared. In Bangladesh, use of colistin is widely used in broiler production. This drug is classified by WHO as Critically important for human health, and resistance in commensal E. coli is a cause for concern. Resistance to this drug was common (25% of isolates) and resistance was shown to be due to presence of the resistance gene, mcr-1. Positive strains were not clonally related suggesting a massive horizontal spread of mcr-1 gene in the production system. Interestingly, the variation in resistance towards colistin varied considerably (MIC from 2 to 128 ug/ml) despite the presence of the same resistance gene with the same gene sequence, suggesting that other genes play a role for the level of resistance. Comparison of gene sequences revealed mutations in genes associated with LPS biosynthesis, but the functional importance of these mutations remains to be investigated.


The presence of commensal E. coli types that appear to be adapted to pigs should be further studied in order to reveal which traits are likely important for the success of E. coli in the intestine of pigs. Such strains may be used to block colonization with pathogenic types. With more knowledge on the factors that determines diversity of the commensal E. coil we may further be able to keep this flora stable in order to prevent colonization with pathogenic types. As mentioned, the presence of a high number of commensal E. coli with colistin resistance is worrisome, and it is highly indicated to determine whether there is frequent transfer of colistin resistant E. coli from broilers to man in Bangladesh.