Phylogenetic analysis of drug resistant environmental Escherichia coli

Abstract

Escherichia coli can be both harmful causing disease in human or harmless in the environment. Considering the diverse nature of E. coli, the main aim of this study was to understand the current dynamics of E. coli in the environment. One hundred and eighty four isolates from different environmental sources including human (n=60), animal (n=54), prawn (n=25) and the abiotic environment (n=45) were investigated. All of the test isolates harbored uspA and uidA genes confirming their identity. Fifty randomly selected isolates represented the same ARDRA (Amplified Ribosomal DNA Restriction Analysis) pattern indicating that the 16s rDNA sequences were conserved. Quadruplex PCR was used for phylogrouping, in which, environmental B1 (46.74%) was found to be the predominant group, followed by commensal group A (28.26%), B2 (1.63%), C (8.15%), D (10.67%), E (3.26%) and F (2.17%). Phylogroups A and B1 were found in all environments, whereas pathogenic B2, D and sister group F were present only in human UTI samples. Both Shannon diversity index for human (1.32) and nonhuman (1.17) and Simpsons diversity index (0.64) for E. coli phylogroup diversity were significantly different (p>0.05) indicating that the two environments are different in terms of phylogroup diversity. According to Pianka’s Pairwise index of similarity the value between human and non-human sources was 0.48, indicating low similarity. The most prevalent virotype was EPEC (1.33%, n=150) followed by ETEC (0.67%, n=150). The eae gene was absent indicating no recent fecal contamination occurred. Class-1 Integron was present only in 30% (n=150) isolates whereas plasmid was detected in 58.67% (n=150) isolates, of which 80.68% isolates were resistant to all of the antibiotics tested. It was observed that there was no specific correlation between the occurrence of Class I Integron or plasmids and multidrug resistance. E. coli of human origin were predominantly resistant to Azithromycin (60%) whereas non-human host isolates were mostly resistant to Cefixime (32.73%). Overall, E. coli isolated from human were more resistant to most of the antibiotics tested compared to their non-human relatives. In terms of diversity in antibiotic resistance, there was no significant difference between the resistance patterns of human and non-human E. coli. This study indicates that environmental E. coli has adapted to live in different environmental types including the human gut, which is of particular concern since these isolates are able to harbour hitherto unknown and potentially harmful genes from the environment. On the other hand, commensal E. coli are predominant residents of the animal gut which contradicts our general understanding about commensals.