Genomic Characterization of Emerging Pathogenic E. coli Cryptic Clade I Isolate from Poultry Intestine

Abstract

Escherichia coli is part of the resident microflora of gut, but it is also known as an opportunistic pathogen because some commensal strains may acquire certain virulence genes and become pathogenic. On the basis of these virulence characteristics, pathogenic ones are broadly classified into Extra-intestinal Pathogenic E. coli (ExPEC) and Intestinal Pathogenic E. coli (IPEC). Genomic distribution has divided E. coli into 9 phylogroups and 5 Cryptic Clades. Among these Cryptic Clades, Clade I have been assigned as a sub-specie of E. coli with the inability to be distinguish phenotypically. In recent times, there has been an emergence of Cryptic Clade I as human intestinal pathogen. As the emergence of human intestinal pathogenic Cryptic Clade I isolates in poultry intestines and its phenotypic identification remains a challenge where we are lacking in knowledge about the population structure and pathogenicity potential of these Clade I strains on a global scale. Therefore, active surveillance and genomic characterization of Cryptic Clade I is essential to design strategies against its potential threats. In this study, for a better understanding of genomic diversity, virulence and resistance determinants a poultry intestinal isolate belonging to Clade I was characterized phenotypically and genotypically along with its comparative genome analysis with global strains was carried out. The Clade I isolate TK.1.1 is a multi-drug resistant, virulent strain with a genome size of 6.0 Mb containing 6509 coding sequences. The strain TK.1.1 belongs to ST770 and have O102:H51 serogroup. It harbors several resistant determinants, five plasmid replicons (designated as Col8282, IncHI2, IncQI, IncI (Gamma), and IncFIB (AP001918), 16 prophage sequences, 2 miniature inverted repeats and several virulence genes. To conclude, acquisition of non-prophage sequences and genomic islands conferring virulence and resistance indicate the genomic plasticity and adaptive potential of Cryptic Clade I. Production of bacteriocins by Cryptic Clade I isolate holds a competitive edge against other E. coli sensu stricto strains. Comparative genome analysis revealed high genetic diversity among Cryptic Clade I strains that are evolving through the acquisition of resistance and virulence genes. These genetic insights will be helpful for effective control measures against this pathogen, for health care providence as well as research and development (R & D) organizations. In future, Appropriate surveillance studies are needed to determine Cryptic Clade I prevalence in our region, transmission between hosts & local antibiotic resistance trends. More Whole Genome 2 Sequences of Cryptic Clade I should be made available in order to accurately estimate the size of pangenome, to study diversity and population structure.