Sequence types of Enteroaggregative Escherichia coli strains recovered from human, animal, and environmental sources, India.

ObjectivesIn the current study, we report whole genome sequencing (WGS) data on EAEC strains from India to identify lineages and different sequence types (STs) in our geographical regions across North India. Material and methodsWe performed WGS comparative genomics characterization to examine the diversity of 122 EAEC strains collected from a large geographic area from clinical (Human sources) and non-clinical sources (animal and environmental sources). M-PCR for 21 virulence genes was performed. A triplex PCR detected phylogenetic groups A, B1, B2, and Dwas done. All strains were genome-sequenced, and bioinformatics analysis was performed. ResultsEAEC isolates belonged to 29 sequence types, further clustered into 11 clonal complexes, among which CC38 was the largest, containing 38 isolates mainly belonging to two ST types (ST38 and ST315). CC10 was the most diverse group, comprising 8 STs (ST43, ST2706, ST1286, ST 10, ST167, ST34, ST227, and ST4305). The most frequently detected virulence gene among the 96 clinical EAEC isolates was astA (87.5%), followed by ORF3 (62.5%), and aap (54.1%). ConclusionThese findings indicate the high diversity of EAEC and different sources of unique ST types of EAEC. Such genetic relatedness may be a favorable factor in exchanging virulence factors and other genes. The results of this study provide genetic evidence that farmed animals may act as a reservoir of EAEC.