Sequence types of enteroaggregative Escherichia coli strains recovered from human, animal, and environmental sources: India

Abstract

In 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. We 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 D was done. All strains were genome-sequenced, and bioinformatics analysis was performed. EAEC 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 %). ST131, known for multidrug resistance and causing various diseases, was detected in acute diarrhea cases and animal sources, underscoring its clinical significance. These findings indicate the high diversity of EAEC and different sources of unique ST types of EAEC. The study reinforces the One Health approach, highlighting the interconnection between human health, animal reservoirs, and environmental sources in EAEC transmission dynamics. The identification of EAEC strains in animals suggests the zoonotic potential of these pathogens, necessitating comprehensive surveillance and control measures. The study emphasizes the need for continued surveillance and a One Health approach to address the complex transmission dynamics of EAEC.