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Background  Intensive aquaculture farming has caused significant degradation of coastal wetlands and has been proposed as a reservoir for pathogenic  Vibrio  spp.    Results  Gut pathogens including  Vibrio  spp.,  Salmonella  spp., and  Klebsiella  spp. were isolated from bird feces, shrimp and wetland water in two typical coastal regions of China in 2015 and 2017 and were subsequently subjected to whole-genome sequencing. Meanwhile, local patient isolates were also selected to confirm the epidemiological links. Bacterial community composition analyses of the sediments that were sampled in 2015 and 2017 were conducted by the hypervariable region 4 of the  16S rRNA  gene. Together with the local clinical isolates, we observed highly related  Vibrio  isolates from waterbirds, wetlands and shrimp. Phylogenetic genome comparisons also demonstrated that sequence types ST3 and ST2414  Vibrio parahaemolyticus  isolates obtained from aquatic animals were clonally related to patient isolates. Likewise, three  Salmonella typhimurium  isolates were also genomically related to one clinical strain. The results showed that farming activities significantly altered the community composition and resulted in the emergence of several pathogens, including  Acinetobacter ,  Mycobacterium  and  Legionella.Conclusions  In conclusion, our results demonstrated that intensive shrimp farming in wetlands has two devastating impacts: pathogen dissemination from aquatic animals into migratory birds and transmission of foodborne pathogens into local communities.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13099-021-00442-4.

One health pathogen surveillance demonstrated the dissemination of gut pathogens within the two coastal regions associated with intensive farming