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Workflow of three pipelines. (A) Amplicon‐based microbial identification, such as 16S rDNA/18S rDNA/ITS genes. (B) SNP‐based source tracking. (C) WGS‐based microbial identification. ANI, Average Nucleotide Identity; ARGs, antibiotic resistance genes; rDNA, recombinant DNA; rRNA, ribosomal RNA; SNP, single‐nucleotide polymorphism; VFGs, virulence factors genes; WGS, whole genome sequencing.
