Local and Environmental Reservoirs ofSalmonella entericaAfter Hurricane Florence Flooding

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Abstract In many regions of the world, including the United States, human and animal fecal genetic markers have been found in flood waters. In this study, we use high‐resolution whole genomic sequencing to examine the origin and distribution ofSalmonella entericaafter the 2018 Hurricane Florence flooding. We specifically asked whetherS. entericaisolated from water samples collected near swine farms in North Carolina shortly after Hurricane Florence had evidence of swine origin. To investigate this, we isolated and fully sequenced 18 independentS. entericastrains from 10 locations (five flooded and five unflooded). We found that all strains have extremely similar chromosomes with only five single nucleotide polymorphisms (SNPs) and possessed two plasmids assigned bioinformatically to the incompatibility groups IncFIB and IncFII. The chromosomal core genome and the IncFIB plasmid are most closely related to environmentalSalmonellastrains isolated previously from the southeastern US. In contrast, the IncFII plasmid was found in environmentalS. entericastrains whose genomes were more divergent, suggesting the IncFII plasmid is more promiscuous than the IncFIB type. We identified 65 antibiotic resistance genes (ARGs) in each of our 18S. entericaisolates. All ARGs were located on theSalmonellachromosome, similar to other previously characterized environmental isolates. All isolates with different SNPs were resistant to a panel of commonly used antibiotics. These results highlight the importance of environmental sources of antibiotic‐resistantS. entericaafter extreme flood events.

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