Richardson

Genomic Analysis of Atypical Aeromonas Hydrophila (Aah) From Catfish Aquaculture in the Southeastern United States With Evidence of Haplotype Shifts From Diagnostic Case Submissions

1Bradley M. Richardson, 2Geoffrey C. Waldbieser, 3Cynthia Ware, 4Mark R. Liles, 3Lester H. Khoo, 3Patricia S. Gaunt, 5Larry A. Hanson, 5Mark L. Lawrence, 1,6David J. Wise, 3Matt J. Griffin

1Department of Wildlife, Fisheries and Aquaculture, College of Forest Resources, Mississippi State University, Mississippi State, MS; 2USDA-ARS, Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center (NWAC), Stoneville, MS; 3Aquatic Research and Diagnostic Laboratory, Department of Pathobiology and Population Medicine, College of Veterinary Medicine, NWAC, Stoneville, MS; 4Department of Biological Sciences, Auburn University, Auburn, AL; 5Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS; 1,6Mississippi Agriculture and Forestry Experiment Station, NWAC, Stoneville, MS

ABSTRACT

Since 2009, atypical Aeromonas hydrophila (aAh) has been associated with acute mortality events resulting in catastrophic losses to catfish aquaculture in the southeastern United States. This study provides a spatial and temporal overview of two aAh haplotypes (ML09-119-like; S14-452-like) from catfish aquaculture with evidence of a shift in haplotype dominance in Mississippi. Data is also presented on potential legacy effects of aAh in the pond environment and an updated genomic analysis of the two haplotypes. These data provide a foundation for future research investigating effective management practices to mitigate aAh losses in farm-raised catfish. Isolates and data from clinical diagnostic submissions were provided by three cooperating diagnostic labs in Mississippi and Alabama. Clinical isolates were identified by duplex polymerase chain reaction (PCR). Draft genomes were sequenced from a subset of isolates using Oxford Nanopore technology. Results revealed that as of 2015, aAh cases in Alabama were strictly due to the ML09-119 haplotype; however, Mississippi cases were attributed to both ML09-119 and S14-452. Approximately 20% of aAh cases in the Mississippi Delta were caused by the S14-452 haplotype in 2014. This percentage increased rapidly to 100% of diagnostic cases in 2017. A similar trend was shown in cases from eastern Mississippi though data was only available for 2016 and 2018. Genomic analysis agreed with previous studies evincing the two haplotypes are highly clonal across the 113 genes investigated. However, as shown in previous studies, the presence of a complete type VI secretion system (T6SS) in S14-452 is an important difference between the two haplotypes. The use of the T6SS in aAh is not fully understood and previous research of other bacterial pathogens have provided evidence of both antagonistic and defensive capabilities. Further research is needed to determine the role of the T6SS in the S14-452 haplotype and any ecological advantages it may provide over the ML09-119 group. The haplotype shift shown in this study suggest increased fitness of S14-452 in the host and/or environment which may have important implications for the management of this pathogen.