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IntroductionSoft rot Pectobacteriaceae (SRP) bacteria are globally dispersed pathogens that cause significant economic loss in potato and other crops. Our understanding of the SRP species diversity has expanded in recent years due to advances and adoption of whole-genome sequence technologies. There are currently 34 recognized SRP species that belong to the Dickeya and Pectobacterium genera.MethodsWe used whole-genome sequencing based analysis to describe the current distribution and epidemiology of SRP isolated from diseased potato samples obtained from commercial potato cropping systems in the United States. Our primary objectives in the present study were to: (1) identify the species of these SRP isolates recovered from potato samples across 14 states in the US, (2) describe the variation among SRP isolates from various US locations and track their temporal changes, and (3) evaluate the evolutionary relationships among these SRP isolates to deduce their source. We collected 118 SRP strains from diseased potato plants and tubers in 14 states between 2015 and 2022.ResultsWe identified three Dickeya and eight Pectobacterium species from diseased potato samples. Dickeya dianthicola, Pectobacterium parmentieri, P. carotovorum, and P. versatile appeared to be the predominant species, constituting 83% of the isolates. Furthermore, all D. dianthicola strains studied here as well as 90% of US D. dianthicola isolates sequenced to date exhibit significant clonality.DiscussionThe prevalence of this specific group of D. dianthicola, temporally and geographically, aligns with the occurrence of blackleg and soft rot outbreaks in the northeastern US after 2014. The genomic diversity observed in P. parmentieri implies multiple introductions to the US from at least four distinct sources, earlier than the arrival of the predominant group of D. dianthicola. In contrast, P. carotovorum and P. versatile appear to be widespread, long-term endemic strains in the US.

Disease-free planting stocks and formal certification systems are critical for the profitable production of vegetatively propagated crops. Propagation through seed tubers is the standard and preferred process for potato production. Seed tuber certification systems are used in the United States and throughout the world to mitigate degeneration and promote the use of high-quality planting stocks. Seed certification uses molecular and serological diagnostic methods for stock testing. While the molecular assays available are well-validated and offer high sensitivity, the rapidly evolving pathogens they target routinely develop mutations that allow them to evade detection. Examples of these limitations are the potato diseases soft rot and blackleg, caused by Pectobacterium and Dickeya species. These diseases are challenging for current diagnostics tools because of high pathogen genomic variability, identical symptom development, and co-infections. Given the rapidly changing genetics of soft rot and blackleg bacteria, metagenomic sequencing should be adopted as a tool for routine validation of currently accepted diagnostic methods, and for the development of new diagnostic assays. We propose metagenome sequencing usage to enhance the diagnostic capabilities and complement molecular epidemiology approaches. We envision that metagenomics will accelerate diagnosis, shorten response time to outbreaks caused by unknown microorganisms, and provide more accurate and sustainable management strategies for seed certification programs. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.