Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America

Details

• Personal Author:
  Boxrud D ; Elnekave E ; Flores-Figueroa C ; Folster JP ; Johnson A ; Johnson TJ ; Kearney A ; Miller EA ; Munoz-Aguayo J ; Nadon CA ; Singer RS ; Tagg KA ; Tschetter L ; Weber BP
• Description:
  Two separate human outbreaks of Salmonella enterica serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole-genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade, isolates clustered into three subclades, including an "emergent" clade that contained only isolates dated 2016 or later, with many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades, suggesting that the apparent success of currently circulating subclades is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S. Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source. IMPORTANCE: Increasingly, outbreak investigations involving foodborne pathogens are difficult due to the interconnectedness of food animal production and distribution, and homogeneous nature of industry integration, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole-genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincided with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in commercial turkeys and ability to cause illness in humans. [Description provided by NIOSH]
• Subjects:
  Food Handling Food Industry Occupational Health Safety
• Keywords:
  Author Keywords: Salmonella Bacterial Infections Clone Disease Transmission Food Genomic Genomics Human Meat Handlers Meat Packing Industry Outbreak Poultry Poultry Industry Turkey

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• ISSN:
  2379-5042
• Document Type:
  Text
• Funding:
  Cooperative Agreement
• Genre:
  Journal Article
• Place as Subject:
  Georgia ; Minnesota ; OSHA Region 4 ; OSHA Region 5
• CIO:
  National Institute for Occupational Safety and Health (NIOSH)
• Topic:
  Workplace Safety & Health
• Location:
  North America
• Volume:
  5
• Issue:
  2
• NIOSHTIC Number:
  nn:20070758
• Citation:
  mSphere 2020 Mar/Apr; 5(2):e00056-20
• Contact Point Address:
  Timothy J. Johnson, Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
• Email:
  tjj@umn.edu
• Federal Fiscal Year:
  2020
• NORA Priority Area:
  Agriculture, Forestry and Fishing
• Performing Organization:
  University of Minnesota
• Peer Reviewed:
  True
• Start Date:
  20110930
• Source Full Name:
  mSphere
• End Date:
  20270929
• Collection(s):
  National Institute for Occupational Safety and Health
• Main Document Checksum:
  urn:sha-512:25d4f67bebd28646efe67c1ae276799bf734b8546298c402c6828ae252266f38bf21d6f045a5ff43edcd8b698fb851ad8fae39efe6bac3e426e1436e07f00568
• Download URL:
  https://stacks.cdc.gov/view/cdc/208923/cdc_208923_DS1.pdf
• File Type:
  [PDF - 3.42 MB ]