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Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains

  • Jang, Hyein1
  • Woo, Jungha1
  • Lee, Youyoung1
  • Negrete, Flavia1
  • Finkelstein, Samantha1
  • Chase, Hannah R.1
  • Addy, Nicole1
  • Ewing, Laura1
  • Beaubrun, Junia Jean Gilles1
  • Patel, Isha1
  • Gangiredla, Jayanthi1
  • Eshwar, Athmanya2
  • Jaradat, Ziad W.3
  • Seo, Kunho4
  • Shabarinath, Srikumar5, 6
  • Fanning, Séamus5, 6
  • Stephan, Roger2
  • Lehner, Angelika2
  • Tall, Ben D.1
  • Gopinath, Gopal R.1
  • 1 U. S. Food and Drug Administration, Center of Food Safety and Applied Nutrition, 8301 Muirkirk Road, Laurel, MD, 20708, USA , Laurel (United States)
  • 2 Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland , Zurich (Switzerland)
  • 3 Jordan University of Science and Technology, Department of Nutrition and Food Technology, Irbid, 22110, Jordan , Irbid (Jordan)
  • 4 Konkuk University, Center for One Health, College of Veterinary Medicine, Seoul, 05029, South Korea , Seoul (South Korea)
  • 5 University College, UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, Dublin, Ireland , Dublin (Ireland)
  • 6 WHO Collaborating Centre for Cronobacter, Belfield, Dublin 4, Ireland , Dublin 4 (Ireland)
Published Article
Standards in Genomic Sciences
Springer (Biomed Central Ltd.)
Publication Date
Nov 29, 2018
DOI: 10.1186/s40793-018-0339-6
Springer Nature


Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazakii, which were obtained from dried spices from the USA, the Middle East, China, and the Republic of Korea. The average genome size of the C. sakazakii genomes was 4393 kb, with an average of 4055 protein coding genes, and an average genome G + C content of 56.9%. The genomes contained genes related to carbohydrate transport and metabolism, amino acid transport and metabolism, and cell wall/membrane biogenesis. In addition, we identified genes encoding proteins involved in osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as virulence-related and heat shock-related proteins. Interestingly, a metabolic island comprised of a variably-sized xylose utilization operon was found within the spice-associated C. sakazakii genomes, which supports the hypothesis that plants may serve as transmission vectors or alternative hosts for Cronobacter species. The presence of the genes identified in this study can support the remarkable phenotypic traits of C. sakazakii such as the organism’s capabilities of adaptation and survival in response to adverse growth environmental conditions (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses provided insights into many aspects of physiology and evolutionary history of this important foodborne pathogen.

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