Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.

Ben Davies Tall*, Jayanthi Gangiredla, Gopal R. Gopinath, Qiongqiong Yan, Hannah R. Chase, Boram Lee, Seongeun Hwang, Larisa Trach, Eunbi Park, Yeon Joo Yoo, Tae Jung Chung, Scott A. Jackson, Isha R. Patel, Venugopal Sathyamoorthy, Monica Pava-Ripoll, Michael L. Kotewicz, Laurenda Carter, Carol Iversen, Franco Pagotto, Roger StephanAngelika Lehner, Séamus Fanning, Christopher J. Grim

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)
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Abstract

Cronobacter species cause infections in all age groups; however neonates are at highest risk and remain the most susceptible age group for life-threatening invasive disease. The genus contains seven species:Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite an abundance of published genomes of these species, genomics-based epidemiology of the genus is not well established. The gene content of a diverse group of 126 unique Cronobacter and taxonomically related isolates was determined using a pan genomic-based DNA microarray as a genotyping tool and as a means to identify outbreak isolates for food safety, environmental, and clinical surveillance purposes. The microarray constitutes 19,287 independent genes representing 15 Cronobacter genomes and 18 plasmids and 2,371 virulence factor genes of phylogenetically related Gram-negative bacteria. The Cronobacter microarray was able to distinguish the seven Cronobacter species from one another and from non-Cronobacter species; and within each species, strains grouped into distinct clusters based on their genomic diversity. These results also support the phylogenic divergence of the genus and clearly highlight the genomic diversity among each member of the genus. The current study establishes a powerful platform for further genomics research of this diverse genus, an important prerequisite toward the development of future countermeasures against this foodborne pathogen in the food safety and clinical arenas.

Original languageEnglish
Article number36
JournalFrontiers in pediatrics
Volume3
DOIs
Publication statusPublished - 30 Apr 2015
Externally publishedYes

Bibliographical note

Funding Information:
We thank the student internship programs of the International Offices of Kyungpook National University, Daegu, and Gachon University, Gyeonggi, Republic of Korea for sponsoring student interns: B. Lee, S. Hwang, E. Park, Y. J. Yoo, T. J. Chung. We thank the office of Undergraduate Research and Internship Programs, Joint institute of Food Safety and Applied Nutrition, University of Maryland, College Park, MD, USA for sponsoring student interns: H. R. Chase and L. Trach. We thank E. Strain of the Office of Analytics and Outreach, Division of Public Health and Biostatistics, CFSAN for providing us the 454 whole genome sequence of C. malonaticus strain ENBT0334. Funds supporting this work were obtained internally through U.S. FDA appropriations. If readers would like the Excel version of Table S3 in Supplementary Material, and the full data set of CEL files, they are available upon request.

Publisher Copyright:
Copyright © 2015 Tall, Gangiredla, Gopinath, Yan, Chase, Lee, Hwang, Trach, Park, Yoo, Chung, Jackson, Patel, Sathyamoorthy, Pava-Ripoll, Kotewicz, Carter, Iversen, Pagotto, Stephan, Lehner, Fanning and Grim.

Keywords

  • Cronobacter
  • genomic diversity
  • microarray
  • pan genomic
  • phylogenic divergence

ASJC Scopus subject areas

  • Pediatrics, Perinatology, and Child Health

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