title: Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.
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.
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Ben Davies
authors.initials: BD
authors.lastname: Tall
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Jayanthi
authors.initials: J
authors.lastname: Gangiredla
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Gopal R
authors.initials: GR
authors.lastname: Gopinath
authors.affiliation: UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin , Dublin , Ireland ; WHO Collaborating Centre for Cronobacter , Dublin , Ireland.
authors.forename: Qiongqiong
authors.initials: Q
authors.lastname: Yan
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Hannah R
authors.initials: HR
authors.lastname: Chase
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Boram
authors.initials: B
authors.lastname: Lee
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Seongeun
authors.initials: S
authors.lastname: Hwang
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Larisa
authors.initials: L
authors.lastname: Trach
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Eunbi
authors.initials: E
authors.lastname: Park
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: YeonJoo
authors.initials: Y
authors.lastname: Yoo
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: TaeJung
authors.initials: T
authors.lastname: Chung
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Isha R
authors.initials: IR
authors.lastname: Patel
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Venugopal
authors.initials: V
authors.lastname: Sathyamoorthy
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , College Park, MD , USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Pava-Ripoll
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Kotewicz
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Laurenda
authors.initials: L
authors.lastname: Carter
authors.affiliation: College of Life Sciences, University of Dundee , Dundee , UK.
authors.forename: Carol
authors.initials: C
authors.lastname: Iversen
authors.affiliation: Food Directorate, Bureau of Microbial Hazards/Health Canada , Ottawa, ON , Canada.
authors.forename: Franco
authors.initials: F
authors.lastname: Pagotto
authors.affiliation: Institute for Food Safety and Hygiene, University of Zurich , Zurich , Switzerland.
authors.forename: Roger
authors.initials: R
authors.lastname: Stephan
authors.affiliation: Institute for Food Safety and Hygiene, University of Zurich , Zurich , Switzerland.
authors.forename: Angelika
authors.initials: A
authors.lastname: Lehner
authors.affiliation: UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin , Dublin , Ireland ; WHO Collaborating Centre for Cronobacter , Dublin , Ireland.
authors.forename: Séamus
authors.initials: S
authors.lastname: Fanning
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Grim
keywords: Cronobacter; genomic diversity; microarray; pan genomic; phylogenic divergence