title: Use of a Pan-Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology.
abstract: Cronobacter(previously known asEnterobacter sakazakii) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the familyEnterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains ofCronobacterspp. and taxonomically-related isolates was determined using a recently reported DNA microarray. TheCronobactermicroarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the sevenCronobacterspecies from one another and from non-Cronobacterspecies. The microarray was also able to cluster strains within each species into well-defined subgroups. These results also support previous studies on the phylogenic separation of species members of the genus and clearly highlight the evolutionary sequence divergence among each species of the genus compared to phylogenetically-related species. This review extends these studies and illustrates how the microarray can also be used as an investigational tool to mine genomic data sets from strains. Three case studies describing the use of the microarray are shown and include: (1) the determination of allelic differences amongCronobacter sakazakiistrains possessing the virulence plasmid pESA3; (2) mining of malonate and myo-inositol alleles among subspecies ofCronobacter dublinensisstrains to determine subspecies identity; and (3) lastly using the microarray to demonstrate sequence divergence and phylogenetic relatedness trends for 13 outer-membrane protein alleles among 240Cronobacterand phylogenetically-related strains. The goal of this review is to describe microarrays as a robust tool for genomics research of this assorted and important genus, a criterion toward the development of future preventative measures to eliminate this foodborne pathogen from the global food supply.
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. ben.tall@fda.hhs.gov.
authors.forename: Ben D
authors.initials: BD
authors.lastname: Tall
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. jayanthi.gangiredla@fda.hhs.gov.
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 20708, USA. Christopher.grim@fda.hhs.gov.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Grim
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. Isha.patel@fda.hhs.gov.
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 20708, USA. scott.jackson@nist.gov.|Complex Microbial Systems Group Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA. scott.jackson@nist.gov.
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 20708, USA. mark.mammel@fda.hhs.gov.
authors.forename: Mark K
authors.initials: MK
authors.lastname: Mammel
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. mahendrakothary@gmail.com.
authors.forename: Mahendra H
authors.initials: MH
authors.lastname: Kothary
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. venugopal.sathyamoorthy@fda.hhs.gov.
authors.forename: Venugopal
authors.initials: V
authors.lastname: Sathyamoorthy
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. laurenda.carter@fda.hhs.gov.
authors.forename: Laurenda
authors.initials: L
authors.lastname: Carter
authors.affiliation: UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin, Belfield, Dublin D04 N2E5, Ireland. sfanning@ucd.ie.
authors.forename: Séamus
authors.initials: S
authors.lastname: Fanning
authors.affiliation: College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK. c.iversen@dundee.ac.uk.
authors.forename: Carol
authors.initials: C
authors.lastname: Iversen
authors.affiliation: Food Directorate, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A 0K9, Canada. Franco.Pagotto@hc-sc.gc.ca.
authors.forename: Franco
authors.initials: F
authors.lastname: Pagotto
authors.affiliation: Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstr. 272, CH-8057 Zurich, Switzerland. stephanr@fsafety.uzh.ch.
authors.forename: Roger
authors.initials: R
authors.lastname: Stephan
authors.affiliation: Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstr. 272, CH-8057 Zurich, Switzerland. lehnera@fsafety.uzh.ch.
authors.forename: Angelika
authors.initials: A
authors.lastname: Lehner
authors.affiliation: Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada. jfarber@uoguelph.ca.
authors.forename: Jeffery
authors.initials: J
authors.lastname: Farber
authors.affiliation: UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin, Belfield, Dublin D04 N2E5, Ireland. qyan07@gmail.com.
authors.forename: Qiong Q
authors.initials: QQ
authors.lastname: Yan
authors.affiliation: Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA. gopal.gopinathrao@fda.hhs.gov.
authors.forename: Gopal R
authors.initials: GR
authors.lastname: Gopinath
keywords: Cronobacter; data mining; microarray