Evaluation of Genomic Diversity and Gene Content Differences among <i>Cronobacter</i> Isolated from Dairy Manufacturing Environments Using a Pan Genome Microarray

Gopinath, Gopal; Gopinath, Gopal

Monday, July 27, 2015

Exhibit Hall (Oregon Convention Center)

Gopal Gopinath , U.S. Food and Drug Administration , Laurel , MD

Jayanthi Gangiredla , U.S. Food and Drug Administration , Laurel , MD

Christopher Grim , U.S. Food and Drug Administration , Laurel , MD

Yi Chen , U.S. Food and Drug Administration-CFSAN , College Park , MD

Scott Jackson , NIST , Gaithersburg , MD

Isha Patel , U.S. Food and Drug Administration , Laurel , MD

Qiongqiong Yan , University College Dublin , Dublin , Ireland

Hannah Chase , U.S. Food and Drug Administration , Laurel , MD

Eunbi Park , U.S. Food and Drug Administration , Laurel , MD

YeonJoo Yoo , U.S. Food and Drug Administration , Laurel , MD

TaeJung Chung , U.S. Food and Drug Administration , Laurel , MD

Venugopal Sathyamoorthy , U.S. Food and Drug Administration , Laurel , MD

Laurenda Carter , U.S. Food and Drug Administration , Laurel , MD

Michael Kotewicz , U.S. Food and Drug Administration , Laurel , MD

Carol Iversen , University of Dundee , Dundee , Scotland

Franco Pagotto , Health Canada , Ottawa , Canada

Roger Stephan , University of Zurich , Zurich , Switzerland

Angelika Lehner , University of Zurich , Zurich , Switzerland

Seamus Fanning , University College Dublin , Dublin , Ireland

Ben D. Tall , U.S. Food and Drug Administration , Laurel , MD

Introduction: Cronobacter sakazakii, C. malonaticus, and C. turicensis have been implicated in neonatal infections and cause septicemia, meningitis, and necrotizing enterocolitis. It has been isolated from a wide range of sources such as, powdered infant formula, powdered milk, lactose, and starches and associated manufacturing environments.

Purpose: Despite a wealth of published genomes of these species, genomics-based epidemiology of the genus is not well established. A diverse group of 195 unknown Cronobacter and other taxonomically-related isolates obtained through an environmental surveillance sampling program of 55 milk powder and cheese manufacturing facilities were analyzed using a novel pan-genome microarray to annotate the gene content, highlight the genomic diversity and phylogenetic relationship among the strains.

Methods: A pan-genome DNA microarray with ~22,000 features from 15 published Cronobacter genomes was developed. Genomic DNA was isolated using a QIAcube workstation following the manufacturer’s recommendations and hybridizations were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual.

Results: The microarray was clearly able to distinguish the seven Cronobacter species from one another, and from related non-Cronobacter species. The interrogation of 115 milk powder Cronobacter isolates with the microarray identified three C. turicensis (Ct), 15 C. dublinensis (Cd), and 97 C. sakazakii (Cs) isolates. Strain-level differences showed that the Cd isolates grouped within two of three Cd clades, the Ct isolates within a single Ct clade, and the Cs isolates within seven of eight Cs clades.

Significance: The microarray showed that the Cd and Ct isolates were more clonal than the Cs isolates. The microarray also showed that all Cd and Ct isolates possessed the common virulence plasmid compared to 94 (97%) of Cs isolates. The current study establishes a powerful platform for further genomics research of this diverse genus, a prerequisite towards development of future countermeasures against this important foodborne pathogen.

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P2-190 Evaluation of Genomic Diversity and Gene Content Differences among Cronobacter Isolated from Dairy Manufacturing Environments Using a Pan Genome Microarray