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.

Ben Tall,Scott Jackson,Jayanthi Gangiredla,Jeffery Farber,Venugopal Sathyamoorthy,Mahendra Kothary,Gopal Gopinath,Qiong Yan,Angelika Lehner,Laurenda Carter,Roger Stephan,Carol Iversen,Mark Mammel,Séamus Fanning,Franco Pagotto,Christopher Grim,Isha Patel

doi:10.3390/microarrays6010006

Abstract

Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. 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 of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray 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 seven Cronobacter species from one another and from non-Cronobacter species. 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 among Cronobacter sakazakii strains possessing the virulence plasmid pESA3; (2) mining of malonate and myo-inositol alleles among subspecies of Cronobacter dublinensis strains 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 240 Cronobacter and 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.

Highlights

Cronobacter spp. are opportunistic foodborne pathogens that are gaining attention for their ability to cause meningitis, septicemia, necrotizing enterocolitis and pneumonia in neonates and older infants [1,2,3,4]
Results from this study showed that the microarray was able to accurately assess each strain’s identity, could differentiate Cronobacter species from their nearest neighbors, and it further defined two phylogenetic lineages among the
The microarray will be just as useful in understanding gene expression or transcriptomics, i.e., understanding the physiology of an organism cultured under specific growth conditions

Summary

Introduction

Cronobacter spp. are opportunistic foodborne pathogens that are gaining attention for their ability to cause meningitis, septicemia, necrotizing enterocolitis and pneumonia in neonates (defined here as infants 28 days old or younger) and older infants [1,2,3,4]. It is clear at this time that contamination can occur intrinsically and extrinsically It has been noted by Jason [5] that 8% (7 out of 82) of infected infants with invasive disease (defined as a culture-positive, confirmed case of septicemia or meningitis) did consume breast milk exclusively (without supplementation with PIF or powdered human milk fortifiers) prior to the onset of illness. The Food and Drug Administration (FDA) and its food safety collaborators share a responsibility to protect public health, and their collective capability is enhanced through the advancement of methods that can rapidly identify and characterize foodborne pathogens [1,2,3] The rapidity of this response ensures that fewer consumers will come in contact with contaminated products and in doing so may prevent larger outbreaks from occurring [1,2,3].

Future Directions

Findings

Conclusions