RESEARCH INTERESTS

Microbial genomics: evolution of pathogens, mechanisms of pathogenicity/virulence, DNA mismatch repair, molecular mechanisms of mutagenesis, microbial forensics

Yearly, in the United States alone, nearly 76 million people fall ill to
foodborne enteric infections, resulting in approximately 325,000 hospitalizations,
5,000 deaths, and societal costs of more than 3.6x10¹¹ dollars.  An enteric
pathogen, if it is to be successful, must survive the sundry challenges of
ever-changing environments, be it in the human biome or the greater
biosphere, and this in turn rests upon the relative diversity in the
microbial population at large. 

Our research investigates the inherent diversity within enteric pathogen
populations of Escherichia coli and Salmonella enterica in order to help
understand the evolution, adaptation, and pathogenesis of these microbes.
In ascertaining the diversity of enteric populations, we use genomic and
bioinformatic approaches to focus our attention on two independent, but
interrelated, topics.

The extent and mechanisms of diversity.  We are using genomic
approaches to explore the extent genetic change (mutation) and exchange
(homologous, homeologous, and illegitimate recombination) contribute to
these processes.  Previous work from our laboratory demonstrated, for
example, that a high mutation rate should be anticipated among a microbial
population under adverse conditions, as it would increase the chances of
spawning the rare mutant needed to survive-whether it is to escape immune
surveillance, to elude therapeutic intervention, or to evade the manifold
barriers meant to keep microbial populations in check.  We are interested,
in particular, with mutators that arise because of defects in
methyl-directed mismatch repair (MMR), as they are unique; i.e., not only
are MMR mutators hypermutable (they exhibit high mutation rates), but they
are promiscuous (they show an increase in recombination) as well.  As these
properties could 'speed' the evolutionary process, MMR-defective
subpopulations may exist as mixing pools where horizontal transfer of genes
within and among species takes place.  Moreover, as many of the horizontal
gene acquisitions in the enterics are phage-encoded sequences, many of which
are subject to inducible SOS-DNA repair, we are investigating host and
ecological conditions that could help frame genomic rearrangements found in
the various pathogenic serovars and serotypes of Salmonella and E. coli,
respectively.

The yin and the yang of diversity.  If diversity is an inherent
property of enteric pathogen populations that can be quantified, so too can
the lack of diversity be used as a measure of genetic relatedness of two
individuals.  The very techniques that we have developed and evaluated for
measuring diversity can therefore be exploited to infer a genetic match
(inclusion) or non-match (exclusion).  We are using DNA, SNP, and phenotypic
arrays, as well as optical mapping, phylogenetics, pyrosequencing, and whole
genome sequencing to characterize and type microbes at (or near) the
individual level, thus permitting more accurate probing of the enteric
pangenomes.  These techniques should allow proper attribution in the
examination of intentional and unintentional contamination by these agents.
We are incorporating all of our data into a centralized database, The
Microbial Rosetta Stone, the aim of which is to help develop and contribute to the burgeoning field of microbial forensics.

REPRESENTATIVE PUBLICATIONS

Kotewicz ML, Mammel MK, LeClerc JE, Cebula TA.  2008.  Optical mapping and
454 sequencing of Escherichia coli O157:H7 isolates linked to the U.S. 2006
spinach associated outbreak.  Microbiology (in press).

Mukherjee A, LeClerc JE, Cebula TA.  2008.  Phenotypic Microarray Approaches
to the Study of Microbes. In:  Genomics: Fundamentals and Applications.  Ed:
S Choudhuri and DB Carlson. Informa Healthcare USA, Inc.  New York, New York
(in press).

Mukherjee A, Mammel MK, LeClerc JE, Cebula TA.  2008. Altered utilization of
N-acetyl-D-galactosamine by Escherichia coli O157:H7 from the 2006 spinach
outbreak.  J. Bacteriol.  190:1710-1717. (published ahead of print
doi:10.1128/JB.01737-07).

Kotewicz ML, Jackson SA, LeClerc JE, Cebula TA.  2007.  Optical maps
distinguish individual strains of Escherichia coli O157:H7.  Microbiology
153:1720-1733.

Jackson SA, Mammel MK, Patel IR, Mays T, Albert TJ, Leclerc JE, Cebula TA.
2007.  Interrogating genomic diversity of E. coli O157:H7 using DNA tiling
arrays.

Welch TJ, Fricke WF, McDermott PF, White DG, Rosso ML, Rasko DA, Mammel MK,
Eppinger M, Rosovitz MJ, Wagner, D, Rahalison L, LeClerc JE, Hinshaw JM,
Lindler LE, Cebula TA, Carniel E, Ravel J.  2007.  Multiple antimicrobial
resistance in plague: an emerging public health risk.   PLos One 2:1-6.

Cebula TA.  2006.  DNA detection strategies:  Sequences, signatures, and
significance. Proc IFT First Annual Food Protection and Defense Conference.
(http://www.ift.org/fooddefense/25-Cebula-Transcript.pdf ahead of print
version).

Budowle B, Schutzer SE, Burans JP, Beecher DJ, Cebula TA, et al.  2006.
Quality sample collection, handling, and preservation for an effective
microbial forensics program.  Appl Environ Microbiol 72:6431-6438.

Shi L et al. (the MAQC Consortium).  2006.  The MicroArray Quality Control
(MAQC) project shows inter- and intraplatform reproducibility of gene
expression measurements. Nature Biotechnology 24:1151-1161.

Mukherjee A, Jackson SA, LeClerc JE, Cebula TA.  2006.  Exploring genotypic
and phenotypic diversity of microbes using microarray approaches. Toxicology
Mechanisms and Methods 16:121-128.

Cebula TA, Brown EW, Jackson SA, Mammel MK, LeClerc JE.  2005.  Molecular
applications for discriminating microbial pathogens in the era of food
security.  Expert Rev Mol Diagn. 5:431-445.

Cebula TA, Jackson SA, Brown EW, Goswami B, LeClerc JE.  2005.  Chips and
SNPs, bugs and thugs: a molecular sleuthing perspective. J Food Prot.
68:1271-1284.

Li B, Brown EW, D'Agostino C, LeClerc JE, Cebula TA.  2005.  Structure and
distribution of phosphoprotein phosphatase genes prpA and prpB among
Shigella subgroups.  Microbiology 151:2671-2683. 

Levy DD, Sharma B, Cebula TA.  2004.  Single Nucleotide Polymorphism
Mutation Spectra and resistance to quinolone antibiotics in with Salmonella enterica Serovar.

Brown EW, Mammel MK, LeClerc JE, Cebula TA.  2003.  Limited boundaries for
extensive horizontal gene transfer among Salmonella pathogens.  Proc. Natl.
Acad. Sci. (USA) 100:15676-15681.

Brown EW, LeClerc JE, Cebula TA.  2003.  Searching for keys under the
devil's lamppost.  Trends Microbiol.  11:454-456.

Kotewicz ML, Brown EW, LeClerc JE, Cebula TA.  2003.  Genomic variability
among enteric pathogens: the case of the mutS-rpoS intergenic region. Trends
Microbiol. 11:2-6.

Li B, Tsui HC, LeClerc JE, Dey M, Winkler ME, Cebula TA.  2003.  Molecular
analysis of mutS expression and mutation in natural isolates of pathogenic
Escherichia coli. Microbiology 149:1323-1331.

Sahu SN, Acharya S, Tuminaro H, Patel I, Dudley K, LeClerc JE, Cebula TA,
Mukhopadhyay S.  2003.  The bacterial adaptive response gene, barA, encodes
a novel conserved histidine kinase regulatory switch for adaptation and
modulation of metabolism in Escherichia coli.  Mol Cell Biochem. 253:
167-177.