THOMAS CEBULA
Biology

Visiting Professor   302 Dunning Hall Department of Biology Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218-2685   Email: tcebula1@jhu.edu Office 410 516-7285 Departmental fax 410 516-5213

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.