Chitrita "Chobi" DebRoy, Ph.D.

  • Clinical Professor
  • Director, E. coli Reference Center
Chitrita "Chobi" DebRoy, Ph.D.
125 Agricultural Sciences and Industries (ASI) Building
University Park, PA 16802

136 ASI Bldg

University Park, PA 16802
Work Phone: 814-863-2630

Areas of Expertise

  • Pathogenic E. coli
  • Shiga toxin- producing E. coli
  • Diarrheagenic E. coli
  • Extraintestinal pathogenic E. coli
  • Diagnostics
  • Whole genome sequencing
  • Microbiome


  1. Post doctoral training, Penn State, Department of Biochemistry and Molecular Biology
  2. PhD, Life Sciences, Jawaharlal Nehru University, New Delhi
  3. MPhil, Life Sciences, Jawaharlal Nehru University, New Delhi
  4. MS, Biology, University of Delhi, Delhi


Sequencing and analyzing O antigen gene clusters of E. coli

E. coli are classified on the basis of O antigens that are lipopolysaccharides present on the outer surface of the bacteria. O-antigens are important virulent factors that are targets of both immune system and bacteriophages. Its specificity is very important for adaptation as its variation plays an important role in evasion of the host defenses. The designation of E. coli serotypes, comprising of O and H antigens, is of great importance in epidemiological studies, in tracing the source of the outbreaks of gastrointestinal or other illness, or for linking the source to the infection. Conventionally O antigens are determined by agglutination reactions using antisera raised in rabbits against the 187 different O serogroups. We now have the complete sequences of all O-antigen gene clusters that have been or soon will be submitted to GenBank. This research will lead to the development of molecular diagnostics where all O-serogroups of E. coli can be detected genotypically.

Extraintestinal Pathogenic E. coli

E. coli can cause intestinal as well as extraintestinal infections. We have, for the first time, shown that extraintestinal pathogenic E. coli (ExPEC) can cause pneumonia in dogs, cats, horses and tigers. We have also shown that many of these ExPEC strains are genetically related to strains that cause urinary tract infection in humans.

Antibiotic resistance in E. coli

The emergence and dissemination of antibiotic resistance in bacterial pathogens is a serious emerging problem world wide. We are trying to elucidate the mechanism by which microorganisms acquire new genes as a result of inter-species (horizontal) transfer of antimicrobial resistance determinants. A potential important factor in the development of antimicrobial resistance stems from animal husbandry practices, in which antimicrobial agents not only are used for treating and preventing animal diseases, but are also administered at sub therapeutic levels to promote faster growth and to improve efficiency of feed conversion into meat. This routine practice may be the driving force in accelerating the emergence of antibiotic resistant bacteria that are subsequently transferred from animals to humans through the food chain, including meat products and fresh produce. Studies on antimicrobial resistance pattern and modes of dissemination in pathogenic strains of E. coli isolated from animals are being conducted in our laboratory.


The E. coli Reference Center is one of the largest repositories for E. coli isolates and a major diagnostic laboratory in North America. Serotyping and molecular diagnostics of E. coli are routinely performed. The presence of more than twenty five virulence attributes of E. coli is determined by PCR to ascertain the pathogenicity of the bacteria that are isolated from humans, animals, food, water and the environment. The characteristics of each isolate are recorded in the database and that can be retrieved easily.

Selected Publications

Johnson JR, Davis G, Clabots C, Johnston BD, Porter S, DebRoy C, Pomputius W, Ender PT, Cooperstock M, Slater BS, Banerjee R, Miller S, Kisiela D, Sokurenko EV, Aziz M, and Price LB. 2016. Household Clustering of Escherichia coliSequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis. Open Forum Infect Dis. In Press

Borges CA, Beraldo LG, Maluta RP, Cardozo MV, Barbosa KB, Guastalli EAL, Kariyawasam S, DebRoy C, Avila  FA.  2016. Multidrug-resistant pathogenic Escherichia coli isolated from wild birds in a veterinary hospital. Avian Pathology. Accepted

Fratamico PM, DebRoy C, Baranzoni GM, Liu Y, Letterman D.  and Feng P.  2016. Advances in Molecular Serotyping and Subtyping of Escherichia coli. Front. Microbiol. 7:644.doi: 10.3389/fmicb.2016.00644

Wang J,  Katani R, Li L, Roberts EL, Kapur V and DebRoy C. 2016 Rapid Detection of E. coli O157 and Shiga Toxins by Lateral Flow Immunoassays.  Toxins, 8: 92; doi:10.3390/toxins8040092

Losada L, DebRoy C, Radune D, Kim M, Sanka R, Brinkac L, Kariyawasam S, Shelton D, Fratamico PM, Kapur V, Feng PCH. 2016 Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids. Plasmid 83:8-11.

DebRoy C, Fratamico PM, Xianghe Y, Baranzoni GM, Liu Y, Needleman DS, Tebbs R, O'Connell CD,  Allred A, Swimley M, Mwangi M, Kapur V, Garay JAR, Roberts EL, Katani R. 2016. Comparison of O-Antigen Gene Clusters of all O-Serogroups of Escherichia coli and Proposal for adopting a new nomenclature for O-Typing of Escherichia coli. PLoS One. 2016 Jan 29;11(1):e0147434. doi: 10.1371/journal.pone.0147434

Ibekwe M, Murinda, S,  Reddy, G and DebRoy C. 2016. Potential Pathogens, Antimicrobial Patterns, and Genotypic Diversity of Escherichia coli Isolates in Constructed Wetlands Treating Swine Wastewater. FEMS Microbiology Ecology. Dec 31;83:8-11. doi: 10.1016/j.plasmid.2015.12.001

Bu RE, Wang JL, DebRoy C, Wu JH, Xi LG, Liu Y, Shen ZQ. 2015. Development of an indirect ELISA for bovine mastitis using Sip protein of Streptococcus agalactiae. Iran J Vet Res. 2015 16(3):283-7

Katani R, Cote R, Garay JR, Li L, Arthur T, DebRoy C, Mwangi M, and Kapur V. 2015. Complete Genome Sequence of SS52, a Strain of Escherichia coli O157:H7 Recovered from Super-shedder Cattle. Genome Announcement. genomeA01569-14 

Liu Y , Yan X, DebRoy C, Fratamico PM, Needleman D S, Li R, Wang W, Losada L, Brinkac L, Radune D, Toro M, Hegde N and Meng  J. 2015. Escherichia coli O-antigen gene clusters of serogroups O62, O68, O131, O140, O142, and O163: DNA sequences and similarity between O62 and O68, and PCR-based serogrouping.  Biosensors Feb 5;5(1):51-68. doi: 10.3390/bios5010051.

Cote  R, Katani R,  Moreau MR, Kudva IT,  Arthur TM, DebRoy C,  Mwangi MM, Albert I, Garay JAR, Li  L, Brandl MT, Carter MQ, Kapur V. 2015. Comparative Analysis of Super-shedder Strains of Escherichia coli O157:H7 Reveals Distinctive Genomic Features and a Strongly Aggregative Adherent Phenotype on Bovine Rectoanal Junction Squamous Epithelial Cells. PloS One Feb 9;10(2):e0116743. doi: 10.1371/journal.pone.0116743.

Carvallo FR., Kerlin Roy, Fredette Claudine, Pisharath H, DebRoy  C, Kariyawasam S, Pardo ID. 2015. Histiocytic typhlocolitis in two colony Beagle dogs. Experimental and Toxicologic Pathology. 67:219-2 

McCluskey K, Scott B, Boundy-Mills  K, Broggiato A, Cova A, Desmeth P, DebRoy C, Fravel D, Garrity G , Gasco MdMJ, Joseph  L, Lindner D,. Lomas MW, Morton J, Nobles D, Turner J,  Ward T, Wertz J, Wiest A, and Geiser D. 2014. Meeting Report: 2nd Workshop of the United States Culture Collection Network. May 19-21, 2014, State College, PA, USA. Standards in Genomic Sciences  9:27.

Wijetunge, D. S. S., Karunathilake, K. H. E. M., Chaudhari, A., Katani, R., Dudley, E. G., Kapur, V., DebRoy, C., and Kariyawasam, S. 2014. Complete nucleotide sequence of pRS218, a large virulent plasmid from the neonatal meningitis associated Escjherichia coli RS218. BMC Microbiol. Accepted.

Seeley, K. E., Baitchman, E., Bartlett, S., DebRoy, C., and Garner, M. M. 2014. Investigation and control of an attaching and effacing Escherichia coli outbreak in a colony of captive budgerigars (Melopsittacus undulates). J Zoo and Wildlife Medicine. Accepted.

Sanjar, F., Hazen, T., Shah, S., Koenig, S., Agrawal, S., Daugherty, S., Sadzewicz, L., Tallon, L.,  Mammel, M., Feng, P., Soderlund, R., Tarr, P., DebRoy, C., Dudley, E., Cebula, T., Ravel, J., Fraser, C.,  Rasko, D., and Eppinger, M. 2014. Genome Sequence of Escherichia coli O157:H7 strain 2886-75 Associated with the First Reported Case of Human Infection in the United States. Genome Announcement.  Jan 9;2(1). pii: e01120-13. doi: 10.1128/genomeA.01120-13.

Brooks, J. W., Roberts, E. L., Kocher, K., Kariyawasam, S., DebRoy, C. 2013. Fatal pneumonia caused by Extraintestinal Pathogenic Escherichia coli (ExPEC)  in a juvenile cat recovered from an animal boarding incident. Vet Micro 167:704-7.

Yin, S., Jensen, M. A., Bai, J., DebRoy, C., Barrangou, R., and Dudley, E. G. 2013. Evolutionary  Divergence of Shiga Toxin-producing Escherichia coli is Reflected in CRISPR Spacer Composition. Appl Environ Microbiol. 79:5710-20  

Gehring, A., Barnett, C., Chu, T., DebRoy, C., D'Souza, D., Eaker, S., Fratamico, P., Gillespie, B., Hegde, N., Jones, K., Lin, J., Oliver, S., Paoli, G., Perera, A., and Uknalis, J. 2013. A high-throughput antibody-based microarray typing platform. Sensors (Basel).  13(5):5737-5748. 

Hegde, N. V., Praul, C., Gehring, A., Fratamico, P. M., and DebRoy, C. 2013. Rapid identification of the six clinically relevant O serogroups of Shiga toxin-producing Escherichia coli by antibody microarray. J. Microbiol.Methods 93:273-276

Svoboda, A. L., Dudley, E.G., DebRoy, C., Mills, E. W., and Cutter, C. N.  2013. Presence of Shiga Toxin-Producing Escherichia coli O-Groups in Small and Very Small Beef Processing Plants and Resulting Ground Beef Detected by a Multiplex Polymerase Chain Reaction Assay.  Foodborne Path Dis. 10:789-795  

Feng, P., Soderlund, R., Cebula, T. A., Tarr, P. I., DebRoy, C., Dudley, E. G. and Ravel, J. 2013. Whole Genome Draft Sequences of Twenty Enterohemorrhagic Escherichia coli O157:H7 Strains. Genome Announcement. Feb 28;1(2):e0013412. doi: 10.1128/genomeA.00134-12.

Chen, C., Lewis, C. R., Goswami, K., Roberts, E. L., DebRoy, C., and Dudley, E. G. 2013. Identification and Characterization of Spontaneous Deletions within the Sp11-Sp12 Prophage Region of Escherichia coli O157:H7 Sakai. Appl. Env. Microbiol. 79: 1934-1941. Jan 11 (e-pub).

Magwedere, K., Dang, H. A., Mills, E., Cutter, C. N., Roberts, E., and DebRoy, C. 2013. Incidence of Shiga toxin-Producing Escherichia coli Strains in Beef, Pork, Chicken, Deer, Boar, Bison and Rabbit Retail Meat. J Vet Diag Inv. 25:254-258.

Johnson, J. R., Tchesnokova, V., Johnston, B., Clabots, C., Roberts, P. L., Billig, M., Riddell, K., Rogers, P., Qin, X., Butler-Wu, S., Price, L. B., Aziz, M., Nicolas-Chanoine, M. H., DebRoy, C., Robicsek, A., Hansen, G., Urban, C., Platell, J., Trott, D., Zhanel, G., Weissman, S. J., Cookson, B. T., Fang, F. C., Limaye, A., Scholes, D., Chattopadhyay, S., Hooper, D. C., Sokurenko, E. V. 2013. Abrupt Emergence of a Single Dominant Multi-Drug-Resistant Strain of Escherichia coli. J Infect Dis. 207(6):919-28  Jan 3(e pub).

Hegde, N. V., Hulet, R.,  Jayarao, B. M., Muldoon, M., Lindpaintner, K., Kapur, V., and DebRoy, C. 2012. Detection of the top six non-O157 Shiga toxin-producing Escherichia coli O groups by ELISA. Foodborne Path. Dis. 9:1044-1048.

Johnson, T. J., Bielak, E. M., Fortini, D., Hansen, L. H., Hasman, H., DebRoy, C., Nolan, L. K., and Carattoli, A. 2012. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae.  Plasmid 68:43-50.

Hegde, N. V., Jayarao, B. M., and DebRoy, C. 2012. Rapid Detection of top six non-O157 Shiga toxin-producing Escherichia coli O groups in Ground Beef by Flow Cytometry. J. Clin. Microbiol. 50:2137-2139.  

Contreras, C. A., Ochoa, T. J., Ruiz, J., Durand, D., Lacher, D. W., DebRoy, C., Lanata, C. F., and Cleary, T. G. 2012. Genetic Diversity of LEE Genes of EPEC isolated from Peruvian children. J. Med Microbiol. 61:1114-1120.

Medina, M., Shelver, W., Fratamico, P., Fortis, L., Narang, N., Cray, W., Jr., Esteban, E., Tillman, G., and DebRoy, C. 2012. Latex Agglutination Assays for Detection and Confirmation of Non-O157 Shiga Toxin-Producing E. coli Serogroups O26, O45, O103, O111, O121 and O145.  J Food Protection 75: 819-826.

Johnson, J. R., Nicolas-Chanoine, M. H., DebRoy, C., Castanheira, M., Robiscek, A., Hansen, G., Weissman, S., Urban, C., Platell, J., Trott, D., Zhanel, G., Clabots, C., Johnston, B. D., Kuskowski, M. A., and the Macrorestriction Analysis of ST131 for Epidemiologic Research (MASTER). Investigators* 2012. Pulsed-Field Gel Electrophoresis Analysis of 579 Escherichia coli Sequence Type ST131 Isolates (1967 - 2009) in Relation to Year, Geography, Ecological Source, and Antimicrobial Resistance Traits. J. Infect. Dis. 18(4):598-607. 

Johnson, T. J., Logue, C. M., Johnson, J. R., Kuskowski, M. A., Sherwood, J. S., Barnes, H. J., DebRoy, C., Wannemuehler, Y. M., Obata-Yasuoka, M., Spanjaard, L., and Nolan, L. K. 2012. Associations between multidrug resistance, plasmid content, and virulence potential among extraintestinal pathogenic and commensal Escherichia coli from humans and poultry. Foodborne Path Dis. 9:37-46.

DebRoy, C., Roberts, E., and Fratamico, P. M. 2011. Detection of O antigens in Escherichia coli. Animal Health Research Reviews 12: 1-16.

Contreras, C. A., Ochoa, T. J., Ruiz, J., Lacher, D. W., Rivera, F. P., Saenz, Y., Chea, E., Zavaleta, N., Gil, A. I., Lanata, C. F., Huicho, L., Maves, R., Torres, C., DebRoy, C., and Cleary, T. G. 2011. Phylogenetic relationships of Shiga toxin-producing Escherichia coli (STEC) isolated from Peruvian children. J. Med. Microbiol. Epub: Feb 3, 2011.

DebRoy, C., Roberts, E., Valadez, A. M., Dudley, E. G., and Cutter, C. N. 2011. Detection of Shiga toxin-producing Escherichia coli O26, O45, O103, O111, O113, O121, O145, and O157 serogroups by multiplex PCR of the wzx gene of the O-antigen gene cluster. Foodborne Path. Dis. 8:651-652.    

Valadez, A. M., DebRoy, C., Dudley, E. G., and Cutter, C. N. 2011. Multiplex PCR detection of Shiga toxin-producing Escherichia coli strains belonging to serogroups O157, O103, O91, O113, O145, O111, and O26 experimentally inoculated in beef carcass swabs, beef trim, and ground beef. J. Food Prot. 74:228-239.

Hollmén, T. E., DebRoy, C., Flint, P. L., Safine, D. E., Schamber, J. L., Riddle, A. E., and Trust, K. A. 2011. Molecular typing of Escherichia coli strains associated with threatened sea ducks and near-shore marine habitats of southwest Alaska. Environ. Microbial. Rep. 3:262-269.

DebRoy, C., Roberts, E., Davis, M. A., and Bumbaugh, A. C. 2010. Detection of Non-serotypable Shiga toxin-producing Escherichia coli Strains Derived from Pigs by Multiplex PCR Assay. Foodborne Path. Dis. 7:1407-1414.

Fratamico, P. M. and DebRoy, C. 2010. Detection of Escherichia coli O157:H7 in Food Using Real-Time Multiplex PCR Assays Targeting the stx1, stx2, wzyO157, and the fliCh7 or eae Genes. Food Analytical Meth. 3:330-337.

Fratamico, P. M., Yan, X., DebRoy, C.,  Bryne, B.,  Monaghan, A.,  Liu, Y., Fanning, S., and Bolton, D. 2010. DNA Sequence of the Escherichia coli O2 and O28ac O Antigen Gene Clusters and Detection of Shiga Toxin-Producing E. coli Serogroup O2 and Enteroinvasive O28ac Strains by Multiplex PCR Assays Targeting Virulence Genes and Genes in the Respective O-Antigen Gene Clusters. Can. J. Microbiol. 56(4):308-16.

Johnson, T. J., DebRoy, C., Belton, S., Lawrence, M., and Nolan, L. K. 2010. Pyrosequencing of the Vir Plasmid of Necrotoxigenic Escherichia coli. J. Vet Micro 144 (2010) 100–109 (epub-  Dec 30, 2009).

Carvallo, F., DebRoy, C., Baeza, E., Hinckley, L., and Gilbert, K. 2010. Extraintestinal pathogenic Escherichia coli induced necrotizing pneumonia in a white tiger cub. J Vet Diag Inv  22 (1): 136-140. In press.

Johnson, J. R., Johnston, B., Clabots, C., Kuskowski, M. A., DebRoy, C., and Rice, J. 2010. Escherichia coli Sequence Type ST131 as an Emerging Fluoroquinolone-Resistant Uropathogen among Renal Transplant Recipients. Antimicrobial Agents Chemo. 54(1): 546-550 (e-pub Nov 16, 2009).

DebRoy, C., Sidhu, M. S., Sarker, U., Jayarao, B. M., Stell, A. L., Bell, N.P., and Johnson, T.J. 2010. Complete sequence of pEC14_114, a highly conserved IncFIB/FIIA plasmid associated with uropathogenic Escherichia coli cystitis strains, and its  prevalence among Extraintestinal Pathogenic isolates from humans and animals. Plasmid 63: 53-60 (e-pub Oct 31, 2009).

Contreras, C. A., Ochoa, T. J., Lacher, D. W., DebRoy, C., Talledo, M., Donnenberg,  M. S., Lanata, C. F., and Cleary, T. G. 2010. Allele variability of critical virulence genes (eae, bfpA and perA) in typical and atypical EPEC from diarrhea cases in Peruvian children. J. Med Microbiol 59: 25-31 ( e- pub Oct 1, 2009).

Johnson, J. R., Miller, S., Johnston, B., Clabots, C., and DebRoy, C. 2009. Sharing of Escherichia coli Sequence Type ST131 and other Multidrug-Resistant Urovirulent E. coli Strains among  Dogs and Cats Within a Household. J. Clin. Microbiol. 47 (11): 3721-3725.

Highland, M. A., Byrne, B. A., DebRoy, C., Samitz, E. M., Peterson, T, S, and Oslund, K., L. 2009. Extraintestinal pathogenic Escherichia coli induced necrohemorrhagic bronchopneumonia and pleuritis in three kittens and fecal prevalence in a cohort population. J. Vet Diagn. Invest. 21 (5):609-615 

Ajiboye, R. M., Solberg, O. D., Lee, B. M., Raphael, E., DebRoy, C., and Riley, L. W. 2009. Global spread of mobile antimicrobial drug resistance determinants in human and animal Escherichia coli and Salmonella strains causing community-acquired infections. Clin Infect Dis.  49:365-71.

Johnson, T. J., Logue, C. M., Wannemuehler, Y., Kariyawasam, S., Doetkott, C., DebRoy, C., White, D. G., and Nolan, L. K. 2009. Examination of the source and extended virulence genotypes of Escherichia coli  contaminating retail poultry meat.  Foodborne Path. Dis. 6:657-667.

Ravindranath, S. P., Mauer, L., DebRoy, C., and Irudayaraj, J. 2009. Bio-functionalized magnetic nanoparticle integrated mid-IR pathogen sensor for food matrices. Anal. Chem. 81: 2840-2846.

Fratamico, P. M., DebRoy, C., Miyamoto, T., and Liu, Y. 2009. Detection of enterohemorrhagic Escherichia coli O145 in food by PCR targeting genes in the E. coli O145 O antigen gene cluster and the shiga toxins 1 and 2 genes. Foodborne Path. Dis.  6:605-611.

DebRoy, C., Roberts, E. Scheuchenzuber, W., Kariyawasam, S., Jayarao, B. M. 2009.  Comparison of genotypes of Escherichia coli strains carrying F18ab and f18ac fimbriae from pigs. J. Vet. Diagn. Invest. 21(3):359-64.

Fratamico, P. M., DebRoy, C., and Liu, Y. 2009. The DNA Sequence of the Escherichia coli O22 O Antigen Gene Cluster and Detection of Pathogenic Strains Belonging to E. coli Serogroups O22 and O91 by Multiplex PCR Assays Targeting Virulence Genes and Genes in the Respective O-Antigen Gene Clusters. Food Anal. Methods. 2:169-179. 

Research Interests

Animal Diagnostic Laboratory Research Faculty


Sequencing and analyzing O antigen gene clusters of E. coli