Chitrita "Chobi" DebRoy MPhil, PhD

Research:

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 174 different O serogroups. We have now sequenced O antigen gene clusters and developed PCR assays of more than 20 pathogenic O groups. This research will lead to the development of molecular diagnostics where all O-serogroups of E. coli can be detected rapidly.

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 and horses. We have also shown that many of these ExPEC strains are 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.

Diagnostics:

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.

Publications: (2009-2013)

Hegde NV,  Praul C, Gehring A, Fratamico PM, DebRoy C. 2013. Rapid identification of the six clinically relevant O serogroups of Shiga toxin-producing Escherichia coli by antibody microarray.  J. Microbiol.Methods Accepted

Svoboda AL., Dudley EG., DebRoy C. Mills EW, and Cutter CN.  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. Accepted

Feng P, Soderlund R, Cebula TA, Tarr PI, DebRoy C, Dudley EG 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 CR, Goswami K, Roberts EL, DebRoy C and Dudley EG. 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 HA, Mills E, Cutter CN, Roberts E, 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 JR, Tchesnokova V, Johnston B, Clabots C, Roberts PL, Billig M, Riddell K, Rogers P, Qin X, Butler-Wu S, Price LB, Aziz M, Nicolas-Chanoine MH, DebRoy C, Robicsek A, Hansen G, Urban C, Platell J, Trott D, Zhanel G, Weissman SJ, Cookson BT, Fang FC, Limaye A, Scholes D, Chattopadhyay S, Hooper DC, Sokurenko EV. 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 NV, Hulet R,  Jayarao BM, 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 TJ, Bielak EM, Fortini  D, Hansen LH, Hasman H, DebRoy C, Nolan LK, 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 NV, Jayarao BM, 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 CA, Ochoa TJ , Ruiz J, Durand D, Lacher DW, DebRoy C, Lanata CF and. Cleary TG. 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 JR, Nicolas-Chanoine MH, DebRoy C, Castanheira M, Robiscek A, Hansen G, Weissman S, Urban C, Platell J, Trott D, Zhanel G, Clabots C,. Johnston BD, Kuskowski MA 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  TJ,  Logue  CM, Johnson JR, Kuskowski MA, Sherwood JS, Barnes HJ, DebRoy C, Wannemuehler YM, Obata-Yasuoka M, Spanjaard L, and Nolan LK. 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, PM. 2011. Detection of O antigens in Escherichia coli. Animal Health Research Reviews 12: 1-16.

Contreras CA, Ochoa TJ, Ruiz J, Lacher DW, Rivera FP, Saenz Y, Chea E, Zavaleta N, Gil AI, Lanata CF, Huicho L, Maves R, Torres C, DebRoy C and Cleary TG. 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 AM, Dudley EG and Cutter CN. 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 AM, DebRoy C, Dudley EG and Cutter CN. 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 TE, DebRoy C, Flint PL, Safine DE, Schamber JL, Riddle AE and Trust KA. 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 MA and Bumbaugh AC. 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 PM 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 PM, 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 TJ, DebRoy C, Belton S, Lawrence M and Nolan LK.  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, 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 JR, Johnston B, Clabots C, Kuskowski MA, 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 MS, Sarker U, Jayarao BM,  Stell AL, Bell NP.,and Johnson TJ. 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 CA, Ochoa TJ. Lacher DW, DebRoy C, Talledo M, Donnenberg  MS,  Lanata,, CF   and Cleary TG. 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 JR, 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 MA, Byrne BA, DebRoy C, Samitz EM, Peterson TS and Oslund KL. 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 RM, Solberg OD, Lee BM., Raphael E, DebRoy C and Riley LW. 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 TJ, Logue CM, Wannemuehler Y, Kariyawasam S, Doetkott C, DebRoy C, White DG and Nolan LK. 2009. Examination of the source and extended virulence genotypes of Escherichia coli  contaminating retail poultry meat.  Foodborne Path. Dis. 6:657-667.

Ravindranath, SP, 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 PM, 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 BM. 2009.  Comparison of genotypes of Escherichia coli strains carrying F18ab and f18ac fimbriae from pigs. J. Vet. Diagn. Invest. 21(3):359-64

Fratamico PM,  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. (Online First)