Genomic diversity of pathogenic Escherichia coliof the EHEC 2 clonal complex (2009)
Abu-Ali, Galeb S, Lacher, David W, Wick, Lukas M, Qi, Weihong, Whittam, Thomas S
Abstract Background Evolutionary analyses of enterohemorrhagic Escherichia coli (EHEC) have identified two distantly related clonal groups: EHEC 1, including serotype O157:H7 and its inferred...
Characterisation of atypical enteropathogenic E. colistrains of clinical origin (2009)
Tennant, Sharon M, Tauschek, Marija, Azzopardi, Kristy, Bigham, Andrea, Bennett-Wood, Vicki, Hartland, Elizabeth L, ...
Abstract Background Enteropathogenic E. coli (EPEC) is a prominent cause of diarrhoea, and is characterised in part by its carriage of a pathogenicity island: the locus for enterocyte effacement...
Bell, Julia A, St Charles, Jessica L, Murphy, Alice J, Rathinam, Vijay AK, Plovanich-Jones, Anne E, Stanley, Erin L, ...
Abstract Background Campylobacter jejuni infection produces a spectrum of clinical presentations in humans – including asymptomatic carriage, watery diarrhea, and bloody diarrhea – and has been...
Shiga Toxin-producing Escherichia coli Strains Negative for Locus of Enterocyte Effacement (2009)
Newton, Hayley J., Sloan, Joan, Bulach, Dieter M., Seemann, Torsten, Allison, Cody C., Tauschek, Marija, ...
Most Shiga toxin–producing Escherichia coli (STEC) infections that are associated with severe sequelae such as hemolytic uremic syndrome (HUS) are caused by attaching and effacing pathogens that...
Shiga Toxin-producing Escherichia coli Strains Negative for Locus of Enterocyte Effacement (2009)
Newton, Hayley J., Sloan, Joan, Bulach, Dieter M., Seemann, Torsten, Allison, Cody C., Tauschek, Marija, ...
Most Shiga toxin–producing Escherichia coli (STEC) infections that are associated with severe sequelae such as hemolytic uremic syndrome (HUS) are caused by attaching and effacing pathogens that...
Cho, Seongbeom, Whittam, Thomas S, Boxrud, David J, Bartkus, Joanne M, Saeed, A Mahdi
Abstract Background Salmonella enterica serotype Enteritidis ( S . Enteritidis) is a zoonotic pathogen, which can be found in many sources including animals and the environment. However, little is...
Dispatches Mutators and Long-Term Molecular Evolution of Pathogenic Escherichia coli O157:H7 (2008)
Thomas S. Whittam, Sean D. Reid, Robert K. Sel
It has been proposed that an increased mutation rate (indicated by the frequency of hypermutable isolates) has facilitated the emergence of Escherichia coli O157:H7. Analysis of the divergence of 12...
Bergholz, Teresa M, Wick, Lukas M, Qi, Weihong, Riordan, James T, Ouellette, Lindsey M, Whittam, Thomas S
Abstract Background: Global patterns of gene expression of Escherichia coli K-12 during growth transitions have been deeply investigated, however, comparable studies of E. coli O157:H7 have not been...
Besser, Thomas E., Shaikh, Nurmohammad, Holt, Nicholas J., Tarr, Phillip I., Konkel, Michael E., Malik-Kale, Preeti, ...
E. coli O157:H7, a zoonotic human pathogen for which domestic cattle are a reservoir host, produces a Shiga toxin(s) (Stx) encoded by bacteriophages. Chromosomal insertion sites of these...
Anantha, Ravi P., McVeigh, Annette L., Lee, Lanfong H., Agnew, Mary K., Cassels, Frederick J., Scott, Daniel A., ...
Colonization factor antigen I (CFA/I) is the archetype of eight genetically related fimbriae of enterotoxigenic Escherichia coli (ETEC) designated class 5 fimbriae. Assembled by the alternate...
David All, David W. Lacher, Manzour Hern, O Hazbón, Alifiya S. Motiwala, Weihong Qi, ...
Mycobacterium tuberculosis strains contain different genomic insertions or deletions called large sequence polymorphisms (LSPs). Distinguishing between LSPs that occur one time versus ones that occur...
Wick, Lukas M., Rouillard, Jean Marie, Whittam, Thomas S., Gulari, Erdogan, Tiedje, James M., Hashsham, Syed A.
Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes...
Zhang, Wei, Qi, Weihong, Albert, Thomas J., Motiwala, Alifiya S., Alland, David, Hyytia-Trees, Eija K., ...
Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the...
Zhang, Wei, Qi, Weihong, Albert, Thomas J., Motiwala, Alifiya S., Alland, David, Hyytia-Trees, Eija K., ...
Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the...
Elena, Santiago F., Whittam, Thomas S., Winkworth, Cynthia L., Riley, Margaret A., Lenski, Richard E.
This report describes the sequencing in the Escherichia coli B genome of 36 randomly chosen regions that are present in most or all of the fully sequenced E. coli genomes. The phylogenetic...
Ravi P. Anantha, Annette L. Mcveigh, Lanfong H. Lee, Mary K. Agnew, Frederick J. Cassels, Daniel A. Scott, ...
Colonization factor antigen I (CFA/I) is the archetype of eight genetically related fimbriae of enterotoxigenic Escherichia coli (ETEC) designated class 5 fimbriae. Assembled by the alternate...
Wang, Gan, Whittam, Thomas S., Berg, Claire M., Berg, Douglas E.
The RAPD (random amplified polymorphic DNA) fingerprinting method, which utilizes low stringency PCR amplification with single primers of arbitrary sequence to generate strain-specific arrays of...
Sreevatsan, Srinand, Pan, Xi, Stockbauer, Kathryn E., Connell, Nancy D., Kreiswirth, Barry N., Whittam, Thomas S., ...
One-third of humans are infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. Sequence analysis of two megabases in 26 structural genes or loci in strains recovered globally...
Carbonic anhydrase is an ancient enzyme widespread in prokaryotes
Smith, Kerry S., Jakubzick, Claudia, Whittam, Thomas S., Ferry, James G.
Carbonic anhydrases catalyze the reversible hydration of CO2 and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (γ class) in a...
Complete genomic sequence of Pasteurella multocida,Pm70
May, Barbara J., Zhang, Qing, Li, Ling Ling, Paustian, Michael L., Whittam, Thomas S., Kapur, Vivek
We present here the complete genome sequence of a common avian clone of Pasteurella multocida, Pm70. The genome of Pm70 is a single circular chromosome 2,257,487 base pairs in length and contains...
Nagy, Béla, Wilson, Richard A., Whittam, Thomas S.
Multilocus enzyme electrophoresis was applied to detect allelic variation and multilocus genotypes (electrophoretic types [ETs]) among 43 Escherichia coli isolates from weaned pigs suffering from...
Reid, Sean D., Betting, David J., Whittam, Thomas S.
A multiplex PCR was designed to detect the eae gene and simultaneously identify specific alleles in pathogenic Escherichia coli. The method was tested on 87 strains representing the diarrheagenic E....
Acquisition of the rfb-gnd Cluster in Evolution of Escherichia coli O55 and O157
Tarr, Phillip I., Schoening, Laura M., Yea, Yoo-Lee, Ward, Teresa R., Jelacic, Srdjan, Whittam, Thomas S.
The rfb region specifies the structure of lipopolysaccharide side chains that comprise the diverse gram-negative bacterial somatic (O) antigens. The rfb locus is adjacent to gnd, which is a...
Davies, Robert L., Whittam, Thomas S., Selander, Robert K.
The molecular evolution of the leukotoxin structural gene (lktA) of Mannheimia (Pasteurella) haemolytica was investigated by nucleotide sequence comparison of lktA in 31 bovine and ovine strains...
Phylogenetic Analysis of Enteroaggregative and Diffusely Adherent Escherichia coli
Czeczulin, John R., Whittam, Thomas S., Henderson, Ian R., Navarro-Garcia, Fernando, Nataro, James P.
The phylogenetics of the various pathotypes of diarrheagenic Escherichia coli are not completely understood. In this study, we identified several plasmid and chromosomal genes in the pathogenic...
Blank, T. Eric, Zhong, Hailang, Bell, Alison L., Whittam, Thomas S., Donnenberg, Michael S.
Typical enteropathogenic Escherichia coli (EPEC) strains produce bundle-forming pili (BFP), type IVB fimbriae that have been implicated in EPEC virulence, antigenicity, autoaggregation, and localized...
Sequence Diversity of Flagellin (fliC) Alleles in Pathogenic Escherichia coli
Reid, Sean D., Selander, Robert K., Whittam, Thomas S.
To study the molecular evolution of flagellin, the protein subunit specifying flagellar (H) antigens, the fliC genes from 15 pathogenic strains of Escherichia coli were amplified by PCR and...
Gene Conservation and Loss in the mutS-rpoS Genomic Region of Pathogenic Escherichia coli
Herbelin, Corinne J., Chirillo, Samantha C., Melnick, Kristen A., Whittam, Thomas S.
The extent and nature of DNA polymorphism in the mutS-rpoS region of the Escherichia coli genome were assessed in 21 strains of enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC)...
Clonal Diversity of Escherichia coli Colonizing Stools and Urinary Tracts of Young Girls
Schlager, Theresa A., Hendley, J. Owen, Bell, Alison L., Whittam, Thomas S.
Intestinal carriage of Escherichia coli in prepubertal girls without a history of urinary tract infection was examined by collecting weekly stools and periurethral and urine samples over 3 to 4 weeks...
Tarr, Cheryl L., Large, Teresa M., Moeller, Chris L., Lacher, David W., Tarr, Phillip I., Acheson, David W., ...
Most illnesses caused by Shiga toxin-producing Escherichia coli (STEC) have been attributed to E. coli serotype O157:H7, but non-O157 STEC infections are now increasingly recognized as public health...
Maidhof, Heinrich, Guerra, Beatriz, Abbas, Sascha, Elsheikha, Hany M., Whittam, Thomas S., Beutin, Lothar
Multiresistant Shiga toxin-producing Escherichia coli (STEC) O118:H16 and O118 nonmotile strains (designated O118:[H16]) were detected by examination of 171 STEC isolates for their antimicrobial...
Davies, Robert L., Campbell, Susan, Whittam, Thomas S.
The mosaic structure and molecular evolution of the leukotoxin operon (lktCABD) was investigated by nucleotide sequence comparison of the lktC, lktB, and lktD genes in 23 Mannheimia (Pasteurella)...
Molecular Evolution of the Intimin Gene in O111 Clones of Pathogenic Escherichia coli
Tarr, Cheryl L., Whittam, Thomas S.
Intimin is an important virulence factor in two groups of enteric pathogens: enteropathogenic Escherichia coli (EPEC), which is a major cause of infant diarrhea in the developing world, and...
Strain, Steven R., Leung, Kamtin, Whittam, Thomas S., De Bruijn, Frans J., Bottomley, Peter J.
An investigation was carried out to determine the genetic structure in soil populations of Rhizobium leguminosarum bv. trifolii and viciae at each of two Oregon sites (A and C) that were 1 km apart....
Anantha, Ravi P., McVeigh, Annette L., Lee, Lanfong H., Agnew, Mary K., Cassels, Frederick J., Scott, Daniel A., ...
Colonization factor antigen I (CFA/I) is the archetype of eight genetically related fimbriae of enterotoxigenic Escherichia coli (ETEC) designated class 5 fimbriae. Assembled by the alternate...
Hyma, Katie E., Lacher, David W., Nelson, Adam M., Bumbaugh, Alyssa C., Janda, J. Michael, Strockbine, Nancy A., ...
A bacterium originally described as Hafnia alvei induces diarrhea in rabbits and causes epithelial damage similar to the attachment and effacement associated with enteropathogenic Escherichia coli....
Evolution of Genomic Content in the Stepwise Emergence of Escherichia coli O157:H7†
Wick, Lukas M., Qi, Weihong, Lacher, David W., Whittam, Thomas S.
Genome comparisons have demonstrated that dramatic genetic change often underlies the emergence of new bacterial pathogens. Evolutionary analysis of Escherichia coli O157:H7, a pathogen that has...
Variation in Acid Resistance among Shiga Toxin-Producing Clones of Pathogenic Escherichia coli†
Large, Teresa M., Walk, Seth T., Whittam, Thomas S.
Pathogenic strains of Escherichia coli, such as E. coli O157:H7, have a low infectious dose and an ability to survive in acidic foods. These bacteria have evolved at least three distinct mechanisms...
Fitch, Brooke R., Sachen, Kacey L., Wilder, Stacey R., Burg, Matthew A., Lacher, David W., Khalife, Walid T., ...
Multilocus sequencing was used to compare Campylobacter sp. strains isolated from retail chicken products and humans with gastroenteritis in central Michigan. Sequence comparisons demonstrated...
DNA Polymorphism and Molecular Subtyping of the Capsular Gene Cluster of Group B Streptococcus†
Manning, Shannon D., Lacher, David W., Davies, H. Dele, Foxman, Betsy, Whittam, Thomas S.
Serotyping and other phenotypic methods are often used to characterize the capsular polysaccharide of group B streptococci (GBS). We describe a capsular genotyping method that utilizes PCR of...
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and...
Wick, Lukas M., Rouillard, Jean Marie, Whittam, Thomas S., Gulari, Erdogan, Tiedje, James M., Hashsham, Syed A.
Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes...
Alland, David, Whittam, Thomas S., Murray, Megan B., Cave, M. Donald, Hazbon, Manzour H., Dix, Kim, ...
The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and...
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
Differentiation of Escherichia coli Pathotypes by Oligonucleotide Spotted Array†
Palaniappan, Raghavan U. M., Zhang, Yu, Chiu, David, Torres, Alfonso, DebRoy, Chobi, Whittam, Thomas S., ...
To accurately determine the pathotypes of Escherichia coli strains, a comprehensive assessment of each strain that targets multiple genes is required. A new approach to the identification and...
Monday, Steven R., Keys, Christina, Hanson, Patricia, Shen, Yuelian, Whittam, Thomas S., Feng, Peter
Produce isolates of the Escherichia coli Ont:H52 serotype carried Shiga toxin 1 and stable toxin genes but only expressed Stx1. These strains had pulsed-field gel electrophoresis profiles that were...
Genetic Changes in Fluctuating Vole Populations: Selective VS. Nonselective Forces
Gaines, Michael S., Whittam, Thomas S.
The Lewontin-Krakauer test for selective neutrality of polymorphisms was applied to temporal variation in gene frequency at five electrophoretic loci in each of four fluctuating vole populations over...
Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
Zhang, Wei, Qi, Weihong, Albert, Thomas J., Motiwala, Alifiya S., Alland, David, Hyytia-Trees, Eija K., ...
Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the...
Sreevatsan, Srinand, Pan, Xi, Stockbauer, Kathryn E., Connell, Nancy D., Kreiswirth, Barry N., Whittam, Thomas S., ...
One-third of humans are infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. Sequence analysis of two megabases in 26 structural genes or loci in strains recovered globally...
Carbonic anhydrase is an ancient enzyme widespread in prokaryotes
Smith, Kerry S., Jakubzick, Claudia, Whittam, Thomas S., Ferry, James G.
Carbonic anhydrases catalyze the reversible hydration of CO2 and are ubiquitous in highly evolved eukaryotes. The recent identification of a third class of carbonic anhydrase (γ class) in a...
Complete genomic sequence of Pasteurella multocida,Pm70
May, Barbara J., Zhang, Qing, Li, Ling Ling, Paustian, Michael L., Whittam, Thomas S., Kapur, Vivek
We present here the complete genome sequence of a common avian clone of Pasteurella multocida, Pm70. The genome of Pm70 is a single circular chromosome 2,257,487 base pairs in length and contains...
Nagy, Béla, Wilson, Richard A., Whittam, Thomas S.
Multilocus enzyme electrophoresis was applied to detect allelic variation and multilocus genotypes (electrophoretic types [ETs]) among 43 Escherichia coli isolates from weaned pigs suffering from...
Reid, Sean D., Betting, David J., Whittam, Thomas S.
A multiplex PCR was designed to detect the eae gene and simultaneously identify specific alleles in pathogenic Escherichia coli. The method was tested on 87 strains representing the diarrheagenic E....
Acquisition of the rfb-gnd Cluster in Evolution of Escherichia coli O55 and O157
Tarr, Phillip I., Schoening, Laura M., Yea, Yoo-Lee, Ward, Teresa R., Jelacic, Srdjan, Whittam, Thomas S.
The rfb region specifies the structure of lipopolysaccharide side chains that comprise the diverse gram-negative bacterial somatic (O) antigens. The rfb locus is adjacent to gnd, which is a...
Davies, Robert L., Whittam, Thomas S., Selander, Robert K.
The molecular evolution of the leukotoxin structural gene (lktA) of Mannheimia (Pasteurella) haemolytica was investigated by nucleotide sequence comparison of lktA in 31 bovine and ovine strains...
Phylogenetic Analysis of Enteroaggregative and Diffusely Adherent Escherichia coli
Czeczulin, John R., Whittam, Thomas S., Henderson, Ian R., Navarro-Garcia, Fernando, Nataro, James P.
The phylogenetics of the various pathotypes of diarrheagenic Escherichia coli are not completely understood. In this study, we identified several plasmid and chromosomal genes in the pathogenic...
Blank, T. Eric, Zhong, Hailang, Bell, Alison L., Whittam, Thomas S., Donnenberg, Michael S.
Typical enteropathogenic Escherichia coli (EPEC) strains produce bundle-forming pili (BFP), type IVB fimbriae that have been implicated in EPEC virulence, antigenicity, autoaggregation, and localized...
Sequence Diversity of Flagellin (fliC) Alleles in Pathogenic Escherichia coli
Reid, Sean D., Selander, Robert K., Whittam, Thomas S.
To study the molecular evolution of flagellin, the protein subunit specifying flagellar (H) antigens, the fliC genes from 15 pathogenic strains of Escherichia coli were amplified by PCR and...
Gene Conservation and Loss in the mutS-rpoS Genomic Region of Pathogenic Escherichia coli
Herbelin, Corinne J., Chirillo, Samantha C., Melnick, Kristen A., Whittam, Thomas S.
The extent and nature of DNA polymorphism in the mutS-rpoS region of the Escherichia coli genome were assessed in 21 strains of enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC)...
Clonal Diversity of Escherichia coli Colonizing Stools and Urinary Tracts of Young Girls
Schlager, Theresa A., Hendley, J. Owen, Bell, Alison L., Whittam, Thomas S.
Intestinal carriage of Escherichia coli in prepubertal girls without a history of urinary tract infection was examined by collecting weekly stools and periurethral and urine samples over 3 to 4 weeks...
Tarr, Cheryl L., Large, Teresa M., Moeller, Chris L., Lacher, David W., Tarr, Phillip I., Acheson, David W., ...
Most illnesses caused by Shiga toxin-producing Escherichia coli (STEC) have been attributed to E. coli serotype O157:H7, but non-O157 STEC infections are now increasingly recognized as public health...
Maidhof, Heinrich, Guerra, Beatriz, Abbas, Sascha, Elsheikha, Hany M., Whittam, Thomas S., Beutin, Lothar
Multiresistant Shiga toxin-producing Escherichia coli (STEC) O118:H16 and O118 nonmotile strains (designated O118:[H16]) were detected by examination of 171 STEC isolates for their antimicrobial...
Davies, Robert L., Campbell, Susan, Whittam, Thomas S.
The mosaic structure and molecular evolution of the leukotoxin operon (lktCABD) was investigated by nucleotide sequence comparison of the lktC, lktB, and lktD genes in 23 Mannheimia (Pasteurella)...
Molecular Evolution of the Intimin Gene in O111 Clones of Pathogenic Escherichia coli
Tarr, Cheryl L., Whittam, Thomas S.
Intimin is an important virulence factor in two groups of enteric pathogens: enteropathogenic Escherichia coli (EPEC), which is a major cause of infant diarrhea in the developing world, and...
Alland, David, Whittam, Thomas S., Murray, Megan B., Cave, M. Donald, Hazbon, Manzour H., Dix, Kim, ...
The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and...
Strain, Steven R., Leung, Kamtin, Whittam, Thomas S., De Bruijn, Frans J., Bottomley, Peter J.
An investigation was carried out to determine the genetic structure in soil populations of Rhizobium leguminosarum bv. trifolii and viciae at each of two Oregon sites (A and C) that were 1 km apart....
Anantha, Ravi P., McVeigh, Annette L., Lee, Lanfong H., Agnew, Mary K., Cassels, Frederick J., Scott, Daniel A., ...
Colonization factor antigen I (CFA/I) is the archetype of eight genetically related fimbriae of enterotoxigenic Escherichia coli (ETEC) designated class 5 fimbriae. Assembled by the alternate...
Hyma, Katie E., Lacher, David W., Nelson, Adam M., Bumbaugh, Alyssa C., Janda, J. Michael, Strockbine, Nancy A., ...
A bacterium originally described as Hafnia alvei induces diarrhea in rabbits and causes epithelial damage similar to the attachment and effacement associated with enteropathogenic Escherichia coli....
Evolution of Genomic Content in the Stepwise Emergence of Escherichia coli O157:H7†
Wick, Lukas M., Qi, Weihong, Lacher, David W., Whittam, Thomas S.
Genome comparisons have demonstrated that dramatic genetic change often underlies the emergence of new bacterial pathogens. Evolutionary analysis of Escherichia coli O157:H7, a pathogen that has...
Variation in Acid Resistance among Shiga Toxin-Producing Clones of Pathogenic Escherichia coli†
Large, Teresa M., Walk, Seth T., Whittam, Thomas S.
Pathogenic strains of Escherichia coli, such as E. coli O157:H7, have a low infectious dose and an ability to survive in acidic foods. These bacteria have evolved at least three distinct mechanisms...
Genetic Changes in Fluctuating Vole Populations: Selective VS. Nonselective Forces
Gaines, Michael S., Whittam, Thomas S.
The Lewontin-Krakauer test for selective neutrality of polymorphisms was applied to temporal variation in gene frequency at five electrophoretic loci in each of four fluctuating vole populations over...
Fitch, Brooke R., Sachen, Kacey L., Wilder, Stacey R., Burg, Matthew A., Lacher, David W., Khalife, Walid T., ...
Multilocus sequencing was used to compare Campylobacter sp. strains isolated from retail chicken products and humans with gastroenteritis in central Michigan. Sequence comparisons demonstrated...
DNA Polymorphism and Molecular Subtyping of the Capsular Gene Cluster of Group B Streptococcus†
Manning, Shannon D., Lacher, David W., Davies, H. Dele, Foxman, Betsy, Whittam, Thomas S.
Serotyping and other phenotypic methods are often used to characterize the capsular polysaccharide of group B streptococci (GBS). We describe a capsular genotyping method that utilizes PCR of...
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and...
Wick, Lukas M., Rouillard, Jean Marie, Whittam, Thomas S., Gulari, Erdogan, Tiedje, James M., Hashsham, Syed A.
Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes...
Filliol, Ingrid, Motiwala, Alifiya S., Cavatore, Magali, Qi, Weihong, Hazbón, Manzour Hernando, Bobadilla Del Valle, Miriam, ...
Differentiation of Escherichia coli Pathotypes by Oligonucleotide Spotted Array†
Palaniappan, Raghavan U. M., Zhang, Yu, Chiu, David, Torres, Alfonso, DebRoy, Chobi, Whittam, Thomas S., ...
To accurately determine the pathotypes of Escherichia coli strains, a comprehensive assessment of each strain that targets multiple genes is required. A new approach to the identification and...
Monday, Steven R., Keys, Christina, Hanson, Patricia, Shen, Yuelian, Whittam, Thomas S., Feng, Peter
Produce isolates of the Escherichia coli Ont:H52 serotype carried Shiga toxin 1 and stable toxin genes but only expressed Stx1. These strains had pulsed-field gel electrophoresis profiles that were...
Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
Zhang, Wei, Qi, Weihong, Albert, Thomas J., Motiwala, Alifiya S., Alland, David, Hyytia-Trees, Eija K., ...
Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the...
Lacher, David W., Steinsland, Hans, Blank, T. Eric, Donnenberg, Michael S., Whittam, Thomas S.
Enteropathogenic Escherichia coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations. Typical EPEC isolates are differentiated from other types of pathogenic E. coli by...
Alland, David, Lacher, David W., Hazbón, Manzour Hernando, Motiwala, Alifiya S., Qi, Weihong, Fleischmann, Robert D., ...
Mycobacterium tuberculosis strains contain different genomic insertions or deletions called large sequence polymorphisms (LSPs). Distinguishing between LSPs that occur one time versus ones that occur...
Besser, Thomas E., Shaikh, Nurmohammad, Holt, Nicholas J., Tarr, Phillip I., Konkel, Michael E., Malik-Kale, Preeti, ...
Escherichia coli O157:H7, a zoonotic human pathogen for which domestic cattle are a reservoir host, produces a Shiga toxin(s) (Stx) encoded by bacteriophages. Chromosomal insertion sites of these...
Cho, Seongbeom, Boxrud, David J, Bartkus, Joanne M, Whittam, Thomas S, Saeed, Mahdi
Simplified multiple-locus variable-number tandem repeat analysis (MLVA) was developed using one-shot multiplex PCR for seven variable-number tandem repeats (VNTR) markers with high diversity...
Walk, Seth T., Mladonicky, Janice M., Middleton, Jaclyn A., Heidt, Anthony J., Cunningham, Julie R., Bartlett, Paul, ...
The widespread agricultural use of antimicrobials has long been considered a crucial influence on the prevalence of resistant genes and bacterial strains. It has been suggested that antibiotic...
Bergholz, Teresa M, Wick, Lukas M, Qi, Weihong, Riordan, James T, Ouellette, Lindsey M, Whittam, Thomas S
Besser, Thomas E., Shaikh, Nurmohammad, Holt, Nicholas J., Tarr, Phillip I., Konkel, Michael E., Malik-Kale, Preeti, ...
Tarr, Cheryl L., Nelson, Adam M., Beutin, Lothar, Olsen, Katharina E. P., Whittam, Thomas S.
Most severe illnesses that are attributed to Shiga toxin-producing Escherichia coli are caused by isolates that also carry a pathogenicity island called the locus of enterocyte effacement (LEE)....
Ziebell, Kim, Konczy, Paulina, Yong, Irene, Frost, Shelley, Mascarenhas, Mariola, Kropinski, Andrew M., ...
Two phylogenetic methods (multilocus sequence typing [MLST] and a multiplex PCR) were investigated to determine whether phylogenetic classification of verocytotoxin-producing Escherichia coli...
Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks
Manning, Shannon D., Motiwala, Alifiya S., Springman, A. Cody, Qi, Weihong, Lacher, David W., Ouellette, Lindsey M., ...
Escherichia coli O157:H7, a toxin-producing food and waterborne bacterial pathogen, has been linked to large outbreaks of gastrointestinal illness for more than two decades. E. coli O157 causes a...
Riordan, James T., Viswanath, Sandeep B., Manning, Shannon D., Whittam, Thomas S.
The rapid and accurate identification of Escherichia coli O157:H7 strains is central to reducing the impact of outbreaks. A real-time PCR-based approach to differentiating major outbreak lineages of...
Pathogenesis of Renal Disease Due to Enterohemorrhagic Escherichia coli in Germ-Free Mice▿
Eaton, Kathryn A., Friedman, David I., Francis, Gayle J., Tyler, Jessica S., Young, Vincent B., Haeger, Jennifer, ...
Enterohemorrhagic Escherichia coli (EHEC) is a food-borne pathogen that causes hemorrhagic colitis and acute renal failure. We used a germ-free mouse model to investigate the role of host factors,...
Konczy, Paulina, Ziebell, Kim, Mascarenhas, Mariola, Choi, Aileen, Michaud, Corinne, Kropinski, Andrew M., ...
The locus of enterocyte effacement (LEE) and genomic O island 122 (OI-122) are pathogenicity islands in verocytotoxin-producing Escherichia coli (VTEC) serotypes that are associated with outbreaks...
Hazbón, Manzour Hernando, Motiwala, Alifiya S., Cavatore, Magali, Brimacombe, Michael, Whittam, Thomas S., Alland, David
Mycobacterium tuberculosis adapts to the environment by selecting for advantageous single-nucleotide polymorphisms (SNPs). We studied whether advantageous SNPs could be distinguished from neutral...
Bell, Julia A, St Charles, Jessica L, Murphy, Alice J, Rathinam, Vijay AK, Plovanich-Jones, Anne E, Stanley, Erin L, ...
Shiga Toxin–producing Escherichia coli Strains Negative for Locus of Enterocyte Effacement
Newton, Hayley J., Sloan, Joan, Bulach, Dieter M., Seemann, Torsten, Allison, Cody C., Tauschek, Marija, ...
The ehx plasmids of these strains are highly related, which suggests acquisition of the large plasmid was central to the strains’ emergence.
Characterisation of atypical enteropathogenic E. coli strains of clinical origin
Tennant, Sharon M, Tauschek, Marija, Azzopardi, Kristy, Bigham, Andrea, Bennett-Wood, Vicki, Hartland, Elizabeth L, ...
Genomic diversity of pathogenic Escherichia coli of the EHEC 2 clonal complex
Abu-Ali, Galeb S, Lacher, David W, Wick, Lukas M, Qi, Weihong, Whittam, Thomas S
Characterization of the Escherichia coli O157:H7 Sakai GadE Regulon▿ †
Kailasan Vanaja, Sivapriya, Bergholz, Teresa M., Whittam, Thomas S.
Integrating laterally acquired virulence genes into the backbone regulatory network is important for the pathogenesis of Escherichia coli O157:H7, which has captured many virulence genes through...
McNamara, Sara E., Srinivasan, Usha, Zhang, Lixin, Whittam, Thomas S., Marrs, Carl F., Foxman, Betsy
Probe hybridization array typing (PHAT) is a previously validated, high-throughput, highly discriminatory binary typing method based on the presence or absence of genetic material. To increase the...
Surveillance for Shiga Toxin–producing Escherichia coli, Michigan, 2001–2005
Manning, Shannon D., Madera, Robbie T., Schneider, William, Dietrich, Stephen E., Khalife, Walid, Brown, William, ...
A surveillance system used different detection methods to estimate prevalence of Shiga toxin–producing Escherichia coli during 2003–2005 and 2001–2002. More non-O157 serotypes were detected by...
Manning, Shannon D., Springman, A. Cody, Lehotzky, Erica, Lewis, Maggi A., Whittam, Thomas S., Davies, H. Dele
Group B streptococci (GBS), a leading cause of neonatal sepsis and meningitis, are transferred to neonates from colonized mothers during childbirth. Prior studies using multilocus sequence typing...