Number of fecal samples from feedlot cattle positive for <i>E</i>. <i>coli</i> O104 and O8/O9/O9a based on PCR assays of <i>wzx</i>_O104 and <i>wbdD</i>_O8/O9/O9a.

<p>Number of fecal samples from feedlot cattle positive for <i>E</i>. <i>coli</i> O104 and O8/O9/O9a based on PCR assays of <i>wzx</i>_O104 and <i>wbdD</i>_O8/O9/O9a.</p

Virulence gene profiles of strains of <i>Escherichia coli</i> O104 isolated from feedlot cattle feces.

<p>Virulence gene profiles of strains of <i>Escherichia coli</i> O104 isolated from feedlot cattle feces.</p

Model-adjusted prevalence estimates of fecal samples from feedlot cattle positive for <i>wzx</i>_O104/<i>wbdD</i>_O8/O9/O9a and <i>wzx</i>_O104 at the feedlot-, lot- and sample- levels.

<p>Model-adjusted prevalence estimates of fecal samples from feedlot cattle positive for <i>wzx</i>_O104/<i>wbdD</i>_O8/O9/O9a and <i>wzx</i>_O104 at the feedlot-, lot- and sample- levels.</p

<i>In silico</i> restriction fragment length polymorphism (RFLP) subtyping of Shiga toxin genes of O104 isolates.

<p>(A) RFLP pattern of Shiga toxin of an O104 isolate; (B) RFLP pattern of <i>stx</i>1c of a reference sequence (Accession no. DQ449666.1); (C) RFLP pattern of <i>stx</i>1a of a reference sequence (Accession no. M16625.1); (D) RFLP pattern of <i>stx</i>1d of a reference sequence (Accession no. AY170851.1)</p

Pulsed-field gel electrophoresis-based clustering of <i>Escherichia coli</i> O104 strains from cattle feces and human clinical strains (O104:H4; O104:H21; and O104:H7).

<p>Pulsed-field gel electrophoresis-based clustering of <i>Escherichia coli</i> O104 strains from cattle feces and human clinical strains (O104:H4; O104:H21; and O104:H7).</p

Number of fecal samples from feedlot cattle positive for <i>wzx</i>_O104 possessing <i>E</i>. <i>coli</i> (serogroups O104 and/or O8/O9/O9a) based on the culture method and <i>wzx</i>_O104-positive isolates that tested positive for <i>wbdD</i>_O8/O9/O9a (serogroups O8/O9/O9a) or negative for <i>wbdD</i>_O8/O9/O9a (serogroup O104).

<p>Number of fecal samples from feedlot cattle positive for <i>wzx</i>_O104 possessing <i>E</i>. <i>coli</i> (serogroups O104 and/or O8/O9/O9a) based on the culture method and <i>wzx</i>_O104-positive isolates that tested positive for <i>wbdD</i>_O8/O9/O9a (serogroups O8/O9/O9a) or negative for <i>wbdD</i>_O8/O9/O9a (serogroup O104).</p

Target genes, primer sequences used and size of amplicons in PCR assays.

<p>Target genes, primer sequences used and size of amplicons in PCR assays.</p

Detection of the six major non-O157 serogroups of <i>Escherichia coli</i>, based on a culture- or multiplex PCR-based method, in fecal samples of feedlot cattle (n = 576).

<p>*Denotes significant difference in proportions within serogroups (<i>P</i> < 0.05).</p

DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying <i>Escherichia coli</i> O104:H7 isolated from feedlot cattle feces

<div><p><i>Escherichia coli</i> O104:H4, a hybrid pathotype reported in a large 2011 foodborne outbreak in Germany, has not been detected in cattle feces. However, cattle harbor and shed in the feces other O104 serotypes, particularly O104:H7, which has been associated with sporadic cases of diarrhea in humans. The objective of our study was to assess the virulence potential of Shiga toxin-producing <i>E</i>. <i>coli</i> (STEC) O104:H7 isolated from feces of feedlot cattle using DNA microarray. Six strains of STEC O104:H7 isolated from cattle feces were analyzed using FDA-<i>E</i>. <i>coli</i> Identification (ECID) DNA microarray to determine their virulence profiles and compare them to the human strains (clinical) of O104:H7, STEC O104:H4 (German outbreak strain), and O104:H21 (milk-associated Montana outbreak strain). Scatter plots were generated from the array data to visualize the gene-level differences between bovine and human O104 strains, and Pearson correlation coefficients (r) were determined. Splits tree was generated to analyze relatedness between the strains. All O104:H7 strains, both bovine and human, similar to O104:H4 and O104:H21 outbreak strains were negative for intimin (<i>eae</i>). The bovine strains were positive for Shiga toxin 1 subtype c (<i>stx</i>1c), enterohemolysin (<i>ehxA</i>), tellurite resistance gene (<i>terD</i>), IrgA homolog protein (<i>iha</i>), type 1 fimbriae (<i>fimH</i>), and negative for genes that code for effector proteins of type III secretory system. The six cattle O104 strains were closely related (r = 0.86–0.98) to each other, except for a few differences in phage related and non-annotated genes. One of the human clinical O104:H7 strains (2011C-3665) was more closely related to the bovine O104:H7 strains (r = 0.81–0.85) than the other four human clinical O104:H7 strains (r = 0.75–0.79). Montana outbreak strain (O104:H21) was more closely related to four of the human clinical O104:H7 strains than the bovine O104:H7 strains. None of the bovine <i>E</i>. <i>coli</i> O104 strains carried genes characteristic of <i>E</i>. <i>coli</i> O104:H4 German outbreak strain and unlike other human strains were also negative for Shiga toxin 2. Because cattle <i>E</i>. <i>coli</i> O104:H7 strains possess <i>stx</i>1c and genes that code for enterohemolysin and a variety of adhesins, the serotype has the potential to be a diarrheagenic foodborne pathogen in humans.</p></div

Splits tree representation of O104 diversity in our collections.

<p>Phylogenetic analysis of 33 O104 strains using the FDA-ECID gene differences data from all the probe sets. The tree was developed using the Neighbor net algorithm using Neighbor joining method (SplitsTree4). Microarray analysis of these strains was able to reveal several large parallel paths, indicative of phylogenetic incompatibilities due to probable recombination. The scale bar represents a 0.01 base substitution (bp) per site.</p