Sample sources that yielded the Shiga toxin-producing <i>E</i>. <i>coli</i> strains, examined in the present study.

<p>Wildlife (32%), watersheds (24%), leafy vegetables (22%), livestock (18%), other vegetables (1%), sediment (1%), soil (1%), and fruit (1%).</p

Data_Sheet_1_Pathogenicity assessment of Shiga toxin-producing Escherichia coli strains isolated from wild birds in a major agricultural region in California.PDF

Shiga toxin-producing Escherichia coli (STEC) consists of diverse strains differing in genetic make-up and virulence potential. To better understand the pathogenicity potential of STEC carried by the wildlife, three STEC and one E. coli strains isolated from wild birds near a major agricultural region in California were selected for comparative pathogenomic analyses. Three American crow (Corvus brachyrhynchos) strains, RM9088, RM9513, and RM10410, belonging to phylogroup A with serotypes O109:H48, O9:H30, and O113:H4, respectively, and a red-winged blackbird (Agelaius phoeniceus) strain RM14516 in phylogroup D with serotype O17:H18, were examined. Shiga toxin genes were identified in RM9088 (stx1a), RM10410 (stx1a + stx2d), and RM14516 (stx2a). Unlike STEC O157:H7 strain EDL933, none of the avian STEC strains harbored the pathogenicity islands OI-122, OI-57, and the locus of enterocyte effacement, therefore the type III secretion system biogenesis genes and related effector genes were absent in the three avian STEC genomes. Interestingly, all avian STEC strains exhibited greater (RM9088 and RM14516) or comparable (RM10410) cytotoxicity levels compared with EDL933. Comparative pathogenomic analyses revealed that RM9088 harbored numerous genes encoding toxins, toxins delivery systems, and adherence factors, including heat-labile enterotoxin, serine protease autotransporter toxin Pic, type VI secretion systems, protein adhesin Paa, fimbrial adhesin K88, and colonization factor antigen I. RM9088 also harbored a 36-Kb high pathogenicity island, which is related to iron acquisition and pathogenicity in Yersinia spp. Strain RM14516 carried an acid fitness island like the one in EDL933, containing a nine gene cluster involved in iron acquisition. Genes encoding extracellular serine protease EspP, subtilase cytotoxin, F1C fimbriae, and inverse autotransporter adhesin IatC were only detected in RM14516, and genes encoding serine protease autotransporter EspI and P fimbriae were only identified in RM10410. Although all curli genes were present in avian STEC strains, production of curli fimbriae was only detected for RM9088 and RM14516. Consistently, strong, moderate, and little biofilms were observed for RM9088, RM14516, and RM10410, respectively. Our study revealed novel combinations of virulence factors in two avian strains, which exhibited high level of cytotoxicity and strong biofilm formation. Comparative pathogenomics is powerful in assessing pathogenicity and health risk of STEC strains.</p

Patterns of presence, absence or divergence in the <i>Campylobacter jejuni</i>-integrated elements.

<p>A detailed genomic analysis of the genomic integrated elements CJIE1 (top) and CJIE2 (bottom) was compiled in GeneSpring version 7.3 with the standard correlation and bootstrapping (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#s2" target="_blank">Materials and Methods</a>). Each column corresponds to a <i>C. jejuni</i> strain designated vertically across the bottom, as described in the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#pone-0002015-g002" target="_blank">Figure 2</a>. The gene status based on cutoff values of absence and presence predictions is shown color-coded: blue, present; light blue, divergent; red, highly divergent or absent; white, no data.</p

MLST analysis of the <i>Campylobacter jejuni</i> strains used in this study.

a<p>Original strain number is designated in parenthesis.</p>b<p>Unk, unknown.</p>c<p>UK, United Kingdom; USA, United States of America; SA, South Africa; MEX, Mexico; CAN, Canada.</p>d<p>GBS, Guillain-Barré syndrome; MFS, Miller Fisher syndrome.</p>e<p>Penner heat-stable (HS) serotypes.</p

Patterns of presence, absence or divergence in the 18 hypervariable regions in <i>Campylobacter jejuni</i> strains.

<p>A detailed genomic analysis of the 18 hypervariable regions (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#pone-0002015-t002" target="_blank">Table 2</a>) was compiled in GeneSpring version 7.3 with the standard correlation and bootstrapping (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#s2" target="_blank">Materials and Methods</a>). Each panel represents a hypervariable region, and each column corresponds to a <i>C. jejuni</i> strain designated vertically across the bottom, as described in the legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#pone-0002015-g002" target="_blank">Figure 2</a>. The gene status based on cutoff values of absence and presence predictions is shown color-coded: blue, present; light blue, divergent; red, highly divergent or absent; white, no data.</p

Dendrogram of <i>Campylobacter jejuni</i> sequence types, including clinical strains from South Africa, Mexico and Canada.

<p>The dendrogram was constructed by using the neighbor-joining algorithm and the Kimura two-parameter distance estimation method. Bootstrap values of >75%, generated from 500 replicates, are shown at the nodes. The scale bar represents substitutions per site.</p

Intraspecies hypervariable regions in <i>Campylobacter jejuni</i>.

a<p>The start and end of each region is shown for genes in strain RM1221 (strain NCTC 11168) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#pone.0002015-Parker3" target="_blank">[40]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#pone.0002015-Taboada1" target="_blank">[42]</a>.</p

Genome comparison of <i>Campylobacter jejuni</i> clinical strains by DNA microarrays analysis.

<p>An average linkage hierarchical clustering of the <i>C. jejuni</i> strains with a distance score scale bar was compiled in GeneSpring version 7.3 with the standard correlation and bootstrapping (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002015#s2" target="_blank">Materials and Methods</a>). The gene status based on cutoff values of absence and presence predictions is shown color-coded: blue, present; light blue, divergent; red, highly divergent or absent; white, no data. <i>C. jejuni</i> strains from South Africa with HS∶41 serotype (yellow), with other serotypes (green), or strains with HS∶41 serotype from Mexico and Canada (white) are designated vertically across the bottom. GBS-associated strains are annotated with stars; MFS-associated strains are annotated with diamonds. The four <i>C. jejuni</i>-integrated elements (CJIEs) and the assigned MLST sequence type (ST) for each strain cluster is indicated.</p

Additional file 1: of Antimicrobial resistance profiles of Shiga toxin-producing Escherichia coli O157 and Non-O157 recovered from domestic farm animals in rural communities in Northwestern Mexico

Antimicrobial agents used in the present study. (DOCX 14 kb

Genotypic Analyses of Shiga Toxin-Producing <em>Escherichia coli</em> O157 and Non-O157 Recovered from Feces of Domestic Animals on Rural Farms in Mexico

<div><p>Shiga toxin-producing <em>Escherichia coli</em> (STEC) are zoonotic enteric pathogens associated with human gastroenteritis worldwide. Cattle and small ruminants are important animal reservoirs of STEC. The present study investigated animal reservoirs for STEC in small rural farms in the Culiacan Valley, an important agricultural region located in Northwest Mexico. A total of 240 fecal samples from domestic animals were collected from five sampling sites in the Culiacan Valley and were subjected to an enrichment protocol followed by either direct plating or immunomagnetic separation before plating on selective media. Serotype O157:H7 isolates with the virulence genes <em>stx2</em>, <em>eae</em>, and <em>ehxA</em> were identified in 40% (26/65) of the recovered isolates from cattle, sheep and chicken feces. Pulse-field gel electrophoresis (PFGE) analysis grouped most O157:H7 isolates into two clusters with 98.6% homology. The use of multiple-locus variable-number tandem repeat analysis (MLVA) differentiated isolates that were indistinguishable by PFGE. Analysis of the allelic diversity of MLVA loci suggested that the O157:H7 isolates from this region were highly related. In contrast to O157:H7 isolates, a greater genotypic diversity was observed in the non-O157 isolates, resulting in 23 PFGE types and 14 MLVA types. The relevant non-O157 serotypes O8:H19, O75:H8, O111:H8 and O146:H21 represented 35.4% (23/65) of the recovered isolates. In particular, 18.5% (12/65) of all the isolates were serotype O75:H8, which was the most variable serotype by both PFGE and MLVA. The non-O157 isolates were predominantly recovered from sheep and were identified to harbor either one or two <em>stx</em> genes. Most non-O157 isolates were <em>ehxA</em>-positive (86.5%, 32/37) but only 10.8% (4/37) harbored <em>eae</em>. These findings indicate that zoonotic STEC with genotypes associated with human illness are present in animals on small farms within rural communities in the Culiacan Valley and emphasize the need for the development of control measures to decrease risks associated with zoonotic STEC.</p> </div