Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities

Abstract

Escherichia coli O157:H7 is a major foodborne human pathogen causing disease worldwide. Cattle are a major reservoir for this pathogen and those that shed E. coli O157:H7 at >104 CFU/g feces have been termed “super-shedders”. A rich microbial community inhabits the mammalian intestinal tract, but it is not known if the structure of this community differs between super-shedder cattle and their non-shedding pen mates. We hypothesized that the super-shedder state is a result of an intestinal dysbiosis of the microbial community and that a “normal” microbiota prevents E. coli O157:H7 from reaching super-shedding levels. To address this question, we applied 454 pyrosequencing of bacterial 16S rRNA genes to characterize fecal bacterial communities from 11 super-shedders and 11 contemporary pen mates negative for E. coli O157:H7. The dataset was analyzed by using five independent clustering methods to minimize potential biases and to increase confidence in the results. Our analyses collectively indicated significant variations in microbiome composition between super-shedding and non-shedding cattle. Super-shedders exhibited higher bacterial richness and diversity than non-shedders. Furthermore, seventy-two operational taxonomic units, mostly belonging to Firmicutes and Bacteroidetes phyla, were identified showing differential abundance between these two groups of cattle. The operational taxonomic unit affiliation provides new insight into bacterial populations that are present in feces arising from super-shedders of E. coli O157:H7.

The impact of the bovine faecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle

“…In contrast to the above studies, faecal microbiome studies with animals supershedding E. coli O157:H7 (>10 4 CFU per gram faeces) were found to have greater richness and diversity in the faecal microbiome than animals not shedding the pathogen (Xu et al . ). We have observed previously that the HC diet exhibited a high degree of variation in the faecal microbiota composition and taxa abundance across individual animals compared to the LC diet (Kim et al .…”

“…Previous research with cattle fed a high concentrate diet also recognized that taxa assigned within Clostridiales were differentially abundant in E. coli O157:H7 nonshedding and supershedding cattle (Xu et al . ). If isolated from bovine faeces and found to confer antagonism or inhibition to E. coli O157:H7, then the species corresponding to the OTUs that were negatively correlated with E. coli O157:H7 prevalence and enumeration may be useful as direct fed microbials to inhibit E. coli O157:H7.…”

“…In contrast, Xu et al . () examined the bacterial microbiome in faeces from 22 finishing cattle in a feedlot study from Canada and reported taxa representing only 17 phyla. The current study provides the first extensive analysis of the faecal bacterial populations from large animal populations and the cattle‐associated foodborne pathogen, E. coli O157:H7, whereas previous research by Xu et al .…”

“…The HC diet was a high concentrate maize-based diet typical to finishing cattle in the United States, and we observed 26 different bacterial phyla from the composited faeces of the 132 animals fed this diet. In contrast, Xu et al (2014) examined the bacterial microbiome in faeces from 22 finishing cattle in a feedlot study from Canada and reported taxa representing only 17 phyla. The current study provides the first extensive analysis of the faecal bacterial populations from large animal populations and the cattle-associated foodborne pathogen, E. coli O157:H7, whereas previous research by Xu et al (2014) only examined 22 animals total.…”

Shiga‐toxin Producing Escherichia coli: Pathogenicity, Supershedding, Diagnostic Methods, Occurrence, and Foodborne Outbreaks

“…Variations in the results would probably be due to the difference between animals, diet, period and duration of the study (Chase‐Topping and others ). In addition, the intestinal microbiome of supershedding species has shown greater diversity among species than non‐shedding animals, detected through feces samples (Xu and others ). Furthermore, in the study of Wang and others (), the rectal tissue of non‐shedding animals may exhibit more effective innate and adaptive immune protection than supershedding animals, due to the presence of down‐regulated genes.…”