Use of multiple-locus variable-number tandem repeat analysis to evaluate Escherichia coli O157 subtype distribution and transmission dynamics following natural exposure on a closed beef feedlot facility

Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California

Escherichia coli serotype O157:H7 is a zoonotic food- and waterborne bacterial pathogen that causes a high hospitalization rate and can cause life-threatening complications. Increasingly, E. coli O157:H7 infections appear to originate from fresh produce. Ruminants, such as cattle, are a prominent reservoir of E. coli O157:H7 in the United States. California is one of the most agriculturally productive regions in the world for fresh produce, beef, and milk. The close proximity of fresh produce and cattle presents food safety challenges on a uniquely large scale. We performed a survey of E. coli O157:H7 on 20 farms in California to observe the regional diversity and prevalence of E. coli O157:H7. Isolates were obtained from enrichment cultures of cow feces. Some farms were sampled on two dates. Genomes from isolates were sequenced to determine their relatedness and pathogenic potential. E. coli O157:H7 was isolated from approximately half of the farms. The point prevalence of E. coli O157:H7 on farms was highly variable, ranging from zero to nearly 90%. Within farms, generally one or a few lineages were found, even when the rate of isolation was high. On farms with high isolation rates, a single clonal lineage accounted for most of the isolates. Farms that were visited months after the first visit might have had the same lineages of E. coli O157:H7. Strains of E. coli O157:H7 may be persistent for months on farms.IMPORTANCE This survey of 20 cow-calf operations from different regions of California provides an in depth look at resident Escherichia coli O157:H7 populations at the molecular level. E. coli O157:H7 is found to have a highly variable prevalence, and with whole-genome sequencing, high prevalences in herds were found to be due to a single lineage shed from multiple cows. Few repeat lineages were found between farms in this area; therefore, we predict that E. coli O157:H7 has significant diversity in this area beyond what is detected in this survey. All isolates from this study were found to have pathogenic potential based on the presence of key virulence gene sequences. This represents a novel insight into pathogen diversity within a single subtype and will inform future attempts to survey regional pathogen populations.

Making the most of clustered data in laboratory animal research using multi-level models

In the following review article, I address the fitting of multi-level models for the analysis of hierarchical data in laboratory animal medicine. Using an example of paternal dietary effects on the weight of offspring in a mouse model, this review outlines the reasons and benefits of using a multi-level modeling approach. To start, the concept of clustered/autocorrelated data is introduced, and the implications of ignoring the effects of clustered data on measures of association/model coefficients and their statistical significance are discussed. The limitations of other methods compared with multi-level modeling for analyzing clustered data are addressed in terms of statistical power, control of potential confounding effects associated with group membership, proper estimation of associations and their statistical significance, and adjusting for multiple levels of clustering. In addition, the benefits of being able to estimate variance partition coefficients and intra-class correlation coefficients from multi-level models is described, and the concepts of more complex correlation structures and various methods for fitting multi-level models are introduced. The current state of learning materials including textbooks, websites, and software for the nonstatistician is outlined to describe the accessibility of multi-level modeling approaches for laboratory animal researchers.

Vaccination of Cattle against Escherichia coli O157:H7

Human infection with Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) is relatively rare, but the consequences can be serious, especially in the very young and the elderly. Efforts to control the flow of STEC O157 during beef processing have meaningfully reduced the incidence of human STEC O157 infection, particularly prior to 2005. Unfortunately, despite early progress, the incidence of STEC O157 infection has not changed meaningfully or statistically in recent years, suggesting that additional actions, for example, targeting the cattle reservoir, are necessary to further reduce STEC O157 illness. Ideally, preharvest interventions against STEC O157 should reduce the likelihood that cattle carry the organism, have practical application within the beef production system, and add sufficient value to the cattle to offset the cost of the intervention. A number of STEC O157 antigens are being investigated as potential vaccine targets. Some vaccine products have demonstrated efficacy to reduce the prevalence of cattle carrying STEC O157 by making the gut unfavorable to colonization. However, in conditions of natural exposure, efficacy afforded by vaccination depends on how the products are used to control environmental transmission within groups of cattle and throughout the production system. Although cattle vaccines against STEC O157 have gained either full or preliminary regulatory approval in Canada and the United States, widespread use by cattle feeders is unlikely until there is an economic signal to indicate that cattle vaccinated against STEC O157 are valued over other cattle.

Animal Reservoirs of Shiga Toxin-Producing Escherichia coli

Shiga toxin-producing Escherichia coli (STEC) strains have been detected in a wide diversity of mammals, birds, fish, and several insects. Carriage by most animals is asymptomatic, thus allowing for dissemination of the bacterium in the environment without detection. Replication of the organism may occur in the gastrointestinal tract of some animals, notably ruminants. Carriage may also be passive or transient, without significant amplification of bacterial numbers while in the animal host. Animals may be classified as reservoir species, spillover hosts, or dead-end hosts. This classification is based on the animal's ability to (i) transmit STEC to other animal species and (ii) maintain STEC infection in the absence of continuous exposure. Animal reservoirs are able to maintain STEC infections in the absence of continuous STEC exposure and transmit infection to other species. Spillover hosts, although capable of transmitting STEC to other animals, are unable to maintain infection in the absence of repeated exposure. The large diversity of reservoir and spillover host species and the survival of the organism in environmental niches result in complex pathways of transmission that are difficult to interrupt.