Predicting zoonotic Salmonella from livestock

Increasingly, routine surveillance and monitoring of foodborne pathogens using whole-genome sequencing is creating opportunities to study foodborne illness epidemiology beyond routine outbreak investigations and case–control studies.

Using a global phylogeny of Salmonella entericaserotype Typhimurium, we found that major livestock sources of the pathogen in the United States can be predicted through whole-genome sequencing data. Relatively steady rates of sequence divergence in livestock lineages enabled the inference of their recent origins. Elevated accumulation of lineage-specific pseudogenes after divergence from generalist populations and possible metabolic acclimation in a representative swine isolate indicates possible emergence of host adaptation.

We developed and retrospectively applied a machine learning Random Forest classifier for genomic source prediction of Salmonella Typhimurium that correctly attributed 7 of 8 major zoonotic outbreaks in the United States during 1998–2013. We further identified 50 key genetic features that were sufficient for robust livestock source prediction.

Zoonotic source attribution of Salmonella Enterica serotype typhimurium using genomic surveillance data, United States

January 2019

Emerging Infectious Diseases vol. 25 no. 1

Shaokang Zhang, Shaoting Li, Weidong Gu, Henk den Bakker, Dave Boxrud, Angie Taylor, Chandler Roe, Elizabeth Driebe, David M. Engelthaler, Marc Allard, Eric Brown, Patrick McDermott, Shaohua Zhao, Beau B. Bruce, Eija Trees, Patricia I. Fields, and Xiangyu Deng


These experts can’t write: how fresh produce growers make decisions about food safety?

If people who write in ALL CAPS are compensating by yelling, people who stress points by writing in italics or excessive use of quotations are compensating for boredom. To paraphrase Strunk and White, let the reader decide what is truly exclamatory and what needs to be emphasized; words, not formatting, can do this.

When people are talking, it’s called air quotes; Jon Stewart famously called them dick fingers in 2008 (video here if you’re in Canada or the U.S.). I call it bad writing.

I also have issues with people who write, “Clearly …” and “we …”

Clear to whom? Who’s we?

Strunk and White agree.

If the reader can get past the writing, a new paper in Food Control supposedly presents a new model for how fresh produce growers make decisions about food safety. I reduce the paper to: don’t care how it’s done, don’t make people barf if you provide food, and talk with growers since they’re growing the food.

I can’t figure out how the “new model” (below) is going to make fewer people barf; guess I’m not into models.

And it’s Powell, not Powel.

Abstract below:

An expert guide to understanding grower decisions related to fresh fruit and vegetable contamination prevention and control
Food Control
Jason Parker, Robyn S. Wilson, Jeffrey LeJeune, Louie Rivers III, Douglas Doohan
This research intends to refocus the on-farm fresh produce food safety paradigm away from an emphasis on knowledge deficit models and ready-made or tightly-coupled, reductionist solutions toward a loosely-coupled systems approach. The dynamic environment of produce farming and multi-dimensional objectives of produce growers create manifold pathways to address farm specific food safety concerns. We propose a systems approach to facilitate increased decision making of growers using farm-specific criteria to improve their efforts. Currently, social and psychological dimensions of fresh produce food safety are overlooked in program development with preference given to bio-physical knowledge and technological solutions. In this paper, we describe a comprehensive model that was developed through a formal expert elicitation and literature review for the purpose of enhancing education and policy development and improving the microbiological safety of fresh and fresh cut produce. This model illuminates the intrinsic interrelationships among farm scale, marketing practices, and the need for appropriate food safety interventions. We further discuss how this loosely-coupled systems perspective can both aid our understanding of grower-decision-making and provide a basis for developing equitable solutions to on-farm food safety issues as part of a social-psychological approach to addressing these issues.
? US farm scale diversity should be part of food safety policy recommendations. ? Experts need to be aware of their biases of produce grower decision-making. ? A grower-centered approach will enhance new policy, standards, and metrics. ? Farmer input is needed to adapt practices to farms of all scales. ? Avoid one-size-fits-all practices developed for large-scale produce production.

Dodd defends: E. coli and salmonella in cattle production

Chuck Dodd looked fairly snappy as he defended his PhD (below, left) today – to go with his MS and DVM – but he spent much of the past three years (right), knee deep in cow poop.

Chuck’s thesis was entitled, Epidemiology of Salmonella and E. coli O157 in Beef Cattle Production Systems and included four interrelated studies:

• effects of Salmonella Newport SRP® vaccine;
• prevalence and persistence of Salmonella;
• relatedness of E. coli O157 in feces and on carcasses; and,
• a simulation model for E. coli O157 interventions.

During his defense, Chuck said he learned “you can’t test or inspect your way to food safety. It’s the entire system.”

Good for him, and best wishes. When he finally washes out the cow smell, Chuck’s off to the Landstufl Regional Medical Center in Germany.