Rise of the machines: Tools to know if Salmonella will hit your 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 enterica serotype 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

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 

Shiga-toxin producing E. coli: Montessori school closed after 2 students hospitalized

The Washington, Monroe Montessori School was closed Wednesday after two young children were hospitalized with E. coli.

The girls are both under the age of 5 and were hospitalized. Only one of the girls has a confirmed kidney issue called HUS, which indicates a more serious case of E. coli. Her condition has not been released.

Sixty other preschoolers and 10 staff members may have been exposed. Everyone who has been at the school since July 11 is being tested.  Test Kits will be sent to parents Thursday, and results can take about five days.

Although it is not the source of the E. coli, the school is also being sanitized.

“The exact source of contamination in E. coli can be very difficult to identify, but at this point we believe the children were likely exposed to livestock near their home,” said Dr. Gary Goldbaum, health officer and director of the Health District.

Australian livestock industries in ‘favorable position’ on antibiotic use

Australia’s first national survey suggests livestock industries have, according to the Bush Telegraph, done a relatively good job of limiting the use of antibiotics.

The survey of 2,600 samples collected through 22 veterinary laboratories around Australia shows a low level of resistance to antibiotics.

ab.use.pigs.austThe labs tested for antibiotic resistance within two types of pathogens – E. coli and Golden Staph (Staphylococcus).

The survey found no resistance to carbapenems, an antibiotic class of last resort in human medicine used against infections when other antibacterial treatments have failed.

However the study identified ‘very low’ frequencies of resistance to other critically important human antimicrobials including fluoroquinolones and 3rd generation cephalosporins.

Professor John Turnidge, senior medical adviser on the Australian Commission on Safety and Quality in Health Care, says “what’s encouraging is the levels of resistance to the critical antibiotics for human health are close to zero.

“In part it’s due to the fact that by good foresight, good management, or good luck about 20 years ago for one particular class of antibiotics, we made a decision at a federal level that these shouldn’t be available for use in food animals and I think we’re reaping the benefit of that now.

“I’m embarrassed to say they (livestock industries) have been doing a better job than the human side.”

Community rallies behind Oklahoma boy battling E. coli infection

Residents in a small town in northwest Oklahoma are rallying behind a young boy, who is fighting for his life after being infected with E. coli.

State health officials in Oklahoma are investigating a spike in a deadly strain of E. coli. Eight-year-old Connor Sneary of Alva, Oklahoma, is one of oklahoma.e.coliat least a dozen people who became hospitalized.

Connor has been in the intensive care unit at OU Children’s Hospital where he remains in critical condition. As part of the treatment, he is undergoing dialysis and blood transfusions.

Connor has a form of E. coli that the family believes may have been contracted at an agricultural event at the Oklahoma State Fair Grounds. Investigators say that is a possibility.

Several organizations are hosting events benefiting Connor’s family. The Oklahoma Blood Institute will have a special blood drive in Alva on Tuesday, April 8, from noon to 6 p.m., at the First Christian Church. All donations will be credited to Connor for his use.

UN agency says surge in diseases of animal origin means new approach to health needed

Holistic is a term academics and those on the conference circuit like to toss around when they have no idea how to actually improve things.

Or sometimes it’s just the PR types who write the fluff.

According to a new report from the Food and Agriculture Organization of the United Nations, population growth, agricultural expansion, and livestockthe rise of globe-spanning food supply chains have dramatically altered how diseases emerge, jump species boundaries, and spread,

A new, more holistic approach to managing disease threats at the animal-human-environment interface is needed, it argues.

Seventy percent of the new diseases that have emerged in humans over recent decades are of animal origin and, in part, directly related to the human quest for more animal-sourced food, according to the report, World Livestock 2013: Changing Disease Landscapes.

The ongoing expansion of agricultural lands into wild areas, coupled with a worldwide boom in livestock production, means that “livestock and wildlife are more in contact with each other, and we ourselves are more in contact with animals than ever before,” said Ren Wang, FAO Assistant Director-General for Agriculture and Consumer Protection.

“What this means is that we cannot deal with human health, animal health, and ecosystem health in isolation from each other – we have to look at them together, and address the drivers of disease emergence, persistence and spread, rather than simply fighting back against diseases after they emerge,” he added.

FAO’s new study focuses in particular on how changes in the way humans raise and trade animals have affected how disease emerge and spread.

“In response to human population growth, income increases and urbanization, world food and agriculture has shifted its main focus from livestock-img01the supply of cereals as staples to providing an increasingly protein-rich diet based on livestock and fishery products,” World Livestock 2013 notes.

While livestock production provides a number of economic and nutrition benefits, the sector’s rapid growth has spawned a number of health-related challenges, it says.

The risk of animal-to-human pathogen shifts varies greatly according to the type of livestock production and the presence of basic infrastructure and services.

While intensive production systems are largely free from high-impact animal and zoonotic diseases, they do present some pitfalls, particularly in developing countries and countries in transition, according to the report.

The report also states, however, that disease emergence in livestock is not specific to large-scale, intensive systems.

Smallholder livestock systems – which tend to involve animals roaming freely over large areas, but still in relatively high densities – often facilitate the disease spread, both among local animal populations and over broad distances.