Horizontal gene transfer in E. coli O104

Escherichia coli O104 is an emergent disease-causing bacterium various strains of which are becoming increasingly well known and troublesome.

beansproutsThe pathogen causes bloody diarrhea as well as and potentially fatal kidney damage, hemolytic uremic syndrome. Infection is usually through inadvertent ingestion of contaminated and incompletely cooked food or other materials, such as animals feces.

Escherichia coli is a gram negative bacterium, commonly found in the intestine of humans and other mammals. Entero-hemorrhagic strains including O157, O26, O103 and O111 and specifically the sub-strain O157:H7 is an important cause of foodborne illness in North America, the UK and Japan.

One particular strain, highlighted by Indian researchers in the International Journal of Bioinformatics Research and Applications, O104:H4, causes serious complications and has developed significant multiple-drug resistance to antibiotics. Moreover, it has acquired genes through horizontal transfer from other strains that make it even more virulent than others.

The team from Madurai Kamaraj University in Madurai, Tamil Nadu, working with colleagues at Genotypic Technology Pvt Ltd in Karnataka, have used the tools of computational molecular biology to identify 38 such horizontal gene transfer elements, prophage elements. These elements the team explains are genetic weapons that protect the bacteria from antibiotics and have been acquired from viruses, known as bacteriophages, that usually infect bacteria.

More than a quarter of the genome of this strain of E. coli comprises prophage elements, the team explains. These elements are also involved in the production of lethal compounds such as Shiga toxin, which give rise to many of the symptoms of infection. As such, they might represent new diagnostic markers or even targets for the development of novel antibiotics that circumvent the protective measures acquired by the bacteria.

Public health has better things to do: Increased outbreaks associated with nonpasteurized milk

The number of US outbreaks caused by nonpasteurized milk increased from 30 during 2007-2009 to 51 during 2010-2012. Most outbreaks were caused by Campylobacter spp. (77%) and by nonpasteurized milk purchased from states in which nonpasteurized milk sale was legal (81%).

rw.milk.outbreaks.2Regulations to prevent distribution of nonpasteurized milk should be enforced.

Increased outbreaks associated with nonpasteurized milk, United States, 2007-2012.

Emerging Infectious Diseases, 2015 Jan;21(1):119-22. doi: 10.3201/eid2101.140447.

Mungai EA, Behravesh CB, Gould LH.


Nosestretcher alert: Invite some germs to dinner

When Michael Pollan endorses an article, I know it’s BS.

sprout.santa_.barf_.xmas_-300x254So it is with Kate Murphy’s piece in the New York Times on Sunday, that says the U.S. food supply is “arguably the safest in the world” and asks “whether our food could perhaps be too clean.”

I’ve been hearing this for 25 years. It’s a tantalizing belief but at this point that’s all it is – a belief.

Cherry-picking data to support a pre-existing theory remains a belief.

I could tell an equal number of stories about my mother who got undulate fever from raw milk as a child, or my aunt who suffered with cyclospora from basil in Florida, or Champan who spent a weekend in our toilet from Campylobacter in Kansas, but it’s not science.

There are research areas worth exploring, but we humans don’t know much about applying this germ theory, especially to the genetically susceptible.

The theory that there might be such a thing as “too clean” food stems from the hygiene hypothesis, which has been gaining traction over the last decade. It holds that our modern germaphobic ways may be making us sick by harming our microbiome, which comprises all the microscopic beasties — bacteria, viruses, fungi, mites, etc. — that live in and on our bodies.

Research so far has focused primarily on the detrimental effects of cesarean births and not breast-feeding, which may inhibit the formation of a robust microbiome, and the use of antibacterial soaps and antibiotics, which diminish the microbiome once it is established.

A result is an immune system that essentially gets bored, spoiling for a fight and apt to react to harmless substances and even attack the body’s own tissues. This could explain the increasing incidence of allergies and autoimmune disorders such as asthma, rheumatoid arthritis and inflammatory bowel syndrome.

It could also explain my latest fart.

There is also the suggestion that a diminished microbiome disrupts hormones that regulate hunger, which can cause obesity and metabolic disorders.

When it comes to foodborne illness, the idea is that fewer good bacteria in your gut means there is less competition to prevent colonization of the bad microbes, leading to more frequent and severe bouts of illness.

Moreover, your underutilized immune system may lose its ability to discriminate between friend and foe, so it may marshal its defenses inappropriately (e.g., against gluten and lactose) or not at all.

All of this is hard to prove.

That should be the headline.

Anyone who has visited a country with less than rigorous sanitation knows the locals don’t get sick from foods that can cause tourists days of toilet-bound torment.

sprouts_sandwich(1)That’s because the susceptible ones have died off.

“We have these tantalizing bits of evidence that to my mind provide pretty good support for the hygiene hypothesis, in terms of foodborne illness,” said Guy Loneragan, an epidemiologist and professor of food safety and public health at Texas Tech.

Yes, it’s tantalizing.

This is not to say we’d be better off if chicken producers eased up on the salmonella inspections, we ate recalled ice cream sandwiches and didn’t rinse our produce.

Rinsing produce ain’t going to do much either way; but may make the consumer feel cleaner.

Murphey says it is worth noting that serious foodborne diseases — the ones that make it into the news, like listeria, salmonella, E. coli, cryptosporidium and campylobacter — are mainly diseases of immuno-compromised populations.


The E. coli O104 outbreak in sprouts in Germany in 2011 that killed 53 and sickened 4,400 primarily struck middle-aged, health women, because they eat more salads.

That’s science.

Seek and ye shall find: E. coli O26:H11 in cows

Escherichia coli O26 has been identified as the most common non-O157 Shiga toxin-producing E. coli (STEC) serogroup to cause human illnesses in the United States and has been implicated in outbreaks around the world. E. coli has high genomic plasticity, which facilitates the loss or acquisition of virulence genes.

cow.poop2Attaching and effacing E. coli (AEEC) O26 strains have frequently been isolated from bovine feces, and there is a need to better characterize the relatedness of these strains to defined molecular pathotypes and to describe the extent of their genetic diversity.

High-throughput real-time PCR was used to screen 178 E. coli O26 isolates from a single U.S. cattle feedlot, collected from May to July 2011, for the presence or absence of 25 O26 serogroup-specific and virulence-associated markers. The selected markers were capable of distinguishing these strains into molecularly defined groups (yielding 18 unique marker combinations). Analysis of the clustered regularly interspaced short palindromic repeat 1 (CRISPR1) and CRISPR2a loci further discriminated isolates into 24 CRISPR types. The combination of molecular markers and CRISPR typing provided 20.8% diversity. The recent CRISPR PCR target SP_O26-E, which was previously identified only in stx2-positive O26:H11 human clinical strains, was identified in 96.4% (161/167 [95% confidence interval, 99.2 to 93.6%]) of the stx-negative AEEC O26:H11 bovine fecal strains. This supports that these stx-negative strains may have previously contained a prophage carrying stx or could acquire this prophage, thus possibly giving them the potential to become pathogenic to humans.

These results show that investigation of specific genetic markers may further elucidate our understanding of the genetic diversity of AEEC O26 strains in bovine feces.

Genetic diversity and pathogenic potential of attaching and effacing Escherichia coli O26:H11 strains recovered from bovine feces in the United States

Applied and Environmental Microbiology

Sarah A. Ison, Sabine Delannoy, Marie Bugarel, Kendra K. Nightingale, Hattie E. Webb, David G. Renter, Tiruvoor G. Nagarajac, Guy H. Loneragana and Patrick Fachb


 Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen that may be responsible for severe human infections. Only a limited number of serotypes, including O26:H11, are involved in the majority of serious cases and outbreaks. The main virulence factors, Shiga toxins (Stx), are encoded by bacteriophages.

cowSeventy-four STEC O26:H11 strains of various origins (including human, dairy, and cattle) were characterized for their stx subtypes and Stx phage chromosomal insertion sites. The majority of food and cattle strains possessed the stx1a subtype, while human strains carried mainly stx1a or stx2a. The wrbA and yehV genes were the main Stx phage insertion sites in STEC O26:H11, followed distantly by yecE and sbcB. Interestingly, the occurrence of Stx phages inserted in the yecE gene was low in dairy strains. In most of the 29 stx-negative E. coli O26:H11 strains also studied here, these bacterial insertion sites were vacant. Multilocus sequence typing of 20 stx-positive or stx-negative E. coli O26:H11 strains showed that they were distributed into two phylogenetic groups defined by sequence type 21 (ST21) and ST29. Finally, an EspK-carrying phage was found inserted in the ssrA gene in the majority of the STEC O26:H11 strains but in only a minority of the stx-negative E. coli O26:H11 strains.

The differences in the stx subtypes and Stx phage insertion sites observed in STEC O26:H11 according to their origin might reflect that strains circulating in cattle and foods are clonally distinct from those isolated from human patients.

 Diversity of shiga toxin-producing Escherichia coli (STEC) O26:H11 strains examined via stx subtypes and insertion sites of stx and espk bacteriophages

Applied and Environmental Microbiology

Ludivine Bonanno, Estelle Loukiadis, Patricia Mariani-Kurkdjian, Eric Oswald, Lucille Garnier, Valérie Michel and Frédéric Auvray


Handwashing is never enough: 32 suspected sick from WA animal contact area

The Whatcom County Health Department is continuing to look for the cause of an E. coli outbreak among schoolchildren who went to the Milk Makers Fest last week in Lynden.

MILK_MAKERS_FEST_020.aurora_standalone.prod_affiliate.39Um, cows? Sheep? Goats?

Six children have been sickened so far with shiga toxin-producing E. coli and up to 32 are reported with symptoms.

The Milk Makers Fest introduces young students to farming. It also gave them a chance to pet farm animals.

Meanwhile, health officials are reminding people that they should wash their hands well, especially after using the bathroom and before preparing food for eating.

“Everybody has to be careful with their hand washing,” said Greg Stern, Whatcom County Health officer.


A table of petting zoo outbreaks is available at http://barfblog.com/wp-content/uploads/2014/04/Petting-Zoo-Outbreaks-Table-4-8-14.xlsx.

Best practices for planning events encouraging human-animal interactions

Zoonoses and Public Health

G. Erdozain , K. KuKanich , B. Chapman  and D. Powell


Educational events encouraging human–animal interaction include the risk of zoonotic disease transmission. It is estimated that 14% of all disease in the US caused by Campylobacter spp., Cryptosporidium spp., Shiga toxin-producing Escherichia coli (STEC) O157, non-O157 STECs, Listeria monocytogenes, nontyphoidal Salmonella enterica and Yersinia enterocolitica were attributable to animal contact. This article reviews best practices for organizing events where human–animal interactions are encouraged, with the objective of lowering the risk of zoonotic disease transmission.

Seek and ye shall find: E. coli O26 testing in UK

Many serogroups of Shiga toxin-producing Escherichia coli (STEC) other than serogroup O157 (non-O157 STEC), for example STEC O26:H11, are highly pathogenic and capable of causing hemolytic uremic syndrome.

beef.stecA recent increase in non-O157 STEC cases identified in England, resulting from a change in the testing paradigm, prompted a review of the current methods available for detection and typing of non-O157 STEC for surveillance and outbreak investigations. Nineteen STEC O26:H11 strains, including four from a nursery outbreak were selected to assess typing methods. Serotyping and multilocus sequence typing were not able to discriminate between the stx-producing strains in the dataset. However, genome sequencing provided rapid and robust confirmation that isolates of STEC O26:H11 associated with a nursery outbreak were linked at the molecular level, had a common source and were distinct from the other strains analysed. Virulence gene profiling of DNA extracted from a polymerase chain reaction (PCR)-positive/culture-negative faecal specimen from a case that was epidemiologically linked to the STEC O26:H11 nursery outbreak, provided evidence at the molecular level to support that link. During this study, we describe the utility of PCR and the genome sequencing approach in facilitating surveillance and enhancing the response to outbreaks of non-O157 STEC.

The utility and public health implications of PCR and whole genome sequencing for the detection and investigation of an outbreak of Shiga toxin-producing Escherichia coli serogroup O26:H11

Epidemiology and Infection, 143, pp 1672-1680




3 first-graders sick: Washington health investigating E. coli cases in children at farm event in Lynden

Sorenne is in grade 1. Her school fete is this Sunday.

They plan to have a petting zoo, and I’ve said, this is a bad idea and let the principal know.

courtlynn.petting.zooWe’ll be at hockey.

At least three Whatcom County first-graders in Washington state, and possibly a fourth, have been sickened by shiga-toxin producing E. coli after attending the Milk Makers Fest in Lynden last week.

About 1,325 first-graders and their chaperones went to the event April 21-23 at the fairgrounds in Lynden. It was put on by the Whatcom County Dairy Women.

The event introduced young students to farming. It also gave the students a chance to pet farm animals, including small horses, sheep, rabbits, chickens and a calf, the dairy women wrote on their Facebook page.

Pasteurized chocolate milk was given to the children but isn’t considered a source of contamination because pasteurization destroys E. coli, according to the Facebook post.

“Nothing’s been ruled out,” said Greg Stern, Whatcom County health officer, on Tuesday, April 28.

 A table of petting zoo outbreaks is available at http://barfblog.com/wp-content/uploads/2014/04/Petting-Zoo-Outbreaks-Table-4-8-14.xlsx.

Best practices for planning events encouraging human-animal interactions

Zoonoses and Public Health

G. Erdozain, K. KuKanich , B. Chapman  and D. Powell


Educational events encouraging human–animal interaction include the risk of zoonotic disease transmission. It is estimated that 14% of all disease in the US caused by Campylobacter spp., Cryptosporidium spp., Shiga toxin-producing Escherichia coli (STEC) O157, non-O157 STECs, Listeria monocytogenes, nontyphoidal Salmonella enterica and Yersinia enterocolitica were attributable to animal contact. This article reviews best practices for organizing events where human–animal interactions are encouraged, with the objective of lowering the risk of zoonotic disease transmission.petting1-791x1024petting2-791x1024


It’s there: Salmonella in irrigation water

Here’s a video featuring farmer Jeff from 2003, before youtube existed.

And an abstract from a paper just published.

farmer.jeff.water.2003Same questions, not many solutions.

Irrigation water has been implicated as a likely source of produce contamination by Salmonella enterica. Therefore, the distribution of S. enterica was surveyed monthly in irrigation ponds (n=10) located within a prime agricultural region in Southern Georgia and Northern Florida.

All ponds and 28.2% of all samples (n=635) were positive for Salmonella with an overall geometric mean concentration (0.26 MPN/L) that was relatively low compared to prior reports for rivers in this region. Salmonella peaks were seasonal; levels correlated with increased temperature and rainfall (p<0.05). Numbers and occurrence were significantly higher in water (0.32 MPN/L and 37%) compared to sediment (0.22 MPN/L and 17%) but did not vary with depth. Representative isolates (n=185) from different ponds, sample types, and seasons were examined for resistance to 15 different antibiotics; most strains were resistant to streptomycin (98.9%), while 20% were multidrug resistant (MDR) for 2-6 antibiotics.

DiversiLab rep-PCR revealed genetic diversity and showed 43 genotypes among 191 isolates, as defined by >95% similarity. Genotypes did not partition by pond, season, or sample type. Genetic similarity to known serotypes indicated Hadar, Montevideo, and Newport as the most prevalent. All ponds achieved the current safety standards for generic Escherichia coli in agricultural water, and regression modeling showed E. coli levels were a significant predictor for the probability of Salmonella occurrence. However, persistent populations of Salmonella were widely distributed in irrigation ponds, and associated risks for produce contamination and subsequent human exposure are unknown, supporting continued surveillance of this pathogen in agricultural settings.

Distribution and Characterization of Salmonella enterica Isolates from Irrigation Ponds in the Southeastern U.S.A.

Applied and Environmnetal Microbiology

Zhiyao Luo, Ganyu Gu, Amber Ginn, Mihai C. Giurcanu, Paige Adams, George Vellidis, Ariena H. C. van Bruggen, Michelle D. Danyluk, and Anita C. Wright


It’s not organic or conventional it’s will it make you barf?

I’ve been drawn into these debates before, and concluded they are mindnumbing.

sprout.santa_.barf_.xmas_1-300x254Yes, organic probably causes a disproportionate number of food safety recalls, but it’s not the production method, it’s the producer.

Either they know about dangerous microorganisms and take steps to reduce them, or they don’t.

 The Western Producer says the “refreshingly candid comments of a University of Saskatchewan professor (Stuart Smyth) interviewed by WP reporter Dan Yates provoked lively discussion.

Except, if accurately quoted, they were as much bullshit as the good professor claims is at the root of organic outbreaks.

Smyth responded to one critic by stating, “In 2011, organic cucumbers containing a lethal level of E. coli were sold in Europe, resulting in over 4,000 cases of illness and 50 deaths. Colleagues of mine at the FAO reported that by the third day of the story, the powerful European organic industry had pressured the media into removing the word organic from all stories. Sadly, removing the word organic contributed to thousands of additional cases of illness and death, as European consumers had no idea it was the organic food that was killing them.

“I stand by my claim: organic food is the most dangerous and unsafe food on the market today. If you want to eat food that will kill you, eat organic.”

Yes, cucumbers were initially fingered as the source of an E. coli O104 outbreak that killed 53 and sickened 4,400 in Europe in 2011, but the source was ultimately determined to be fenugreek sprout seeks imported from Egypt.

If you’re going to cast stones, get it right.

Queensland Health? Hello? Petting zoo ignorance

Petting zoos at a mall or a school without proper handwashing facilities is a bad idea.

Even with proper facilities, it’s a bad idea.

An alert reader sent this in from the Greenslopes mall, a few km from our house in Brisbane.

There is hand sanitizer in the upper right, but no handwashing facilities.

And no idea if anyone is using the sanitizer.

A table of petting zoo outbreaks is available at http://barfblog.com/wp-content/uploads/2014/04/Petting-Zoo-Outbreaks-Table-4-8-14.xlsx.