Category Archives: Research

Research – Norovirus – Applied math reveals the key to stopping Norovirus lies — literally — in our own hands

Science Daily 


From stately cruise ships to Olympic host cities, recent headline-grabbing outbreaks prove that norovirus, an incapacitating stomach bug, can strike anywhere and anytime. A new study uses mathematical modelling and data from real-world cruise ship outbreaks to find the best way of stopping the disease’s spread. Their surprising results reveal that washing your hands is more effective than surface cleaning or even quarantine at breaking the chain of transmission.

USA – Multistate Outbreak of Salmonella Agbeni Infections Linked to Pet Turtles, 2017 (Final Update)

CDC Salm2

Outbreak Advisory





  • CDC and multiple states investigated a multistate outbreak of human Salmonella infections linked to contact with pet turtles.
  • A total of 76 people infected with the outbreak strain of Salmonella Agbeni were reported from 19 states.
    • Illnesses started on dates ranging from March 1, 2017 to December 1, 2017.
    • Of 63 people with available information, 30 were hospitalized. No deaths were reported.
    • 24 (32%) ill people were children younger than 5.
  • Epidemiologic and laboratory findings linked this outbreak of human Salmonella Agbeni infections to contact with turtles or their environments, such as water from a turtle habitat.
    • In interviews, ill people answered questions about contact with animals during the week before becoming ill. Twenty-three (38%) of the 60 people interviewed reported contact with turtles or their environments, such as water from a turtle habitat, before getting sick.
    • Of the 23 ill people who had contact with turtles, 14 (61%) reported contact with small turtles that had a shell length of less than four inches. They reported purchasing the turtle from a street vendor or receiving the turtle as a gift.
    • In 2015, state and local health officials collected samples from turtles at a street vendor. Whole genome sequencing( showed that the Salmonella Agbeni isolated from ill people in this outbreak was closely related genetically to the Salmonella Agbeni isolates from the turtles at the street vendor. This close genetic relationship means that illnesses in this outbreak were likely linked to turtles.
  • Whole genome sequencing( did not identify predicted antibiotic resistance in 43 of 44 isolates from ill people
    • One isolate from an ill person had predicted resistance to nalidixic acid and ciprofloxacin. The resistance in this isolate is unlikely to affect treatment for most outbreak-associated cases.
  • Testing of four outbreak isolates using standard antibiotic susceptibility testing( methods by CDC’s National Antimicrobial Resistance Monitoring System (NARMS)( laboratory did not show any resistance.
  • Do not buy small turtles as pets or give them as gifts.
  • All turtles, regardless of size, can carry Salmonella bacteria even if they look healthy and clean. These outbreaks are a reminder to follow simple steps( to enjoy pet reptiles and keep your family healthy.
  • This outbreak investigation is over. Illnesses could continue because people may not know they could get a Salmonella infection from contact with pet turtles.

Research – Multistate Outbreak of Salmonella Virchow Infections Linked to a Powdered Meal Replacement Product — United States, 2015–2016

Oxford Academic



Nontyphoidal Salmonella is the leading cause of bacterial gastroenteritis in the United States. Meal replacement products containing raw and ‘superfood’ ingredients have gained increasing popularity among consumers in recent years. In January 2016, we investigated a multistate outbreak of infections with a novel strain of Salmonella Virchow.


Cases were defined using molecular subtyping procedures. Commonly reported exposures were compared with responses from healthy people interviewed in the 2006–2007 FoodNet Population Survey. Firm inspections and product traceback and testing were performed.


Thirty-five cases from 24 states were identified; 6 hospitalizations and no deaths were reported. Thirty-one (94%) of 33 ill people interviewed reported consuming a powdered supplement in the week before illness; of these, 30 (97%) reported consuming Product A, a raw organic powdered shake product consumed as a meal replacement. Laboratory testing isolated the outbreak strain of Salmonella Virchow from: leftover Product A collected from ill people’s homes, organic moringa leaf powder (an ingredient in Product A), and finished product retained by the firm. Firm inspections at three facilities linked to Product A production did not reveal contamination at the facilities. Traceback identified that the contaminated moringa leaf powder was imported from South Africa.


This investigation identified a novel outbreak vehicle and highlighted the potential risk with similar products not intended to be cooked by consumers before consuming. The company issued a voluntary recall of all implicated products. As this product has a long shelf-life, the recall likely prevented additional illnesses.


Research – Scientists find single letter of genetic code that makes African Salmonella so dangerous

Outbreak News Today

Scientists at the University of Liverpool have identified a single genetic change in Salmonella that is playing a key role in the devastating epidemic of bloodstream infections currently killing around 400,000 people each year in sub-Saharan Africa.

Invasive non-typhoidal Salmonellosis (iNTS) occurs when Salmonella bacteria, which normally cause gastrointestinal illness, enter the bloodstream and spread through the human body. The African iNTS epidemic is caused by a variant of Salmonella Typhimurium (ST313) that is resistant to antibiotics and generally affects individuals with immune systems weakened by malaria or HIV.

In a new study published in PNAS, a team of researchers led by Professor Jay Hinton at the University of Liverpool have identified a specific genetic change, or single-nucleotide polymorphism (SNP), that helps the African Salmonella to survive in the human bloodstream.

Professor Hinton explained: “Pinpointing this single letter of DNA is an exciting breakthrough in our understanding of why African Salmonella causes such a devastating disease, and helps to explain how this dangerous type of Salmonella evolved.”

SNPs represent a change of just one letter in the DNA sequence and there are thousands of SNP differences between different types of Salmonella. Until now, it has been hard to link an individual SNP to the ability of bacteria to cause disease.

Research – Water troughs are key to toxic E. coli spread in cattle

Cornell Chronicle 19243

A major study led by Cornell researchers reveals for the first time that water troughs on farms are a conduit for the spread of toxic E. coli in cattle, which can then spread the pathogen to people through bacteria in feces. The study was published Feb. 7 in the journal PLOS ONE.

“Water troughs appeared in our mathematical model as a place where water can get contaminated and a potential place where we could break the cycle,” said Renata Ivanek, associate professor of epidemiology in the College of Veterinary Medicine and the paper’s senior author. The hypothesis was then tested in the field – with surprising results.

People commonly acquire infections from shiga toxin-producing E. coli through cow feces-contaminated beef and salad greens. The main shiga toxin-producing strain, E. coli 0157:H7, causes more than 63,000 illnesses per year and about 20 deaths, according to the Centers for Disease Control. Though cows carry and spread E. coli 0157:H7 when they defecate, the bacteria do not make them sick.


Research – Outbreak of Fluoroquinolone-Resistant Campylobacter jejuni Infections Associated with Raw Milk Consumption from a Herdshare Dairy — Colorado, 2016



In August 2016, a local public health agency (LPHA) notified the Colorado Department of Public Health and Environment (CDPHE) of two culture-confirmed cases of Campylobacter infection among persons who consumed raw (unpasteurized) milk from the same herdshare dairy. In Colorado, the sale of raw milk is illegal; however, herdshare programs, in which a member can purchase a share of a herd of cows or goats, are legal and are not regulated by state or local authorities. In coordination with LPHAs, CDPHE conducted an outbreak investigation that identified 12 confirmed and five probable cases of Campylobacter jejuni infection. Pulsed-field gel electrophoresis (PFGE) patterns for the 10 cases with available isolates were identical using the enzyme Sma. In addition, two milk samples (one from the dairy and one obtained from an ill shareholder) also tested positive for the outbreak strain. Five C. jejuni isolates sent to CDC for antimicrobial susceptibility testing were resistant to ciprofloxacin, tetracycline, and nalidixic acid (1). Although shareholders were notified of the outbreak and cautioned against drinking the milk on multiple occasions, milk distribution was not discontinued. Although its distribution is legal through herdshare programs, drinking raw milk is inherently risky (2). The role of public health in implementing control measures associated with a product that is known to be unsafe remains undefined.

UK – Scotland – Understanding the sources of human Campylobacter infection in Scotland

Food Standards Scotland 


Research published today shows that chicken remains the biggest source of campylobacter infection in Scotland.

We commissioned the University of Aberdeen to compare clinical strains of campylobacter from the Grampian area with strains isolated from chickens, cattle, sheep, pigs and wild birds. This was used to determine the proportion of infections in Scotland from these potential sources.

While campylobacter remains the most common source of foodborne illness there has been a reduction in those contracting campylobacter from chicken. The proportion of cases attributed to chicken decreased from 55-75% to 52-68% when compared to data collected between 2012-2015.