News Scan for Jun 13, 2016

Flour confirmed as E coli source
MCR-1 in Japan and Colombia
Chikungunya tops 2M cases

FDA confirms multistate E coli outbreak's link to General Mills flour

The US Food and Drug Administration (FDA) has confirmed that Escherichia coli O121 found in a sample of General Mills flour from the home of one of the patients in a 38-case outbreak matches the strain infecting people.

Whole-genome sequencing of E coli O121 isolates from the patient's flour showed that they were "closely genetically related [to] the clinical isolates from human illnesses," the FDA said in a Jun 10 statement. "The flour came from a lot that General Mills has recalled."

Minneapolis-based General Mills recalled 10 million pounds of flour on May 31 because of the outbreak, though it said no E coli O121 had been found in the flour at that point. The products are sold nationwide under the names Gold Medal, Signature Kitchens, and Gold Medal Wondra.

The FDA said General Mills also sells bulk flour to customers who use it to make other products, and the company has informed them of the recall. "Because of legal restrictions on commercial confidential information, FDA is not at this time authorized to release the names of these customers or the products they make with the flour," the agency said.

The outbreak involved 38 people in 20 states, with 10 hospitalizations but no deaths or cases of hemolytic uremic syndrome (kidney failure), the Centers for Disease Control and Prevention (CDC) reported Jun 1. The FDA statement mentions the same numbers, and the CDC has not updated its outbreak report since Jun 1.

Flour was implicated in the outbreak because a number of patients reported they had used flour in the week before they got sick, and some reported eating raw homemade dough or batter. Noting that flour has a long shelf life, the FDA is advising consumers to get rid of the recalled flour.
Jun 10 FDA statement
Related Jun 1 CIDRAP News item


MCR-1 found in isolate collections from Japan, Colombia

An analysis of Escherichia coli samples collected from sick pigs in Japan from 1991 to 2014 detected the MCR-1 resistance gene as far back as 2007, with the number of positives rising rapidly since 2009, Japanese researchers reported in a letter to Emerging Infectious Diseases.

The MCR-1 resistance gene, first identified by Chinese researchers in November 2015, disables the ability of the last-line antibiotic colistin to combat resistant bacteria. Its recent identification has spurred major efforts by scientists across the globe to pinpoint how widely the gene has spread in agricultural settings, the food supply, and in humans. The new report is the second one from Japan.

In the latest lab investigation the researchers looked at 984 E coli strains collected from diseased pigs throughout Japan. Of those, 309 were colistin-resistant, and the MCR-1 gene was detected in 90 strains. The first detection was in a sample from 2007, with the proportion rising, especially since 2009. For the years 2013 and 2014, about half of the E coli strains were positive for MCR-1.

Researchers said rates of colistin-resistance and E coli strains positive for MCR-1 from healthy animals are low, which may result from judicious use of colistin in Japan. However, they added that the recent dissemination of MCR-1 in swine-pathogenic E coli in the country may reflect use of colistin to treat sick animals. They noted that the sharp increase still poses a threat of transmission to strains that infect humans, "a serious concern for human medicine."

The team concluded that more active surveillance of MCR-1 colistin-resistant bacteria is needed in human and animal environments.
Jun 10 Emerg Infect Dis letter
Jan 8 CIDRAP News story "New MCR-1 reports warn of untreatable infection threat"

In related news, the Pan American Health Organization (PAHO) on Jun 10 posted an epidemiologic alert on MCR-1 and implications for the Americas. It reviewed recent detections in the Americas that have appeared in the medical literature, along with an account of the first MCR-1 detection in the United States.

In addition, it said MCR-1 was detected in three Salmonella Typhimurium isolates from patients from three different cities in Colombia and from one E coli isolate from a patient in Santander. The findings were from a retrospective analysis of isolates from 2014 to May 2016.

PAHO urged its member countries to implement and strengthen surveillance to detect MCR-1 and to implement control measures.
Jun 10 PAHO report


PAHO reports 9,400 new chikungunya cases; outbreak total tops 2 million

PAHO late last week reported 9,424 new chikungunya cases, to bring the 2016 total in the Americas to 127,253 cases and the overall total since the outbreak began past 2 million.

The previous 2 weeks saw increases of only 1,184 and 2,446 suspected and confirmed cases, respectively. PAHO's latest update was posted on Jun 10.

The vast majority of new cases are from Bolivia, which reported 8,821 such cases over 9 weeks, bringing its 2016 total to 15,721. Colombia added 278 cases this past week; it now has 15,903 for the year. El Salvador logged 101 new cases and now has 4,949 for the year.

PAHO reported no new chikungunya-related deaths, keeping that figure at 16 for the year.

The outbreak was first reported in December 2013 on St. Martin in the Caribbean with the first recorded cases of the disease in the Americas. Since then PAHO has reported 2,007,220 suspected or confirmed cases, including 284 deaths.
Jun 10 PAHO update

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