News Scan for Dec 21, 2015

Two Chipotle E coli outbreaks
Ebola test, lessons learned
More avian flu in France
New chikungunya cases

CDC now investigating 2 Chipotle E coli outbreaks totaling 58 cases

The Centers for Disease Control and Prevention (CDC) is now investigating two separate Escherichia coli outbreaks tied to Chipotle restaurants, one involving 53 cases and the other 5, the agency said today in an update.

The CDC first reported the larger outbreak on Nov 4. Today the agency said the event has expanded by one case in Pennsylvania since its previous update on Dec 4. The most recent case-patient did not report eating at Chipotle Mexican Grill in the week before becoming ill, but genetic fingerprinting identified the case as matching the outbreak strain of E coli O26.

To date, 46 (88%) of 52 outbreak patients interviewed reported eating at Chipotle before falling sick. "The investigation is still ongoing to identify common meal items or ingredients causing illness," the CDC said. Illness-onset dates range from Oct 19 to Nov 14. Twenty cases (38%) required hospitalization.

So far nine states have reported cases in the 53-case outbreak, with the vast majority in Washington (27 cases) and Oregon (13).

The smaller outbreak also involves Shiga toxin–producing E coli O26 (STEC O26), but a rare form of that strain, the agency said in the update. Three cases have been reported in Oklahoma, and one each in Kansas and North Dakota—states that haven't been involved in the larger outbreak. All five reported eating at Chipotle in the week before they became ill.
Dec 21 CDC update


Ebola studies note utility of sequencing test, lessons learned in Netherlands

Separate Ebola studies published late last week in Emerging Infectious Diseases noted the efficacy of a field sequencing test and lessoned learned by Dutch healthcare professionals from the first case there.

In the first study, an international team of researchers detailed the field performance of an approach based on reverse transcription polymerase chain reaction in which whole-virus genomes were amplified in overlapping fragments to sequence Ebola virus RNA. After the approach was validated in non-human primates, the team tested it in Ebola patients in Monrovia, Liberia, from August 2014 through May 2015.

Complete-genome phylogenetic analysis of viruses from the patients showed them being clearly distinct from Sierra Leone or early Guinea sequences but clustering well with all other sequences found in samples from Liberia, suggesting that Ebola viruses in Liberia resulted from a single or very few introductions.

The authors conclude, "Because of the device’s small size and comparatively modest resource requirements, nanopore sequencing has tremendous potential for use in remote and resource-limited areas, and its implementation could revolutionize the capacity of public health professionals to perform sequencing during future disease outbreaks."
Dec 18 Emerg Infect Dis study on sequencing test

In the second study, scientists from the University Medical Centre of Utrecht in the Netherlands reported the preparation involved and the lessons learned from treating the only Ebola patient in that country, who was admitted on Dec 6, 2014.

They noted that waste management—a task that was ultimately outsourced—was their greatest concern. They also noted that the maximum time that healthcare personnel were allowed to wear the extensive personal protective equipment was 45 minutes, with an additional 20 minutes of recovery.

They concluded that even treating just one patient was demanding on staff resources.
Dec 18 Emerg Infect Dis Dutch report


France's high-path avian flu outbreaks grow to 53

The number of highly pathogenic avian influenza (HPAI) outbreaks in France has grown by 23 in the past 3 days, to 53, with one newly affected region, according to recent updates from French officials, including one today.

On Dec 18 France's agriculture ministry reported 12 new H5 HPAI events, including the first reported in Midi-Pyrenees region. Then today the ministry noted 11 new HPAI outbreaks, primarily in Pyrenees-Atlantiques and Gers regions. Officials, following the tradition of their most recent reports, did not specify the exact strains of HPAI involved or details on the affected poultry. Both reports were translated and posted by Avian Flu Diary (AFD), an infectious disease blog.

In recent weeks French authorities have reported outbreaks of HPAI involving the H5N1, H5N2, and H5N9 strains, as well as low-pathogenic avian flu outbreaks involving H5N2 and H5N3. Details of the outbreaks have tapered in the most recent reports.
Dec 19 AFD blog post
Dec 21 AFD blog post


PAHO reports 2nd straight week of low chikungunya numbers

Cases of chikungunya in the Americas and Caribbean rose by only 1,191 last week, marking the second straight week of low numbers and bringing the outbreak total to 1,790,681, according to a Dec 18 Pan American Health Organization (PAHO) update.

The agency's previous two updates included 17,398 and 1,432 new cases, respectively, with the former (and earlier) update including 2 weeks' worth of data. The new infections bring the total this year to 643,912 suspected and confirmed cases. No new deaths were reported, keeping that total at 77.

There is no indication that the low numbers represent a slow-down in the outbreak, however, which began in late 2013. Only Colombia, Mexico, Venezuela, and the United States provided updated figures, and the vast majority of countries in the region have not provided updates to PAHO for many weeks.

Of the 1,191 new cases, 907 were in Colombia, which often has had the most weekly cases this year. Its 2015 total is now at 356,254 cases. Mexico had 149 new cases and 11,219 for the year.

The epidemic began in December 2013 with the first locally acquired chikungunya case ever reported in the Americas, on St. Martin in the Caribbean.
Dec 18 PAHO update

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