Flu Scan for Apr 01, 2016

News brief

US flu activity continues retreating, but 3 pediatric deaths reported

By most measures, the seasonal influenza epidemic in the United States waned further last week, the Centers for Disease Control and Prevention (CDC) said in an update today, continuing a trend first apparent a week earlier.

Just two states, New Jersey and New Mexico, and Puerto Rico still had high influenza-like illness (ILI) activity for the week, down from seven states and Puerto Rico the week before. Seven states and New York City had moderate activity.

Flu cases continued to be geographically widespread in 29 states last week, but that was 10 fewer than the previous week. Meanwhile, the share of clinic visits prompted by ILI dropped to 2.9%, from 3.2% the week before, but remained above the national baseline of 2.1%.

Three flu-related deaths of children were reported during the week, one more than the previous week. Those cases raised the season total to 33. One death was attributed to an influenza A/H1N1 virus, one to a type B virus, and one to a type A virus that was not subtyped.

The share of respiratory samples testing positive for flu dropped again, to 18.3% of 21,959 samples, compared with 20.1% of 23,946 the week before.

Flu-related hospitalizations reported last week raised the estimated cumulative incidence for the season to 21.4 per 100,000 people, up from 18.2 per 100,000 a week earlier.

One flu marker that rose was the share of deaths related to pneumonia and flu as measured by the CDC's 122 Cities Mortality Reporting system, which was 7.7%, versus 7.3% the week before. That was just above the epidemic threshold of 7.2% for the week.

The CDC's other system for counting deaths due to flu and pneumonia, operated by the National Center for Health Statistics (NCHS), put the number for the week ending Mar 12 at 7.3%, which was below the epidemic threshold of 7.6% and down from 7.4% the week before. The NCHS system lags 2 weeks behind the 122 Cities system.
Apr 1 CDC FluView report

Flu vaccine 42% effective during H1N1-dominated flu season in UK

Influenza vaccination has shown significant effectiveness in preventing primary care visits in the United Kingdom (UK), especially those due to confirmed H1N1 infection, according to a study yesterday in Eurosurveillance.

Researchers analyzed 1,548 samples from 182 people with confirmed influenza and 1,366 controls midway through the 2015/16 flu season. From Oct 1, 2015, to Jan 22, most case-patients with flu had H1N1 (151), while the remainder were positive for H3N2 (3), unknown type A viruses (9), and type B (20).

When compared with controls, H1N1 cases were more likely to occur in children under the age of 5 (16.8% of 198 children under 5 presenting to a primary care clinic) and people who had not received the flu vaccine (11.1% of 1,215). The highest percentage of H1N1 cases occurred in January (23.2% of 333 primary care visits), the authors said.

In terms of preventing confirmed flu infections resulting in primary care consultations, the flu vaccine had an overall effectiveness of 41.5% (95% confidence interval [CI], 3%-64.7%), an effectiveness of 49.1% against H1N1 infections (95% CI, 9.3%-71.5%), and effectiveness of 47.3% against all type A infections (95% CI, 9%-69.5%).

The authors observed some variation in the H1N1 hemagglutinin gene, though changes appeared to have little effect on the virus's antigenic properties. As the flu season continues, shifts in strain predominance in the UK may affect vaccine effectiveness, the authors said.
Mar 31 Eurosurveillance study

Studies find high-path avian flu viruses rare in US wild birds

Surveillance during an outbreak of highly pathogenic avian influenza (HPAI) H5N2 in Minnesota garnered only two HPAI isolates from wild birds, according to a study yesterday in Emerging Infectious Diseases. A similar study reported yesterday in Virology Journal revealed no evidence for HPAI circulation among migratory wild birds in Alaska.

Researchers in Minnesota tested 104 sick or dead wild birds and took 3,139 waterfowl fecal samples between Mar 9 and Jun 4, 2015, roughly the same period as an outbreak of H5N2 in 23 Minnesotan counties.

HPAI viruses were isolated from a Cooper's hawk found in Yellow Medicine County in April 2015 and in a black-capped chickadee submitted by a wildlife rehabilitation center in July 2015, the authors said. Among 148 fecal samples taken near the site of the first outbreak, low-pathogenic avian influenza (LPAI) was identified in two pooled samples. Thirty pooled samples from 85 birds in other locations were LPAI-positive.

The researchers concluded that HPAI viruses were not prevalent in wild birds during the 2015 outbreak.
Mar 31 Emerg Infect Dis study

A similar study of 1,129 migratory birds on Alaska's Yukon-Kuskokwim Delta during the spring and summer of 2015 found no evidence of HPAI viruses.

Five LPAI viruses were isolated from cackling and greater white-fronted geese, including four viruses of combined subtypes H6N1, H6N2, and H9N2, and one virus composed of H3 and N7 gene segments. Three genetic segments were similar to HPAI H5 viruses recently detected in North American birds, the authors said.

Though HPAI did not appear to circulate in geese during the spring and summer, genetic evidence demonstrates intercontinental avian flu virus exchange in migratory birds, the authors said.
Mar 31 Virol J study

News Scan for Apr 01, 2016

News brief

Saudi Arabia reports new MERS case in Buraydah

Saudi Arabia's Ministry of Health (MOH) today reported a new, fatal MERS-CoV case in Buraydah, the first there this month after the city reported 34 MERS cases in March.

Today's MERS-CoV (Middle East respiratory syndrome coronavirus) case involves a 75-year-old Saudi woman whose infection was contracted in a healthcare setting, as have most of the cases in the Buraydah cluster, which was first noted on Mar 3. The woman died from her infection. She had preexisting disease and was not a healthcare worker, the MOH said.

Her case brings the MERS-CoV total in Saudi Arabia since the outbreak began in 2012 to 1,363 infections, including 583 deaths. Thirteen patients are still undergoing treatment, the MOH said.
Apr 1 MOH update

Study: Raw milk can harbor Campylobacter even after negative tests

Raw milk can harbor dangerous bacteria, even when routine testing results show it to be uncontaminated, says a report from Utah on a 2014 outbreak of confirmed or suspected campylobacteriosis in 99 individuals. The report appears in today's issue of Morbidity Mortality Weekly Report (MMWR).

The outbreak began in May 2014 with three patients who tested positive on pulsed field gel electrophoresis for Campylobacter jejuni. They had all consumed raw milk from an unnamed dairy in Weber County in northern Utah. The dairy's routine testing, which is required monthly of dairies selling raw milk in Utah and consists of somatic cell and coliform counts, had yielded results within acceptable levels (<400,000 somatic cells/mL and <10 coliform colony forming units/mL).

Enhanced testing after the illnesses were identified showed C jejuni in the dairy's milk.

Officials suspended the dairy's permit in August and then reinstated it Oct 1 after follow-up cultures were negative. However, seven more C jejuni cases occurred by Nov 4, and the permit was permanently revoked Dec 1.

In total, 99 people in Utah, 85 (86%) of them from northern counties, were identified through lab testing and patient interviews as having confirmed (59) or probable (40) cases of campylobacteriosis from May 9 to Nov 6, 2014. Patients ranged in age from 1 to 74 years; 10 were hospitalized, and 1 died.

Of the 98 patients for whom exposure history was available, 53 reported drinking raw milk, 52 of them milk from the Weber Country dairy; 4 drank raw milk but could not name the dairy where it was purchased, and 14 bought raw milk at the dairy but did not report drinking it.

The authors point out that "Current raw milk testing standards do not readily detect contamination." They recommend more education of consumers about the dangers associated with consuming unpasteurized milk, and they conclude, "The safest alternative is to consume pasteurized milk."
Apr 1 MMWR study

President's advisory council publishes draft antibiotic resistance report

Yesterday the US Presidential Advisory Council on Combating Antibiotic Resistant Bacteria (PACCARB) released a draft report recommending steps to advance the goals of the National Action Plan on Combating Antibiotic Resistant Bacteria (CARB), such as focusing on "one health" surveillance and bolstering antibiotic research and development (R&D).

The move was met with approval from leading infectious disease groups.

In addition to its one-health approach—which means cross-discipline collaborations surrounding human, animal, and environment health—and drug R&D, the PACCARB report calls for a federal champion of the CARB initiative, coordination of the federal response to the problem, adequate funding, development of critical partnerships, and employing economic incentives for scientific advances.

"I am pleased to see national progress that will drive lasting change on all the different facets of antibiotic resistance," said Louise M. Dembry, MD, MS, MBA, president of the Society for Healthcare Epidemiology of America (SHEA), in a press release. "The foundation of good antibiotic resistance prevention and control efforts include not only antibiotic stewardship but also solid infection prevention interventions such as hand hygiene, environmental disinfection and careful use of medical devices, to name just a few. Preventing transmission is part of protecting patients from getting an antibiotic-resistant bacterial infection."

The Infectious Diseases Society of America (IDSA) approved of the comprehensive approach. The organization said in a news release yesterday, "We were particularly pleased that the recommendations included investment in a strong [infectious disease] physician workforce, which will be necessary for leading antibiotic stewardship programs; conducting clinical trials for new antibiotics, diagnostics and vaccines; and leading other activities to combat resistance.

"We also welcome the PACCARB support for the Limited Population Antibacterial Drug (LPAD) approval pathway that will facilitate R&D of some of the most urgently needed new antibiotics to address unmet medical needs."
Mar 31 PACCARB draft report
Mar 31 SHEA press release
Mar 31 IDSA news release

MCR-1 gene detected in Spanish hospital patients

In one of the few reports of the MCR-1 antibiotic resistance gene detection in humans, Spanish researchers yesterday reported on findings from a collection of Escherichia coli isolates collected between 2012 and 2015 from a single hospital in Barcelona. They published the details in Eurosurveillance.

The MCR-1 gene disables the antibiotic colistin, an older drug that is often used in raising food animals. However, the drug is considered a last-line treatment in the battle against multidrug-resistant infections. Chinese researchers first described MCR-1 in November 2015. Since then, several research teams have found the gene in their bacterial collections, though mainly from food and agricultural sources.

In the new report, researchers looked at 10,011 E coli clinical specimens collected from a teaching hospital. Colistin resistance was found in 53 (0.5%), with the MCR-1 found in 15 samples, which ranged from blood, urine, sputum, and a surgical wound. No epidemiologic links were found among the patients. One was from a nursing home, and nine had been hospitalized in the previous year. None of the patients had traveled abroad.

Seven of the isolates weren't multidrug-resistant (MDR), which the authors said might not be clinically relevant, but still raises concerns that the problem could get worse owing to the exchange of resistance genes across different microbiome populations—food animals, environment, and humans. They added that colistin use varies in hospitals and that its use increased 14-fold at their hospital from 2007 to 2014.

The researchers emphasized that urgent global actions are needed to curb veterinary use of the drug to guard its usefulness for treating MDR gram-negative bacteria.
Mar 31 Eurosurveill report

Cold-attenuated polio vaccine called safe, highly immunogenic

A newly developed polio vaccine cannot replicate at normal body temperature and provokes a high immune response, according to findings published yesterday in PLOS Pathogens.

Researchers from Janssen Infectious Diseases and Vaccines in the Netherlands developed an attenuated alternative to oral polio vaccine, which contains live attunuated viruses that can become virulent in certain circumstances, and to conventional inactivated polio vaccine (cIPV), which is safer but more expensive and is made from virulent wild-type strains. The CAVA (cold-adapted viral attenuation) vaccine replicates in human cells only at temperatures of 26 to 30 degrees C, far below the normal body temperature of 37 degrees C.

Three CAVA vaccine prototypes combine 31 mutations from 3 poliovirus clones to create a synthetic viral genome. Fourteen of these mutations were particularly successful in preventing replication of poliovirus types 1, 2, and 3 at normal body temperature. Genes from cIPV were added to enhance immunogenicity.

More than 360 human cells injected with the CAVA strains remained healthy when kept at normal body temperature for two weeks. In mouse models, the CAVA vaccines did not become neurovirulent at 37 degrees C, the authors said.

All three CAVA vaccines produced high antibody titers that at 150% of the vaccine dose were comparable to the immune response provoked by cIPV, and one CAVA prototype had a similar immunogenicity profile to the conventional vaccine at 100% of the dose.

Given the ongoing biosafety risks associated wth manufacturing of cIPV, cold-attenuated strains deserve more research to determine safety and immunogenicity as a potential replacement, the authors said.
Mar 31 PLOS Pathog study