News Scan for Mar 20, 2017

News brief

Saudi MOH: 2 new MERS cases, 3 deaths

The Saudi Arabian Ministry of Health (MOH) reported two new cases of MERS and three deaths in previously reported patients in recent days. Both of the new cases were linked to camel contact.

A 63-year-old Saudi man from Badr was diagnosed as having MERS-CoV (Middle East respiratory syndrome coronavirus) infection on Mar 16. He is in stable condition, and had direct contact with camels. On the same day, the MOH said that a 67-year-old Riyadh man had passed away from the disease. He had preexisting disease.

On Mar 17, the MOH said a 54-year-old Saudi man in Jeddah had died from MERS. Finally, on Mar 18 a 20-year-old expatriate man in Hafar Al Batin died from MERS after having direct contact with camels.

So far Saudi Arabia has reported 1,580 MERS-CoV cases, 659 of them fatal, since the virus was first detected in humans in 2012. Ten people are still being treated for their infections, the MOH said.
Mar 16 MOH report
Mar 17 MOH report
Mar 18 MOH report

CDC reports 15 new drug-resistant Salmonella cases, ends investigation

The investigation into a multistate outbreak of multidrug-resistant (MDR) Salmonella Heidelberg infections tied to contact with dairy bull calves is now over after the pathogen sickened at least 36 people, hospitalizing 13, the Centers for Disease Control and Prevention (CDC) said today.

The update includes 15 new cases, including 5 hospitalizations, since the CDC first reported the outbreak on Nov 28, 2016. Illness-onset dates go back to Jan 27, 2015, with the latest being Jan 16 of this year. All but 8 of the patients, though, fell ill in June 2016 or later. Patients range in age from less than 1 year to 72 years, with a median of 18 years.

Ten states reported cases, with Wisconsin (15), Missouri (6), Minnesota (4), and South Dakota (4) having the most. No deaths were reported.

"This outbreak investigation is over," the CDC said. "However, infections in calves continue to be reported and people can still get a Salmonella infection from contact with livestock." The agency recommends washing hands thoroughly with soap and water immediately after contacting livestock or its surroundings, among other disease-prevention steps.

Among all 36 outbreak patients, 25 (69%) reported contact with dairy bull calves or other cattle before becoming sick. Some of the patients said they fell ill after their dairy bull calves became sick or died. The outbreak strain was identified in one patient's dairy calves.

All isolates tested from patients proved to be MDR. All five isolates tested were resistant to amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftriaxone, streptomycin, sulfisoxazole, and tetracycline and showed reduced susceptibility to ciprofloxacin. All, however, were susceptible to azithromycin, gentamicin, and meropenem. Four of the five isolates were also resistant to trimethoprim-sulfamethoxazole, and two of these were resistant to chloramphenicol and nalidixic acid.
Mar 20 CDC final update
Nov 28, 2016, CIDRAP News scan on original notice

PAHO reports 7,000 new chikungunya cases, mostly in Brazil

Three weeks' worth of new data from Brazil helped boost the chikungunya total in the Americas this year by 7,091 cases, the Pan American Health Organization (PAHO) noted in an update late last week.

The case count for 2017 has now reached 12,244, PAHO said in its Mar 17 update.

Brazil, reporting new cases through late February, added 6,540 confirmed and suspected cases, raising its 2017 total to 10,294. Bolivia reported the next-highest increase as it noted its first 242 cases of the year. Nicaragua had 110 new cases and 317 total, while Paraguay reported 85 new infections, bringing its 2017 total to 508 cases.

The outbreak began in late 2013 on the Caribbean island of St. Martin and has now sickened at least 2,399,237 people.
Mar 17 PAHO update

TB/HIV co-infections up 40% in Europe over past 5 years

According to new data released today by the European Centre for Disease Prevention and Control (ECDC), co-infection of tuberculosis (TB) and HIV has risen 40% in Europe over the past 5 years, despite overall decreases of TB cases. The news comes ahead of World TB Day, on Mar 24.

The ECDC and the World Health Organization (WHO) said that new TB cases and deaths in the 53 countries of the WHO European Region declined each year by 4.3% and 8.5%, respectively, from 2011 through 2015, but that trend was not reflected in at-risk populations. Among drug users, HIV-positive people, and the homeless, TB rates increased during the same period.

"The flare-up of TB/HIV co-infections from 2011 to 2015, together with persistently high rates of drug-resistant tuberculosis, seriously threaten progress made towards ending TB, the goal that European and world leaders have committed to achieve by 2030," says Zsuzsanna Jakab, MD, WHO regional director for Europe, in a press release.

TB is a leading killer of those with HIV/AIDs. In 2015, there were 2 million cases of HIV in Europe. According to the WHO, people with HIV are seven times more likely to fail treatment for TB or perish from either disease.
Mar 20 ECDC/WHO statement
Mar 20 ECDC World TB Day release

Study: Following up on negative urine cultures aids antibiotic stewardship

Better follow-up of negative urine cultures substantially reduced the number of antibiotic days among pediatric urgent care patients, according to a new study in Pediatrics. The authors say the findings highlight empiric antibiotic treatment of urinary tract infection (UTI) in children as an important target for antibiotic stewardship.

For the study, researchers at Nationwide Children's Hospital (NCH)—an academic children's hospital in Columbus, Ohio, with a network of urgent care centers—set out to develop and implement a protocol for follow-up management on negative urine culture results. The purpose was to reduce inappropriate antibiotic exposure in patients with acute UTI at their urgent care centers. UTI is a common infection in children, but because physicians have to wait up to 48 hours for urine culture results, they frequently prescribe empiric antibiotic therapy based on symptoms. Prior to the study, NCH had no consistent mechanism in place to follow up on negative culture results and discontinue unnecessary antibiotic therapy.

The protocol standardized a process in which a nurse reviews the urine culture result and forwards a negative result to a physician, who then decides if antibiotic discontinuation is appropriate based on the results and clinical presentation. The nurse then notifies the patient or caregiver of the recommendation, and the physician documents the discontinuation of the antibiotics in the electronic medical record.

During the study period (July 2013 through December 2015), 910 patients received empiric antibiotic therapy for UTIs but had negative urine culture results. Among these patients, the rate of documented antibiotic discontinuation following a negative urine culture rose from a baseline mean of 4% to a mean of 84%, avoiding 3,429 (40%) of 8,648 antibiotic days prescribed. In addition, of the 46 patients who returned to an NCH urgent care center after antibiotic discontinuation, none were subsequently diagnosed as having a UTI.

"Our results highlight an essential opportunity in outpatient settings to introduce quality and stewardship measures for UTI management that will affect many patients and avoid a substantial number of antibiotic days," the authors write.
Mar 16 Pediatrics study

New AMR diagnostic tool outperforms competitors in analysis

A new diagnostic tool that identifies antimicrobial resistance (AMR) genes directly from paired sequencing reads outperformed other diagnostic tools in a new study in bioRxiv, a preprint server.

The tool, called ARIBA (Antimicrobial Resistance Identification by Assembly), uses a combined mapping/alignment and targeted local assembly approach to identify AMR genes and their variants efficiently and accurately from paired sequencing reads. This approach is considered less limited than other widely used diagnostic tools that either align sequencing reads to a set of reference genes or search for reference gene matches in de novo assembled sequences.

In head-to-head comparisons with the diagnostic tools SRST2 and KmerResistance, ARIBA was found to be just as accurate in identifying resistance genes in Enterococcus faecium and Shigella sonnei but was also able to identify and classify variants involved in AMR. In addition, it was able to report the presence of variants, and interpret their consequences, in Neisseria gonorrhea isolates. ARIBA was also faster and required fewer computational resources.

ARIBA was developed by researchers from the Wellcome Trust Sanger Institute.
Mar 18 bioRxiv abstract

Flu Scan for Mar 20, 2017

News brief

Low-path H7N9 confirmed in one of Alabama's outbreaks

Alabama officials have received results on samples collected from one of the state's recently announced avian flu outbreaks, indicating low-pathogenic H7N9 detected in guinea fowl at the TaCo-Bet Trade Day flea market in Jackson County.

According to a Mar 16 statement form the Alabama Department of Agriculture and Industries (ADAI), the source of the guinea fowl, also in Jackson County, is under quarantine and continued surveillance, and the remaining birds have been culled.

Tests to confirm the subtype were conducted by the US Department of Agriculture National Veterinary Services Laboratory (NVSL) in Ames, Iowa. Testing is still under way on samples from two other outbreak locations in north Alabama, from a commercial farm in Lauderdale County and from a backyard holding in Madison County.

Alabama authorities, however, suspect that the two other outbreaks involve the low-pathogenic strain as well, because neither flock showed signs of illness. Out of an abundance of caution, the company that owns the commercial breeding farm opted to depopulate the flock, as did the owner of the backyard birds.

The low-pathogenic H7N9 finding is the second recent detection in the United States. On Mar 10, Tennessee officials announced low-pathogenic H7N9 at a farm in Giles County. Tennessee has also reported two recent highly pathogenic H7N9 outbreaks in Lincoln County. The Tennessee outbreak locations border Alabama's outbreak areas. Genetic tests so far have shown the H7N9 viruses recently detected in the United States are related to North American wild bird lineages and have no connection to the H7N9 strain sickening people and poultry in China.
Mar 16 ADAI press release
Mar 14 CIDRAP News story "Alabama officials investigate 3 avian flu detections"

China's fifth wave H7N9 total climbs by 21

Hong Kong's Centre for Health Protection (CHP) on Mar 17 announced in one of its regular updates that China reported 21 more H7N9 avian influenza cases, 4 of them fatal, from Mar 10 to Mar 16. The mainland continues to report a steady stream of cases in its fifth and biggest wave of H7N9 activity, which peaked in February.

Illness onsets for the latest group of patients range from Feb 28 to Mar 13. The latest cases are in seven different provinces, with about half from Guangxi and Hunan. Eighteen of the people had known exposure to poultry or poultry markets.

China has now reported at least 565 cases and 174 deaths in the fifth H7N9 wave. Hong Kong, Taiwan, and Macao have also reported cases that were imported from the mainland.
Mar 17 CHP statement

US flu continues to decline, but 5 new pediatric deaths reported

Indicators of US influenza activity showed elevated but declining flu activity, but five new flu-related deaths in kids were confirmed, the Centers for Disease Control and Prevention (CDC) said in its weekly update on Mar 17.

Flu was geographically widespread in 36 states for the week ending Mar 11, the CDC said, down from 39 the week before. Eleven states reported regional flu activity, up from 8 the week before.

The percentage of respiratory samples that tested positive for flu was 18.3%, down from 18.6% the week before. The proportion of outpatient visits for influenza-like illness (ILI) was 3.7% , up from 3.6% the week before and still well above the national baseline of 2.2%. Flu activity has now remained elevated for 13 straight weeks.

Last week 18 states reported high ILI activity, which was up from 14 the week before. Seven states saw moderate ILI activity, compared with 12 the week before. Seven of 10 regions noted ILI above baseline levels, compared with 8 the week before.

Another marker that rose slightly was hospitalization rate, which climbed from 43.5 lab-confirmed flu hospitalizations per 100,000 population to 46.9 per 100,000. Among those 65 and older, the rate rose from 198.8 to 214.0 per 100,000 population. In 2012-13, another season dominated by the H3N2 "A" strain, the overall hospitalization rate at this point in the season was 40.4 per 100,000 population.

Two of the pediatric deaths were caused by H3N2, one by an influenza A virus that wasn't subtyped, and two by influenza B. The deaths happened in late January through early March. The CDC reported eight pediatric deaths the week before and have now confirmed 53 flu-related deaths in that population for the season. That compares with 111 for the entire 2013-14 season, 148 in 2014-15, and 89 last season.

For the week ending Mar 11, 61.1% of flu specimens were influenza A and 38.9% were influenza B, compared with 68.6% and 31.4%, respectively, the week before. (The late-season flu B surge is typical.) Of the "A" strains that were subtyped, 97% were H3N2.
Mar 17 CDC FluView report
Mar 17 CDC summary of FluView findings