News Scan for Mar 20, 2017

Saudi MERS cases
Drug-resistant Salmonella outbreak
More chikungunya
TB/HIV in Europe
Stewardship in peds urgent care
New AMR diagnostic tool

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


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

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