New online hub for antimicrobial resistance data launches

News brief

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) today announced the launch of a new online hub for global antimicrobial resistance (AMR) data.

Launched with the aim of making global AMR data more accessible and usable for researchers, the AMR portal will collect and present data on resistance phenotypes, AMR genes, and genome sequences, along with sample metadata, including information about the included bacteria, experimental methods, and the provenance of the dataset. The first release is based on a dataset from Imperial College London.

"Working with EMBL-EBI to create the AMR portal means these data are openly accessible, allowing the global research community to explore resistance mechanisms more effectively, build stronger evidence to support public health decisions, and promote the development of more accurate diagnostics," Leonid Chindelevitch, PhD, of Imperial College London, said in an EMBL press release.

EMBL-EBI officials say the next step will be to lower the barrier to allow more people to contribute data to the portal.

"As more groups contribute, this portal will naturally expand and become an increasingly powerful resource for the global AMR community, enabling the creation of benchmarking datasets for AMR prediction tools, and helping track resistance trends over time," said John Lees, PhD, group leader at EMBL-EBI

Indiana tracks more avian flu outbreaks in poultry

News brief

Stephanie Soucheray, MA

The latest update from the US Department of Agriculture's Animal and Plant Health Inspection Service (APHIS) notes that more Indiana poultry farms have been hit with highly pathogenic H5N1 avian flu.

The largest outbreak involved a poultry operation in Elkhart County with 48,800 birds. And four more facilities in LaGrange County reported activity, including a commercial duck breeder with 14,700 birds. The other affected farms housed flocks of 10,500, 19,500, and 25,600 poultry.

LaGrange County has been a hotbed of avian flu activity this month, with more than 20 detections, many in large commercial duck facilities. Indiana is the leading duck producer in the country.

Backyard flocks hit in Oklahoma, Oregon, Washington

APHIS also reported detections in smaller, backyard poultry flocks in Grady and McClain counties in Oklahoma, Washington state, and Oregon.

H5N1 detections have risen sharply this fall, as wild birds spread the virus during their migration. Over the past 30 days, 83 confirmed flocks (36 commercial and 47 backyard) have been hit by H5N1 outbreaks, and 1.82 million birds have been affected.

CWD hits another Richland County, Wisconsin, deer farm

News brief

Mary Van Beusekom, MS

White-tailed buck — Deb Watson / Flickr cc

A 3-year-old buck on a Richland County, Wisconsin, deer farm has tested positive for chronic wasting disease (CWD), the Wisconsin Department of Agriculture, Trade and Consumer Protection (DATCP) announced yesterday.

The positive result was confirmed by the National Veterinary Services Laboratories in Ames, Iowa. The farm is now quarantined while the DATCP and US Department of Agriculture conduct an epidemiologic investigation. Richland County is located in the southwestern part of the state, which is endemic for CWD in free-ranging deer, per the Wisconsin Department of Resources.

The DATCP regulates deer farms for registration, recordkeeping, disease testing, movement, and permit requirements. This detection is not the first on a deer farm in Richland County, DATCP data show. Previous detections occurred in 2014 (eight CWD-positive deer) and 2018 (one).

Spreads from deer to deer and via the environment

CWD is a fatal, neurodegenerative disease of cervids such as deer, elk, and moose caused by misfolded infectious proteins called prions, which spread from deer to deer and through environmental contamination. CWD falls under the umbrella of transmissible spongiform encephalopathies, which also include prion diseases such as bovine spongiform encephalopathy ("mad cow" disease) in cattle, scrapie in sheep, and Creutzfeldt-Jakob disease in people.