The FDA recently released its 2014-2015 Retail Meat Interim Report, summarizing data from the National Antimicrobial Resistance Monitoring System (NARMS). The report focuses specifically on salmonella, one of the most common food-borne pathogens associated with eat and one of particular concern in terms of antibiotic resistance.

Also, for the first time, the analysis includes whole-genome sequencing data for Salmonella, a new component of NARMS surveillance that allows FDA to report isolate-level data on its website.

The retail meat arm of the NARMS program collects samples of grocery store chicken, ground turkey, ground beef and pork chops, and tests for non-typhoidal Salmonella, Campylobacter, Escherichia coli and Enterococcus, to measure and monitor trends in pathogen resistance to antibiotics used in human and veterinary medicine.

Encouraging trends in the new interim report include:

·         The prevalence of Salmonella in retail poultry is at its lowest since testing began in 2002. In ground turkey, the prevalence of Salmonella has declined from a high of 19% in 2008 to 6% in 2014. In retail chicken over the same time period, it has dropped from 15% to 9%.

·         Salmonella resistance to ceftriaxone from chicken sources continued to decline steadily from a high of 38% in retail chicken meats in 2009 to 18% in 2014, and 5% during the first half of 2015. In ground turkey isolates, ceftriaxone resistance was detected in 7% of 2014 isolates and 4% of 2015 isolates collected through June, which represents an 80% decline since 2011 when resistance peaked at 22%.

·         Ciprofloxacin-resistant Salmonella was not isolated from poultry and beef, while a single isolate was found in pork. Ciprofloxacin belongs to the fluoroquinolone class of antibiotics, which are classified as critically important for the treatment of Salmonella infections.

·         All Salmonella from retail meats were susceptible to azithromycin, a medically important antibiotic used in treatment of Salmonella and other intestinal pathogens.

·         Multidrug resistance in Salmonella continued to decline. In 2011 testing, the NARMS program found multidrug resistance in bacteria from show a downward drift in 45% of chicken samples and 50% of turkey. During the first half of 2015, the data show a prevalence of 20% and 36% in chicken and turkey respectively.

The report also notes some findings of concern, including:

·         FDA identified the first instance of ciprofloxacin resistance in an isolate from retail pork, and identified the genes associated with this resistance for future tracking.

·         One ceftriaxone-resistant retail chicken isolate from 2014 had the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-65. This is the first time this important class of resistance gene was detected in the U.S. This ESBL gene causes resistance to β-lactam antibiotics, including third generation cephalosporins.

·         Sampling revealed three isolates of Salmonella serotype Dublin ground beef in 2014. While uncommon, those isolates exhibited multidrug resistance, with resistance to nine to 12 of14 drugs tested.

According to the interim report, whole genome sequencing (WGS) of pathogens provides power to greatly enhance diagnosis, tracking and treatment. WGS has become an inexpensive and rapid tool for characterizing bacteria, with potential to replace a number of long-standing laboratory methods.

For the first time, FDA has included comprehensive WGS in this NARMS report, listing the antimicrobial resistance genes and resistance-associated mutations for Salmonella. The report notes that WGS helped identify antibiotic resistant genes in the form of diverse quinolone resistance mechanisms. Also, the WGS data has allowed FDA to understand the mechanisms underlying each of the resistance phenotypes observed, and how they differ by source. For instance, the predominant β-lactamases in ground turkey and pork chop isolates were blaTEM enzymes, the report notes, while blaCMY were more prevalent in retail chicken and ground beef isolates,.

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