A new interim report from the U.S. Food and Drug Administration (FDA) measuring antimicrobial resistance in Salmonella isolated from raw retail meat and poultry found both encouraging and concerning trends. The report included whole-genome sequencing data for the first time, FDA noted, and analyzed data from January 2014 through June 2015 collected through the National Antimicrobial Resistance Monitoring System (NARMS). 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 determine whether such bacteria are resistant to various antibiotics used in human and veterinary medicine. However, this latest interim report, released April 28, only tested for Salmonella. Information reported includes serotype distribution, prevalence by food source and state, selected resistance patterns, and a list of all the identified antimicrobial resistance genes. FDA reported “encouraging improvements” in the 2014-2015 data. These included:

• The prevalence of Salmonella in retail poultry is at its lowest level since testing began in 2002. In ground turkey, the prevalence of Salmonella has declined from a high of 19 percent in 2008 to 6 percent in 2014. In retail chicken over the same time period, it has dropped from 15 percent to 9 percent, FDA reported.
• Salmonella resistance to ceftriaxone (an important antibiotic used to treat seriously ill patients) from chicken sources continued to decline steadily from a high of 38 percent in retail chicken meats in 2009 to 18 percent in 2014, and 5 percent during the first half of 2015. In ground turkey isolates, ceftriaxone resistance was detected in 7 percent of 2014 isolates and 4 percent of 2015 isolates collected through June, which represents an 80-percent decline since 2011 when resistance peaked at 22 percent, the agency noted.
• Fluoroquinolones like ciprofloxacin are classified as critically important for the treatment of Salmonella infections. Ciprofloxacin resistance was absent in Salmonella from poultry and beef, although a single isolate was found in pork.
• All Salmonella from retail meats were susceptible to azithromycin, another important antibiotic recommended for the treatment of Salmonella and other intestinal pathogens.
• Multidrug resistance in Salmonella continued to show a downward drift in chicken and turkey from 2011 levels of 45 percent and 50 percent, respectively, to 20 percent and 36 percent in June 2015, FDA stated.

The agency also noted some “findings of concern” in the 2014-2015 data. They were:

• 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 bla_CTX-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, resulting in fewer treatment options for infected patients, FDA reported.
• While only three isolates of Salmonella serotype Dublin were recovered from meats (ground beef) in 2014, they exhibited extensive resistance patterns as in the past, showing resistance to 9-12 of 14 drugs tested.

Whole-genome sequencing (WGS) data can be used to predict antimicrobial resistance for a number of bacteria, including the foodborne pathogens Salmonella, Campylobacter, and E. coli, FDA noted. In addition, WGS data reveal the range of genes causing resistance to a particular antibiotic. The agency has included comprehensive genetic data for the first time in a NARMS report, listing the antimicrobial resistance genes and resistance-associated mutations for Salmonella. Whole genome sequence data are published for all 271 retail meat isolates from 2014 and 114 Salmonella isolated in the first half of 2015. These data for Salmonella will be a component of routine NARMS surveillance practices and the isolate-level data is now posted here. To provide NARMS data in a timelier manner, FDA intends to issue retail meat interim reports twice per year.  NARMS was established in 1996 as a partnership between FDA, the Centers for Disease Control and Prevention, and the U.S. Department of Agriculture to track antibiotic resistance in foodborne bacteria for drugs that are considered important in human medicine, including whether they are multidrug resistant (resistant to three or more classes of antibiotics). NARMS monitors trends in antimicrobial resistance among foodborne bacteria collected from humans, retail meats and food animals and assists FDA in making data-driven decisions on the approval of safe and effective antimicrobial drugs for animals.

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