The 2014-2015 Retail Meat Interim Report from the US Food and Drug Administration (FDA) contains data from January 2014-June 2015 that measures antimicrobial resistance for Salmonella isolated from raw retail meat and poultry.
The National Antimicrobial Resistance Monitoring System (NARMS) tracks antibiotic resistance in foodborne bacteria for drugs that are considered important in human medicine.
Mixed findings
The report found prevalence of Salmonella in retail poultry was at its lowest level since testing began in 2002. In ground turkey, the prevalence has declined from a high of 19% in 2008 to 6% in 2014. In retail chicken over the same time period, it dropped from 15% to 9%.
On the other hand, FDA identified the first instance of ciprofloxacin resistance in an isolate from retail pork, and identified the associated genes for future tracking.
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, E. coli and Enterococcus, to determine whether they are resistant to antibiotics used in human and veterinary medicine.
Salmonella resistance to ceftriaxone (an antibiotic used to treat seriously ill patients) from chicken sources declined from 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%.
However, three isolates of Salmonella serotype Dublin recovered from meats (ground beef) in 2014, showed resistance to nine to 12 of 14 drugs tested.
Interim report reaction
Ashley Peterson, National Chicken Council (NCC) SVP of scientific and regulatory affairs, said it was pleased to see positive trends continue and added that analyzing resistance patterns is much more meaningful to public health outcomes than examining antibiotic sales data.
“Reports like this provide a strong case that the continued judicious use of antibiotics by poultry producers, coupled with ongoing strategies to reduce Salmonella, are aiding in the reduction of the pathogen and the reduction in resistance. Most chicken producers are well ahead of the December deadline to phase out medically important antibiotics for growth purposes.
“One thing consumers should remember is that all pathogens potentially found on raw chicken, regardless of strain or resistance profile, are fully destroyed by handling the product properly and cooking it to an internal temperature of 165°F.”
In a blog for the Natural Resources Defense Council (NRDC), Carmen Cordova said the results show only one bacterium instead of four and it is missing half of the most recent year’s data for 2015.
“On top of missing three of the four bacteria…this report includes only data from the first six months of 2015 in its analysis. Why? With literally half the year’s data missing, it isn’t appropriate to make conclusions about possible trends which include 2015.
“There is some good news, mostly around poultry, but part of that is associated with bans on the use of the antibiotic classes themselves. FDA states that this is one of two reports that will be released this year, so perhaps the bulk of the analysis and other data will be published then?
“After reading this report, it’s hard to make heads or tails on progress of antibiotic resistance on retail meat and in livestock with so many pieces of the puzzle missing.”
Dr Adina Howe, assistant professor, Agricultural and Biosystems Engineering, Iowa State University, said it is important to recognize the presence of a specific gene demonstrates the potential for resistance but does not demonstrate functional resistance or susceptibility to an antibiotic.
"While a single isolate is not enough evidence to suggest widespread antibiotic resistance, it is concerning that the Salmonella ciprofloxacin-resistant gene, like many other resistance genes, was found on a plasmid,” she said.
“The location of resistance genes on plasmids is of great concern as this is a mechanism that allows genes to move between bacteria and spread.”
Inclusion of WGS
FDA also included whole genome sequencing data for the first time for Salmonella.
The agency said WGS data has allowed it to understand the mechanisms underlying each of the resistance phenotypes observed, and how they differ by source.
Dr Howe said WGS is an ‘exciting and affordable new technology’ that has changed the resolution that microbes can be characterized by in the environment.
“Combined with many other technologies, including microscopy and cell sorting techniques, sequencing helps us to understand complex microbial communities in our environment. In particular, whole genome sequencing allows us to very specifically identify strains of interest and their genes,” she said.
“The ability to resolve the locations of genes in relationship to one other is a powerful benefit to sequencing strategies. Our biological toolbox to understand diverse environments, containing trillions of species, is growing and helping us to shed light on the role of AMR in agriculture."