Source poultry with lower loads of Salmonella: FDA NARMS retail meat report recites FightBac BS

The U.S. Food and Drug Administration has released a new interim report that measures antimicrobial resistance in Salmonella isolated from raw retail meat and poultry collected through the National Antimicrobial Resistance Monitoring System (NARMS).

AnimalHouse.satanThe 2014-2015 Retail Meat Interim Report contains data from January 2014 – June 2015. It focuses only on Salmonella, a major pathogen of concern in foodborne disease outbreaks. Information includes serotype distribution, prevalence by food source and state, selected resistance patterns, and a list of all the identified antimicrobial resistance genes. To provide data in a timelier manner, the FDA intends to issue retail meat interim reports twice per year. In this report FDA also includes, for the first time, whole-genome sequencing data for Salmonella as a new component of routine NARMS surveillance practices and has placed all the isolate-level data on its website.

NARMS was established in 1996 as a partnership between the 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 is critically important for monitoring trends in antimicrobial resistance among foodborne bacteria collected from humans, retail meats and food animals. In particular, it assists the FDA in making data-driven decisions on the approval of safe and effective antimicrobial drugs for animals.

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. Enterococcus and most E. coli are not considered major foodborne pathogens but are included because they are helpful in understanding how resistance occurs and spreads.

Consumers can help protect themselves from foodborne bacteria, including antibiotic-resistant bacteria, by following four basic food safety tips: clean, separate, cook, chill. Learn more at

2014-2015 Retail Meat Interim Report

In many important categories, encouraging improvements found in 2011 continued to be evident in the latest data.

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% in 2008 to 6% in 2014. In retail chicken over the same time period, it has dropped from 15% to 9%.

FunkyChickenHiSalmonella resistance to ceftriaxone (an important antibiotic used to treat seriously ill patients) 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%.

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% and 50%, respectively, to 20% and 36% in June 2015.

Findings of Concern

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 (see below).

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, resulting in fewer treatment options for infected patients.

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

Whole genome sequencing (WGS) has ushered in a new age in infectious disease science, with the power to greatly enhance diagnosis, tracking and treatment. Because WGS has become an inexpensive and rapid tool for characterizing bacteria, it has the potential to replace a number of long-standing laboratory methods such as biochemical tests to identify species, and the subtyping methods of serotyping and pulsed-field gel electrophoresis, each of which requires specialized training and separate lab processes. Whole genome sequence data are published for all 271 retail meat isolates from 2014 and 114 Salmonella isolated in the first half of 2015. All of the WGS data for NARMS isolates are now publicly available in GenBank bioproject PRJNA290865.

WGS data can be used to predict antimicrobial resistance for a number of bacteria, including the foodborne pathogens Salmonella, Campylobacter, and E. coli. In addition, WGS data reveal the range of genes causing resistance to a particular antibiotic. FDA has included comprehensive genetic data for the first time in a NARMS report, listing the antimicrobial resistance genes and resistance-associated mutations for Salmonella. Some notable findings from WGS in this report include:

WGS helped identify antibiotic resistant genes in the form of diverse quinolone resistance mechanisms. In addition to two isolates with well-known DNA gyrase mutations associated with quinolone resistance, two isolates possessed the plasmid-mediated qnr genes, one with qnrS and one with qnrB. This analysis revealed that the single ciprofloxacin-resistant isolate from pork carried the qnrS gene. The presence of such plasmid-associated resistance genes is of particular concern due to the potential for transmissibility to other strains of Salmonella. This appears to be the first report of qnr genes present in retail meat Salmonella isolated in the United States. Despite these findings, Salmonella largely remained susceptible to ciprofloxacin and other first line human clinical therapies, including azithromycin, during 2014 and the first half of 2015.

As noted above, 2014 was the first year FDA found a blaCTX-M-65 ESBL in Salmonella from a retail meat sample in the United States. This was identified by WGS and was seen in a single isolate. Studies are ongoing to see if this finding points to a broader distribution of this important trait in Salmonella from other sources.

The WGS data has allowed FDA, for the first time, 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, whereas in retail chicken and ground beef isolates, blaCMY were more prevalent.blaCMY genes are generally associated with more extended activity, and confer resistance to third-generation cephalosporins, important drugs in the treatment of Salmonella infections. The tetA gene predominated among tetracycline resistant isolates from retail chicken, ground turkey, and ground beef isolates, while in pork chop isolates tetB was most common. Additional genetic information over multiple years will be necessary to determine whether these differences are stable over time and may be used to help determine the source of resistant infections in isolates recovered from humans.

All the isolate-level data, including links to the WGS data, can be found at  

Ups and downs in report on drug-resistant foodborne bacteria

CIDRAP reports that an annual federal report released this week on drug resistance in bacterial foodborne illness culprits mainly showed encouraging patterns but raised concerns about multidrug resistance in two Salmonella serotypes. findings are from the National Antimicrobial Resistance Monitoring System (NARMS), a collaboration of three federal agencies that between them track resistant bacteria in humans, retail meat, and food animals. The respective agencies include the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), and the US Department of Agriculture (USDA).

The report focuses on foodborne pathogens that resist antibiotics considered crucial to human medicine and on multidrug resistant bacteria—those that resist agents in three or more antibiotic classes. The system screens for nontyphoidal Salmonella, Campylobacter, Escherichia coli, and Enterococcus; Salmonella and Campylobacter are the leading bacterial causes of foodborne illness.

Methodology and testing changes

This year’s report for the first time covers multiple years, 2012 and 2013, and has a new format that includes 10 interactive graphs to help show resistance patterns in Salmonella and Campylobacter in humans, retail foods, and animals through 2013, the FDA said in a press release yesterday. It added that the report also reflects improvements in NARMS testing. For example, animal testing now includes cecal (intestinal) testing of food-producing animals before slaughter, which may provide a more accurate picture of animals’ microbial status in farm settings.

Also, the FDA said it is using epidemiologic cut-off values that move toward global harmonization of Campylobacter surveillance methods as well as updating measurements for cefepime in response to changes made to best practices for international testing. Cefepime is an antibiotic used to screen for extended-spectrum beta-lactamase (ESBL) production, a mechanism linked to drug resistance.

In encouraging findings, the NARMS study found that overall, Salmonella isolates are holding the line against resistance. About 80% of human Salmonella isolates aren’t resistant to any tested antibiotics, a number that hasn’t changed over the past decade. Resistance to the three most important drugs used to treat human Salmonella isolates—ceftriaxone, azithromycin, and quinolones—remains below 3%.

Similarly, Salmonella multidrug resistance in human, cattle, and chicken isolates hasn’t changed in the last 10 years, remaining at about 10%. Also, the number of multidrug-drug resistant Salmonella isolates in retail chicken has decreased to around 3%, according to the report.

For Campylobacter jejuni, the subtype that causes most human campylobacteriosis cases, resistance to ciprofloxacin, the drug most commonly used for treatment, declined to its lowest level in retail chicken to date (11%).

Among the worrisome findings, multidrug resistance in human isolates of the common Salmonella serotype l 4,[5],12:i:- is still rising, and has doubled from 18% in 2011 to 46% in 2013, according to the FDA.

The report also pointed to another concern, an increase in multidrug resistance and ceftriaxone resistance in Salmonella Dublin subtypes isolated from cattle and humans.

US CDC says antibiotic resistance in foodborne germs is an ongoing threat

It’s nice that the scientists and PR-types at CDC, who for decades insisted that foodborne illness be publicly attributed to bacteria or viruses or parasites, out of scientific accuracy, are now referring to them as germs.

Family guy barfPeople really care about what is going to make them barf, not what it’s called.

Antibiotic resistance in foodborne germs, an ongoing public health threat, continued to show both positive and challenging trends in 2013, according to human illness data posted online today by the Centers for Disease Control and Prevention (CDC). Efforts are underway to curb the injudicious use of antibiotics, but each year, antibiotic-resistant infections from foodborne germs cause an estimated 440,000 illnesses in the United States.

The National Antimicrobial Resistance Monitoring System (NARMS) tracks changes in the antibiotic resistance of six types of common foodborne germs found in ill people, retail meats, and food animals. In 2013, NARMS tested more than 5,000 germs from sick people for antibiotic resistance and compared them with previous years’ data to assess changes in resistance patterns.

Among the findings in the new NARMS report on human illnesses:

The good news is that multidrug resistance (resistance to 3 or more classes of antibiotics) in Salmonella overall stayed steady, remaining at 10 percent of infections.

However, resistance in some types of Salmonella is increasing. For example, multidrug resistance in a common Salmonella serotype called I4,[5],12:i:- was 46 percent, more than double the rate from two years before. In the United States, resistance in this serotype to four drugs (ampicillin, streptomycin, sulfonamides, and tetracycline) rose from 18 percent in 2011 to 46 percent in 2013. Human illness with this serotype has been linked to animal exposure and consumption of pork or beef, including meats purchased from live animal markets.

NARMS also tests Campylobacter, another germ that is transmitted by food. One in four Campylobacter samples from sick people are still resistant to quinolones like ciprofloxacin.

Most Salmonella and Campylobacter infections cause diarrheal illness that resolves within a week without antibiotics. These germs can also cause infection of the bloodstream and other sites. In more serious infections and when germs are resistant, antibiotics may be ineffective, increasing the chance of a severe illness.

The 2013 NARMS Annual Human Isolates Report is now available at

CDC: Antibiotic resistance in foodborne germs is an ongoing threat

In a report that is sure to be interpreted by the political lenses of various groups, the U.S. Centers for Disease Control and Prevention reports that in 2012 that multi-drug resistant Salmonella decreased during the past 10 years and resistance to two important groups of drugs – cephalosporins and fluoroquinolones – remained low in 2012. However, in Salmonella typhi, the germ that causes typhoid fever, resistance to quinolone drugs increased to 68 percent in 2012, raising concerns that one of the common treatments for typhoid fever may not work in many cases.

chickenpurseAbout 1 in 5 Salmonella Heidelberg infections was resistant to ceftriaxone, a cephalapsorin drug. This is the same Salmonella serotype that has been linked to recent outbreaks associated with poultry. Ceftriaxone resistance is a problem because it makes severe Salmonella infections harder to treat, especially in children.

The data are part of the latest report of the National Antimicrobial Resistance Monitoring System (NARMS), a tri-agency surveillance system that has tracked antibiotic resistance in humans (CDC), retail meats (Food and Drug Administration), and food animals (U.S. Department of Agriculture) since 1996.  The report from CDC NARMS compares resistance levels in human samples in 2012 to a baseline period of 2003-2007. 

“Our latest data show some progress in reducing resistance among some germs that make people sick but unfortunately we’re also seeing greater resistance in some pathogens, like certain types of Salmonella,” said Robert Tauxe, M.D., M.P.H, deputy director of CDC’s Division of Foodborne, Waterborne, and Environmental Diseases. “Infections with antibiotic-resistant germs are often more severe. These data will help doctors prescribe treatments that work and to help CDC and our public health partners identify and stop outbreaks caused by resistant germs faster and protect people’s health.”

Among the other findings in the 2012 report:

*Campylobacter resistance to ciprofloxacin remained at 25 percent, despite FDA’s 2005 withdrawal of its approval for the use of enrofloxacin in poultry. Ciprofloxacin and enrofloxacin are both in the fluoroquinolone class of drugs.

*Shigella resistance to ciprofloxacin (2 percent) and azithromycin (4 percent) is growing. However, no Shigella strains were resistant to both drugs.

*Although fluoroquinolone resistance remained low in 2012, Salmonella enteritidis – the most common Salmonella type – accounted for 50 percent of infections resistant to the fluoroquinolone drug nalidixic acid, which is used in laboratory testing for resistance. Resistance to nalidixic acid relates to decreased susceptibility to ciprofloxacin, a widely used fluoroquinolone drug. Other work shows that many of the nalidixic acid resistant Salmonella enteritidis infections are acquired during travel abroad.

The full 2012 NARMS report is available on the CDC website at For more information about NARMS,  visit

In Australia, researchers from the Australian National University’s Research School of Biology tested more than 90 packages of chicken bought from several Canberra retailers for the presence of E. coli. 

chicken.south.parkProfessor of microbial population biology and evolution, David Gordon, said almost 200 samples were found to contain E. coli and of those, about two-thirds were discovered to be antibiotic-resistant.

Just four strains of E. coli were found to be resistant to antibiotics known as fluoroquinolone, which were not used by Australia’s poultry industry, he said. 

Professor Gordon said the E. coli strains researchers found were rare in the samples. 

He said it was unlikely the strains of fluoroquinolone-resistent E. coli were in the chicken before slaughtering, and the “most logical, although not necessarily true, explanation for their presence in poultry is post-processing contamination.”

An ACT Health spokeswoman said although the directorate had not seen the study, the presence of resistant bacteria in chicken meat highlighted the importance of good food handling and preparation when eating chicken, including thorough cooking and cleaning of food-preparation surfaces. 

“This is important to prevent bacterial food-borne illness regardless of whether bacteria are resistant to an antibiotic,” she said. 

An Australian Pesticides and Veterinary Medicines Authority spokeswoman said the authority was responsible for the assessment and registration of veterinary medicines, including antibiotics, in Australia.

She said fluoroquinolones have never been registered for use in food-producing animals in Australia.

“State and territory governments are responsible for controlling the use of pesticides and veterinary medicines beyond the point of retail sale,” she said.