Thursday, 08 December 2016 15:05

Carbapenem-resistant bacteria isolated from a pig farm in the United States

Written by 
Published in mBiosphere
Do these Enterobacteriaceae harbor antibiotic resistance genes? Do these Enterobacteriaceae harbor antibiotic resistance genes?

Carbapenems are beta-lactam antibiotics considered to be the last line of defense for many infections. Despite antibiotic stewardship programs, outbreaks of carbapenem-resistant bacteria do sometimes occur, mostly in healthcare settings. Because of the importance of this antibiotic class, there are restrictions for carbapenems in farm animal use.

While carbapenems aren’t allowed to be given to feedlot animals, other beta-lactam antibiotics are. This is a large class of drugs that includes extended-spectrum cephalosporin drugs. There is no direct line between the use of these extended-spectrum cephalosporins and selection for carbapenem resistance, but some scientists worry this may be the case, since the genes that confer carbapenem resistance can also confer extended-spectrum cephalosporin resistance.

Carbapenem-resistant bacteria have now been found for the first time on a farm in the United States. This comes after multiple incidents where carbapenem-resistant bacteria were isolated in Europe and Asia. The case is documented in Antimicrobial Agents and Chemotherapy.

Click to read the study

The study focused on a single farm, taking samples from fecal samples, fecal swabs, and environmental samples over the course of 2015. Samples were grown in the presence of meropenem to identify carbapenem-resistant isolates, and positive cultures were tested via biochemical assays for species identification. The genotype of carbapenem-resistant isolates was assessed using PCR and sequencing to determine the resistance genes.

The scientists found three carbapenem-resistant isolates (representing 7% of environmental isolates tested) in the first round of environmental samples (July 2015). Although surveillance found different bacterial species such as Escherichia coli and Proteus mirabilis to be resistant, these species carried the same resistance gene (blaIMP-27), as well as a mixture of resistance genes to other antibiotics. While the subsequent month found no carbapenem-resistant isolates, 15 of 100 environmental isolates contained the same carbapenemase gene (IMP-27) in October 2015.

The resistance gene origin is a bit mysterious, given that the farm has bred its own animals for 50 years without introducing new, outside animals. It’s possible that a human or non-pig animal distributed the detected isolates, since no pigs tested positive for carbapenem-resistant bacteria. However, no positive samples were detected on doorknobs or feed bin handles, weakening the argument that the isolates came from humans. The ubiquity of the same resistance gene, IMP-27, suggests the initial spread of a resistant bacterial strain followed by horizontal gene transfer between species. Unpublished data in a forthcoming study was able to pinpoint some of the pigs as positive for carbapenemase-carrying bacteria, and future studies will hopefully help the scientists find the source of the contamination.

IMP-27 is a resistance gene not commonly observed in clinical bacterial infection isolates. Monitoring the resistance profiles of clinical pathogens will help determine the role played by farm animals in spreading resistant bacteria to humans. Although care is taken when slaughtering animals, there is good evidence that enteric flora from the animal can end up packaged with the meat products and become distributed over a wide geographical area.

ABX structuresCore structure of a cephalosporin (L) and a carbapenem (R) molecule. Source (1) and (2)

Do the non-carbapenem beta-lactam antibiotics used on farms select for carbapenem resistant strains? The authors didn’t study this idea systematically, but they did note that the majority of their resistant strains came from a part of the barn where ceftiofur, a cephalosporin-class beta lactam, is frequently used, with fewer isolates coming from areas where antibiotics are only occasionally used. This is consistent with selection by extended-spectrum beta lactamases for carbapenem resistance.

How to deal with emerging bacterial resistance on a farm? Removing antibiotics isn’t a viable option for livestock farms. Just like hospitals and citizens must do, farms must make sure to use good antibiotic stewardship and ensure proper dosing and administration of antibiotics to sick animals. Farms can undergo extensive contamination removal procedures, but these are time- and resource-expensive (and not always effective). When it comes to antibiotic resistance, the old adage holds true: an ounce of prevention is worth a pound of cure.

Last modified on Thursday, 08 December 2016 17:09
Julie Wolf

Julie Wolf is the ASM Science Communications Specialist. She contributes to the ASM social media and blog network and hosts the Meet the Microbiologist podcast. She also runs workshops at ASM conferences to help scientists improve their own communication skills. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.

Julie earned her Ph.D. from the University of Minnesota, focusing on medical mycology and infectious disease. Outside of her work at ASM, she maintains a strong commitment to scientific education and teaches molecular biology at the community biolab, Genspace. She lives in beautiful New York City.