Stewardship / Resistance Scan for Jan 15, 2019

Antibiotic resistance on pig farms
Resistance genes in Bolivian river

Pig farm study notes ties between resistome, antimicrobials, biosecurity

A study of pig farms in nine European countries suggests antimicrobial use during the fattening phase is associated with antimicrobial resistance, researchers from the European Union Ecology from Farm to Fork Of microbial drug Resistance and Transmission (EFFORT) project reported yesterday in the Journal of Antimicrobial Chemotherapy.

The analysis, conducted from June 2014 to Dec 2015, looked at fecal samples from 176 conventional pig farms in Belgium, Bulgaria, Denmark, France, Germany, Italy, the Netherlands, Poland, and Spain. The investigators also surveyed farms about practices such as antimicrobial use. Resistomes—the profile of resistance genes in microorganisms and microbial populations—were determined using shotgun metagenomics and the Resfinder reference database.

For the positive association the researchers found between fattening and antibiotic use, the pattern was especially evident for widely used macrolides and tetracyclines, with antimicrobial resistance genes corresponding to their respective antimicrobial classes. However, they didn't see the same link for beta lactams, and they saw only a few colisitin resistance genes, despite the drug class's high use in younger pigs.

Increased biosecurity was related to higher abundance of resistance genes, mainly those that encode macrolide resistance. Adjusted models suggested that biosecurity effects were independent of antimicrobial use.

The authors said the study was the first of its kind and adds accuracy to earlier observations of the associations between antimicrobial use and antimicrobial resistance.
Jan 14 J Antimicrob Chemother abstract


Study finds diarrheal pathogens, resistance genes in Bolivian river

A team of Bolivian and Swedish researchers has found evidence of diarrheal pathogens and antibiotic-resistant bacteria in samples from an urban waterway in Bolivia, according to a study yesterday in PLOS One.

In the study, the researchers aimed to analyze the occurrence and bacterial load of diarrheal pathogens in water, soil, and vegetable samples from the Choqueyapu River—which receives wastewater from urban, medical, and industrial sources—and other affluent rivers in the La Paz River basin. They collected samples from four different points from April 2013 to March 2014 and conducted quantitative real-time polymerase chain reaction (qPCR) to detect the presence of genes indicating enterobacterial contamination. They also tested for the presence of diarrheagenic Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Shigella spp, and for antibiotic resistance genes.

The most abundant genes found in the water, soil, and vegetable samples were gapA, which indicates the presence of enterobacteria, and eltB, an indicator of enterotoxigenic E coli carrying the heat labile toxin. Pathogen levels in the samples were significantly positively associated with high water conductivity—which can signify high levels of metals, pollutants, and bacteria in the water—and low water temperature.

In addition, 101 bacterial isolates obtained from the samples were found to be resistant to multiple antibiotics, and qPCR identified the extended-spectrum beta-lactamase (ESBL) gene blaCTX-M, along with several other resistance genes and a high number of plasmids. Whole-genome sequencing identified three of the isolates as E coli and one as Enterobacter cloacae. The E coli isolates belonged to three emerging, globally disseminated, multidrug-resistant lineages.

"In conclusion, this study evidences the risk of transmission of diarrheal diseases directly or indirectly from the Choqueyapu River and its basin due to the presence of diarrheal pathogens in river water, vegetables and agricultural soils," the authors of the study wrote. "Bacterial isolates carrying ESBL genes and conjugative resistant plasmids obtained from the basin indicate that the risk is not only associated with the transmission of infectious bacteria, but also with the possibility of transmission of antibiotic resistant bacteria and the resistance genes they carry from the environment to the community."
Jan 14 PLOS One study

Newsletter Sign-up

Get CIDRAP news and other free newsletters.

Sign up now»


Unrestricted financial support provided by

Bentson Foundation 3MAccelerate DiagnosticsGilead 
Grant support for ASP provided by


  Become an underwriter»