ARS | Publication request: Linking microbial community structure and function to characterize antibiotic resistant bacteria and antibiotic resistant genes from cattle feces

Submitted to: ASA-CSSA-SSSA Annual Meeting Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: June 27, 2011
Publication Date: October 16, 2011
Citation: Durso, L.M. 2011. Linking microbial community structure and function to characterize antibiotic resistant bacteria and antibiotic resistant genes from cattle feces [abstract]. ASA-CSSA-SSSA Annual Meeting Abstracts. Poster No. 355-4(135). Available: http://a-c-s.confex.com/crops/2011am/webprogram/Session8331.html.

Interpretive Summary: The use of antibiotics in animal agriculture is an important issue. Few details are known, however, about how antibiotic resistant bacteria and antibiotic resistance genes travel through animals and the environment. The bacteria carry the genes inside themselves, as part of their own DNA. It has been suggested that one way to monitor the spread of antibiotic resistance on farms is to track just the genes, not the bacteria. Antibiotic resistant bacteria from cattle intestines travel out of the animal in the feces. How do we sort out which bacteria and genes are important for understanding the use of antibiotics in cattle? The first step is to figure out what bacteria are carrying these genes. We used modern DNA sequencing tools to look at the antibiotic resistance genes in cattle feces, and to link individual genes with the bacteria that are most likely carrying that gene. We know that antibiotic resistance genes can be found almost everywhere, including pristine habitats like Antarctic lakes. We compared the bacteria responsible for antibiotic resistance in pristine habitats with bacteria responsible for antibiotic resistance in agricultural habitats. While many of the bacterial groups were the same, the ratios of one group to another differed for feces vs. rumen vs. Antarctic lake. These data mean that tracking antibiotic resistant bacteria will give different results than tracking antibiotic resistance genes. This work also shows how new DNA-based tools can help identify which bacteria were the source of antibiotic resistance genes in cattle feces.

Technical Abstract: There is widespread interest in monitoring the development of antibiotic resistant bacteria and antibiotic resistance genes in agriculturally impacted environments, however little is known about the relationships between bacterial community structure, and antibiotic resistance gene profiles. Cattle manure serves as the vehicle by which intestinal bacteria carrying antibiotic resistance genes are transferred to the environment. Thus, the first step in tracking the transmission of antibiotic resistant bacteria and antibiotic resistance genes is to understand these parameters in the fecal source material. Whole community DNA sequencing was used to characterize the antibiotic resistant genes in feedlot cattle feces, and identify the bacteria likely carrying these genes. Additionally, public metagenomic databases were mined to compare community structure and antibiotic resistant gene profiles from other environments. Results indicate that in feedlot cattle feces, the detected fluoroquinolone resistance genes likely belong to 59 bacteria genera. The majority (50%) are carried by members of the Bacteroides genus, followed by Clostridium sp. (15%). At the level of class, the predominant bacteria carrying fluoroquinolone resistance genes in cattle feces are Bacteroidetes, Clostridia, and Bacilli in a 9:3:1 ratio, compared to 1:2:1 in cattle rumen, and 1:6:3 in Antarctic marine derived lake. Whole community DNA sequencing using high-throughput techniques provides information on both taxonomic and functional genes from a sample. While the current “second-generation” pyrosequencing tools are not readily accessible to most researchers at this time, new sequencing platforms have recently been introduced that have the potential to make sequencing-based approaches more accessible by reducing the cost of a sequencing run to under $800. New tools are publicly available that link functional gene assignments to taxonomic information, allowing insight into which bacteria are potentially carrying the genes of interest. We used these tools to identify which bacteria were carrying antibiotic resistance genes in cattle feces.