DNA Microarray Detection of Antimicrobial Resistance Genes in Bacteria Co-Cultured from Swine Feces

Authors: Frye, Jonathan; Jackson, Charlene; Englen, Mark; Meinersmann, Richard - Rick; Berrang, Mark; Bailey, Joseph; RONDEAU, GAELLE - SIDNEY KIMMEL CANCER CTR; LONG, FRED - SIDNEY KIMMEL CANCER CTR; PORWOLLIK, STEFFEN - SIDNEY KIMMEL CANCER CTR; MCCLELLAND, MICHAEL - SIDNEY KIMMEL CANCER CTR

Submitted to: American Society for Microbiology Conference
Publication Type: Abstract Only
Publication Acceptance Date: 2/16/2007
Publication Date: 5/23/2007
Citation: Frye, J.G., Jackson, C.R., Englen, M.D., Meinersmann, R.J., Berrang, M.E., Bailey, J.S., Rondeau, G., Long, F., Porwollik, S., Mcclelland, M. 2007. Dna microarray detection of antimicrobial resistance genes in bacteria co-cultured from swine feces. American Society for Microbiology Conference. 167/A(A-076):17.

Interpretive Summary:

Technical Abstract: One factor leading to the spread of antimicrobial resistance (AR) in bacteria is the horizontal transfer of resistance genes. To study this, a DNA microarray was recently developed to detect these genes. To maximize the capability of this microarray, probes were designed and added to detect all AR genes found in the NCBI database. AR gene sequences were identified by keyword search, redundant sequences were removed, and annotations were evaluated to eliminate erroneous sequences. For each of the 684 genes identified a 70-mer oligonucleotide probe was designed using OligoWiz 2.0 and added to the previous array (Frye, et al., IJAA, 2006. Feb;27(2):138-150) for a total of 775 gene probes. Array printing, DNA extraction, labeling, hybridization, scanning, data analysis, controls and validation hybridizations were performed as previously described. The microarray was used to analyze Salmonella, Escherichia coli, Campylobacter spp. and Enterococcus spp. co-cultured from on-farm swine fecal samples. Over 220 different AR genes and mobile elements were detected in Salmonella and E. coli isolates, while 41 genes were detected in Campylobacter and Enterococcus spp. At least five pairs of Salmonella and E. coli isolated from the same fecal sample had common genes detected including ones encoding resistance to aminoglycosides (aadA, aadB, and aph(3)-I), '-lactams (blaAMPC and blaTEM), sulfanilamide (sulI), tetracycline (tetA, tetB, and tetR) and mobile elements (intI, tnpA, and tnpR). However, very few common AR genes were found between Salmonella and E. coli and the other isolates. All Campylobacter isolates had AR genes for '-lactams (blaCAM-1), tetracycline (tetO), and the efflux pump (cmeABC) and two had an aminoglycoside resistance gene (aphA-3). Isolates of Enterococcus spp. had few genes identified encoding resistance to aminoclycosides (aac(3’)-II) and tetracycline (tetM and tetW) as well as a transposon (tnpAB). These data demonstrate the power of this technique and presents some evidence of either horizontal exchange of AR genes between isolates from the same fecal sample or a common source of AR genes for Salmonella and E. coli.