Scientific Publications by FDA Staff

Antimicrob Agents Chemother 2013 Nov;57(11):5398-405

Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes.

Chen Y, Mukherjee S, Hoffmann M, Kotewicz ML, Young S, Abbott J, Luo Y, Davidson MK, Allard M, McDermott P, Zhao S

Aminoglycoside resistance in Campylobacter has been routinely monitored in the United States in clinical isolates since 1996 and in retail meats since 2002. Gentamicin resistance first appeared in a single human isolate of Campylobacter coli in 2000 and a single chicken meat isolate in 2007, after which it increased rapidly to account for 11.3% human isolates and 12.5% of retail isolates in 2010. Pulsed-field gel electrophoresis analysis indicated that gentamicin resistant C. coli isolates from retail meat were clonal. We sequenced the genomes of two strains in this clone using a next generation sequencing technique in order to investigate the genetic basis for the resistance. The gaps of one strain were closed using optical mapping and Sanger sequencing, and it is the first completed genome of C. coli. The two genomes are highly similar to each other. A self-transmissible plasmid carrying multiple antibiotics resistance genes was revealed within both genomes, encoding genes resistant to gentamicin, kanamycin, streptomycin, streptothricin, and tetracycline. Bioinformatics analysis and experimental results showed that gentamicin resistance was due to a phosphotransferase gene aph(2'')-Ig not described previously. The phylogenetic relationship of this newly emerged clone to other Campylobacter sp. was determined by whole genome single nucleotide polymorphisms (SNPs) and showed that it clustered with the other poultry isolates and was separated from isolates from livestock.