Percentage of the genome among 37 Escherichia and Shigella strains which code for genes related to antibiotic resistance. This shows that antibiotic resistance genes are over-represented on plasmids. Bars show the mean percentage (±s.e.) in all replicons (either on the chromosome, n = 37, or on plasmids, n = 53, including 38 plasmid genomes which contained no antibiotic resistance genes). The genomes are from 37 Escherichia and Shigella strains, including all chromosomal and plasmid genes in each genome (data obtained from the NCBI at http://www.ncbi.nlm.nih.gov/genomes/ webcite). There were a total of 174,862 genes, with 170,709 on all 37 chromosomes and 4,153 on all 53 plasmids. For comparison with known genes involved in antibiotic resistance, the "Antibiotic Resistance Database" [http://ardb.cbcb.umd.edu/ webcite- ] was used to identify genes involved in antibiotic resistance (homologues were identified using an E-value of 10-10 and percentage of sequence identity between 60-95%). From this, there were a total of 817 genes involved in antibiotic resistance, with 765 carried by the bacterial chromosomes (and 0.48% of all chromosomal genes) and 52 carried by plasmids (1.25% of all plasmid genes). A χ2 test revealed that antibiotic resistance genes were significantly over-represented on plasmids, compared to on the bacterial chromosome (Pearson's χ2 with Yates' continuity correction: χ2 = 54.6, p < 10-12, df = 1).
Svara and Rankin BMC Evolutionary Biology 2011 11:130 doi:10.1186/1471-2148-11-130