The aphA1 kanamycin and neomycin resistance gene originated in Klebsiella michiganensis.

Background: The origins of several antibiotic resistance genes have been traced to intrinsic genes present in bacterial chromosomes. The aphA1 gene, which confers resistance to the aminoglycosides kanamycin and neomycin, is commonly found in diverse Gram-negative bacterial pathogens, and is associated with several different mobile genetic elements. However, its origin had not been identified.

Objectives: To determine whether the aphA1-containing segments in novel compound and pseudo-compound transposons found in three historic plasmids, pIE545, R478 and Rts1, are found in the chromosome of a specific bacterial species.

Methods: Passenger segments of transposons containing the aphA1 gene were compared to one another and to chromosomal sequences in GenBank using BLAST.

Results: In pIE545, aphA1 is in a 5424 bp compound transposon, TnaphA1-pIE545, that is bounded by directly oriented copies of IS102. The 3.3 kb aphA1-containing passenger segment is >99% identical to a contiguous part of several Klebsiella michiganensis chromosomes. The 4.3 kb aphA1-containing segment of the IS26-bounded pseudo-compound transposon PTnaphA1-R478 in R478 is also >99% identical to a contiguous part of several K. michiganensis chromosomes that differ in the gene content surrounding aphA1. The 2.2 kb passenger segment of the IS26-bounded PTn2680 from Rts1 arose via a third independent acquisition from a K. michiganensis chromosome.

Conclusions: The aphA1 gene has been captured and mobilized on at least three occasions from K. michiganensis chromosomes with related but distinct surrounding configurations.