Staphylococci on ICE: Overlooked agents of horizontal gene transfer

Abstract

Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus, which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn916 was capable of transfer from Enterococcus to Staphylococcus. However, recent work has begun to thaw this field. To date, 2 families of ICEs have been identified among staphylococci - Tn916 that includes the Tn5801 subfamily, and ICE6013 that includes at least 7 subfamilies. Both Tn5801 and ICE6013 commonly occur in clinical strains of S. aureus. Tn5801 is the most studied of the Tn916 family elements in staphylococci and encodes tetracycline resistance and a protein that, when expressed in Escherichia coli, inhibits restriction barriers to incoming DNA. ICE6013 is among the shortest known ICEs, but it still includes many uncharacterized open reading frames. This element uses an IS30-like transposase as its recombinase, providing some versatility in integration sites. ICE6013 also conjugatively transfers among receptive S. aureus strains at relatively higher frequency than Tn5801. Continued study of these mobile genetic elements may reveal the full extent to which ICEs impact horizontal gene transfer and the evolution of staphylococci.

Keywords: ICE6013; Staphylococcus aureus; Tn5801; Tn916; conjugation; horizontal gene transfer; integrative conjugative elements.

Figure 1.

Comparison of Tn916 family elements from staphylococci and other species, as classified previously. Sequences are numbered and labeled by species, strain, and ICE identifier. Gene map shows orfs (open reading frames) predicted by Prodigal v1.2 as arrows and are colored according to the following: red for recombinase proteins, blue for regulation-related proteins, purple for tetM, and green for conjugation-related proteins. Black indicates orfs not present in the founding Tn916 element. Vertical pink arrowheads indicate insertions of transposons described elsewhere, which were removed to facilitate comparison. Percent nucleotide identity determined by BLASTn analysis is shown under sequences as red shading (EasyFig 2.2.2). A matrix of pairwise mean reciprocal ANI (average nucleotide identities) was computed using JSpecies v1.2.1 with default parameters, and colored according to the scale.

Figure 2.

Comparison of ICE6013 family elements, as classified previously. Sequences are numbered by, species, strain, and subfamily. orfs (open reading frames) predicted by Prodigal v1.2 analysis are shown as arrows and are colored according to the following: red for IS30-like DDE transposase and green for conjugation-related proteins. Black indicates unknown function. Vertical pink arrowhead indicates insertion of Tn552 in strain HDG2, which was removed to facilitate comparison. Percent nucleotide identity determined by BLASTn analysis is shown under sequences as red shading (EasyFig 2.2.2). A matrix of pairwise mean reciprocal ANI (average nucleotide identities) was computed using JSpecies v1.2.1 with default parameters, and colored according to the scale.