Major Families of Multiresistant Plasmids from Geographically and Epidemiologically Diverse Staphylococci

Abstract

Staphylococci are increasingly aggressive human pathogens suggesting that active evolution is spreading novel virulence and resistance phenotypes. Large staphylococcal plasmids commonly carry antibiotic resistances and virulence loci, but relatively few have been completely sequenced. We determined the plasmid content of 280 staphylococci isolated in diverse geographical regions from the 1940s to the 2000s and found that 79% of strains carried at least one large plasmid >20 kb and that 75% of these large plasmids were 20–30 kb. Using restriction fragment length polymorphism (RFLP) analysis, we grouped 43% of all large plasmids into three major families, showing remarkably conserved intercontinental spread of multiresistant staphylococcal plasmids over seven decades. In total, we sequenced 93 complete and 57 partial staphylococcal plasmids ranging in size from 1.3 kb to 64.9 kb, tripling the number of complete sequences for staphylococcal plasmids >20 kb in the NCBI RefSeq database. These plasmids typically carried multiple antimicrobial and metal resistances and virulence genes, transposases and recombinases. Remarkably, plasmids within each of the three main families were >98% identical, apart from insertions and deletions, despite being isolated from strains decades apart and on different continents. This suggests enormous selective pressure has optimized the content of certain plasmids despite their large size and complex organization.

Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus

“…The presence of multiple ICE6013 subfamilies within S. aureus strains that are associated with food animals (e.g., ED98 and S0385) may also indicate both the lack of exclusion mechanisms that prevent the introduction of multiple copies of the element and the possibility that strains infecting food animals act as reservoirs for the element. Finally, our results unify genetic elements previously classified as a transposon, a plasmid, and different ICEs (26,34,35) within the ICE6013 family of integrative conjugative elements, which demonstrates the difficulty of classifying ICEs.…”

“…These additional ORFs are poorly annotated in general, but they do not include known antimicrobial resistance determinants. Notably, the genetic elements variously classified as Tn6012 (34), plasmid SAP077B (35), and ICESa1 and ICESa2 (26) all fell within these ICE6013 subfamilies (Fig. 5).…”

The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials

“…Nowadays, plasmid categorization is relevant from the public and environmental health perspective to follow the movement of genes coding for resistance to antimicrobials (antibiotics, heavy metals, biocides), colonization and virulence factors for humans and animals, and/or other adaptive traits that drive ecological success (bacteriocins, metabolic traits) and consequently increase the population size of bacteria harboring MGEs. In fact, only a "representative diversity" of bacterial plasmids has been systematically analyzed in a few genera of multihost opportunistic pathogens of interest in biomedicine, with a particular emphasis on species of the Enterobacteriaceae, Pseudomonadaceae, Staphylococcaceae, and Enterococcaceae families (7,(50)(51)(52)(53). The diversity of plasmids from Lactococcus (54), Lactobacillus (55), C. perfringens (56), Micrococcus (57), and Bifidobacterium (58) has also been analyzed from different perspectives.…”

“…Rep_3 plasmids play a relevant role as vehicles of AbR among staphylococci. Plasmids from S. aureus are overrepresented by closely related variants containing Rep 5 , which are associated with genes coding for penicilinase and resistance to heavy metals (cadmium and arsenic) (51,53,66,84). Staphylococcal plasmids within this group include AbR plasmids from coagulasenegative strains of animal origin, some of them with RIPs that would not be detected by current typing systems (97,98).…”

“…5) (9,(211)(212)(213). Comprehensive reviews address the essentially clonal population structure of S. aureus (214)(215)(216) and other staphylococcal species (207) and also the impact of HGT in the evolutionary history of staphylococcal populations (9,(217)(218)(219), with emphasis on the description of the plasmids associated with AbR genetic elements (9,51,84,220) and their influence on the variability of lineages (217,219,(221)(222)(223)(224).…”