The smr gene resides on a novel plasmid pSP187 identified in a Staphylococcus pasteuri isolate recovered from unpasteurized milk

A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack the mating pore of a conjugative element for their own transfer. However, knowledge of their prevalence and diversity is still severely lacking. In this work, an extensive analysis of 124 genomes from 27 species of Streptococcus reveals 144 IMEs. These IMEs encode either tyrosine or serine integrases. The identification of IME boundaries shows that 141 are specifically integrated in 17 target sites. The IME-encoded relaxases belong to nine superfamilies, among which four are previously unknown in any mobilizable or conjugative element. A total of 118 IMEs are found to encode a non-canonical relaxase related to rolling circle replication initiators (belonging to the four novel families or to MobT). Surprisingly, among these, 83 encode a TcpA protein (i.e., a non-canonical coupling protein (CP) that is more closely related to FtsK than VirD4) that was not previously known to be encoded by mobilizable elements. Phylogenetic analyses reveal not only many integration/excision module replacements but also losses, acquisitions or replacements of TcpA genes between IMEs. This glimpse into the still poorly known world of IMEs reveals that mobilizable elements have a very high prevalence. Their diversity is even greater than expected, with most encoding a CP and/or a non-canonical relaxase.

The qacC Gene Has Recently Spread between Rolling Circle Plasmids of Staphylococcus, Indicative of a Novel Gene Transfer Mechanism

Resistance of Staphylococcus species to quaternary ammonium compounds, frequently used as disinfectants and biocides, can be attributed to qac genes. Most qac gene products belong to the Small Multidrug Resistant (SMR) protein family, and are often encoded by rolling-circle (RC) replicating plasmids. Four classes of SMR-type qac gene families have been described in Staphylococcus species: qacC, qacG, qacJ, and qacH. Within their class, these genes are highly conserved, but qacC genes are extremely conserved, although they are found in variable plasmid backgrounds. The lower degree of sequence identity of these plasmids compared to the strict nucleotide conservation of their qacC means that this gene has recently spread. In the absence of insertion sequences or other genetic elements explaining the mobility, we sought for an explanation of mobilization by sequence comparison. Publically available sequences of qac genes, their flanking genes and the replication gene that is invariably present in RC-plasmids were compared to reconstruct the evolutionary history of these plasmids and to explain the recent spread of qacC. Here we propose a new model that explains how qacC is mobilized and transferred to acceptor RC-plasmids without assistance of other genes, by means of its location in between the Double Strand replication Origin (DSO) and the Single-Strand replication Origin (SSO). The proposed mobilization model of this DSO-qacC-SSO element represents a novel mechanism of gene mobilization in RC-plasmids, which has also been employed by other genes, such as lnuA (conferring lincomycin resistance). The proposed gene mobility has aided to the wide spread of clinically relevant resistance genes in Staphylococcus populations.

Safety-related properties of staphylococci isolated from food and food environments

AIMS

To test some safety-related properties within 321 staphylococci strains isolated from food and food environments.

METHODS AND RESULTS

The isolates were identified as Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus saprophyticus, Staphylococcus pasteuri, Staphylococcus sciuri, Staphylococcus warneri and Staphylococcus xylosus. Decarboxylase activity was quite common for the various Staphylococcus spp., and tyrosine was the most frequently decarboxylated amino acid. The frequency of antibiotic resistance was highest in Staph. pasteuri and Staph. xylosus. Several of the isolates were tolerant to QAC compounds, and in some cases, QAC tolerance was present in antibiotic-resistant strains. Most of the strains displayed moderate to high adhesion rates to stainless steel and Teflon(®). The strains that readily formed biofilms belonged to the species Staph. aureus, Staph. epidermidis and Staph. pasteuri.

CONCLUSIONS

An high incidence of some safety hazards was found within the staphylococcal strains of food origin tested in this study. In particular, amino acid decarboxylase activity and biofilm-forming ability were common within strains, and antibiotic resistance and tolerance to QAC-based compounds occurred frequently as well. These characteristics are an important safety concern for food industry.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work gives a first picture of safety hazards within staphylococcal species isolated from food environments. The presence of disinfectant-resistant staphylococci is a concern because resistance can be genetically transferred between the various Staphylococcus species. This could lead an increase and spread of resistant enterotoxic staphylococci and/or pathogenic staphylococci.