Abstract
The claimed role of gene reservoir of coagulase-negative staphylococci (CoNS) could be contradicted by estimates that CRISPR/Cas systems are found in the genomes of 40–50% of bacteria, as these systems interfere with plasmid uptake in staphylococci. To further correlate this role with presence of CRISPR, we analyzed, by computational methods, 122 genomes from 15 species of CoNS. Only 15% of them harbored CRISPR/Cas systems, and this proportion was much lower for S. epidermidis and S. haemolyticus, the CoNS most frequently associated with opportunistic infections in humans. These systems are of type II or III, and at least two of them are located within SCCmec, a mobile genetic element of Staphylococcus bacterial species. An analysis of the spacers of these CRISPRs, which come from exogenous origin, allowed us to track the transference of the SCCmec, which was exchanged between different strains, species and hosts. Some of the spacers are derived from plasmids described in Staphylococcus species that are different from those in which the CRISPR are found, evidencing the attempt (and failure) of plasmid transference between them. Based on the polymorphisms of the cas1 gene in CRISPRs of types II and III, we developed a multiplex polymerase chain reaction (PCR) suitable to screen and type CRISPR systems in CoNS. The PCR was tested in 59 S. haemolyticus strains, of which only two contained a type III cas1. This gene was shown to be expressed in the exponential growth, stationary phase and during biofilm formation. The low abundance of CRISPRs in CoNS is in accordance with their role as gene reservoirs, but when present, their spacers sequence evidence and give an insight on the dynamics of horizontal genetic transfer among staphylococci.
Highlights
Coagulase-negative staphylococci (CoNS) were for a long time considered as harmless residents of the normal microbiota of skin and mucous membranes of humans, but are increasingly being recognized as central causative agents of healthcare-associated infections (Becker et al, 2014; Asaad et al, 2016)
Horizontal gene transfer is greatly limited in staphylococci by the presence of clustered regularly interspaced short palindromic repeats – CRISPR (Marraffini and Sontheimer, 2008; Cao et al, 2016), which are believed to be present in approximately 40–50% and 90% of bacterial and archaeal genomes, respectively (Sorek et al, 2008)
A total of 122 sequenced genomes available from GenBank (Supplementary Table S1) were used for the computational analysis. They belong to 15 different species of coagulase negative Staphylococcus that have been detected in humans, among other sources (Becker et al, 2014): S. auricularis (n = 1), S. capitis (n = 7), S. epidermidis (n = 34), S. haemolyticus (n = 32), S. hominis (n = 6), S. lugdunensis (n = 9), S. massiliensis (n = 1), S. pettenkoferi (n = 1), S. saprophyticus (n = 8), S. schleiferi (n = 5), S. sciuri (n = 1), S. simulans (n = 3), S. succinus (n = 1), S. warneri (n = 10), and S. xylosus (n = 3)
Summary
Coagulase-negative staphylococci (CoNS) were for a long time considered as harmless residents of the normal microbiota of skin and mucous membranes of humans, but are increasingly being recognized as central causative agents of healthcare-associated infections (Becker et al, 2014; Asaad et al, 2016). The establishment of biofilms provide an environment of high cell density, increased genetic competence and availability of mobile genetic elements that altogether make an ideal setting for horizontal transference of resistance genes (Flemming et al, 2016). Evidences show that CoNS may act as reservoirs of genes that may be transferred between related and to more pathogenic bacteria, such as Staphylococcus aureus, enhancing its potential to resist antimicrobial treatment (Otto, 2013; Rossi et al, 2016a). The evidences for transfer of important elements, such as plasmids and the staphylococcal cassette chromosome mec (SCCmec, which harbors the mecA gene coding for an alternative penicillin binding protein), from CoNS to S. aureus are quite strong as observed by sequence homology (Barbier et al, 2010; Otto, 2013). Horizontal gene transfer is greatly limited in staphylococci by the presence of clustered regularly interspaced short palindromic repeats – CRISPR (Marraffini and Sontheimer, 2008; Cao et al, 2016), which are believed to be present in approximately 40–50% and 90% of bacterial and archaeal genomes, respectively (Sorek et al, 2008)
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