CRISPR-Cas Systems Features and the Gene-Reservoir Role of Coagulase-Negative Staphylococci

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.

Underrated Staphylococcus species and their role in antimicrobial resistance spreading

“…Pet animals have been shown to act as reservoirs of resistant bacteria, which in turn act as reservoirs of mobile genetic elements that carry antimicrobial resistance genes (Guardabassi et al, 2004;Rossi et al, 2017a). In fact, the relationship between the animals and their owners signifi-cantly shapes the microbiota of both counterparts (Song et al, 2013).…”

“…Then, even if one staphylococcal species is not a common pathogen, it can be a potential threat, because it may be capable of transferring antimicrobial resistance genes to more pathogenic species, such as S. aureus, thereby enhancing its capacity to resist drug therapy (Haaber et al, 2017). For that reason, some CoNS have been suggested to act as antimicrobial genes reservoirs within the Staphylococcus genus (Cafini et al, 2016;Rossi et al, 2017a). The acquisition of antimicrobial resistance genes is mainly credited to the occurrence of conjugation and bacteriophage transduction and the presence of dozens of insertion sequences in staphylococcal genomes, whose rearrangements contribute to genome plasticity and strains' phenotypic diversification (Takeuchi et al, 2005;Haaber et al, 2017).…”

“…Later, Hatoum-Aslan et al (2014) constructed mutants for all the nine cas/csm genes of the type III-A system in Staphylococcus epidermidis RP62a and showed that many mutations affected interference by impacting the interference complex formation or the crRNA biogenesis. At least 4% of the spacers within staphylococcal CRISPRs are identical to publicly available plasmid sequences, thus demonstrating their antiplasmid activity (Rossi et al, 2017a). This percentage may be underrated due to under-sampling of mobile genetic elements and, as a consequence, their relative scarcity in public databases (Mojica et al, 2005).…”

“…Genomic analyses indicate that many of the genetic determinants of resistance may have been exchanged between several staphylococcal species from different environments and hosts (Rolo et al, 2017;Rossi et al, 2017a;Kohler et al, 2018;). This includes species that are understudied and/or underestimated, either for having been recently discovered, rarely involved with infectious diseases, or for lacking canonical staphylococcal virulence factors.…”

“…This includes species that are understudied and/or underestimated, either for having been recently discovered, rarely involved with infectious diseases, or for lacking canonical staphylococcal virulence factors. However, recent evidence shows that these underrated species, despite not being usual pathogens, may have an important role in the exchange of antimicrobial resistance genes, by acting as gene-reservoirs for more pathogenic species, such as S. aureus (Otto, 2013;Rossi et al, 2017aRossi et al, , 2019.…”