Abstract
Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical relevance, annotation of genes potentially involved in pathogenicity and/or antibiotic resistance in the CoNS species Staphylococcus arlettae (SAR) is currently very limited. In the current work we describe the genome of a novel methicillin resistant isolate of SAR, which we named Bari, and present a comprehensive analysis of predicted antibiotic resistance profiles and virulence determinants for all the 22 currently available SAR genomes. By comparing predicted antibiotic resistance and virulence-associated genes with those obtained from a manual selection of 148 bacterial strains belonging to 14 different species of staphylococci and to two “outgroup” species, Bacillus subtilis (BS) and Macrococcus caseoliticus (MC), we derived some interesting observations concerning the types and number of antibiotic resistance-related and virulence-like genes in SAR. Interestingly, almost 50% of the putative antibiotic resistance determinants identified in this work, which include the clinically relevant mec, van, and cls genes, were shared among all the SAR strains herein considered (Bari included). Moreover, comparison of predicted antibiotic resistance profiles suggest that SAR is closely related to well-known pathogenic Staphylococcus species, such as Staphylococcus aureus (SA) and Staphylococcus epidermidis (SE). A similar analysis of predicted virulence factors, revealed that several genes associated with pathogenesis (including, for example, ica, nuc, and ssp), which are commonly found in the genomes of pathogenic staphylococci such as Staphylococcus haemolyticus (SH) and Staphylococcus saprophyticus (SS), are observed also in the SAR strains for which a genomic sequence is available. All in all, we believe that the analyses presented in the current study, by providing a consistent and comprehensive annotation of virulence and antibiotic resistance-related genes in SAR, can constitute a valuable resource for the study of molecular mechanisms of opportunistic pathogenicity in this species.
Highlights
The first strains of Staphylococcus arlettae (SAR) were reported in 1984, isolated from the skin and nares of poultry and goats [1]
Both TCS and Average Nucleotide Identity (ANI) suggested the classification of the isolate as a novel SAR strain, which was named Staphylococcus arlettae Bari
The majority of candidate antibiotic resistance proteins identified by RGI were associated with efflux-based mechanisms of antibiotic resistance (52%), with other hits correlated to resistance mechanisms involving antibiotic target alteration, protection and replacement (31%), and antibiotic inactivation (17%) (Figure 1)
Summary
The first strains of Staphylococcus arlettae (SAR) were reported in 1984, isolated from the skin and nares of poultry and goats [1]. SAR strains were isolated from bovine mastitis, pig exudative epidermidis, dairy goat intramammary infection, a human patient affected by rheumatic mitral stenosis, as well as from blood clinical samples [7,8,9]. A plasmid encoding for nine antibiotic resistance genes, cfr, erm(C), tet(L), erm(T), aadD, fosD, fexB, aacA-aphD, and erm(B), was characterized in SA-01, a SAR strain isolated from a chicken farm. Independent studies have identified several multidrug efflux pumps (e.g., norA) coding genes as well as other genes related to resistance to antibiotics such as chloramphenicol (e.g., fexA), tetracycline (e.g., tetL), and erythromycin (e.g., msrA, mphC) in the genomes of SAR strains isolated from chicken farm and dairy herds affected by mastitis [10,12,13]. Since fosD-resistance genes are typically located in mobile genetic elements, they may contribute to multi-resistant traits to other staphylococci [14,15,16]
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