Methicillin resistance in Staphylococcus pseudintermedius encoded within novel staphylococcal cassette chromosome mec (SCCmec) variants.

BACKGROUND: Staphylococcus pseudintermedius is a common opportunistic pathogen of companion dogs and an occasional human pathogen. Treatment is hampered by antimicrobial resistance including methicillin resistance encoded by mecA within the mobile genetic element SCCmec. OBJECTIVES: SCCmec elements are diverse, especially in non-Staphyloccocus aureus staphylococci, and novel variants are likely to be present in S. pseudintermedius. The aim was to characterize the SCCmec elements found in four canine clinical isolates of S. pseudintermedius. MATERIAL AND METHODS: Isolates were whole-genome sequenced and SCCmec elements were assembled, annotated and compared to known SCCmec types. RESULTS AND DISCUSSION: Two novel SSCmec are present in these isolates. SCCmec7017-61515 is characterized by a novel combination of a Class A mec gene complex and a type 5 ccr previously only described in composite SCCmec elements. The other three isolates share a novel composite SCCmec with features of SCCmec types IV and VI. CONCLUSIONS: S. pseudintermedius is a reservoir of novel SSCmec elements that has implications for understanding antimicrobial resistant in veterinary and human medicine.

Streptococcus hillyeri sp. nov., isolated from equine trachea.

Strain 28462T, which had Gram-stain-positive, catalase-negative coccus-shaped cells, was isolated from a routine tracheal sample from a 3 year old thoroughbred horse. 16S rRNA gene sequence analysis revealed it to be most closely related to, but distinct from, Streptococcus henryi (95.7 % identity), Streptococcusplurextorum (95.8 %), Streptococcusporci (96.4 %) and Streptococcus caprae (95.1 %). Similarity values derived from sequences from sodA and rpoB genes were consistent with strain 28462T belonging to a species distinct from these four streptococci. At the whole genome level, strain 28462T had an average nucleotide identity value <95 % and an inferred DNA-DNA hybridization value <70 % when compared to S. henryi, Streptococcus. plurextorum and S. porci with no S. caprae genome sequence being available. Finally, various phenotypic characteristics distinguish strain 28462T from each of these species. Based on the genotypic and phenotypic results, it is proposed that strain 28462T is a novel species, with the name Streptococcus hillyeri sp. nov. The type strain is 28462T (=DSM 107591T=CCUG 72762T).

Staphylococcus pseudoxylosus sp. nov., isolated from bovine mastitis.

Strain S04009T, a Gram-stain-positive, coagulase-negative staphylococcus, was isolated from bovine mastitis in France. 16S rRNA gene analysis revealed it to be closely related to the coagulase-negative species Staphylococcusxylosus, Staphylococcussaprophyticus, Staphylococcuscaeli and Staphylococcus edaphicus. At the whole-genome level, strain S04009T had an average nucleotide identity value <95 % and an inferred DNA-DNA hybridization value <70 % when compared to these species. Furthermore, phenotypic characteristics distinguished S04009T from those species. From these related species only strain S04009T and S. xylosus are able to ferment xylose and these two can be distinguished by the inability of strain S04009T to express urease activity. Based on the genotypic and phenotypic results, it is proposed that this isolate is a novel species, with the name Staphylococcus pseudoxylosus sp. nov. The type strain is S04009T (=DSM 107950T=CCUG 72763T=NCTC 14184T).

Staphylococcus caeli sp. nov., isolated from air sampling in an industrial rabbit holding.

Strain 82T, a Gram-stain-positive, coagulase-negative staphylococcus was isolated from an air sample obtained from an industrial rabbit holding in Italy. It is phylogenetically closely related to the coagulase-negative species Staphylococcus saprophyticus, Staphylococcus xylosus and Staphylococcus edaphicus. However, it could be distinguished from these species by sequence differences between the 16S rRNA, hsp60, rpoB, dnaJ and gap genes. At the whole genome level, the isolate had an average nucleotide identity of <95 % and an inferred DNA-DNA hybridization of <70 % when compared to these species. Based on the genotypic results, it is proposed that this isolate is a novel species, with the name Staphylococcus caeli sp. nov. The type strain is 82BT (=NCTC 14063T=CCUG 71912T).

A mecC allotype, mecC3, in the CoNS Staphylococcus caeli, encoded within a variant SCCmecC.

BACKGROUND: Methicillin resistance in staphylococci is conferred by an alternative PBP (PBP2a/2') with low affinity for most ß-lactam antibiotics. PBP2a is encoded by mecA, which is carried on a mobile genetic element known as SCCmec. A variant of mecA, mecC, was described in 2011 and has been found in Staphylococcus aureus from humans and a wide range of animal species as well as a small number of other staphylococcal species from animals. OBJECTIVES: We characterized a novel mecC allotype, mecC3, encoded by an environmental isolate of Staphylococcus caeli cultured from air sampling of a commercial rabbit holding. METHODS: The S. caeli isolate 82BT was collected in Italy in 2013 and genome sequenced using MiSeq technology. This allowed the assembly and comparative genomic study of the novel SCCmec region encoding mecC3. RESULTS: The study isolate encodes a novel mecA allotype, mecC3, with 92% nucleotide identity to mecC. mecC3 is encoded within a novel SCCmec element distinct from those previously associated with mecC, including a ccrAB pairing (ccrA5B3) not previously linked to mecC. CONCLUSIONS: This is the first description of the novel mecC allotype mecC3, the first isolation of a mecC-positive Staphylococcus in Italy and the first report of mecC in S. caeli. Furthermore, the SCCmec element described here is highly dissimilar to the archetypal SCCmec XI encoding mecC in S. aureus and to elements encoding mecC in other staphylococci. Our report highlights the diversity of mecC allotypes and the diverse staphylococcal species, ecological settings and genomic context in which mecC may be found.