Complete genome sequencing of three human clinical isolates of Staphylococcus caprae reveals virulence factors similar to those of S. epidermidis and S. capitis

Abstract

BackgroundStaphylococcus caprae is an animal-associated bacterium regarded as part of goats’ microflora. Recently, S. caprae has been reported to cause human nosocomial infections such as bacteremia and bone and joint infections. However, the mechanisms responsible for the development of nosocomial infections remain largely unknown. Moreover, the complete genome sequence of S. caprae has not been determined.ResultsWe determined the complete genome sequences of three methicillin-resistant S. caprae strains isolated from humans and compared these sequences with the genomes of S. epidermidis and S. capitis, both of which are closely related to S. caprae and are inhabitants of human skin capable of causing opportunistic infections. The genomes showed that S. caprae JMUB145, JMUB590, and JMUB898 strains contained circular chromosomes of 2,618,380, 2,629,173, and 2,598,513 bp, respectively. JMUB145 carried type V SCCmec, while JMUB590 and JMUB898 had type IVa SCCmec. A genome-wide phylogenetic SNP tree constructed using 83 complete genome sequences of 24 Staphylococcus species and 2 S. caprae draft genome sequences confirmed that S. caprae is most closely related to S. epidermidis and S. capitis. Comparative complete genome analysis of eight S. epidermidis, three S. capitis and three S. caprae strains revealed that they shared similar virulence factors represented by biofilm formation genes. These factors include wall teichoic acid synthesis genes, poly-gamma-DL-glutamic acid capsule synthesis genes, and other genes encoding nonproteinaceous adhesins. The 17 proteinases/adhesins and extracellular proteins known to be associated with biofilm formation in S. epidermidis were also conserved in these three species, and their biofilm formation could be detected in vitro. Moreover, two virulence-associated gene clusters, the type VII secretion system and capsular polysaccharide biosynthesis gene clusters, identified in S. aureus were present in S. caprae but not in S. epidermidis and S. capitis genomes.ConclusionThe complete genome sequences of three methicillin-resistant S. caprae isolates from humans were determined for the first time. Comparative genome analysis revealed that S. caprae is closely related to S. epidermidis and S. capitis at the species level, especially in the ability to form biofilms, which may lead to increased virulence during the development of S. caprae infections.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5185-9) contains supplementary material, which is available to authorized users.

Coagulase-Negative Staphylococci Pathogenomics

“…We identified eight studies for S. epidermidis [ 29 , 30 , 40 , 41 , 42 , 43 , 44 , 45 ], four for S. capitis [ 46 , 47 , 48 , 49 ], three for S. lugdunensis [ 32 , 50 , 51 ], two for S. haemolyticus [ 52 , 53 ], and one for S. caprae [ 54 ] and S. saprophyticus [ 55 ].…”

Identification and characterization of mutations responsible for the β-lactam resistance in oxacillin-susceptible mecA-positive Staphylococcus aureus

“…Genomic DNA was extracted from OS-MRSA and its mutants using the phenol–chloroform method and purified using a QIAamp DNA mini kit (Qiagen, Hilden, Germany) following previously developed methods 66 . The genomic sequences of parent strains were determined via mate-pair sequencing as previously described 66 , 67 .…”

“…Genomic DNA was extracted from OS-MRSA and its mutants using the phenol–chloroform method and purified using a QIAamp DNA mini kit (Qiagen, Hilden, Germany) following previously developed methods 66 . The genomic sequences of parent strains were determined via mate-pair sequencing as previously described 66 , 67 . Briefly, a mate-pair library was prepared using a Nextera mate-pair library prep kit (Illumina, Inc., San Diego, CA, USA), and sequencing was performed using an Illumina MiSeq platform with the MiSeq reagent kit version 3 (Illumina).…”

Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia

“…The assembled genomes were then circularized using the Circlator tool (version 1.5.5 3 ) (Hunt et al, 2015), and all of the resulting assemblies that produced contiguous sequences were polished with the nanopolish algorithm (version 0.11.0 4 ) (Loman et al, 2015). Genome sequencing of all of the above strains was performed using the MiSeq platform as previously described (Watanabe et al, 2016(Watanabe et al, , 2018. The draftgenomes generated by MinION were then polished again with the reads generated by MiSeq with the Pilon automated genome assembly improvement and variant detection tool (version 1.22; Broad Institute, Cambridge, MA, United States) (Walker et al, 2014).…”